[Wien] w2web + lava queuing system
Dear all, I fixed the problem. Best, C?line Hin. celhin celhin at MIT.EDU a ??crit??: Dear wien2k users, I try to launch jobs on lava queuing system from w2web. In the execution type, I have bsub=cat %f w2web-job;bsub -n4 hp2.bsub. Below is the hp2.bsub script. This does not work. Any idea what's wrong? In addition, where can I find the master-job-template qsub-job0_lapw? I do not find it in $WIENROOT. Best, C?line Hin. Script: #!/bin/csh #BSUB -o job.out #BSUB -e job.err cd /home/celine/wienessaie/Wienessaie_mpi/Si9 # copy the machines file in #cp $TMPDIR/machines.wien2k .machines set mpijob=1 echo nodes for this job: $LSB_HOSTS set proclist=`echo $LSB_HOSTS` set nproc=$#proclist echo number of processors: $nproc echo '#' .machines # example for an MPI parallel lapw0 #echo -n 'optimize.job:' .machines #set i=1 #while ($i = $nproc ) #echo -n $proclist[$i] .machines #@ i = $i + 1 #end #echo ' ' .machines #example for k-point and mpi parallel lapw1/2 set i=1 while ($i = $nproc ) echo -n '1:' .machines @ i1 = $i + $mpijob @ i2 = $i1 - 1 echo $proclist[$i-$i2] .machines set i=$i1 end echo 'granularity:1' .machines echo 'extrafine:1' .machines ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Interstitial N-N pair in GaP supercell
Dear Wien2k users! I am trying to minimize the GaP supercell with Nitrogen-Nitrogen interstitial pair using min -i 100 -s 10 -j 'run_lapw -p -I -i 40 -ec 0.001 -fc 1.0 -cc 0.001' I constructed the supercell with 64 atoms and replaced one P atom by the pair of interstitial N atoms. After 16 cycles the program stopped with following message: . . . . . . . . . . . in cycle 16ETEST: .0996 CTEST: -.0009901 ec cc and fc_conv 1 1 1 stop Fallback to compatibility mode with old save_lapw broyden files deleted, clm*, dmat*, vorb*, vresp*, eece*, scf and struct files saved under GaPNN_1 27.977u 0.412s 0:28.89 98.2% 0+0k 0+20648io 0pf+0w 0.844u 0.336s 0:01.66 70.4%0+0k 1272+16896io 8pf+0w clmextrapol_lapw has generated a new GaPNN.clmsum and calculations were renewed. Further, after 12 cycles, the program stopped again with the message: . . . . . . . . in cycle 12ETEST: .0406 CTEST: -.0009842 ec cc and fc_conv 1 1 1 stop :WARNING: Step size reduced due to overlapping spheres -- check RMT 28.185u 0.408s 0:29.11 98.1% 0+0k 0+20648io 0pf+0w 0.872u 0.320s 0:01.53 77.7%0+0k 0+16896io 0pf+0w clmextrapol_lapw has generated a new GaPNN.clmsum and so on without ending. Initially the RMTs for Ga and P atoms were RMT(Ga,P)=2.0 and for N atom ? RMT(N)=1.3 In isolated nitrogen molecule the interatomic distance is approximately 1.295 Angstrom. I guessed that the interatomic distance between the interstitial N atoms in GaP supercell would be larger then 1.295 A. So I reduced the RMT for N atom and took RMT(N)=1.0, aiming to prevent the overlapping of spheres for N-N pair. (2*RMT(N)=1.06 A 1.295 A). In spite of that, the result of ?mini? remains the same ? the interatomic distance between the interstitial N atoms becomes even smaller (!!!) then that in isolated nitrogen molecule and I still have the problem with overlapping spheres.
[Wien] Interstitial N-N pair in GaP supercell
In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion.
[Wien] Interstitial N-N pair in GaP supercell
Dear Kakhaber Jandieri Sir, First of all I am sorry because I am not able to answer your question instead of I am humbelly asking you a question. You have replaced one P atom by a pair of N atom. I am interested to know that how do you able to replace one atom by two atoms? With regards, On Sun, Jul 4, 2010 at 5:17 PM, Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de wrote: In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Shamik Chakrabarti Research Scholar Dept. of Physics Meteorology Material Processing Solid State Ionics Lab IIT Kharagpur Kharagpur 721302 INDIA -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100704/bed04396/attachment.htm
[Wien] Interstitial N-N pair in GaP supercell
Hello, first of all I think you can't replace one atom by a pair of atoms. Set 5% less RMT for all types of atoms instead of reduction of RMT of N only and run mini. best wishes. swati --- On Sun, 4/7/10, Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de wrote: From: Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de Subject: [Wien] Interstitial N-N pair in GaP supercell To: wien at zeus.theochem.tuwien.ac.at Date: Sunday, 4 July, 2010, 5:17 PM In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Interstitial N-N pair in GaP supercell
Dear Swati, Thank you for advice, but I still want to clarify some questions: first of all I think you can't replace one atom by a pair of atoms. My final goal is to obtain the relaxed atom positions in GaP supercell where one of the P atoms is replaced by the interstitial pair of Nitrogen-Nitrogen atoms. To say truth, I am not sure in correctness of my approach but I did the following: Step1 - Using the program supercell I generated 2x2x2 supercell for GaP containing 64 atoms Step2 - I construct a new supercell with 64 inequivalent atoms using the positions obtained in Step1 Step3 - I split one P atom in 2 atoms Step4 - I changed the atoms obtained in Step3 from P to N Step5 - I ran x sgroup. It converted my p supercell with 65 inequivalent atoms into the 111_p-42m supercell with 16 inequivalent atoms Step6 - I ran the program mini. Could you advice me the correct way for constructing the supercell with interstitial pair of N-N atoms in GaP matrix? Set 5% less RMT for all types of atoms instead of reduction of RMT of N only and run mini In interstitial N-N pair the interatomic distance between N atoms might be significantly smaller then the distance between Ga and P atoms. If instead of 2.0 I take 5% less RMT, then how cam I prevent the overlapping of spheres between the N atoms in the interstitial pair? Beforehand thankfull, Kakha swati chaudhury wrote: Hello, first of all I think you can't replace one atom by a pair of atoms. Set 5% less RMT for all types of atoms instead of reduction of RMT of N only and run mini. best wishes. swati --- On Sun, 4/7/10, Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de wrote: From: Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de Subject: [Wien] Interstitial N-N pair in GaP supercell To: wien at zeus.theochem.tuwien.ac.at Date: Sunday, 4 July, 2010, 5:17 PM In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Interstitial N-N pair in GaP supercell
Dear Shamik, You have replaced one P atom by a pair of N atom. I am interested to know that how do you able to replace one atom by two atoms? I described in details the corresponding procedures in my reply to Swati Chaudhury. I already mentioned in this reply that I am not sure in the correctness of these procedures, but just now I do not know the correct alternative. Best wishes, Kakha shamik chakrabarti wrote: Dear Kakhaber Jandieri Sir, First of all I am sorry because I am not able to answer your question instead of I am humbelly asking you a question. You have replaced one P atom by a pair of N atom. I am interested to know that how do you able to replace one atom by two atoms? With regards, On Sun, Jul 4, 2010 at 5:17 PM, Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de wrote: In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Interstitial N-N pair in GaP supercell
If you want to study a pair of interstitial N atoms, you must add two N atoms, not replace P. Or if you are replacing P by two interstitial N atoms, you remove one P and add two N at new positions. Interstitial means the atoms are not on lattice sites. If the reduced cell has 16 inequivalent atoms, it sounds as though you have 64 not 65 atoms, so possibly you have just replaced P by N on four sites. Are you trying to add an interstitial N2 molecule? If not why do you need two N atoms? Elaine A. Moore From: Kakhaber Jandieri [kakhaber.jandi...@physik.uni-marburg.de] Sent: 04 July 2010 15:04 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Interstitial N-N pair in GaP supercell Dear Swati, Thank you for advice, but I still want to clarify some questions: first of all I think you can't replace one atom by a pair of atoms. My final goal is to obtain the relaxed atom positions in GaP supercell where one of the P atoms is replaced by the interstitial pair of Nitrogen-Nitrogen atoms. To say truth, I am not sure in correctness of my approach but I did the following: Step1 - Using the program supercell I generated 2x2x2 supercell for GaP containing 64 atoms Step2 - I construct a new supercell with 64 inequivalent atoms using the positions obtained in Step1 Step3 - I split one P atom in 2 atoms Step4 - I changed the atoms obtained in Step3 from P to N Step5 - I ran x sgroup. It converted my p supercell with 65 inequivalent atoms into the 111_p-42m supercell with 16 inequivalent atoms Step6 - I ran the program mini. Could you advice me the correct way for constructing the supercell with interstitial pair of N-N atoms in GaP matrix? Set 5% less RMT for all types of atoms instead of reduction of RMT of N only and run mini In interstitial N-N pair the interatomic distance between N atoms might be significantly smaller then the distance between Ga and P atoms. If instead of 2.0 I take 5% less RMT, then how cam I prevent the overlapping of spheres between the N atoms in the interstitial pair? Beforehand thankfull, Kakha swati chaudhury wrote: Hello, first of all I think you can't replace one atom by a pair of atoms. Set 5% less RMT for all types of atoms instead of reduction of RMT of N only and run mini. best wishes. swati --- On Sun, 4/7/10, Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de wrote: From: Kakhaber Jandieri Kakhaber.Jandieri at physik.uni-marburg.de Subject: [Wien] Interstitial N-N pair in GaP supercell To: wien at zeus.theochem.tuwien.ac.at Date: Sunday, 4 July, 2010, 5:17 PM In addition to my previous letter. I thought that may be the problem is in very large difference between the RMT(Ga,P)=2.0 and RMT (N)=1.0, but I cannot increase the RMT(N) because of overlapping spheres and, on the other hand, I cannot decrease the RMT(Ga,P) because of charge leakage. Could somebody advice the solution of this problem? I will be extremely thankful for any suggestion. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England Wales and a charity registered in Scotland (SC 038302).
