From yaldouri at yahoo.com Sun Aug 4 11:53:00 2002 From: yaldouri at yahoo.com (Dr Yarub Al-Douri) Date: Sun, 4 Aug 2002 02:53:00 -0700 (PDT) Subject: [CPMD-list] (no subject) Message-ID: <20020804095300.99732.qmail@web21411.mail.yahoo.com> Dear sir, I have the honor to write to you. I would like to exit myself from mailing list memberships and to unsubscribe from a list. Thank you very much. Best regards, Yarub --------------------------------- Do You Yahoo!? Yahoo! Health - Feel better, live better -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020804/cc93fa62/attachment.html From kwu at physchem.ox.ac.uk Mon Aug 5 12:14:24 2002 From: kwu at physchem.ox.ac.uk (kwu) Date: Mon, 5 Aug 2002 11:14:24 +0100 Subject: [CPMD-list] (no subject) Message-ID: <000a01c23c68$df713980$c91a01a3@pcl.ox.ac.uk> Hi, All Where can I find more sample input files ? Wu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020805/e5612f02/attachment.html From c00ycl00 at nchc.gov.tw Mon Aug 5 13:18:31 2002 From: c00ycl00 at nchc.gov.tw (c00ycl00) Date: Mon, 05 Aug 2002 19:18:31 +0800 Subject: [CPMD-list] Where can I find more examples? Message-ID: <3D4E5F073AC.85DEC00YCL00@smtp.nchc.gov.tw> Dear all, I also have the same question. Where can I find more examples of cpmd input file? Yung-Chiang Lan From kwu at physchem.ox.ac.uk Mon Aug 5 17:57:37 2002 From: kwu at physchem.ox.ac.uk (kwu) Date: Mon, 5 Aug 2002 16:57:37 +0100 Subject: [CPMD-list] pseudopotential Message-ID: <002a01c23c98$d1fc1790$c91a01a3@pcl.ox.ac.uk> Dear all, where can we find more pseudopotentials, such as norm-conserving Troullier-Martins pseudopotential and Car-von Barth analytical? wu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020805/43678d11/attachment.html From atte.sillanpaa at oulu.fi Wed Aug 7 09:32:08 2002 From: atte.sillanpaa at oulu.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Wed, 7 Aug 2002 10:32:08 +0300 (EEST) Subject: [CPMD-list] GGA does not work with Vanderbilt pseudo generator? Message-ID: Hello, we were trying to generate Vandrbilt pseudopotentials with the 7.3.3 generator. Everything works fine with plain Ceperley-Alder functional, but the using of any of the available gradient correction functionals (exfact other than 0.0) causes the code to stop after the all electron calculation with the message: beginning execution pseudopotential program version 7.3.3 make: The error code from the last command is 168. The all electron results seem reasonable. The ??_ps.out file is zero size. Is this a bug in the compilation or is there another possible reason? An older version (7.0) works fine with similar input. Cheers, atte.sillanpaa at oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From cakmak at gazi.edu.tr Wed Aug 7 12:12:55 2002 From: cakmak at gazi.edu.tr (Dr.Mehmet Cakmak) Date: Wed, 07 Aug 2002 12:12:55 EEST Subject: [CPMD-list] (no subject) Message-ID: Dear All, I am a bit puzzle to calculate lattice parameter of Si. Please see the below table. When I take bigger lattice parameter, the energy is getting smaller and smaller. There should be turning point which is going to be theoretical lattice parameter of Si. So any idea what could be the reason? or do i know something wrong? E_tot a_lat ------- ----- -7.14 5.0 -7.31 5.1 -7.36 5.2 -7.39 5.3 -7.43 5.4 -7.72 5.41 -7.73 5.42 -7.74 5.43 -7.74 5.44 -7.75 5.45 -7.78 5.5 -7.83 5.6 -7.87 5.7 -mehmet From Ari.P.Seitsonen at iki.fi Wed Aug 7 15:47:24 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 7 Aug 2002 15:47:24 +0200 Subject: [CPMD-list] (no subject) In-Reply-To: (cakmak@gazi.edu.tr) References: Message-ID: <200208071347.g77DlO624699@cragno.cscs.ch> Dear Mehmet, > I am a bit puzzle to calculate lattice parameter of Si. > Please see the below table. When I take bigger lattice > parameter, the energy is getting smaller and smaller. > There should be turning point which is going to be > theoretical lattice parameter of Si. So any idea what could > be the reason? or do i know something wrong? > > E_tot a_lat > ------- ----- > -7.14 5.0 > -7.31 5.1 > -7.36 5.2 > -7.39 5.3 > -7.43 5.4 > -7.72 5.41 > -7.73 5.42 > -7.74 5.43 > -7.74 5.44 > -7.75 5.45 > -7.78 5.5 > -7.83 5.6 > -7.87 5.7 I presume that the energies are in eV, the lattice constants in ?ngstr?ms (Angstroms), or? Did you use k points, or a big cell with only the Gamma point? Could you please send your input to the mailing list, so that we might better get an idea of what goes wrong? Greetings, apsi PS To everyone: Please ALWAYS use the mailing list also for the answers, unless it gets VERY, VERY personal; we need to know if someone already has answered the questions -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From y.kong at mf.mpg.de Thu Aug 8 13:52:19 2002 From: y.kong at mf.mpg.de (Yong Kong) Date: Thu, 08 Aug 2002 13:52:19 +0200 Subject: [CPMD-list] Re: CPMD-list References: <200208081001.MAA20466@cpmd.org> Message-ID: <20020808115220.19C4DC38@mail.mf.mpg.de> Dear Mehmet and APSI, Actually I met the same problem when I made test run on Si. I guess you use a FCC cell containing 2 atoms. If you use a SC cell with 8 atoms, the results would be reasonable. I think it may be the problem of single-k point (I am not sure). By the way, the results on graphite is similar: The calculated bond length and interlayer spacing with hexagonal cell are much larger than 1.421 and 3.35 Angstrom, but too smaller with an orthorhombic cell. So my question to APSI: what should I do? use multi-k points? It seems that one can only do that with Lanczos diagonalisation. Is there other methods to resolve this problem? best regards Yong >Dear All, > >I am a bit puzzle to calculate lattice parameter of Si. >Please see the below table. When I take bigger lattice >parameter, the energy is getting smaller and smaller. >There should be turning point which is going to be >theoretical lattice parameter of Si. So any idea what could >be the reason? or do i know something wrong? > > E_tot a_lat >------- ----- >-7.14 5.0 >-7.31 5.1 >-7.36 5.2 >-7.39 5.3 >-7.43 5.4 >-7.72 5.41 >-7.73 5.42 >-7.74 5.43 >-7.74 5.44 >-7.75 5.45 >-7.78 5.5 >-7.83 5.6 >-7.87 5.7 > > -mehmet From hutter at pci.unizh.ch Thu Aug 8 14:40:52 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 8 Aug 2002 14:40:52 +0200 (MEST) Subject: [CPMD-list] (no subject) In-Reply-To: Message-ID: Hi I assume the problem is related to the small cell you are using. Certainly, the points raised by the others are also important, but I think that your problem is directly related to a NOT converged real space Ewald sum. The default in CPMD is to sum up the real space contributions of the Ewald sum only within the original supercell. If your cell is too small and you change the cell size you will see contributions of this. Check this assumption by running the simulations with TESR 4 Of course to get "good" results with small cells you should also have converged the cutoff (especially if you change the cell size) and k-points are important also. In addition I advice everybody to use more than the default value for the spline interpolation points for the pseudopotentials. SPLINE POINTS 3000 is a good start. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 7 Aug 2002, Dr.Mehmet Cakmak wrote: > Dear All, > > I am a bit puzzle to calculate lattice parameter of Si. > Please see the below table. When I take bigger lattice > parameter, the energy is getting smaller and smaller. > There should be turning point which is going to be > theoretical lattice parameter of Si. So any idea what could > be the reason? or do i know something wrong? > > E_tot a_lat > ------- ----- > -7.14 5.0 > -7.31 5.1 > -7.36 5.2 > -7.39 5.3 > -7.43 5.4 > -7.72 5.41 > -7.73 5.42 > -7.74 5.43 > -7.74 5.44 > -7.75 5.45 > -7.78 5.5 > -7.83 5.6 > -7.87 5.7 > > -mehmet > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From erichu_linux at yahoo.com Thu Aug 8 19:11:12 2002 From: erichu_linux at yahoo.com (eric hu) Date: Thu, 8 Aug 2002 10:11:12 -0700 (PDT) Subject: [CPMD-list] compile for myrinet Message-ID: <20020808171112.58247.qmail@web13401.mail.yahoo.com> Hi, I tried to compile CPMD 3.5 for myrinet mpich. The job stops after reading all the input info and starting to broadcast into each processor. I wonder if anyone has met similar situation or the code needed to be modified for myrinet. Thanks! Eric | Pseudopotential Report Thu Nov 30 13:19:26 1995 | ------------------------------------------------------------ | Atomic Symbol : O | | Atomic Number : 8 | | Number of core states : 1 | | Number of valence states : 2 | | Exchange-Correlation Functional : | | Slater exchange : .6667 | | LDA correlation : Lee-Yang-Parr | | Exchange GC : Becke (1988) | | Correlation GC : Lee-Yang-Parr | | Electron Configuration : N L Occupation | | 1 S 2.0000 | | 2 S 2.0000 | | 2 P 4.0000 | | Full Potential Total Energy -75.023693 | | Trouiller-Martins normconserving PP | | n l rc energy | | 2 S 1.0500 -.87404 | | 2 P 1.0500 -.33186 | | 3 D 1.0500 -.33186 | | Number of Mesh Points : 631 | | Pseudoatom Total Energy -15.775323 | ============================================================ **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * H 1.0080 1.2000 NO S LOCAL * * C 12.0112 1.2000 NO KLEINMAN S NONLOCAL * * P LOCAL * * O 15.9994 1.2000 NO KLEINMAN S NONLOCAL * * P LOCAL * **************************************************************** (stops here in the queue) __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From tfysg at fy.chalmers.se Fri Aug 9 00:24:41 2002 From: tfysg at fy.chalmers.se (Shiwu Gao) Date: Fri, 09 Aug 2002 00:24:41 +0200 Subject: [CPMD-list] EWALD SUM not equal in real and Q-space References: Message-ID: <3D52EFA9.863B0DE4@fy.chalmers.se> Hi, I got a trouble in running CPMD with the Vanderbildt uspp, which I generated myself. The program stops and complains that the Ewald sum does not equal in real and Fourier Q-space, Typical error message looks like this **************************************************************** CPU TIME FOR WAVEFUNCTION INITIALIZATION: 8.73 SECONDS *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 13844 kBYTES *** EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS IN FOURIER SPACE: 360.000005713858 IN REAL SPACE: 359.999999999984 ***************************************************************** Note the charge should be 360 in this case. Tested many uspp's including the potential included in the latest uspp package. All have the same problem. Note that the sum in real space is usually OK with an error less than 10^-10, while the error in Q-space is large, 10^-5--10^-6. Has anybody met this problem with uspp? What is the way out of it? Thanks in advance, Shiwu Gao From cakmak at gazi.edu.tr Fri Aug 9 17:31:39 2002 From: cakmak at gazi.edu.tr (Dr.Mehmet Cakmak) Date: Fri, 09 Aug 2002 17:31:39 EEST Subject: [CPMD-list] (no subject) Message-ID: No. I have still the same problem. Any other ideas. If you are carrefully check my input file, you can easly see that I have made the bulk like calculations,i.e, fcc lattice with two basis atosms are fixed in their bulk like positions with using different lattice parameters and then I was tring to calculate the energies. thank you Mehmet Cakmak > Hi > > I assume the problem is related to the small cell you are > using. Certainly, the points raised by the others are > also important, but I think that your problem is directly > related to a NOT converged real space Ewald sum. > The default in CPMD is to sum up the real space > contributions of the Ewald sum only within the > original supercell. If your cell is too small and you > change the cell size you will see contributions > of this. Check this assumption by running the > simulations with > > TESR > 4 > > Of course to get "good" results with small cells > you should also have converged the cutoff (especially > if you change the cell size) and k-points are important > also. In addition I advice everybody to use more > than the default value for the spline interpolation > points for the pseudopotentials. > > SPLINE POINTS > 3000 > > is a good start. > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : 41 1 635 4491 > Physical Chemistry Institute FAX : 41 1 635 6838 > University of Zurich E-mail: hutter at pci.unizh.ch > Winterthurerstrasse 190 > CH-8057 Zurich, Switzerland > ---------------------------------------------------------- > > > On Wed, 7 Aug 2002, Dr.Mehmet Cakmak wrote: > > > Dear All, > > > > I am a bit puzzle to calculate lattice parameter of Si. > > Please see the below table. When I take bigger lattice > > parameter, the energy is getting smaller and smaller. > > There should be turning point which is going to be > > theoretical lattice parameter of Si. So any idea what could > > be the reason? or do i know something wrong? > > > > E_tot a_lat > > ------- ----- > > -7.14 5.0 > > -7.31 5.1 > > -7.36 5.2 > > -7.39 5.3 > > -7.43 5.4 > > -7.72 5.41 > > -7.73 5.42 > > -7.74 5.43 > > -7.74 5.44 > > -7.75 5.45 > > -7.78 5.5 > > -7.83 5.6 > > -7.87 5.7 > > > > -mehmet > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > From Ari.P.Seitsonen at iki.fi Sat Aug 10 19:34:59 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sat, 10 Aug 2002 19:34:59 +0200 Subject: [CPMD-list] (no subject) In-Reply-To: (cakmak@gazi.edu.tr) References: Message-ID: <200208101734.g7AHYxe29137@cragno.cscs.ch> > No. I have still the same problem. > Any other ideas. Here's an input which seems to work: ---------------------------------------------------------------------- &CPMD WAVEFUNCTION OPTIMIZATION SPLINE POINTS 5000 LANCZOS DIAGONALISATION ANDERSON MIXING 0.2 &END &DFT FUNCTIONAL PZ &END &SYSTEM SYMMETRY 2 CELL 10.2612 1.0 1.0 0.0 0.0 0.0 CUTOFF 36. KPOINTS MONKHORST-PACK 4 4 4 STATES 4 POINT GROUP AUTO TESR 4 4 4 SCALED &END &ATOMS *SI_SGS KLEINMAN-BYLANDER LMAX=D 2 0.00 0.00 0.00 0.25 0.25 0.25 &END ---------------------------------------------------------------------- Notes: - The k points were in the wrong section, they must be in the '&SYSTEM' ... '&END', not with the '&ATOMS' ... '&END' - One has to use a diagonalisation scheme (Lanczos in my input) with k points, ODIIS doesn't work - I switched to the automatic generation of k points, just as it was easier - The same applies for using 'SCALED' coordinates - I went for the 'LMAX=D' in the pseudo and to KLEINMAN-BYLANDER Yours, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From hutter at pci.unizh.ch Sun Aug 11 16:37:13 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 11 Aug 2002 16:37:13 +0200 (MEST) Subject: [CPMD-list] EWALD SUM not equal in real and Q-space In-Reply-To: <3D52EFA9.863B0DE4@fy.chalmers.se> Message-ID: Hi I can't reproduce this problem. Could you post an input for a system (as small as possible) where this error occurs? Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 9 Aug 2002, Shiwu Gao wrote: > Hi, > > I got a trouble in running CPMD with the Vanderbildt uspp, > which I generated myself. The program stops and complains that > the Ewald sum does not equal in real and Fourier Q-space, > > Typical error message looks like this > > **************************************************************** > > CPU TIME FOR WAVEFUNCTION INITIALIZATION: 8.73 SECONDS > *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 13844 kBYTES *** > EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS > IN FOURIER SPACE: 360.000005713858 > IN REAL SPACE: 359.999999999984 > > ***************************************************************** > > Note the charge should be 360 in this case. Tested many uspp's including > the potential included in the latest uspp package. All have the same > problem. Note that the sum in real space is usually OK with an error > less than 10^-10, while the error in Q-space is large, 10^-5--10^-6. > > Has anybody met this problem with uspp? What is the way out of it? > > Thanks in advance, > > Shiwu Gao > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Mon Aug 12 08:44:47 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 12 Aug 2002 08:44:47 +0200 (MEST) Subject: [CPMD-list] EWALD SUM not equal in real and Q-space In-Reply-To: <3D56A36D.8EC74564@fy.chalmers.se> Message-ID: Hi I still can't reproduce your problem. However, as you sent me a binary pseudopotential I was not able to use it. I replaced it by another pp and the charge densities were accurate to machine precision both in real and G space. There are now two possibilities: 1) the problem is connected to your pp -> please send the input files to the atomic code 2) the problem is connected to your computer/compiler/os etc. -> try the input on another type of computer Juerg PS: send mails also to the mailing list. There might be other people interested in this problem, or people that can help. ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sun, 11 Aug 2002, Shiwu Gao wrote: > Dear Juerg, > > Attached please find a test case, where I still have probem. > For smaller systems (than this one), there is no such problems. > In the tar.gz file you also find the output and uspp that > I use. Please let me what you find and where the problem > is. > > Many thanks again, > > Shiwu > > PS > > For you information: > > The test case is a 2-layer slab model of Pt(111) surface in > p(3x3) 2-D symmetry, and the calculation was done my laptop > with RedHat Linux 7.2 as OS. > > > Juerg Hutter wrote: > > > > Hi > > > > I can't reproduce this problem. Could you post an input > > for a system (as small as possible) where this error > > occurs? > > > > Juerg > > > > ---------------------------------------------------------- > > Juerg Hutter Phone : ++41 1 635 4491 > > Physical Chemistry Institute FAX : ++41 1 635 6838 > > University of Zurich E-mail: hutter at pci.unizh.ch > > Winterthurerstrasse 190 > > CH-8057 Zurich, Switzerland > > ---------------------------------------------------------- > > > > On Fri, 9 Aug 2002, Shiwu Gao wrote: > > > > > Hi, > > > > > > I got a trouble in running CPMD with the Vanderbildt uspp, > > > which I generated myself. The program stops and complains that > > > the Ewald sum does not equal in real and Fourier Q-space, > > > > > > Typical error message looks like this > > > > > > **************************************************************** > > > > > > CPU TIME FOR WAVEFUNCTION INITIALIZATION: 8.73 SECONDS > > > *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 13844 kBYTES *** > > > EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS > > > IN FOURIER SPACE: 360.000005713858 > > > IN REAL SPACE: 359.999999999984 > > > > > > ***************************************************************** > > > > > > Note the charge should be 360 in this case. Tested many uspp's including > > > the potential included in the latest uspp package. All have the same > > > problem. Note that the sum in real space is usually OK with an error > > > less than 10^-10, while the error in Q-space is large, 10^-5--10^-6. > > > > > > Has anybody met this problem with uspp? What is the way out of it? > > > > > > Thanks in advance, > > > > > > Shiwu Gao > > > _______________________________________________ > > > CPMD-list mailing list > > > CPMD-list at cpmd.org > > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list From tfysg at fy.chalmers.se Mon Aug 12 09:06:07 2002 From: tfysg at fy.chalmers.se (Shiwu Gao) Date: Mon, 12 Aug 2002 09:06:07 +0200 Subject: [CPMD-list] EWALD SUM not equal in real and Q-space References: Message-ID: <3D575E5F.FA073F38@fy.chalmers.se> Hi Juerg, Attached please find the working directory of pseudopotential generation for Pt, which contains both the input and output for the atomic calculation and ps generation. Note that the case that I sent you does not have any problem, if I use other forms of pp. It is only problematic when running with uspp. This might be a problem with uspp then. However I tested with the pseudopotential for 022-Ti, which comes with the uspp package, and was generated by Vanderbildt? The same problems occurs. So I am not sure whether the problem is related to my pseudopotential, or uspp implementation in CPMD. I also tested on other machines here. The same problems. So it is unlikely to be a fault of computer/OS. Best regards, Shiwu Juerg Hutter wrote: > > Hi > > I still can't reproduce your problem. However, as you sent > me a binary pseudopotential I was not able to use it. > I replaced it by another pp and the charge densities were > accurate to machine precision both in real and G space. > There are now two possibilities: > 1) the problem is connected to your pp > -> please send the input files to the atomic code > 2) the problem is connected to your computer/compiler/os etc. > -> try the input on another type of computer > > Juerg > > PS: send mails also to the mailing list. There might be > other people interested in this problem, or people > that can help. > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4491 > Physical Chemistry Institute FAX : ++41 1 635 6838 > University of Zurich E-mail: hutter at pci.unizh.ch > Winterthurerstrasse 190 > CH-8057 Zurich, Switzerland > ---------------------------------------------------------- > > On Sun, 11 Aug 2002, Shiwu Gao wrote: > > > Dear Juerg, > > > > Attached please find a test case, where I still have probem. > > For smaller systems (than this one), there is no such problems. > > In the tar.gz file you also find the output and uspp that > > I use. Please let me what you find and where the problem > > is. > > > > Many thanks again, > > > > Shiwu > > > > PS > > > > For you information: > > > > The test case is a 2-layer slab model of Pt(111) surface in > > p(3x3) 2-D symmetry, and the calculation was done my laptop > > with RedHat Linux 7.2 as OS. > > > > > > Juerg Hutter wrote: > > > > > > Hi > > > > > > I can't reproduce this problem. Could you post an input > > > for a system (as small as possible) where this error > > > occurs? > > > > > > Juerg > > > > > > ---------------------------------------------------------- > > > Juerg Hutter Phone : ++41 1 635 4491 > > > Physical Chemistry Institute FAX : ++41 1 635 6838 > > > University of Zurich E-mail: hutter at pci.unizh.ch > > > Winterthurerstrasse 190 > > > CH-8057 Zurich, Switzerland > > > ---------------------------------------------------------- > > > > > > On Fri, 9 Aug 2002, Shiwu Gao wrote: > > > > > > > Hi, > > > > > > > > I got a trouble in running CPMD with the Vanderbildt uspp, > > > > which I generated myself. The program stops and complains that > > > > the Ewald sum does not equal in real and Fourier Q-space, > > > > > > > > Typical error message looks like this > > > > > > > > **************************************************************** > > > > > > > > CPU TIME FOR WAVEFUNCTION INITIALIZATION: 8.73 SECONDS > > > > *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 13844 kBYTES *** > > > > EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS > > > > IN FOURIER SPACE: 360.000005713858 > > > > IN REAL SPACE: 359.999999999984 > > > > > > > > ***************************************************************** > > > > > > > > Note the charge should be 360 in this case. Tested many uspp's including > > > > the potential included in the latest uspp package. All have the same > > > > problem. Note that the sum in real space is usually OK with an error > > > > less than 10^-10, while the error in Q-space is large, 10^-5--10^-6. > > > > > > > > Has anybody met this problem with uspp? What is the way out of it? > > > > > > > > Thanks in advance, > > > > > > > > Shiwu Gao > > > > _______________________________________________ > > > > CPMD-list mailing list > > > > CPMD-list at cpmd.org > > > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > > > > > > > _______________________________________________ > > > CPMD-list mailing list > > > CPMD-list at cpmd.org > > > http://www.cpmd.org/mailman/listinfo/cpmd-list -------------- next part -------------- A non-text attachment was scrubbed... Name: 078-pt.tar.gz Type: application/x-gzip Size: 382620 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020812/2462fafa/attachment.gz From hutter at pci.unizh.ch Mon Aug 12 15:00:23 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 12 Aug 2002 15:00:23 +0200 (MEST) Subject: [CPMD-list] EWALD SUM not equal in real and Q-space In-Reply-To: <3D575E5F.FA073F38@fy.chalmers.se> Message-ID: Hi the problem seems to be realted to the PGI compiler only. If you replace in rhov.F the REAL by DREAL (line 105) the problem should disappear IF(GEQ0) THEN RSUMV=DREAL(DELTAR(1)) ELSE RSUMV=0.0D0 ENDIF PS: some tricks to be considered using USPP SPLINE QFUNCTIONS may reduce the time for initialization and the memory requirements. BIG MEMORY increases the memory requirements again, but usually saves some CPU time in USPP calculations. PPS: the SURFACE keyword is only effective together with SYMMETRY 0 and requires special care of orienting the system! Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 12 Aug 2002, Shiwu Gao wrote: > Hi Juerg, > > Attached please find the working directory of pseudopotential > generation for Pt, which contains both the input and output > for the atomic calculation and ps generation. Note that the > case that I sent you does not have any problem, if I use other > forms of pp. It is only problematic when running with uspp. > This might be a problem with uspp then. However I tested with > the pseudopotential for 022-Ti, which comes with the uspp > package, and was generated by Vanderbildt? The same problems > occurs. So I am not sure whether the problem is related to > my pseudopotential, or uspp implementation in CPMD. > > I also tested on other machines here. The same problems. So > it is unlikely to be a fault of computer/OS. > > Best regards, > > Shiwu > > > Juerg Hutter wrote: > > > > Hi > > > > I still can't reproduce your problem. However, as you sent > > me a binary pseudopotential I was not able to use it. > > I replaced it by another pp and the charge densities were > > accurate to machine precision both in real and G space. > > There are now two possibilities: > > 1) the problem is connected to your pp > > -> please send the input files to the atomic code > > 2) the problem is connected to your computer/compiler/os etc. > > -> try the input on another type of computer > > > > Juerg > > > > PS: send mails also to the mailing list. There might be > > other people interested in this problem, or people > > that can help. > > > > ---------------------------------------------------------- > > Juerg Hutter Phone : ++41 1 635 4491 > > Physical Chemistry Institute FAX : ++41 1 635 6838 > > University of Zurich E-mail: hutter at pci.unizh.ch > > Winterthurerstrasse 190 > > CH-8057 Zurich, Switzerland > > ---------------------------------------------------------- > > > > On Sun, 11 Aug 2002, Shiwu Gao wrote: > > > > > Dear Juerg, > > > > > > Attached please find a test case, where I still have probem. > > > For smaller systems (than this one), there is no such problems. > > > In the tar.gz file you also find the output and uspp that > > > I use. Please let me what you find and where the problem > > > is. > > > > > > Many thanks again, > > > > > > Shiwu > > > > > > PS > > > > > > For you information: > > > > > > The test case is a 2-layer slab model of Pt(111) surface in > > > p(3x3) 2-D symmetry, and the calculation was done my laptop > > > with RedHat Linux 7.2 as OS. > > > > > > > > > Juerg Hutter wrote: > > > > > > > > Hi > > > > > > > > I can't reproduce this problem. Could you post an input > > > > for a system (as small as possible) where this error > > > > occurs? > > > > > > > > Juerg > > > > > > > > ---------------------------------------------------------- > > > > Juerg Hutter Phone : ++41 1 635 4491 > > > > Physical Chemistry Institute FAX : ++41 1 635 6838 > > > > University of Zurich E-mail: hutter at pci.unizh.ch > > > > Winterthurerstrasse 190 > > > > CH-8057 Zurich, Switzerland > > > > ---------------------------------------------------------- > > > > > > > > On Fri, 9 Aug 2002, Shiwu Gao wrote: > > > > > > > > > Hi, > > > > > > > > > > I got a trouble in running CPMD with the Vanderbildt uspp, > > > > > which I generated myself. The program stops and complains that > > > > > the Ewald sum does not equal in real and Fourier Q-space, > > > > > > > > > > Typical error message looks like this > > > > > > > > > > **************************************************************** > > > > > > > > > > CPU TIME FOR WAVEFUNCTION INITIALIZATION: 8.73 SECONDS > > > > > *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 13844 kBYTES *** > > > > > EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS > > > > > IN FOURIER SPACE: 360.000005713858 > > > > > IN REAL SPACE: 359.999999999984 > > > > > > > > > > ***************************************************************** > > > > > > > > > > Note the charge should be 360 in this case. Tested many uspp's including > > > > > the potential included in the latest uspp package. All have the same > > > > > problem. Note that the sum in real space is usually OK with an error > > > > > less than 10^-10, while the error in Q-space is large, 10^-5--10^-6. > > > > > > > > > > Has anybody met this problem with uspp? What is the way out of it? > > > > > > > > > > Thanks in advance, > > > > > > > > > > Shiwu Gao > > > > > _______________________________________________ > > > > > CPMD-list mailing list > > > > > CPMD-list at cpmd.org > > > > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > > > > > > > > > > _______________________________________________ > > > > CPMD-list mailing list > > > > CPMD-list at cpmd.org > > > > http://www.cpmd.org/mailman/listinfo/cpmd-list From ct at chemie.hu-berlin.de Tue Aug 13 12:39:18 2002 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Tue, 13 Aug 2002 12:39:18 +0200 Subject: [CPMD-list] problem with parallel CPMD binary (Linux IFC) Message-ID: <20020813123918.B194242@atlas.chemie.hu-berlin.de> Dear all, I tried to compile CPMD 3.5.2 with the IFC (6.0) to get a parallel binary. Since the Configure script doesn't provide defaults for this case I used the following setup: ... FFLAGS = -pc64 -unroll -w90 -w95 LFLAGS = -L/global-work/ct/ATLAS_ifc/lib/Linux_ATHLONSSE1_2 -llapack \ -lf77blas -lcblas -latlas -Vaxlib CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC \ -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET CC = /global-work/ct/mpich124sh_intel/bin/mpicc FC = /global-work/ct/mpich124sh_intel/bin/mpif77 -c -O3 -tp p6 -axiM LD = /global-work/ct/mpich124sh_intel/bin/mpif77 -O3 -tp p6 -axiM ... MPICH was used as the MPI library, built with the Intel compilers as well. At link time everything seems to work - no error messages. (By the way, why don't I need to link with the MPICH libs?) Running this parallel binary on only one processor (mpirun -np 1 ...) works fine. But as soon as I start a job on more than one processor (mpirun -np 2 ...) I get this error message: /global-work/ct/SOURCE352MPI_INTEL/cpmd.x: error while loading shared libraries: libcxa.so.1: cannot open shared object file: No such file or directory When I say > ldd /global-work/ct/SOURCE352MPI_INTEL/cpmd.x I get libm.so.6 => /lib/libm.so.6 (0x40023000) libcxa.so.1 => /usr/loc/intel/compiler60/ia32/lib/libcxa.so.1 (0x40046000) libc.so.6 => /lib/libc.so.6 (0x400b4000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) But the file /usr/loc/intel/compiler60/ia32/lib/libcxa.so.1 exists! Does anybody have an idea what went wrong? Thanks, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Aug 14 14:18:56 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (axel.kohlmeyer at theochem.ruhr-uni-bochum.de) Date: Wed, 14 Aug 2002 14:18:56 +0200 Subject: [CPMD-list] problem with parallel CPMD binary (Linux IFC) In-Reply-To: <20020813123918.B194242@atlas.chemie.hu-berlin.de> Message-ID: <200208141218.g7ECIv530845@yello.theochem.ruhr-uni-bochum.de> On Tue, 13 Aug 2002 12:39:18 +0200 Christian Tuma wrote: > Dear all, > > I tried to compile CPMD 3.5.2 with the IFC (6.0) to get a parallel > binary. Since the Configure script doesn't provide defaults for this > case I used the following setup: > > ... > FFLAGS = -pc64 -unroll -w90 -w95 > LFLAGS = -L/global-work/ct/ATLAS_ifc/lib/Linux_ATHLONSSE1_2 -llapack \ > -lf77blas -lcblas -latlas -Vaxlib > CFLAGS = > CPP = /lib/cpp -P -C -traditional > CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC \ > -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET > CC = /global-work/ct/mpich124sh_intel/bin/mpicc > FC = /global-work/ct/mpich124sh_intel/bin/mpif77 -c -O3 -tp p6 -axiM > LD = /global-work/ct/mpich124sh_intel/bin/mpif77 -O3 -tp p6 -axiM > ... > > MPICH was used as the MPI library, built with the Intel compilers as well. > At link time everything seems to work - no error messages. (By the way, > why don't I need to link with the MPICH libs?) > > Running this parallel binary on only one processor (mpirun -np 1 ...) > works fine. But as soon as I start a job on more than one processor > (mpirun -np 2 ...) I get this error message: > > /global-work/ct/SOURCE352MPI_INTEL/cpmd.x: error while loading shared librari es: libcxa.so.1: cannot open shared object file: No such file or directory > > When I say > > > ldd /global-work/ct/SOURCE352MPI_INTEL/cpmd.x > > I get > > libm.so.6 => /lib/libm.so.6 (0x40023000) > libcxa.so.1 => /usr/loc/intel/compiler60/ia32/lib/libcxa.so.1 (0x4004 6000) > libc.so.6 => /lib/libc.so.6 (0x400b4000) > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > But the file /usr/loc/intel/compiler60/ia32/lib/libcxa.so.1 exists! > > Does anybody have an idea what went wrong? yes. libcxa.so.1 is one of the intel compiler runtime libraries. you either need to create a static binary or install/copy the intel compiler (or only the runtime libraries) on all machines where you want to run the binary. cheers, axel. > > Thanks, > Christian. > > -- > Christian Tuma Humboldt-Universitaet Berlin > ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) > phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY > fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer > > > > --__--__---- > --195.176.20.84.506.15598.1029319206.351.24030 > Content-type: text/plain; charset=us-ascii > Content-description: Digest Footer > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > --195.176.20.84.506.15598.1029319206.351.24030-- > > End of CPMD-list Digest > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ct at chemie.hu-berlin.de Wed Aug 14 15:42:44 2002 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Wed, 14 Aug 2002 15:42:44 +0200 Subject: [CPMD-list] problem with parallel CPMD binary (Linux IFC) In-Reply-To: <200208141218.g7ECIv530845@yello.theochem.ruhr-uni-bochum.de>; from axel.kohlmeyer@theochem.ruhr-uni-bochum.de on Wed, Aug 14, 2002 at 02:18:56PM +0200 References: <20020813123918.B194242@atlas.chemie.hu-berlin.de> <200208141218.g7ECIv530845@yello.theochem.ruhr-uni-bochum.de> Message-ID: <20020814154244.C197933@atlas.chemie.hu-berlin.de> On Wed, Aug 14, 2002 at 02:18:56PM +0200, axel.kohlmeyer at theochem.ruhr-uni-bochum.de wrote: > > libcxa.so.1 is one of the intel compiler runtime libraries. you > either need to create a static binary or install/copy the intel > compiler (or only the runtime libraries) on all machines where > you want to run the binary. > > cheers, > axel. Ok, the library is available on all machines ... My environment variable LD_LIBRARY_PATH was set as well and pointed into the correct directory as already suggested by other people - well, not really ... since I'm using ssh for the TCP/IP connections my ~/.profile wasn't read and so LD_LIBRARY_PATH was NOT set at runtime! As I read from the ssh manpage a file ~/.ssh/environment had to be created containing environment variable definitions. I did so for the variable LD_LIBRARY_PATH, now it works fine ... maybe this can help others as well. Thanks to all who gave hints, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From WANGYI at engr.sc.edu Wed Aug 14 16:22:12 2002 From: WANGYI at engr.sc.edu (WANG, YIXUAN ) Date: Wed, 14 Aug 2002 10:22:12 -0400 Subject: [CPMD-list] memory problem Message-ID: Dear all, I am learning how to use CPMD. For an isolated systems (30 atoms), cubc cell (15.0), cutoff (30.0), I always have memory allocation problem, details of input as well as output are attached. Please give me a hint. another question is how to define required memory. I just found the command (big/small memory) may be related to the question. Thanks. Yixuan Wang Depart Chem. Engineering Uinv S Carolina ---- input &CPMD OPTIMIZE GEOMETRY ISOLATED MOLECULE &END &SYSTEM SYMMETRY 0 ANGSTROM CELL 15.00 1.0 1.0 0.0 0.0 0.0 CUTOFF 30.0 &END ---output **************************************************************** PROCESSOR 0 ALLOCATION OF 15138800 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 151781 kBYTES *** ================================================================ BIG MEMORY ALLOCATIONS SCR 4161001 C0 3027752 C2 3027752 YF 2060602 XF 2060602 HGPOT 1030301 GK 758832 VPS 758832 RHOPS 758832 INYH 379417 ---------------------------------------------------------------- [PEAK NUMBER 55] PEAK MEMORY 15256479 = 122.1 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (PME) From ymxiong at icpm.syb.ac.cn Thu Aug 15 02:08:11 2002 From: ymxiong at icpm.syb.ac.cn (Xiong Yuming) Date: Thu, 15 Aug 2002 8:8:11 +0800 Subject: [CPMD-list] (no subject) Message-ID: <200208150007.CAA07564@internet-fence.zurich.ihost.com> Dear Co. I have added my email address to the cpmd-mail-list. ps post it on. thanks. and how can I ask my question. is it work if I send my questions to cpmd-list at cpmd.org? thanks anyway. best regards yours xiong ????????????????????????????Xiong Yuming ????????????????????????????ymxiong at icpm.syb.ac.cn ??????????????????????????????????2002-08-15 From aulucfph at iitr.ernet.in Thu Aug 15 11:40:38 2002 From: aulucfph at iitr.ernet.in (Prof. Sushil Auluck) Date: Thu, 15 Aug 2002 15:25:38 +0545 Subject: [CPMD-list] equation of state for liquids. Message-ID: <3D5B7716.BF0B138E@iitr.ernet.in> hi, i am interested in knowning if some has obtained the equation of state for liquids using the CPMD code.if so i would like to have some information about the input file/files. best wishes s.auluck -- **************************************************************************** Prof. Sushil Auluck Phone: +91-1332-74075(Home) Department of Physics +91-1332-85010(Home) Indian Institute of Technology +91-1332-85745(Work) Roorkee 247 667 Uttranchal Fax: +91-1332-73560 India e-mail: aulucfph at iitr.ernet.in http://www.iitr.ernet.in/acads/depts/physics/faculty/aulak.htm **************************************************************************** From zimmerli at inf.ethz.ch Thu Aug 15 11:50:43 2002 From: zimmerli at inf.ethz.ch (Urs Zimmerli) Date: Thu, 15 Aug 2002 11:50:43 +0200 (CEST) Subject: [CPMD-list] Surface Setup -- inconsistent behaviour? Message-ID: <60116.148.187.130.154.1029405043.squirrel@spurious.biz> Dear all, I'm currently experiencing peculiar behaviour of simulations using the SURFACE setup. I do not know whether this is a problem of my input statements or of CPMD. To illustrate how I use the SURFACE setup, please refer to the inserted input fragment. ----- BEGIN INPUT FRAGMENT ---------------- &CPMD OPTIMIZE GEOMETRY &END &DFT FUNCTIONAL HCTH &END &SYSTEM SYMMETRY 0 CELL 27.9025 0.865908160639909 1.0 0.0 0.0 0.0 CUTOFF 70. SURFACE &END &ATOMS *O_MT_HCTH.psp KLEINMANN-BYLANDER LMAX=P 1 11.811 10.000 10.000 O *H_MT_HCTH.psp KLEINMAN-BYLANDER LMAX=S 2 10.000 10.000 10.000 H 12.265 10.111 8.250 H &END ----- END INPUT FRAGMENT ---------------- I'm confronting this simulation to different simulations in an orthorhombic setup of the cell, thus the only difference in the input file being in the SYSTEM section (Note that the lateral dimensions of the cell remain the same): ----- BEGIN DIFFERENCE ------------------ &SYSTEM SYMMETRY 8 CELL 27.9025 0.865908160639909 1.0 0.0 0.0 0.0 CUTOFF 70. &END ----- BEGIN DIFFERENCE ------------------ Not only does this lead to completely different total Energies: SURFACE -17.3248 ORTHORHOMBIC -17.2737 but also the resulting geometry of the water molecule is different: SETUP Bond length [a.u.] Bond Angle SURFACE 1.851 111.5 ORTHORHOMBIC 1.825 104.7 Furthermore does the total energy in the SURFACE setup strongly depend on the orientation of the water molecule. The final geometry is orientated along the longest diagonal of the box. In the case of the 'normal' orthorhombic setup the total Energy is almost independent on the rotation of the water molecule (variation approximately 1e-4 a.u.) The differences do not get smaller upon changing the dimensions of the simulation cells. Did anybody experience similar behaviour at some point? What might be the reason for this behaviour? Am I using the wrong input options? With best regards and thank you for any help urs From Ari.P.Seitsonen at iki.fi Thu Aug 15 13:53:41 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 15 Aug 2002 13:53:41 +0200 Subject: [CPMD-list] linux-cpmd help In-Reply-To: <200208151105.NAA06934@internet-fence.zurich.ihost.com> (ymxiong@icpm.syb.ac.cn) References: <200208151105.NAA06934@internet-fence.zurich.ihost.com> Message-ID: <200208151153.g7FBrfp00777@magadino.cscs.ch> Dear Xiong, > ]0;yuming at localhost:~/cpmd/source[yuming at localhost source]$ ./configure PC-PGI > Makefile > ... > ]0;yuming at localhost:~/cpmd/source[yuming at localhost source]$ make > lf95 -c -fast -Mr4 -pc32 -Msignextend -Msecond_underscore ./csize.f -o ./csize.o > f95: warning: -pc32 cannot be specified. > f95: warning: Invalid suboption ast specified for -f. > f95: Compilation abnormally ended due to SIGSEGV. > > Internal compiler error. > Please forward the code to: > Lahey Technical Support. > 865 Tahoe Blvd. > P. O. Box 6091 > Incline Village NV 89451 > Email: support at lahey.com Your compiler is not supported, so please modify the Makefile according to your needs, e.g. the erf() function and the runtime libraries for the Lahey compiler. Also the option '-Msecond_underscore' might cause problems, if it indeed gets interpreted by the Lahey compiler. Since we don't have a Lahey compiler probably we, unfortunately, cannot help more. Yours, apsi PS Please, again, always reply also to the list when answering the mails!! -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From Ari.P.Seitsonen at iki.fi Thu Aug 15 13:56:06 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 15 Aug 2002 13:56:06 +0200 Subject: [CPMD-list] Surface Setup -- inconsistent behaviour? In-Reply-To: <60116.148.187.130.154.1029405043.squirrel@spurious.biz> (zimmerli@inf.ethz.ch) References: <60116.148.187.130.154.1029405043.squirrel@spurious.biz> Message-ID: <200208151156.g7FBu6x00871@magadino.cscs.ch> Hi Urs, After consulting "highly respected sources" I would suggest you to try using the Poisson solver of Jens Mortensen (POISSON SOLVER MORTENSEN), as this is most likely much better tested with the SURFACE option than the default Hockney solver. Yours, apsi PS Please always reply also to the mailing list when answering mails!! -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From jarek at elrond.chem.uni.wroc.pl Thu Aug 15 23:58:29 2002 From: jarek at elrond.chem.uni.wroc.pl (jarek at elrond.chem.uni.wroc.pl) Date: Thu, 15 Aug 2002 23:58:29 +0200 (CEST) Subject: [CPMD-list] Size of cell for SURFACE/POLYMER ? Message-ID: Dear CPMD users, I have a question related to the latest discussion on the 2D calculations in CPMD. What is the required cell length in the "non-periodic dimensions" for SURFACE, POLYMER or, while we are at it, ISOLATED MOLECULE? The standard supercell approach would require the sufficiently large length for decoupling of the periodic images, but what about the options listed above? Should we include, say, 3 or 4 A of "free space" from the most protruding atoms? If anyone has got either a theoretical explanation or the empirical rule of thumb, I would be happy for hearing it. And, of course, happy summer holidays to you all! Jaroslaw Panek Faculty of Chemistry, University of Wroclaw ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland From konopka at elf.stuba.sk Fri Aug 16 15:44:37 2002 From: konopka at elf.stuba.sk (Martin Konopka) Date: Fri, 16 Aug 2002 15:44:37 +0200 (MET DST) Subject: [CPMD-list] crashes during saving RESTART file, using Vanderbilt PPs Message-ID: Hello all, does anybody know how to fix the following problem with CPMD-3.5.2 ? Molecular-dynamics runs (CP, with Vanderbilt pseudopotentials!) crash during saving the RESTART file to disk. It happens AFTER step no. 499. (I.e. either at the end of the run or during the run when saving is forced by the STORE option. The current step number must be > 499 (or 400? I have not tested this detail)). The problem occurs regardless I use the OLDCODE or the NEWCODE option. The problem occured on all tested platforms (linux-intel, linux-alpha, IBM SP) both for serial and parallel runs. There are thousands of pointer values and the final error message at the end of the output file: PROGRAM STOPS IN SUBROUTINE FREEM| NO SUCH POINTER The RESTART file is corrupted. Below I give an example of my input file. Thank you. Martin Konopka. &CPMD RESTART WAVEFUNCTIONS COORDINATES LATEST STORE 100 MOLECULAR DYNAMICS CP TEMPERATURE 300.0D0 MAXSTEP 10000 NOSE IONS MASSIVE 300.0D0 5000.0D0 EMASS 400.0D0 TIMESTEP 5.0D0 ISOLATED MOLECULE SPLINE POINTS 2001 CENTER MOLECULE OFF MEMORY BIG &END &DFT OLDCODE GRADIENT CORRECTION PBEX PBEC GC-CUTOFF 5.0D-5 &END &SYSTEM SYMMETRY 0 POISSON SOLVER TUCKERMAN CELL 18.0D0 1.0D0 1.0D0 0.0D0 0.0D0 0.0D0 TESR 4 CUTOFF 25.0 CHARGE 0 &END &ATOMS *H.uspp BINARY NEWF TPSEU LMAX=S 4 12.283219853612 14.043432067385 14.632547670938 12.283219884482 10.523007602818 14.632547559271 12.283219848402 14.043432086306 9.933892047691 12.283219878999 10.523007612781 9.933892062564 *C.uspp BINARY NEWF TPSEU LMAX=P 2 12.283219923634 12.283219856387 13.545674119898 12.283219817584 12.283219892904 11.020765631812 &END ----------------------------------------- Martin Konopka Department of Physics, FEI STU Ilkovicova 3, 842 19 Bratislava, Slovakia tel: +421 2 60291 714 fax: +421 2 6541 1483 http://www.ccms.elf.stuba.sk/konopka.html ----------------------------------------- From erichu_linux at yahoo.com Fri Aug 16 23:44:43 2002 From: erichu_linux at yahoo.com (eric hu) Date: Fri, 16 Aug 2002 14:44:43 -0700 (PDT) Subject: [CPMD-list] circular dependency dropped In-Reply-To: Message-ID: <20020816214443.94332.qmail@web13401.mail.yahoo.com> Hi,I'm trying to use pgf90 to compile cpmd 3.5 on intel redhat 6.2. I have the following error: make: Circular cpmd.f <- cpmd.f dependency dropped. pgf90 -c -O4 -w -F -fast -I/home/users/erichu/pgi/linux86/include -I/home/users/erichu/mpich/include cpmd.f pgf90-Error-Output would overwrite file cpmd.f make: *** [cpmd.o] Error 1 Before this, compiling needs cpmd.f which is cpmd.F in the source code. Any suggestions are welcome. Eric __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From Ari.P.Seitsonen at iki.fi Sat Aug 17 14:01:36 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sat, 17 Aug 2002 14:01:36 +0200 Subject: [CPMD-list] circular dependency dropped In-Reply-To: <20020816214443.94332.qmail@web13401.mail.yahoo.com> (message from eric hu on Fri, 16 Aug 2002 14:44:43 -0700 (PDT)) References: <20020816214443.94332.qmail@web13401.mail.yahoo.com> Message-ID: <200208171201.g7HC1aH01072@magadino.cscs.ch> Ciao Eric, > Hi,I'm trying to use pgf90 to compile cpmd 3.5 on > intel redhat 6.2. I have the following error: > > make: Circular cpmd.f <- cpmd.f dependency dropped. > pgf90 -c -O4 -w -F -fast > -I/home/users/erichu/pgi/linux86/include > -I/home/users/erichu/mpich/include cpmd.f > pgf90-Error-Output would overwrite file cpmd.f > make: *** [cpmd.o] Error 1 > > Before this, compiling needs cpmd.f which is cpmd.F in > the source code. Any suggestions are welcome. Strange - for us this has always worked fine. How did you create the Makefile, just './Configure PC-PGI > Makefile'? Did you modify the Makefile after this? Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From hutter at pci.unizh.ch Sat Aug 17 15:11:43 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sat, 17 Aug 2002 15:11:43 +0200 (MEST) Subject: [CPMD-list] Size of cell for SURFACE/POLYMER ? In-Reply-To: Message-ID: Hi here some information on the keywords for isolated system calculations. There is some information in the manual and a discussion in the review - D. Marx and J. Hutter "Ab-initio Molecular Dynamics: Theory and Implementation", Modern Methods and Algorithms in Quantum Chemistry, Forschungzentrum Juelich, NIC Series, vol. 1, (2000). www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf All methods require that the charge density is zero at the border of the box. For normal systems this means that about 3 Angstrom space between the outermost atoms and the box should be enough. However, for some systems and for high accuracy this may not be enough. Some methods have additional requirements I will discuss later. ISOLATED SYSTEM keyword has only an effect on the calculation of the degrees of freedom (3N-6 vs. 3N-3 for periodic systems). CENTER MOLECULE ON/OFF: The main purpose of this is to center the molecule (center of mass) in the box. This is needed for the HOCKNEY Poisson solver. This solver gives wrong results if the charge density is not centered in the computational box. All other solvers behave like the periodic counterpart, i.e. the relative position of the charge density and the box are not important. Isolated systems (i.e. decoupling of the electrostatic images in the Poisson solver) are initialized with SYMMETRY 0 The box is assumed to be orthorhombic. Poisson solvers available are POISSON SOLVER {HOCKNEY,TUCKERMAN,MORTENSEN} HOCKNEY Method: - molecule has to be in the center of the box - box size molecule + 3 A border - expensive for very small systems - not available for some response calculations - SURFACE/POLYMER available but not tested use at own risk TUCKERMAN Method - box size : molecule + 3 A border AND 2*size of charge distribution - expensive for large systems, smaller boxes might be used without loosing too much accuracy SURFACE/POLYMER not available MORTENSEN Method - same as TUCKERMAN, but using analytic formulas made possible by using special boundary conditions (sphere, rod) - SURFACE/POLYMER available, should be save to use Remember: for many systems using a large enough cell and periodic boundary conditions is also an option! ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 15 Aug 2002 jarek at elrond.chem.uni.wroc.pl wrote: > Dear CPMD users, > > I have a question related to the latest discussion on the 2D calculations > in CPMD. What is the required cell length in the "non-periodic dimensions" > for SURFACE, POLYMER or, while we are at it, ISOLATED MOLECULE? The > standard supercell approach would require the sufficiently large length > for decoupling of the periodic images, but what about the options listed > above? Should we include, say, 3 or 4 A of "free space" from the most > protruding atoms? If anyone has got either a theoretical explanation or > the empirical rule of thumb, I would be happy for hearing it. > > And, of course, happy summer holidays to you all! > > Jaroslaw Panek > Faculty of Chemistry, University of Wroclaw > ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Sat Aug 17 16:07:47 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sat, 17 Aug 2002 16:07:47 +0200 (MEST) Subject: [CPMD-list] crashes during saving RESTART file, using Vanderbilt PPs In-Reply-To: Message-ID: Hi Martin you have found a real bug in the code! To fix this problem add the line ICON=1 in file forcedr.F after line 42 DO I=1,NUMX CALL UNITMX(XMAT1(1,I),NSTATE) ENDDO ICON=1 !new line ENDIF Thank you very much for reporting this problem. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 16 Aug 2002, Martin Konopka wrote: > Hello all, > > does anybody know how to fix the following problem with CPMD-3.5.2 ? > > Molecular-dynamics runs (CP, with Vanderbilt pseudopotentials!) crash > during saving the RESTART file to disk. > It happens AFTER step no. 499. (I.e. either at the end of the run or during > the run when saving is forced by the STORE option. The current step number > must be > 499 (or 400? I have not tested this detail)). > The problem occurs regardless I use the OLDCODE or the NEWCODE option. > > The problem occured on all tested platforms (linux-intel, linux-alpha, IBM SP) > both for serial and parallel runs. > There are thousands of pointer values and the final error message at the > end of the output file: > PROGRAM STOPS IN SUBROUTINE FREEM| NO SUCH POINTER > > The RESTART file is corrupted. Below I give an example of my input file. > Thank you. > > Martin Konopka. > > &CPMD > RESTART WAVEFUNCTIONS COORDINATES LATEST > STORE > 100 > MOLECULAR DYNAMICS CP > TEMPERATURE > 300.0D0 > MAXSTEP > 10000 > NOSE IONS MASSIVE > 300.0D0 5000.0D0 > EMASS > 400.0D0 > TIMESTEP > 5.0D0 > ISOLATED MOLECULE > SPLINE POINTS > 2001 > CENTER MOLECULE OFF > MEMORY BIG > &END > > &DFT > OLDCODE > GRADIENT CORRECTION PBEX PBEC > GC-CUTOFF > 5.0D-5 > &END > > &SYSTEM > SYMMETRY > 0 > POISSON SOLVER TUCKERMAN > CELL > 18.0D0 1.0D0 1.0D0 0.0D0 0.0D0 0.0D0 > TESR > 4 > CUTOFF > 25.0 > CHARGE > 0 > &END > > &ATOMS > *H.uspp BINARY NEWF TPSEU > LMAX=S > 4 > 12.283219853612 14.043432067385 14.632547670938 > 12.283219884482 10.523007602818 14.632547559271 > 12.283219848402 14.043432086306 9.933892047691 > 12.283219878999 10.523007612781 9.933892062564 > *C.uspp BINARY NEWF TPSEU > LMAX=P > 2 > 12.283219923634 12.283219856387 13.545674119898 > 12.283219817584 12.283219892904 11.020765631812 > &END > > > ----------------------------------------- > Martin Konopka > Department of Physics, FEI STU > Ilkovicova 3, 842 19 Bratislava, Slovakia > > tel: +421 2 60291 714 > fax: +421 2 6541 1483 > http://www.ccms.elf.stuba.sk/konopka.html > ----------------------------------------- > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From kissed at postech.ac.kr Sun Aug 18 10:27:31 2002 From: kissed at postech.ac.kr (kissed at postech.ac.kr) Date: Sun, 18 Aug 2002 17:27:31 +0900 Subject: [CPMD-list] =?iso-8859-1?B?TUQgY3Jhc2ggd2l0aCBtb3JlIHRoYW4gMiBub2RlIHVzaW5nIFZhbmRl?= =?iso-8859-1?B?cmJpbHQgUFBzIA==?= Message-ID: <20020818.AAA1029657792@postech.ac.kr> Dear All, I perform MD with 64 water using Vanderbilt PPs Molecular Dynamics runs crash if I use more than 2 nodes. With 1 node it does run. But with more than 2 cpus, it crash without any error messages. It stop after printing 192 H 5.738890 -0.027930 4.325696 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 576 EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS Thanks in advance SeungBum Suh &CPMD MOLECULAR DYNAMICS CP RESTART WAVEFUNCTION LATEST TRAJECTORY SAMPLE 10 TEMPERATURE 300. NOSE IONS MASSIVE 300.0D0 5000.0D0 MAXSTEP 1000 &END &SYSTEM ANGSTROM SYMMETRY 1 CELL 12.42066 1.0 1.0 0.0 0.0 0.0 CUTOFF 25. &END &DFT FUNCTIONAL BLYP GC-CUTOFF 5.D-5 &ATOMS *o_ps.uspp BINARY NEWF LMAX=P 64 -0.17126 -5.41610 0.28145 2.42316 -3.20667 -4.14817 -0.53403 -2.54222 0.35198 4.80161 -3.02471 4.40582 6.09046 5.96596 -2.27829 -3.41869 -2.57178 6.21276 -4.37821 5.44021 5.43889 -4.08700 1.60953 -0.51872 -5.26265 4.25588 0.53714 -0.77168 2.93568 -3.83648 -5.47005 0.42751 2.12088 4.00045 1.62657 -4.14302 -2.78215 4.15620 -1.21420 3.47914 -1.76760 6.34347 -3.43156 -2.33441 2.42388 -6.24424 -2.36158 2.21336 -2.43578 3.69615 3.35991 -5.25082 4.08025 3.31371 3.64274 5.75768 0.01891 1.79144 4.77391 2.30176 -4.00900 0.44235 5.83465 -5.50786 -4.40763 5.49496 -0.63109 4.46922 0.93437 4.36474 3.18870 0.35805 3.52892 -5.68090 -5.78709 -2.11450 -6.05570 -3.04451 0.24128 4.74218 -5.68843 2.16133 1.39663 5.61323 -5.27055 0.05798 -3.02493 2.85769 -3.78325 2.66752 0.71284 2.20911 0.35020 6.11184 -0.32698 -0.57160 -2.41116 -4.68944 1.63353 1.55802 3.98583 -2.77965 1.07942 -5.05263 -6.20751 0.20556 -4.18058 3.75533 5.56169 -3.89943 -4.62270 -1.01576 -3.46217 -4.84091 -1.48783 -1.97152 4.31933 -0.71629 0.11196 1.97306 5.02643 2.41201 2.96002 4.18600 4.56302 -3.43618 5.85441 -0.14821 -5.36109 1.30217 -1.60648 -1.51701 3.10854 1.82097 -1.59976 4.11271 -2.32757 -0.26337 1.21210 -1.09466 5.02285 -0.19417 0.98183 -1.88017 5.27948 -4.58827 0.92635 -3.03581 1.02445 3.08360 -2.14869 -0.78669 -0.93660 -2.39516 -5.60869 4.22371 3.21610 -4.45847 -1.76738 5.97877 -3.75652 -1.89803 -3.95814 -5.65363 -0.39767 2.71061 -0.06800 0.36588 3.74102 5.09289 4.29713 0.61641 6.65811 -2.44167 -4.39407 4.78246 -4.20190 -3.75957 2.14420 -4.23539 -3.74366 -2.72166 -1.85602 0.35851 -1.14328 -3.96970 -0.10272 3.08971 4.64402 3.21194 0.41042 3.15290 *h_ps.uspp BINARY NEWF LMAX=S 128 -0.14720 -6.27224 0.74485 0.22850 -5.69748 -0.57412 2.93553 -2.71516 -4.83168 2.18162 -3.99726 -4.66839 -0.42217 -3.50531 0.50143 0.23178 -2.37637 -0.22404 5.35619 -2.86686 3.60625 5.34644 -3.73879 4.80798 6.73170 5.35949 -2.70418 5.25826 5.71948 -2.73604 -2.66671 -2.71136 6.82195 -2.95517 -2.36641 5.37260 -3.61285 5.97444 5.13442 -4.61716 4.99291 4.59804 -4.72698 0.92776 -0.21437 -3.30121 1.04485 -0.67026 -4.80516 3.39856 0.42084 -6.08635 4.05073 0.04442 -1.74575 2.99092 -3.74106 -0.58583 2.28109 -3.12288 -5.86259 1.15064 2.64864 -4.53041 0.51445 2.35141 -3.48529 3.57844 -0.84991 -3.02858 4.13988 -2.16689 3.38530 1.53926 -4.90220 4.60796 0.87347 -4.30489 3.84088 -2.35356 5.64341 4.18351 -1.08357 6.40443 -2.68995 -2.04777 2.99047 -3.09907 -3.21564 2.17170 -5.29132 -2.56961 2.32487 -6.19804 -1.38645 2.20316 -3.38363 3.92501 3.30471 -2.05004 4.39115 2.78382 -5.80799 3.28779 3.19888 -5.12789 4.37309 2.39206 4.45913 6.16966 0.35227 3.40750 6.40763 -0.67966 0.91070 4.75440 1.86830 2.32283 5.12962 1.55681 -4.10981 0.22257 4.88968 -3.35967 -0.21949 6.13692 -4.75346 -3.81558 5.70222 -5.07573 -5.27807 5.59654 -1.42205 4.29288 0.38331 -0.03898 3.74003 0.64191 3.86215 4.01313 0.17829 4.15123 2.70089 -0.46503 3.88179 -6.42502 -5.25752 3.70328 -6.01216 -6.69003 -2.89886 -6.34693 -3.54616 -2.45694 -6.13693 -2.12715 0.09139 4.28485 -6.54055 -0.10687 4.05419 -5.08142 2.93787 1.57196 5.03557 1.47971 1.97168 5.20983 -4.62431 -0.68006 -2.96716 -5.64114 -0.00417 -2.12036 3.27795 -4.40384 2.04023 3.60946 -3.58624 3.26806 1.64096 1.87226 0.26773 0.34390 1.82895 -0.47833 5.42401 -1.01201 -0.70232 6.10284 -0.29445 0.41052 -3.03599 -5.11011 0.99651 -1.58905 -4.97510 1.18933 0.94301 3.55886 -3.40797 1.80284 3.25135 -2.17177 2.05398 -5.12674 -6.30011 0.90192 -5.88528 -5.71888 0.55947 -4.56938 4.57272 1.02743 -3.85703 3.32547 4.86547 -4.46495 -5.00286 6.22100 -3.89422 -5.35172 -0.52295 -4.18605 -5.27975 -1.70143 -3.94730 -4.33239 -0.62894 -1.55206 4.53862 -1.14827 -2.80924 3.94076 -0.38951 -0.80414 1.86143 0.03544 0.65958 1.67810 4.50234 2.43608 2.12858 4.57302 1.69245 3.45154 4.28034 3.68481 -3.86135 3.23063 4.53845 -3.21178 6.63188 0.06925 -5.90943 6.25822 -0.29945 -4.48865 1.82177 -2.35804 -1.89003 0.78658 -1.35931 -2.32158 3.57809 1.66097 -2.44417 3.20955 0.94874 -1.16667 4.34469 -2.99729 -0.94262 4.01618 -2.90002 0.53286 1.67691 -1.53454 5.75815 1.37948 -0.16495 5.24412 0.10897 0.63349 -2.74501 -0.59403 0.17867 -1.49805 5.61156 -3.80883 1.42851 5.69800 -4.38706 0.05678 -2.33945 0.51783 2.62134 -2.55411 1.86562 3.22000 -2.73425 -1.48221 -1.31079 -1.77030 -1.25934 -0.16609 -2.52766 -5.38801 3.27666 -1.48480 -5.26771 4.36689 2.33516 -4.88609 -1.84246 3.26769 -4.02907 -2.63955 5.87936 -4.72397 -1.99733 5.70875 -3.48800 -2.79131 -4.24088 -6.58315 -0.26236 -4.72368 -5.33905 -0.91547 2.06501 -0.43280 -0.28503 3.38785 -0.77569 0.37114 2.95917 5.13262 3.71046 4.18691 4.29853 3.96100 -0.15638 6.53226 -3.03614 1.06427 5.79911 -2.63059 -4.52883 4.93638 -5.15560 -4.58052 3.82136 -4.18131 -3.90869 1.66129 -5.07771 -4.42450 1.70038 -3.66457 -3.39213 -3.56409 -1.52108 -4.68808 -2.91136 -1.98057 -0.43465 -1.68911 -4.16111 1.04889 -1.70251 -4.39379 -1.06466 3.20145 4.49473 0.21845 3.12190 3.71923 2.96108 -0.30991 3.76887 3.03689 -0.01478 2.28906 &END -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020818/f034d0d9/attachment.html From kissed at postech.ac.kr Sun Aug 18 14:58:22 2002 From: kissed at postech.ac.kr (kissed at postech.ac.kr) Date: Sun, 18 Aug 2002 21:58:22 +0900 Subject: [CPMD-list] =?iso-8859-1?B?TUQgY3Jhc2ggd2l0aCBtb3JlIHRoYW4gMiBub2RlcyB1c2luZyBWYW5k?= =?iso-8859-1?B?ZXJiaWx0IFBQcyAocmVwb3N0KQ==?= Message-ID: <20020818.AAA1029675398@postech.ac.kr> Dear All, I perform MD with 64 water using Vanderbilt PPs Molecular Dynamics runs crash if I use more than 2 nodes. With 1 node it does run. But with more than 2 cpus , it crash without any error messages. It stops after printing 192 H 5.738890 -0.027930 4.325696 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 576 EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS Thanks in advance SeungBum Suh &CPMD MOLECULAR DYNAMICS CP RESTART WAVEFUNCTION LATEST TRAJECTORY SAMPLE 10 TEMPERATURE 300. NOSE IONS MASSIVE 300.0D0 5000.0D0 MAXSTEP 1000 &END &SYSTEM ANGSTROM SYMMETRY 1 CELL 12.42066 1.0 1.0 0.0 0.0 0.0 CUTOFF 25. &END &DFT FUNCTIONAL BLYP GC-CUTOFF 5.D-5 &ATOMS *o_ps.uspp BINARY NEWF LMAX=P 64 -0.17126 -5.41610 0.28145 2.42316 -3.20667 -4.14817 -0.53403 -2.54222 0.35198 4.80161 -3.02471 4.40582 6.09046 5.96596 -2.27829 -3.41869 -2.57178 6.21276 -4.37821 5.44021 5.43889 -4.08700 1.60953 -0.51872 -5.26265 4.25588 0.53714 -0.77168 2.93568 -3.83648 -5.47005 0.42751 2.12088 4.00045 1.62657 -4.14302 -2.78215 4.15620 -1.21420 3.47914 -1.76760 6.34347 -3.43156 -2.33441 2.42388 -6.24424 -2.36158 2.21336 -2.43578 3.69615 3.35991 -5.25082 4.08025 3.31371 3.64274 5.75768 0.01891 1.79144 4.77391 2.30176 -4.00900 0.44235 5.83465 -5.50786 -4.40763 5.49496 -0.63109 4.46922 0.93437 4.36474 3.18870 0.35805 3.52892 -5.68090 -5.78709 -2.11450 -6.05570 -3.04451 0.24128 4.74218 -5.68843 2.16133 1.39663 5.61323 -5.27055 0.05798 -3.02493 2.85769 -3.78325 2.66752 0.71284 2.20911 0.35020 6.11184 -0.32698 -0.57160 -2.41116 -4.68944 1.63353 1.55802 3.98583 -2.77965 1.07942 -5.05263 -6.20751 0.20556 -4.18058 3.75533 5.56169 -3.89943 -4.62270 -1.01576 -3.46217 -4.84091 -1.48783 -1.97152 4.31933 -0.71629 0.11196 1.97306 5.02643 2.41201 2.96002 4.18600 4.56302 -3.43618 5.85441 -0.14821 -5.36109 1.30217 -1.60648 -1.51701 3.10854 1.82097 -1.59976 4.11271 -2.32757 -0.26337 1.21210 -1.09466 5.02285 -0.19417 0.98183 -1.88017 5.27948 -4.58827 0.92635 -3.03581 1.02445 3.08360 -2.14869 -0.78669 -0.93660 -2.39516 -5.60869 4.22371 3.21610 -4.45847 -1.76738 5.97877 -3.75652 -1.89803 -3.95814 -5.65363 -0.39767 2.71061 -0.06800 0.36588 3.74102 5.09289 4.29713 0.61641 6.65811 -2.44167 -4.39407 4.78246 -4.20190 -3.75957 2.14420 -4.23539 -3.74366 -2.72166 -1.85602 0.35851 -1.14328 -3.96970 -0.10272 3.08971 4.64402 3.21194 0.41042 3.15290 *h_ps.uspp BINARY NEWF LMAX=S 128 -0.14720 -6.27224 0.74485 0.22850 -5.69748 -0.57412 2.93553 -2.71516 -4.83168 2.18162 -3.99726 -4.66839 -0.42217 -3.50531 0.50143 0.23178 -2.37637 -0.22404 5.35619 -2.86686 3.60625 5.34644 -3.73879 4.80798 6.73170 5.35949 -2.70418 5.25826 5.71948 -2.73604 -2.66671 -2.71136 6.82195 -2.95517 -2.36641 5.37260 -3.61285 5.97444 5.13442 -4.61716 4.99291 4.59804 -4.72698 0.92776 -0.21437 -3.30121 1.04485 -0.67026 -4.80516 3.39856 0.42084 -6.08635 4.05073 0.04442 -1.74575 2.99092 -3.74106 -0.58583 2.28109 -3.12288 -5.86259 1.15064 2.64864 -4.53041 0.51445 2.35141 -3.48529 3.57844 -0.84991 -3.02858 4.13988 -2.16689 3.38530 1.53926 -4.90220 4.60796 0.87347 -4.30489 3.84088 -2.35356 5.64341 4.18351 -1.08357 6.40443 -2.68995 -2.04777 2.99047 -3.09907 -3.21564 2.17170 -5.29132 -2.56961 2.32487 -6.19804 -1.38645 2.20316 -3.38363 3.92501 3.30471 -2.05004 4.39115 2.78382 -5.80799 3.28779 3.19888 -5.12789 4.37309 2.39206 4.45913 6.16966 0.35227 3.40750 6.40763 -0.67966 0.91070 4.75440 1.86830 2.32283 5.12962 1.55681 -4.10981 0.22257 4.88968 -3.35967 -0.21949 6.13692 -4.75346 -3.81558 5.70222 -5.07573 -5.27807 5.59654 -1.42205 4.29288 0.38331 -0.03898 3.74003 0.64191 3.86215 4.01313 0.17829 4.15123 2.70089 -0.46503 3.88179 -6.42502 -5.25752 3.70328 -6.01216 -6.69003 -2.89886 -6.34693 -3.54616 -2.45694 -6.13693 -2.12715 0.09139 4.28485 -6.54055 -0.10687 4.05419 -5.08142 2.93787 1.57196 5.03557 1.47971 1.97168 5.20983 -4.62431 -0.68006 -2.96716 -5.64114 -0.00417 -2.12036 3.27795 -4.40384 2.04023 3.60946 -3.58624 3.26806 1.64096 1.87226 0.26773 0.34390 1.82895 -0.47833 5.42401 -1.01201 -0.70232 6.10284 -0.29445 0.41052 -3.03599 -5.11011 0.99651 -1.58905 -4.97510 1.18933 0.94301 3.55886 -3.40797 1.80284 3.25135 -2.17177 2.05398 -5.12674 -6.30011 0.90192 -5.88528 -5.71888 0.55947 -4.56938 4.57272 1.02743 -3.85703 3.32547 4.86547 -4.46495 -5.00286 6.22100 -3.89422 -5.35172 -0.52295 -4.18605 -5.27975 -1.70143 -3.94730 -4.33239 -0.62894 -1.55206 4.53862 -1.14827 -2.80924 3.94076 -0.38951 -0.80414 1.86143 0.03544 0.65958 1.67810 4.50234 2.43608 2.12858 4.57302 1.69245 3.45154 4.28034 3.68481 -3.86135 3.23063 4.53845 -3.21178 6.63188 0.06925 -5.90943 6.25822 -0.29945 -4.48865 1.82177 -2.35804 -1.89003 0.78658 -1.35931 -2.32158 3.57809 1.66097 -2.44417 3.20955 0.94874 -1.16667 4.34469 -2.99729 -0.94262 4.01618 -2.90002 0.53286 1.67691 -1.53454 5.75815 1.37948 -0.16495 5.24412 0.10897 0.63349 -2.74501 -0.59403 0.17867 -1.49805 5.61156 -3.80883 1.42851 5.69800 -4.38706 0.05678 -2.33945 0.51783 2.62134 -2.55411 1.86562 3.22000 -2.73425 -1.48221 -1.31079 -1.77030 -1.25934 -0.16609 -2.52766 -5.38801 3.27666 -1.48480 -5.26771 4.36689 2.33516 -4.88609 -1.84246 3.26769 -4.02907 -2.63955 5.87936 -4.72397 -1.99733 5.70875 -3.48800 -2.79131 -4.24088 -6.58315 -0.26236 -4.72368 -5.33905 -0.91547 2.06501 -0.43280 -0.28503 3.38785 -0.77569 0.37114 2.95917 5.13262 3.71046 4.18691 4.29853 3.96100 -0.15638 6.53226 -3.03614 1.06427 5.79911 -2.63059 -4.52883 4.93638 -5.15560 -4.58052 3.82136 -4.18131 -3.90869 1.66129 -5.07771 -4.42450 1.70038 -3.66457 -3.39213 -3.56409 -1.52108 -4.68808 -2.91136 -1.98057 -0.43465 -1.68911 -4.16111 1.04889 -1.70251 -4.39379 -1.06466 3.20145 4.49473 0.21845 3.12190 3.71923 2.96108 -0.30991 3.76887 3.03689 -0.01478 2.28906 &END From hutter at pci.unizh.ch Sun Aug 18 17:46:41 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 18 Aug 2002 17:46:41 +0200 (MEST) Subject: [CPMD-list] =?iso-8859-1?B?TUQgY3Jhc2ggd2l0aCBtb3JlIHRoYW4gMiBub2RlIHVzaW5nIFZhbmRl?= =?iso-8859-1?B?cmJpbHQgUFBzIA==?= In-Reply-To: <20020818.AAA1029657792@postech.ac.kr> Message-ID: Hi the problem is in file noforce.F : you have to change line 171. C ==--------------------------------------------------------------== C == ROTATE ELECTRONIC FORCE BACK INTO NONORTHOGONAL BASIS == C ==--------------------------------------------------------------== IF(PARENT) CALL DCOPY(NSTATE*NSTATE,XMAT2(1,1),1,SMAT(1),1) ^^^^^^^^^^ || this is new This should fix the code. BTW. I assume you are familiar with the implications of the option : NOSE IONS MASSIVE ------- If not, I propose to use the standard thermostats (NOSE IONS). regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sun, 18 Aug 2002 kissed at postech.ac.kr wrote: > Dear All, > > I perform MD with 64 water using Vanderbilt PPs > Molecular Dynamics runs crash if I use more than 2 nodes. > With 1 node it does run. > But with more than 2 cpus, it crash without any error messages. > It stop after printing > > 192 H 5.738890 -0.027930 4.325696 > **************************************************************** > > > DEGREES OF FREEDOM FOR SYSTEM: 576 > > EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS > > Thanks in advance > > SeungBum Suh > > > > &CPMD > MOLECULAR DYNAMICS CP > RESTART WAVEFUNCTION LATEST > TRAJECTORY SAMPLE > 10 > TEMPERATURE > 300. > NOSE IONS MASSIVE > 300.0D0 5000.0D0 > MAXSTEP > 1000 > &END > &SYSTEM > ANGSTROM > SYMMETRY > 1 > CELL > 12.42066 1.0 1.0 0.0 0.0 0.0 > CUTOFF > 25. > &END > &DFT > FUNCTIONAL BLYP > GC-CUTOFF > 5.D-5 > &ATOMS > *o_ps.uspp BINARY NEWF > LMAX=P > 64 > -0.17126 -5.41610 0.28145 > 2.42316 -3.20667 -4.14817 > -0.53403 -2.54222 0.35198 > 4.80161 -3.02471 4.40582 > 6.09046 5.96596 -2.27829 > -3.41869 -2.57178 6.21276 > -4.37821 5.44021 5.43889 > -4.08700 1.60953 -0.51872 > -5.26265 4.25588 0.53714 > -0.77168 2.93568 -3.83648 > -5.47005 0.42751 2.12088 > 4.00045 1.62657 -4.14302 > -2.78215 4.15620 -1.21420 > 3.47914 -1.76760 6.34347 > -3.43156 -2.33441 2.42388 > -6.24424 -2.36158 2.21336 > -2.43578 3.69615 3.35991 > -5.25082 4.08025 3.31371 > 3.64274 5.75768 0.01891 > 1.79144 4.77391 2.30176 > -4.00900 0.44235 5.83465 > -5.50786 -4.40763 5.49496 > -0.63109 4.46922 0.93437 > 4.36474 3.18870 0.35805 > 3.52892 -5.68090 -5.78709 > -2.11450 -6.05570 -3.04451 > 0.24128 4.74218 -5.68843 > 2.16133 1.39663 5.61323 > -5.27055 0.05798 -3.02493 > 2.85769 -3.78325 2.66752 > 0.71284 2.20911 0.35020 > 6.11184 -0.32698 -0.57160 > -2.41116 -4.68944 1.63353 > 1.55802 3.98583 -2.77965 > 1.07942 -5.05263 -6.20751 > 0.20556 -4.18058 3.75533 > 5.56169 -3.89943 -4.62270 > -1.01576 -3.46217 -4.84091 > -1.48783 -1.97152 4.31933 > -0.71629 0.11196 1.97306 > 5.02643 2.41201 2.96002 > 4.18600 4.56302 -3.43618 > 5.85441 -0.14821 -5.36109 > 1.30217 -1.60648 -1.51701 > 3.10854 1.82097 -1.59976 > 4.11271 -2.32757 -0.26337 > 1.21210 -1.09466 5.02285 > -0.19417 0.98183 -1.88017 > 5.27948 -4.58827 0.92635 > -3.03581 1.02445 3.08360 > -2.14869 -0.78669 -0.93660 > -2.39516 -5.60869 4.22371 > 3.21610 -4.45847 -1.76738 > 5.97877 -3.75652 -1.89803 > -3.95814 -5.65363 -0.39767 > 2.71061 -0.06800 0.36588 > 3.74102 5.09289 4.29713 > 0.61641 6.65811 -2.44167 > -4.39407 4.78246 -4.20190 > -3.75957 2.14420 -4.23539 > -3.74366 -2.72166 -1.85602 > 0.35851 -1.14328 -3.96970 > -0.10272 3.08971 4.64402 > 3.21194 0.41042 3.15290 > *h_ps.uspp BINARY NEWF > LMAX=S > 128 > -0.14720 -6.27224 0.74485 > 0.22850 -5.69748 -0.57412 > 2.93553 -2.71516 -4.83168 > 2.18162 -3.99726 -4.66839 > -0.42217 -3.50531 0.50143 > 0.23178 -2.37637 -0.22404 > 5.35619 -2.86686 3.60625 > 5.34644 -3.73879 4.80798 > 6.73170 5.35949 -2.70418 > 5.25826 5.71948 -2.73604 > -2.66671 -2.71136 6.82195 > -2.95517 -2.36641 5.37260 > -3.61285 5.97444 5.13442 > -4.61716 4.99291 4.59804 > -4.72698 0.92776 -0.21437 > -3.30121 1.04485 -0.67026 > -4.80516 3.39856 0.42084 > -6.08635 4.05073 0.04442 > -1.74575 2.99092 -3.74106 > -0.58583 2.28109 -3.12288 > -5.86259 1.15064 2.64864 > -4.53041 0.51445 2.35141 > -3.48529 3.57844 -0.84991 > -3.02858 4.13988 -2.16689 > 3.38530 1.53926 -4.90220 > 4.60796 0.87347 -4.30489 > 3.84088 -2.35356 5.64341 > 4.18351 -1.08357 6.40443 > -2.68995 -2.04777 2.99047 > -3.09907 -3.21564 2.17170 > -5.29132 -2.56961 2.32487 > -6.19804 -1.38645 2.20316 > -3.38363 3.92501 3.30471 > -2.05004 4.39115 2.78382 > -5.80799 3.28779 3.19888 > -5.12789 4.37309 2.39206 > 4.45913 6.16966 0.35227 > 3.40750 6.40763 -0.67966 > 0.91070 4.75440 1.86830 > 2.32283 5.12962 1.55681 > -4.10981 0.22257 4.88968 > -3.35967 -0.21949 6.13692 > -4.75346 -3.81558 5.70222 > -5.07573 -5.27807 5.59654 > -1.42205 4.29288 0.38331 > -0.03898 3.74003 0.64191 > 3.86215 4.01313 0.17829 > 4.15123 2.70089 -0.46503 > 3.88179 -6.42502 -5.25752 > 3.70328 -6.01216 -6.69003 > -2.89886 -6.34693 -3.54616 > -2.45694 -6.13693 -2.12715 > 0.09139 4.28485 -6.54055 > -0.10687 4.05419 -5.08142 > 2.93787 1.57196 5.03557 > 1.47971 1.97168 5.20983 > -4.62431 -0.68006 -2.96716 > -5.64114 -0.00417 -2.12036 > 3.27795 -4.40384 2.04023 > 3.60946 -3.58624 3.26806 > 1.64096 1.87226 0.26773 > 0.34390 1.82895 -0.47833 > 5.42401 -1.01201 -0.70232 > 6.10284 -0.29445 0.41052 > -3.03599 -5.11011 0.99651 > -1.58905 -4.97510 1.18933 > 0.94301 3.55886 -3.40797 > 1.80284 3.25135 -2.17177 > 2.05398 -5.12674 -6.30011 > 0.90192 -5.88528 -5.71888 > 0.55947 -4.56938 4.57272 > 1.02743 -3.85703 3.32547 > 4.86547 -4.46495 -5.00286 > 6.22100 -3.89422 -5.35172 > -0.52295 -4.18605 -5.27975 > -1.70143 -3.94730 -4.33239 > -0.62894 -1.55206 4.53862 > -1.14827 -2.80924 3.94076 > -0.38951 -0.80414 1.86143 > 0.03544 0.65958 1.67810 > 4.50234 2.43608 2.12858 > 4.57302 1.69245 3.45154 > 4.28034 3.68481 -3.86135 > 3.23063 4.53845 -3.21178 > 6.63188 0.06925 -5.90943 > 6.25822 -0.29945 -4.48865 > 1.82177 -2.35804 -1.89003 > 0.78658 -1.35931 -2.32158 > 3.57809 1.66097 -2.44417 > 3.20955 0.94874 -1.16667 > 4.34469 -2.99729 -0.94262 > 4.01618 -2.90002 0.53286 > 1.67691 -1.53454 5.75815 > 1.37948 -0.16495 5.24412 > 0.10897 0.63349 -2.74501 > -0.59403 0.17867 -1.49805 > 5.61156 -3.80883 1.42851 > 5.69800 -4.38706 0.05678 > -2.33945 0.51783 2.62134 > -2.55411 1.86562 3.22000 > -2.73425 -1.48221 -1.31079 > -1.77030 -1.25934 -0.16609 > -2.52766 -5.38801 3.27666 > -1.48480 -5.26771 4.36689 > 2.33516 -4.88609 -1.84246 > 3.26769 -4.02907 -2.63955 > 5.87936 -4.72397 -1.99733 > 5.70875 -3.48800 -2.79131 > -4.24088 -6.58315 -0.26236 > -4.72368 -5.33905 -0.91547 > 2.06501 -0.43280 -0.28503 > 3.38785 -0.77569 0.37114 > 2.95917 5.13262 3.71046 > 4.18691 4.29853 3.96100 > -0.15638 6.53226 -3.03614 > 1.06427 5.79911 -2.63059 > -4.52883 4.93638 -5.15560 > -4.58052 3.82136 -4.18131 > -3.90869 1.66129 -5.07771 > -4.42450 1.70038 -3.66457 > -3.39213 -3.56409 -1.52108 > -4.68808 -2.91136 -1.98057 > -0.43465 -1.68911 -4.16111 > 1.04889 -1.70251 -4.39379 > -1.06466 3.20145 4.49473 > 0.21845 3.12190 3.71923 > 2.96108 -0.30991 3.76887 > 3.03689 -0.01478 2.28906 > &END > > > > > > From kissed at postech.ac.kr Mon Aug 19 06:14:58 2002 From: kissed at postech.ac.kr (SeungBum Suh) Date: Mon, 19 Aug 2002 13:14:58 +0900 Subject: [CPMD-list] writing Density every few steps Message-ID: <021c01c24736$fb4081b0$407fdf8d@LocalHost> Dear all, I want to investigate Density change during a MD simulation. To do this, I have to write density every few steps. There is subroutine DHOPRI which writes density files. Can I put this routine in main MD loop? Is this routine change some variables? Thanks in advance SeungBum Suh From kissed at postech.ac.kr Mon Aug 19 06:47:27 2002 From: kissed at postech.ac.kr (SeungBum Suh) Date: Mon, 19 Aug 2002 13:47:27 +0900 Subject: [CPMD-list] ibm p690 64bit compile problem Message-ID: <026901c2473b$848338b0$407fdf8d@LocalHost> Dear all I compiled CPMD in ibm p690 with MPI & 64bit mode. With 32bit mode, It does not have any problem. But with 64bit mode, It write core with 'ERROR: 0031-250 task 0: Segmentation fault' I think there is problem in memory allocation. Thanks in advance SeungBum Suh From tfysg at fy.chalmers.se Mon Aug 19 08:35:25 2002 From: tfysg at fy.chalmers.se (Shiwu Gao) Date: Mon, 19 Aug 2002 08:35:25 +0200 Subject: [CPMD-list] Slow convergence with surface calculations References: Message-ID: <3D6091AD.B6846C17@fy.chalmers.se> Hi, I was trying to optimize the wavefunction of a Ag(110) surface with CPMD. The convergence is extemely slow. At some stage, the calculation can not gets better, the typical output looks this, ---------------------------------------------------------------------- 586 1.826E-03 1.439E-04 -3211.132742 6.223E-03 27.70 ODIIS| Insufficient progress; reset! 587 3.384E-04 3.336E-05 -3211.138854 -6.112E-03 26.41 588 3.097E-03 2.982E-04 -3211.130273 8.581E-03 26.11 589 7.925E-04 6.519E-05 -3211.138705 -8.432E-03 26.96 590 3.273E-04 1.751E-05 -3211.139188 -4.824E-04 26.77 591 3.376E-04 1.319E-05 -3211.139248 -5.974E-05 26.92 592 3.427E-04 9.324E-06 -3211.139297 -4.982E-05 27.05 593 3.372E-04 7.054E-06 -3211.139344 -4.654E-05 26.85 594 3.388E-04 1.027E-05 -3211.139451 -1.070E-04 26.97 595 1.293E-03 1.008E-04 -3211.135294 4.157E-03 27.09 596 3.386E-04 7.014E-06 -3211.139096 -3.802E-03 26.46 597 3.395E-04 6.826E-06 -3211.139109 -1.347E-05 27.85 598 3.350E-04 1.909E-05 -3211.138445 6.640E-04 27.78 599 3.353E-04 2.010E-05 -3211.138577 -1.318E-04 26.41 ODIIS| Insufficient progress; reset! 600 8.653E-04 9.429E-05 -3211.135636 2.941E-03 26.42 601 1.010E-02 1.010E-03 -3211.046595 8.904E-02 26.14 602 1.548E-03 1.165E-04 -3211.134862 -8.827E-02 26.24 603 4.091E-04 3.887E-05 -3211.136805 -1.943E-03 26.94 604 4.192E-04 3.997E-05 -3211.136854 -4.923E-05 26.38 605 3.237E-04 1.982E-05 -3211.137049 -1.949E-04 26.23 ----------------------------------------------------------------------- When running the same cell with FP-LAPW method. The calculation converges within 15-20 iterations, although each iteration with FLAPW takes more than 20 time longer time than an electronic step in CPMD. I understand that slow convergence is not a unfamiliar problem with CPMD in a surface calculation. My questions is: Is there any tricks one can play in CPMD to accelerate the convergences? Or we should turn to other methods for a surface calculation? Thanks for any hint/help, Shiwu -------------------------------------------------------------------------- My input file for a Ag(110) surface is as follows # O2 on Ag(110) 5x3x5--12 slab &CPMD OPTIMIZE WAVEFUNCTION ODIIS 60 STRUCTURE BONDS ANGLES DIHEDRAS SPLINE QFUNCTIONS POINTS 6000 BIG MEMORY &END &SYSTEM SYMMETRY 8 SURFACE TESR 4 CELL ABSOLUTE DEGREE 27.299375 23.164300 32.759236 90.000000 90.000000 90.000000 CUTOFF 25. POISSON SOLVER MORTENSEN &END &ATOMS *ag_ps.uspp BINARY NEWF LMAX=D 75 0.00000000 0.00000000 16.37961800 5.45987500 0.00000000 16.37961800 21.83950000 0.00000000 16.37961800 ................... 10.91975000 7.72143326 10.91974522 21.83950000 15.44286674 21.83949078 5.45987500 7.72143326 10.91974522 &END &DFT FUNCTIONAL PBE &END &PROP PROJECT WAVEFUNCTION &END From Ari.P.Seitsonen at iki.fi Mon Aug 19 10:22:43 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Mon, 19 Aug 2002 10:22:43 +0200 Subject: [CPMD-list] ibm p690 64bit compile problem In-Reply-To: <026901c2473b$848338b0$407fdf8d@LocalHost> (kissed@postech.ac.kr) References: <026901c2473b$848338b0$407fdf8d@LocalHost> Message-ID: <200208190822.g7J8MhD24388@magadino.cscs.ch> Dear SeungBum, > I compiled CPMD in ibm p690 with MPI & 64bit mode. > With 32bit mode, It does not have any problem. > But with 64bit mode, It write core with > 'ERROR: 0031-250 task 0: Segmentation fault' > I think there is problem in memory allocation. Did you compile the code with or without the option '-DPOINTER8' for the preprocessor? I seem to remember that changing this helped... (We don't have access to the p690 currently so I cannot check which way it should be) Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From Ari.P.Seitsonen at iki.fi Mon Aug 19 12:08:19 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Mon, 19 Aug 2002 12:08:19 +0200 Subject: [CPMD-list] Slow convergence with surface calculations In-Reply-To: <3D6091AD.B6846C17@fy.chalmers.se> (message from Shiwu Gao on Mon, 19 Aug 2002 08:35:25 +0200) References: <3D6091AD.B6846C17@fy.chalmers.se> Message-ID: <200208191008.g7JA8JT00699@magadino.cscs.ch> Dear Shiwu, > I was trying to optimize the wavefunction of a Ag(110) > surface with CPMD. The convergence is extemely slow. At some > stage, the calculation can not gets better, the typical output > looks this, > ---------------------------------------------------------------------- > 597 3.395E-04 6.826E-06 -3211.139109 -1.347E-05 27.85 > 598 3.350E-04 1.909E-05 -3211.138445 6.640E-04 27.78 > 599 3.353E-04 2.010E-05 -3211.138577 -1.318E-04 26.41 > ODIIS| Insufficient progress; reset! > 600 8.653E-04 9.429E-05 -3211.135636 2.941E-03 26.42 > 601 1.010E-02 1.010E-03 -3211.046595 8.904E-02 26.14 > 602 1.548E-03 1.165E-04 -3211.134862 -8.827E-02 26.24 > 603 4.091E-04 3.887E-05 -3211.136805 -1.943E-03 26.94 > 604 4.192E-04 3.997E-05 -3211.136854 -4.923E-05 26.38 > 605 3.237E-04 1.982E-05 -3211.137049 -1.949E-04 26.23 > ----------------------------------------------------------------------- > > When running the same cell with FP-LAPW method. The calculation > converges > within 15-20 iterations, although each iteration with FLAPW takes > more than 20 time longer time than an electronic step in CPMD. > I understand that slow convergence is not a unfamiliar problem with CPMD > in a surface calculation. My questions is: Is there any tricks one can > play in CPMD to accelerate the convergences? Or we should turn to > other methods for a surface calculation? You don't use any broadening of the occupation numbers, which is most likely done in the FLAPW calculation (or maybe you use the tetrahedron method to integrate over the Brillouin zone). The convergence is VERY difficult, if not impossible, to achieve without a trick there. Maybe the mixing of the electron density would work, maybe switching to the finite temperature formalism (yet this is heavier than pure ODIIS in the current implementation). However, I would probably first try to anneal the wave functions in an MD run, and then use the Nos? thermostat during the MD (in case you are planning to do dynamics on your system). Sincerely, apsi > -------------------------------------------------------------------------- > My input file for a Ag(110) surface is as follows > > # O2 on Ag(110) 5x3x5--12 slab > &CPMD > OPTIMIZE WAVEFUNCTION > ODIIS > 60 > STRUCTURE BONDS ANGLES DIHEDRAS > SPLINE QFUNCTIONS POINTS > 6000 > BIG MEMORY > &END > &SYSTEM > SYMMETRY > 8 > SURFACE > TESR > 4 > CELL ABSOLUTE DEGREE > 27.299375 23.164300 32.759236 90.000000 90.000000 90.000000 > CUTOFF > 25. > POISSON SOLVER MORTENSEN > &END > &ATOMS > *ag_ps.uspp BINARY NEWF > LMAX=D > 75 > 0.00000000 0.00000000 16.37961800 > 5.45987500 0.00000000 16.37961800 > 21.83950000 0.00000000 16.37961800 > ................... > 10.91975000 7.72143326 10.91974522 > 21.83950000 15.44286674 21.83949078 > 5.45987500 7.72143326 10.91974522 > > &END > _______________________________________________ -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From chrirena at techunix.technion.ac.il Tue Aug 6 14:33:48 2002 From: chrirena at techunix.technion.ac.il (Irena Efremenko) Date: Tue, 06 Aug 2002 15:33:48 +0300 Subject: [CPMD-list] lattice parameters Message-ID: <3D4FC22C.8060404@tx.technion.ac.il> Dear CPMD users, I am new in periodic DFT calculations. As I understand, before modeling a surface, I have to optimize lattice parameters in bulk in order to choose appropriate size of supercell. Can somebody here explain me how to perform this first calculation? Thanks in advance, Irena -- Dr. Irena Efremenko Wolfson Department of Chemical Engineering Technion - Israel Institute of Technology Haifa 32000, Israel Phone: 972-4-8293561 Fax: 972-4-8230476 From b.zarychta at phys.keele.ac.uk Thu Aug 15 15:09:44 2002 From: b.zarychta at phys.keele.ac.uk (Zak) Date: Thu, 15 Aug 2002 14:09:44 +0100 Subject: [CPMD-list] cpmd2cube Message-ID: <000f01c2445d$065b76e0$5f5005a0@phys.keele.ac.uk> One and all, I have recently compiled cpmd2cube sucessfully, however I cannot get it to process any files succesfully. Does any one have a working examples of input/output files for cpmd with which they have used with cpmd2cube ? Any help would be greatly appreciated Zak -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020815/35db62bd/attachment.html From sbsuh at csm50.postech.ac.kr Fri Aug 16 08:39:08 2002 From: sbsuh at csm50.postech.ac.kr (SeungBum Suh) Date: Fri, 16 Aug 2002 15:39:08 +0900 Subject: [CPMD-list] Ultra pseudo-potential question & problem compile on ibm with 64bit Message-ID: <016401c244ef$a09b73d0$407fdf8d@LocalHost> Dear All, I have two question. 1. I heard that there is problem in CPMD doing MD simulation with ultra soft pseudo-potential. Is the error corrected in the new version 3.5.2 fully? 2. I compiled CPMD in ibm p690 with MPI & 64bit mode. With 32bit mode, It does not have any problem. But with 64bit mode, It write core with 'ERROR: 0031-250 task 0: Segmentation fault'. I think there is problem in memory.F. Thanks in advance. SeungBum Suh From urs at zimmer.li Fri Aug 16 17:59:02 2002 From: urs at zimmer.li (Urs Zimmerli) Date: Fri, 16 Aug 2002 08:59:02 -0700 Subject: [CPMD-list] Surface Setup -- inconsistent behaviour? References: <60116.148.187.130.154.1029405043.squirrel@spurious.biz> <200208151156.g7FBu6x00871@magadino.cscs.ch> Message-ID: <3D5D2146.6080605@zimmer.li> Dear Ari, dear all, I would just like to confirm consistent behaviour when using the Poisson Solver of Jens Mortensen. The Geometries and Energies of the SURFACE setup are consistent again, with the ones of a super cell setup. With best regards and thank you for your help urs Ari.P.Seitsonen at iki.fi wrote: >Hi Urs, > > After consulting "highly respected sources" I would suggest you to >try using the Poisson solver of Jens Mortensen (POISSON SOLVER >MORTENSEN), as this is most likely much better tested with the SURFACE >option than the default Hockney solver. > > Yours, > > apsi > >PS Please always reply also to the mailing list when answering mails!! > From Ari.P.Seitsonen at iki.fi Mon Aug 19 13:12:28 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Mon, 19 Aug 2002 13:12:28 +0200 Subject: [CPMD-list] cpmd2cube In-Reply-To: <000f01c2445d$065b76e0$5f5005a0@phys.keele.ac.uk> (b.zarychta@phys.keele.ac.uk) References: <000f01c2445d$065b76e0$5f5005a0@phys.keele.ac.uk> Message-ID: <200208191112.g7JBCSb02692@magadino.cscs.ch> Dear Zak, > I have recently compiled cpmd2cube sucessfully, however I cannot get > it to process any files succesfully. Could you please be a bit more specific; what went wrong, what is the output, which options did you give to the code? (-double) If you ran on linux/PGI compiler, did you use more or less the same options for the compiler, i.e. no exchange of the bytes etc? > Does any one have a working examples of input/output files for cpmd > with which they have used with cpmd2cube ? Since the input is in general binary, one has to be careful with such a trial (e.g. see above about the linux/PGI/byte order). Alas, if you could provide a bit more insight to what you did we might be able to help you. Yours, apsi PS Please always use the mailing list for the replys!! -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From Ari.P.Seitsonen at iki.fi Mon Aug 19 13:30:17 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Mon, 19 Aug 2002 13:30:17 +0200 Subject: [CPMD-list] population analysis used in CPMD code In-Reply-To: (message from Raj Pala on Thu, 25 Jul 2002 15:57:19 -0600 (MDT)) References: Message-ID: <200208191130.g7JBUHC03009@magadino.cscs.ch> Dear Raj, Have you already got a reply to this one? > Is there a reference to the method employed for performing population > analysis used in CPMD code. More precisely, I would like to know the > following: > > 1) Do you use some kind of a wigner-seitz radius (this radius is > 'arbitrary') within which spherical harmonic are defined, and project > the wavefunction onto this atomic orbitals? > > 2) Or is there a less arbitrary way in which population analysis is being > done? > > We are working on oxides, & I would greatly appreciate if anyone can > clarify the above questions. It would also help if references are provided > for the way this is coded in the program, and also references to some work > which has used the method used in CPMD code. CPMD needs a _localised_ basis as input for the projection, and this solves the problem (over-counting/-projection of electrons) to major extent. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From cur Mon Aug 19 14:34:47 2002 From: cur (Alessandro Curioni) Date: Mon, 19 Aug 2002 14:34:47 +0200 Subject: [CPMD-list] New CPMD version 3.5.3 Message-ID: <200208191234.OAA13056@cpmd.org> Dear CPMD users, the new CPMD version 3.5.3 is now available at www.cpmd.org. This minor update contains the correction of some small bugs, especially related with the new implementation of the VDB pseudopotentials. Thank you very much to everybody for the many useful suggestions and bug reports. Regards, Your cpmd.org team. From eyvaz_isaev at yahoo.com Tue Aug 20 14:09:46 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 20 Aug 2002 05:09:46 -0700 (PDT) Subject: [CPMD-list] IFC compiler instead Lahey In-Reply-To: <200208200306.FAA05374@internet-fence.zurich.ihost.com> Message-ID: <20020820120946.88825.qmail@web40011.mail.yahoo.com> Dear Xiong, Certainly, g77 compiler is not suitable to compile the CPMD code due to the fact that some subroutins use f90 syntax. I advice you to use Intel Fortran Compiler which is free of charge (you can download it from www.intel.com) and never I (guess somebody, too) had problems compiling the code. By the way I have just compiled v.3.5.3 using it on SuSE 7.3. Regards, Eyvaz. Theoretical Physics Department Moscow Steel and Alloys Institute --- ?????? wrote: > > Dear All, > I dont know whether I can compile the cpmd > without portland Group fortran compiler or not. > In fact, I can not compile the project using the g77 > of redhat 7.3 on my pc P4 1.6G. > Last time, I asked some question about Lahey Linux > Fortran compiler, but till now, I can > not settle the question. I can not find the > functions which I should modify. Anybody can help > me. > I scan the past list archives, there is another > person use the lf95, and I met the same > problems as him. > thanks > yours xiong > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From hutter at pci.unizh.ch Tue Aug 20 14:51:14 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 20 Aug 2002 14:51:14 +0200 (MEST) Subject: [CPMD-list] compiler In-Reply-To: <200208200306.FAA05374@internet-fence.zurich.ihost.com> Message-ID: Hi there is no way to compile CPMD with g77. g77 is missing an essential extension to F77 (POINTER). You need one of the commercial compilers on Linux (ABSOFT, PGI, INTEL, LAHEY). We do not support the Lahey compiler at the moment. However, I downloaded the trial version of the compiler and was able to get a working executable with little effort. The Makefile options were FFLAGS = LFLAGS = -lfj9i6 -lblas -llapack -lf2c CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT CC = gcc -O2 -Wall FC = lf95 -c LD = lf95 I had to change the file csize.F (see attachment) This can certainly be optimized by choosing the correct compiler flags. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On 2002 xxx 2020, ?????? wrote: > > Dear All, > I dont know whether I can compile the cpmd without portland Group fortran compiler or not. > In fact, I can not compile the project using the g77 of redhat 7.3 on my pc P4 1.6G. > Last time, I asked some question about Lahey Linux Fortran compiler, but till now, I can > not settle the question. I can not find the functions which I should modify. Anybody can help me. > I scan the past list archives, there is another person use the lf95, and I met the same > problems as him. > thanks > yours xiong > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -------------- next part -------------- C ================================================================== SUBROUTINE CSIZE(C2,NSTATE,GEMAX,CNORM) C ==--------------------------------------------------------------== IMPLICIT NONE INCLUDE 'system.h' INCLUDE 'elct.inc' INCLUDE 'kpts.inc' INCLUDE 'spin.inc' C Arguments INTEGER NSTATE COMPLEX*16 C2(NGWK,NSTATE) REAL*8 GEMAX,CNORM C Variables DIMENSION F(NSTATE) COMPLEX*16 ZGIVE REAL*8 DDOT,DOTP,GU,GD INTEGER NOCC,I,IABS,NOU,NOD, & IZAMAX C ==--------------------------------------------------------------== IF(TLSD) THEN NOU=0 DO I=1,NSUP IF(F(I).GT.1.D-5) NOU=NOU+1 ENDDO IABS=IZAMAX(NOU*NGWK,C2,1) GEMAX=CDABS(ZGIVE(C2(1,1),IABS)) IF(NOU.EQ.0) GU=0.0D+00 ! cmb NOD=0 DO I=NSUP+1,NSTATE IF(F(I).GT.1.D-5) NOD=NOD+1 ENDDO IABS=IZAMAX(NOD*NGWK,C2(1,NSUP+1),1) GEMAX=MAX(CDABS(ZGIVE(C2(1,NSUP+1),IABS)),GEMAX) IF(NOD.EQ.0) GD=0.0D+00 ! cmb NOCC=NOD+NOU CNORM=0.0D0 IF(TKPNT) THEN DO I=1,NOU CNORM=CNORM+DDOT(2*NGWK,C2(1,I),C2(1,I)) ENDDO DO I=NSUP+1,NSUP+NOD CNORM=CNORM+DDOT(2*NGWK,C2(1,I),C2(1,I)) ENDDO ELSE DO I=1,NOU CNORM=CNORM+DOTP(NGW,C2(1,I),C2(1,I)) ENDDO DO I=NSUP+1,NSUP+NOD CNORM=CNORM+DOTP(NGW,C2(1,I),C2(1,I)) ENDDO ENDIF ELSE NOCC=0 DO I=1,NSTATE IF(F(I).GT.1.D-5) NOCC=NOCC+1 ENDDO IABS=IZAMAX(NOCC*NGWK,C2,1) GEMAX=CDABS(ZGIVE(C2(1,1),IABS)) CNORM=0.0D0 IF(TKPNT) THEN DO I=1,NOCC CNORM=CNORM+DDOT(2*NGWK,C2(1,I),C2(1,I)) ENDDO ELSE DO I=1,NOCC CNORM=CNORM+DOTP(NGW,C2(1,I),C2(1,I)) ENDDO ENDIF ENDIF #ifdef PARALLEL CALL GLOSUM(1,CNORM) CALL GLOMAX(1,GEMAX) #endif CNORM=DSQRT(CNORM/(NOCC*NGWKS)) C ==--------------------------------------------------------------== RETURN END C ================================================================== From bryk at uh.edu Tue Aug 20 18:46:32 2002 From: bryk at uh.edu (Taras Bryk) Date: Tue, 20 Aug 2002 11:46:32 -0500 (CDT) Subject: [CPMD-list] Stress calculations with USPP Message-ID: Guys, is anyone able to calculate stress tensor in simulations with ultrasoft Vanderbilt PPs ? Both versions 3.5.2 and 3.5.3 give me the following message before crashing: ================================================================ == FORCES INITIALIZATION == ================================================================ EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS *** STRESS| THE NEW SIZE OF THE PROGRAM IS 139280 kBYTES *** *** DQVAN2| THE NEW SIZE OF THE PROGRAM IS 139280 I've got the same crash on multiprocessor SunFire machine and Linux workstations, but have never had problems with the stress calculations while using norm-conserving PPs (even with much more memory). Taras ----------------------------------------------------------------- Taras Bryk email bryk at uh.edu Department of Chemistry phone (713)743-5101 University of Houston fax (713)743-2709 4800 Calhoun Houston, TX 77204-5003 From baki at chemres.hu Thu Aug 22 10:58:42 2002 From: baki at chemres.hu (Bako Imre) Date: Thu, 22 Aug 2002 10:58:42 +0200 Subject: [CPMD-list] question about the optimalization of cell parameter Message-ID: <3.0.6.32.20020822105842.00900100@mailgw.chemres.hu> Dear All I tried to optimize the Si lattize use the following input file &CPMD OPTIMIZE GEOMETRY RESTART WAVEFUNCTION COORDINATES LATEST SPLINE POINTS 5000 CONVERGENCE CELL 0.1 &END &DFT FUNCTIONAL PZ &END &SYSTEM SYMMETRY 2 CELL 10.2612 1.0 1.0 0.0 0.0 0.0 CUTOFF 36. KPOINTS MONKHORST-PACK 4 4 4 STATES 4 POINT GROUP AUTO TESR 4 4 4 SCALED &END &ATOMS *Si_SG_LDA KLEINMAN-BYLANDER LMAX=D 2 0.00 0.00 0.00 0.25 0.25 0.25 &END After the second iteration I got the following answer ATOM COORDINATES GRADIENTS 1 Si 0.0000 0.0000 0.0000 0.000E+00 0.000E+00 0.000E+00 2 Si -2.5653 2.5653 2.5653 0.000E+00 0.000E+00 0.000E+00 **************************************************************** *** TOTAL STEP NR. 2 GEOMETRY STEP NR. 1 *** *** GNMAX= 0.000000E+00 ETOT= -7.923217 *** *** GNORM= 0.000000E+00 DETOT= 0.000E+00 *** *** CNSTR= 0.000000E+00 TCPU= 0.73 *** **************************************************************** ================================================================ = END OF GEOMETRY OPTIMIZATION = ================================================================ Can you explain somebody me this behaviour? Best regards Imre Bako Bak? Imre MTA K?miai Kutat?k?zpont, K?miai Int?zet 1525 Budapest Pf. 17 Telefon From Ari.P.Seitsonen at iki.fi Thu Aug 22 16:55:20 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 22 Aug 2002 16:55:20 +0200 Subject: [CPMD-list] question about the optimalization of cell parameter In-Reply-To: <3.0.6.32.20020822105842.00900100@mailgw.chemres.hu> (message from Bako Imre on Thu, 22 Aug 2002 10:58:42 +0200) References: <3.0.6.32.20020822105842.00900100@mailgw.chemres.hu> Message-ID: <200208221455.g7MEtKN11665@magadino.cscs.ch> Dear Imre, > I tried to optimize the Si lattize use the following input file > &CPMD > OPTIMIZE GEOMETRY > RESTART WAVEFUNCTION COORDINATES LATEST > SPLINE POINTS > 5000 > CONVERGENCE CELL > 0.1 > &END > &DFT > FUNCTIONAL PZ > &END > &SYSTEM > SYMMETRY > 2 > CELL > 10.2612 1.0 1.0 0.0 0.0 0.0 > CUTOFF > 36. > KPOINTS MONKHORST-PACK > 4 4 4 > STATES > 4 > POINT GROUP > AUTO > TESR > 4 4 4 > SCALED > &END > &ATOMS > *Si_SG_LDA KLEINMAN-BYLANDER > LMAX=D > 2 > 0.00 0.00 0.00 > 0.25 0.25 0.25 > &END > After the second iteration I got the following answer > ATOM COORDINATES GRADIENTS > 1 Si 0.0000 0.0000 0.0000 0.000E+00 0.000E+00 0.000E+00 > 2 Si -2.5653 2.5653 2.5653 0.000E+00 0.000E+00 0.000E+00 > **************************************************************** > *** TOTAL STEP NR. 2 GEOMETRY STEP NR. 1 *** > *** GNMAX= 0.000000E+00 ETOT= -7.923217 *** > *** GNORM= 0.000000E+00 DETOT= 0.000E+00 *** > *** CNSTR= 0.000000E+00 TCPU= 0.73 *** > **************************************************************** > ================================================================ > = END OF GEOMETRY OPTIMIZATION = > ================================================================ > Can you explain somebody me this behaviour? Hmm, everything seems to go fine, or? In bulk silicon there are no geometrical degrees of freedom to be optimised, so "OPTIMISE GEOMETRY" doesn't make sense (i.e. doesn't do anything), and the optimisation stops when it notices that the energy doesn't change at all (as the atoms didn't move). Or did I misunderstand something? Did you want to relax the lattice constant also? This most likely doesn't work with the k points, but someone please correct me if this is not true. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From konopka at elf.stuba.sk Thu Aug 22 20:18:26 2002 From: konopka at elf.stuba.sk (Martin Konopka) Date: Thu, 22 Aug 2002 20:18:26 +0200 (MET DST) Subject: [CPMD-list] crash of parallel CP slab calculations with Vanderbilt PPs Message-ID: Hello all, Does anybody know how to fix the folowing problem? CPMD 3.5.2 crashes after I start a large parallel Car-Parinello MD job on IBM SP with a slab of copper atoms (and apparently many other systems, too). Features: * No error message in the standart output file * The folowing messages in the standart error file: ERROR: 0031-250 task 0: Terminated ERROR: 0031-250 task 1: Segmentation fault ERROR: 0031-250 task 2: Segmentation fault ......... ERROR: 0031-250 task 15: Segmentation fault (I.e., it is a 16-processor run.) * one core file created by each process (may be not by the 0th one, I forgot) * The crash occurs at the beginning of the run. The last part of the stdout file looks like 47 Cu 14.531590 9.687727 8.621875 48 Cu 14.531590 14.531590 8.621875 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 144 EWALD SUM IN REAL SPACE OVER 5* 5* 5 CELLS ================================================================================ Job sp5cws.rz.uni-karlsruhe.de.156990.0 stopped at 22.08.2002/16:51:11 (RC=139) * I am using a Vanderbilt pseudopotential. * No crash occurs when I do just wavefunction or geometry optimization. * No crash occurs even when I do Car-Parinello MD with Cu2 molecule. (tested on 4 and 16 processors) * Crash occurs for both tested Cu slabs: with 48 and 96 atoms. * Crash occurs for both OLDCODE and NEWCODE. I am using a version of CPMD 3.5.2 that has at least two bugs fixed (one concerns MD and was fixed by some patch and the other was causing crashes when RESTART files where saved after the 400th MD step.) I have not tested this behaviour on other platforms. Below I add parts of my input file. Thank you for your interest. Martin Konopka. &CPMD RESTART WAVEFUNCTIONS COORDINATES LATEST RESTFILE 2 STORE 150 MOLECULAR DYNAMICS CP TEMPERATURE 1000.0D0 MAXSTEP 1000 NOSE IONS MASSIVE 1000.0D0 1000.0D0 EMASS 400.0D0 TIMESTEP 5.0D0 ALEXANDER MIXING 0.3D0 SPLINE POINTS QFUNCTIONS 2001 CENTER MOLECULE OFF MEMORY BIG &END &DFT OLDCODE GRADIENT CORRECTION PBEX PBEC GC-CUTOFF 5.0D-5 &END &SYSTEM CELL VECTORS 19.37545337626741472795D0 0.0D0 0.0D0 0.0D0 19.37545337626741472795D0 0.0D0 0.0D0 0.0D0 22.0D0 TESR 4 CUTOFF 25.0D0 CHARGE 0 &END &ATOMS *Cu.uspp BINARY NEWF TPSEU LMAX=D 48 0.0000000000 0.0000000000 15.4721327209 .......................... 14.5315900317 14.5315900317 8.6218754857 &END ----------------------------------------- Martin Konopka Department of Physics, FEI STU Ilkovicova 3, 842 19 Bratislava, Slovakia tel: +421 2 60291 714 fax: +421 2 6541 1483 http://www.ccms.elf.stuba.sk/konopka.html ----------------------------------------- From Ari.P.Seitsonen at iki.fi Thu Aug 22 20:53:56 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 22 Aug 2002 20:53:56 +0200 Subject: [CPMD-list] Stress calculations with USPP In-Reply-To: (message from Taras Bryk on Tue, 20 Aug 2002 11:46:32 -0500 (CDT)) References: Message-ID: <200208221853.g7MIrut17647@magadino.cscs.ch> Dear Taras, > is anyone able to calculate stress tensor in > simulations with ultrasoft Vanderbilt PPs ? > > Both versions 3.5.2 and 3.5.3 give me the > following message before crashing: > ================================================================ > == FORCES INITIALIZATION == > ================================================================ > EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS > *** STRESS| THE NEW SIZE OF THE PROGRAM IS 139280 kBYTES *** > *** DQVAN2| THE NEW SIZE OF THE PROGRAM IS 139280 > > I've got the same crash on multiprocessor SunFire machine and > Linux workstations, but have never had problems with the stress > calculations while using norm-conserving PPs (even with much more > memory). Uhh... You hit a known "feature": The exchange correlation part of the stress tensor is not correctly implemented at the momemt. Here's an earlier discussion: # Dear Toshi-san, # # Just a short note: I discussed about the problem with other persons, # they said that the part in xcstr.F with the xc energy table is there # because the stress arising from the gradient part is calculated # elsewhere but from the LDA part, and thus in xcstr.F the part arising # from the LDA is calculated. Unfortunately it hasn't been upgraded to # work also with the option 'NEWCODE'... So what should probably be done # here is to try to call the corresponding LDA routine instead of using # the xc tables. How easy this is - in the general case with different # possible LDA parametrisations - I don't know. I also don't have much # time to look at it now, I'm leaving for holidays on Wednesday, I'll be # back in the second week of August. # # Greetings, # # apsi # # > Thanks for your commnets. # > # > After checking the CPMD codes for a while, # > I identified the origin of the error message. # > # > The stress calculation of uspp is impimented in CPMD. # > It uses subroutine 'xcstr.F' which calculates stress from uspp xc-energy. # > The subroutine 'xcstr.F' uses a table of xc-energy tabulated in 'genxc.F'. # > However 'genxc.F' generates # > xc-energy table only for 'OLDCODE'. Therefore when I use 'NEWCODE' for # > xc-functionals, 'noforce.F' referes to a empty table and produce # > a 'division by zero' error. # > # > For a quick fix, I commented out IF((TOLDCODE) THEN ....ENDIF in # > 'genxc.F'. It seems to work, but I do not know if it gives # > correct answer. I will check it and report you later. So if anyone is willing to look at and fix the problem, please tell us...!! One could start first check that LDA works, then with GGA etc. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From chwang at rain.vislab.olemiss.edu Fri Aug 23 01:26:53 2002 From: chwang at rain.vislab.olemiss.edu (Haibo Wang) Date: Thu, 22 Aug 2002 18:26:53 -0500 Subject: [CPMD-list] CPMD for Beowulf Cluster Message-ID: Hi, I am new to CPMD software. I just installed CPMD on the SGI O2K without problem. We have a Pentium 4 processor Linux Beowulf Cluster with PGI compiler. Is there anyone who can share the experience with me on configuration? I cannot find the specific platform from the list for the Beowulf Cluster. Thanks, Haibo Haibo Wang Supercomputer User Consultant Mississippi Center for Supercomputing Research Office of Information Technology System Administrator Hearin Center for Enterprise Science School of Business Administration Phone: 662-915-7353 Homepage: http://www.olemiss.edu/~chwang Office: http://www.mcsr.olemiss.edu From ct at chemie.hu-berlin.de Fri Aug 23 12:25:38 2002 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Fri, 23 Aug 2002 12:25:38 +0200 Subject: [CPMD-list] CPMD for Beowulf Cluster In-Reply-To: ; from chwang@rain.vislab.olemiss.edu on Thu, Aug 22, 2002 at 06:26:53PM -0500 References: Message-ID: <20020823122538.A214550@atlas.chemie.hu-berlin.de> Hello Haibo, you can try $ ./Configure PC-PGI-MPI > Makefile You can consider the following points to get improved performance: (I did some tests with different options to build CPMD 3.5.2, I'm not totally sure whether my results are true in general) 1. Instead of the PGI math-libs (lapack, blas) use the ATLAS-libs tuned for your processor type (see ATLAS web pages). Don't forget to build a complete liblapack.a since the ATLAS-lapack is incomplete (see ATLAS web pages for instructions as well). Compared to the PGI-libs the ATLAS-libs give an impressing performance boost (my tests have shown improved timings of up to 30 % ...) 2. Using the Intel compiler suite (6.0) instead of PGI compilers can improve the performance only slightly. Since I don't have a Pentium4 at hand I didn't test the option "-tp p7" of the Intel compiler for Pentium4-processors and therefore cannot compare to the PGI-compiler. 3. MPI-software: On our Linux cluster (Athlon 1800+, 100Mbit ethernet) the LAM-MPI 6.5.6 gave better wall times compared to MPICH 1.2.4 by about 15 %. Although pure CPU times (from the CPMD output) are better with MPICH the communication between the boxes seems to be more effective using LAM-MPI (although the processor load is still in the range of 0.7 ... 0.8). Good luck, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From mpj at fyslab.hut.fi Fri Aug 23 17:41:55 2002 From: mpj at fyslab.hut.fi (MANUEL PEREZ JIGATO) Date: Fri, 23 Aug 2002 18:41:55 +0300 (EEST) Subject: [CPMD-list] CPMD response functions calculations Message-ID: hi i have seen some options in cpmd to compute response properties and dipole moments. magnetic responses for NMR seem to be clearly documented is there any optical response or dynamical response/ dynamic dielectric functions implemented as a reference point i would mention a tddft paper on finite systems apperaing in the publication list at the cpmd website: Doltsinis NL, Sprik M Electronic excitation spectra from time-dependent density functional response theory using plane-wave methods CHEM PHYS LETT 330 (5-6): 563-569 NOV 17 2000 i would appreciate any information on dynamical response (optical) on periodic systems. ( i have the impresion that if cpmd can do magnetic response, it must be able to do with no effort optical response). regads mpj From hutter at pci.unizh.ch Sat Aug 24 15:07:05 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sat, 24 Aug 2002 15:07:05 +0200 (MEST) Subject: [CPMD-list] crash of parallel CP slab calculations with Vanderbilt PPs In-Reply-To: Message-ID: Dear Martin I'm not sure that this will help, but attached is a new version of the file noforce.F that fixes a scratch space bug. After changing this file I was able to run an input similar to yours. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- -------------- next part -------------- C ================================================================== SUBROUTINE NOFORCE(C0,C2,SC0,TAU0,FION,EIGV, & RHOE,PSI,XMAT1,XMAT2,SCR,LSCR,NSTATE,TFOR) C ==--------------------------------------------------------------== C == COMPUTES FOR A SET OF NONORTHOGONAL ORBITALS == C == THE TOTAL ENERGY == C == THE ELECTRONIC FORCES == C == THE FORCES ON THE IONS == C ==--------------------------------------------------------------== IMPLICIT NONE INCLUDE 'system.h' INCLUDE 'elct.inc' INCLUDE 'norm.inc' INCLUDE 'pslo.inc' INCLUDE 'ropt.inc' INCLUDE 'cppt.inc' INCLUDE 'nlps.inc' INCLUDE 'sfac.inc' INCLUDE 'ions.inc' INCLUDE 'nort.inc' INCLUDE 'cvan.inc' INCLUDE 'spin.inc' INCLUDE 'geq0.inc' C Arguments INTEGER NSTATE,LSCR COMPLEX*16 C0(NGW,*),C2(NGW,*),SC0(NGW,*),PSI(NNR1) REAL*8 TAU0(*),FION(*),EIGV(*),RHOE(NNR1),SCR(LSCR) LOGICAL TFOR REAL*8 XMAT1(NSTATE,NSTATE),XMAT2(NSTATE,NSTATE) C Variables REAL*8 GAM(NSTATE,NSTATE),AUXC(*),SMAT(NSTATE*NSTATE) REAL*8 DDIA(*) POINTER (IP_GAM,GAM),(IP_AUXC,AUXC),(IP_SMAT,SMAT) POINTER (IP_DDIA,DDIA) DIMENSION F(NSTATE) CHARACTER TAG*30 REAL*8 FNL(NAT,NHXS,NSTATE),DFNL(*), & DOTP INTEGER ISUB,I,IJ,J,IABS,IERR, & IL_GAM,IL_AUXC,IL_SMAT,IL_DDIA,LNOFORCE, & IZAMAX, & ICON DATA ICON /0/ SAVE ICON #ifdef PARALLEL INTEGER MSGLEN #endif #ifdef POINTER8 INTEGER*8 GET_ADDR #else INTEGER GET_ADDR #endif C ==--------------------------------------------------------------== CALL TISET(' NOFORCE',ISUB) IF(IMAGP.EQ.2) CALL STOPGM('NOFORCE','K-POINT NOT IMPLEMENTED') C ==--------------------------------------------------------------== C SCR partition CALL GIVE_SCR_NLFORCE(IL_GAM,IL_AUXC,IL_SMAT,NSTATE) IF(PRTEIG.AND.PARENT) THEN IL_AUXC=MAX(IL