From prakashprem373 at gmail.com Fri Apr 8 11:49:36 2022 From: prakashprem373 at gmail.com (Prem Prakash) Date: Fri, 8 Apr 2022 15:19:36 +0530 Subject: [ADF-LIST] Query regarding NBO analysis on ADF Message-ID: Dear ADF developers, Greetings of the day! I am a beginner on ADF and was trying a simple NBO calculation of water by following through this tutorial show in the website- https://www.scm.com/doc/ADF/Examples/H2O_ADFNBO.html I was not clear regarding how to use the GENNBO, as it seems confusing to me. And this is how I was getting an error in my .out file- *ADFNBO 2021.106 RunTime: Apr08-2022 01:29:45 ShM Nodes: 1 Procs: 1 Temporary files are created in /scratch/kid_0.1623875899 (0x6969) naos, nspin, naosx 54 1 1485 nbas, nmo, nocc 54 48 5 entering READ mode lspher, nbasis = T 48 ERROR OPENING ONE OF THE NBO DATA FILES ******************************************************************************* U T I L S E X I T ============ Timer stack: ------------ 1649395784.90 Utils ============ error opening NBO data file* So, kindly guide me to tackle this problem, so that I can get the NBO analysis successfully done and then proceed for the analysis with my relevant project molecules. I am also enclosing my sample input for your reference. Thanks and Regards! Prem Indian Institute of Technology, Hyderabad, India -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: H2O.run Type: application/octet-stream Size: 995 bytes Desc: not available URL: From vanlenthe at scm.com Fri Apr 8 12:09:07 2022 From: vanlenthe at scm.com (Erik van Lenthe) Date: Fri, 8 Apr 2022 12:09:07 +0200 Subject: [ADF-LIST] Query regarding NBO analysis on ADF In-Reply-To: References: Message-ID: <26926c3b-484b-6153-1f10-1ae4bb8ce582@scm.com> Dear Prem Prakash, To use gennbo6 you need to have a license for NBO6 in the SCM license file. Next, like in the example https://www.scm.com/doc/ADF/Examples/H2O_ADFNBO.html you refer to you have to include: FULLFOCK SAVE TAPE15 If you do not use the GUI to run this file H2O.run, you have to change the lines cp "${AMS_RESULTSDIR-${AMS_JOBNAME-ams}.results}/adf.rkf" TAPE21 cp "${AMS_RESULTSDIR-${AMS_JOBNAME-ams}.results}/TAPE15" TAPE15 to cp ams.results/adf.rkf TAPE21 cp ams.results/TAPE15 TAPE15 Best regards, Erik van Lenthe SCM You wrote: > Dear ADF developers, > Greetings of the?day! > > I am a beginner on ADF and was trying a simple NBO calculation of > water by following through this tutorial show in the website- > > https://www.scm.com/doc/ADF/Examples/H2O_ADFNBO.html > > I was not clear regarding how to use the GENNBO, as it seems confusing > to me. > > And this is how I was getting an error in my .out file- > > *ADFNBO 2021.106 ?RunTime: Apr08-2022 01:29:45 ?ShM Nodes: 1 ?Procs: 1 > > ?Temporary files are created in /scratch/kid_0.1623875899 (0x6969) > > ?naos, nspin, naosx ? ? ?54 ? ? ? 1 ? ?1485 > ?nbas, nmo, nocc ? ? ?54 ? ? ?48 ? ? ? 5 > ?entering READ mode > ?lspher, nbasis = T ? ? ? ? ?48 > ?ERROR OPENING ONE OF THE NBO DATA FILES > ?******************************************************************************* > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?U T I L S ? E X I T > > ?============ > ?Timer stack: > ?------------ > ? 1649395784.90 ?Utils > ?============ > > ?error opening NBO data file* > > So, kindly guide me to tackle this problem, so that I can get the NBO > analysis successfully done and then proceed for the analysis with my > relevant project molecules. > > I am also enclosing my sample input for your reference. > > Thanks and Regards! > Prem > Indian Institute of Technology, Hyderabad, India > > > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist -------------- next part -------------- An HTML attachment was scrubbed... URL: From prakashprem373 at gmail.com Fri Apr 8 13:08:34 2022 From: prakashprem373 at gmail.com (Prem Prakash) Date: Fri, 8 Apr 2022 16:38:34 +0530 Subject: [ADF-LIST] Query regarding NBO analysis on ADF In-Reply-To: <26926c3b-484b-6153-1f10-1ae4bb8ce582@scm.com> References: <26926c3b-484b-6153-1f10-1ae4bb8ce582@scm.com> Message-ID: Thank you sir, for your quick response to my previous query regarding NBO analysis of water. But I guess, I am still not able to tackle the problem. I tried both approaches, one on GUI (water.run file), and the other on server (h2o.run file), but still I am failing somewhere to execute it properly. I am enclosing the input and output files for both of them, for your reference. Please, do let me know, if I am still making some mistakes, so that I can rectify it and get it done properly. Thank you in advance! Prem On Fri, Apr 8, 2022 at 3:39 PM Erik van Lenthe wrote: > Dear Prem Prakash, > > To use gennbo6 you need to have a license for NBO6 in the SCM license file. > Next, like in the example > https://www.scm.com/doc/ADF/Examples/H2O_ADFNBO.html you refer to you > have to include: > FULLFOCK > SAVE TAPE15 > > If you do not use the GUI to run this file H2O.run, you have to change the > lines > cp "${AMS_RESULTSDIR-${AMS_JOBNAME-ams}.results}/adf.rkf" TAPE21 > cp "${AMS_RESULTSDIR-${AMS_JOBNAME-ams}.results}/TAPE15" TAPE15 > to > cp ams.results/adf.rkf TAPE21 > cp ams.results/TAPE15 TAPE15 > > Best regards, > Erik van Lenthe > SCM > > You wrote: > > Dear ADF developers, > Greetings of the day! > > I am a beginner on ADF and was trying a simple NBO calculation of water by > following through this tutorial show in the website- > > https://www.scm.com/doc/ADF/Examples/H2O_ADFNBO.html > > I was not clear regarding how to use the GENNBO, as it seems confusing to > me. > > And this is how I was getting an error in my .out file- > > > > > > > > > > > > > > > > > > > > > *ADFNBO 2021.106 RunTime: Apr08-2022 01:29:45 ShM Nodes: 1 Procs: 1 > Temporary files are created in /scratch/kid_0.1623875899 (0x6969) naos, > nspin, naosx 54 1 1485 nbas, nmo, nocc 54 48 > 5 entering READ mode lspher, nbasis = T 48 ERROR OPENING ONE OF > THE NBO DATA FILES > ******************************************************************************* > U T I L S E X I T ============ Timer > stack: ------------ 1649395784.90 Utils ============ error opening > NBO data file* > > So, kindly guide me to tackle this problem, so that I can get the NBO > analysis successfully done and then proceed for the analysis with my > relevant project molecules. > > I am also enclosing my sample input for your reference. > > Thanks and Regards! > Prem > Indian Institute of Technology, Hyderabad, India > > > > > _______________________________________________ > ADFlist mailing listADFlist at scm.comhttps://lists.scm.com/mailman/listinfo/adflist > > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: water.run Type: application/octet-stream Size: 743 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: h2o.run Type: application/octet-stream Size: 873 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: water.out Type: application/octet-stream Size: 52785 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: h2o.out Type: application/octet-stream Size: 59207 bytes Desc: not available URL: From prakashprem373 at gmail.com Thu Apr 21 14:46:48 2022 From: prakashprem373 at gmail.com (Prem Prakash) Date: Thu, 21 Apr 2022 18:16:48 +0530 Subject: [ADF-LIST] (no subject) Message-ID: Dear ADF developers, Greetings of the day! I was performing a single-point calculation, the SCF iterations were running, and suddenly the calculation got stopped with this message- SCF Error: norm([F,P])= 1.737318096647, max([F,P])= 0.216085820784 ***** SPIN 1 ***** orbitals (Q,E): --------------- A :456...467 ( 1.00 -0.1156) ( 1.00 -0.1149) ( 1.00 -0.1087) ( 1.00 -0.1082) ( 1.00 -0.1060) ( 1.00 -0.1043) ( 1.00 -0.1009) ( 1.00 -0.0999) ( 1.00 -0.0952) ( 1.00 -0.0945) ( 0.50 -0.0870) ( 0.00 -0.0866) ***** SPIN 2 ***** orbitals (Q,E): --------------- A :456...467 ( 1.00 -0.1156) ( 1.00 -0.1149) ( 1.00 -0.1087) ( 1.00 -0.1082) ( 1.00 -0.1060) ( 1.00 -0.1043) ( 1.00 -0.1009) ( 1.00 -0.0999) ( 1.00 -0.0952) ( 1.00 -0.0945) ( 0.50 -0.0870) ( 0.00 -0.0866) Spin polar: 0 (Spin_A minus Spin_B electrons) CYCLE 17 *============ Timer stack: ------------ 1650105376.18 AMS 1650105377.99 ADFEngine%Solve 1650106083.94 Cycle_ScalableSCF 1650117747.15 FMatAO 1650117747.44 MirkoHF-CalcExchangeMatrix 1650117747.46 HF1234 1650117748.00 pp 1650117931.78 M5 1650117931.79 M5_a323f ============Process received SIGTERM WARNING: Nr of shared arrays in use at the end: 27 Names of the Shared Arrays that have not been deleted projCoeff projCoeff projCoeff projCoeff projCoeff projCoeff activefrag%initialMOs%A%_A%eigbas activefrag%initialMOs%A%_B%eigbas activefrag%initialMOs%A%_A%eigbas activefrag%initialMOs%A%_B%eigbas grid%coords grid%w grid%distance2atoms grid%neighbors projCoeff fullGrid SerializedTensorsType SerializedTensorsType SerializedTensorsType kMatExchange zlmToCart pMatZlm kMatZlm pMatPermuted SerializedTensorsType* Can anyone let me know why I am getting this, which stopped my calculation? Also, suggest to me how I can avoid such in future. Thanks and Regards! Prem -------------- next part -------------- An HTML attachment was scrubbed... URL: From yakovlev at scm.com Thu Apr 21 15:29:55 2022 From: yakovlev at scm.com (Alexei Yakovlev) Date: Thu, 21 Apr 2022 15:29:55 +0200 Subject: [ADF-LIST] (no subject) In-Reply-To: References: Message-ID: <13be2a7e-32a0-ce8b-793b-5e9277c9b850@scm.com> Dear Prem, The "Process received SIGTERM" message means that the calculation has probably been terminated by a user or by the system. It could run out of the allocated time. Another possible reason is that it could be killed by the MPI runtime because one of the ranks encountered an error. In this case, you should see some ams.kidXX.out files where you will find more details about the error. Kind regards, Alexei On 21/04/2022 14:46, Prem Prakash wrote: > Dear ADF developers, > Greetings of the?day! > I was performing a single-point calculation, the SCF iterations were > running, and suddenly the calculation got stopped with this message- > > SCF Error: norm([F,P])= ? ? ?1.737318096647, max([F,P])= ? ? > ?0.216085820784 > ?***** SPIN 1 ***** > ?orbitals (Q,E): > ?--------------- > ?A :456...467 ? ? ? ?( 1.00 ? ?-0.1156) ?( 1.00 ? ?-0.1149) ?( 1.00 ? > ?-0.1087) ?( 1.00 ? ?-0.1082) > ? ? ? ? ? ? ? ? ? ? ?( 1.00 ? ?-0.1060) ?( 1.00 ? ?-0.1043) ?( 1.00 ? > ?-0.1009) ?( 1.00 ? ?-0.0999) > ? ? ? ? ? ? ? ? ? ? ?( 1.00 ? ?-0.0952) ?( 1.00 ? ?-0.0945) ?( 0.50 ? > ?-0.0870) ?( 0.00 ? ?-0.0866) > ?***** SPIN 2 ***** > ?orbitals (Q,E): > ?--------------- > ?A :456...467 ? ? ? ?( 1.00 ? ?-0.1156) ?( 1.00 ? ?-0.1149) ?( 1.00 ? > ?-0.1087) ?( 1.00 ? ?-0.1082) > ? ? ? ? ? ? ? ? ? ? ?( 1.00 ? ?-0.1060) ?( 1.00 ? ?-0.1043) ?( 1.00 ? > ?-0.1009) ?( 1.00 ? ?-0.0999) > ? ? ? ? ? ? ? ? ? ? ?( 1.00 ? ?-0.0952) ?( 1.00 ? ?-0.0945) ?( 0.50 ? > ?-0.0870) ?( 0.00 ? ?-0.0866) > > ?Spin polar: 0 (Spin_A minus Spin_B electrons) > > ?CYCLE ? 17 > > *============ > ?Timer stack: > ?------------ > ? 1650105376.18 ?AMS > ? 1650105377.99 ?ADFEngine%Solve > ? 1650106083.94 ?Cycle_ScalableSCF > ? 1650117747.15 ?FMatAO > ? 1650117747.44 ?MirkoHF-CalcExchangeMatrix > ? 1650117747.46 ?HF1234 > ? 1650117748.00 ?pp > ? 1650117931.78 ?M5 > ? 1650117931.79 ?M5_a323f > ?============ > > Process received SIGTERM > ?WARNING: Nr of shared arrays in use at the end: 27 > ?Names of the Shared Arrays that have not been deleted > ?projCoeff > ?projCoeff > ?projCoeff > ?projCoeff > ?projCoeff > ?projCoeff > ?activefrag%initialMOs%A%_A%eigbas > ?activefrag%initialMOs%A%_B%eigbas > ?activefrag%initialMOs%A%_A%eigbas > ?activefrag%initialMOs%A%_B%eigbas > ?grid%coords > ?grid%w > ?grid%distance2atoms > ?grid%neighbors > ?projCoeff > ?fullGrid > ?SerializedTensorsType > ?SerializedTensorsType > ?SerializedTensorsType > ?kMatExchange > ?zlmToCart > ?pMatZlm > ?kMatZlm > ?pMatPermuted > ?SerializedTensorsType* > > Can anyone let me know why I am getting this, which stopped my > calculation? Also, suggest to me how I can avoid such in future. > > Thanks and Regards! > Prem > > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist -------------- next part -------------- An HTML attachment was scrubbed... URL: From ibadran at qu.edu.qa Thu Apr 21 18:19:59 2022 From: ibadran at qu.edu.qa (Ismail Badran) Date: Thu, 21 Apr 2022 16:19:59 +0000 Subject: [ADF-LIST] Help with Fe3O4 In-Reply-To: References: <8bb58802.AU4AAFNG32IAAAAAAAAAAP-XPaYAASKLT0kAAAAAAAm5ZgBiMvmu@mailjet.com> <2b53e37b-fcd6-5d88-d987-b71c2019a688@scm.com> <164212a5a6174830a2935467c197063d@qu.edu.qa> <1090172f-001a-78c2-6e38-49e869ea3cec@scm.com> <284ab87aa4b945f9b35c05fa0b9f86f9@qu.edu.qa>, <78c3fcd1-2a61-79c7-3226-2d9e371ca450@scm.com>, Message-ID: <9942247450a94449bad34cd1603fdc54@qu.edu.qa> Over the last week, I was attempting to work with an Fe3O4 lattice. All jobs I summitted using the BAND engine have failed. I guess now the problem is with setting the correct spin polarization to the different Fe2+ and Fe3+ atoms. Have anyone worked with Fe3O4 (111) slabs? Any successwith BAND? Dr. Ismail Badran Associate Professor of Physical Chemistry Department of Chemistry and Earth Sciences, Qatar University BCR, Corridor E, ROOM E121 P.O. Box: 2713, Doha, Qatar ibadran at qu.edu.qa Profile: http://qufaculty.qu.edu.qa/ibadran -------------- next part -------------- An HTML attachment was scrubbed... URL: From philipse at scm.com Fri Apr 22 11:19:45 2022 From: philipse at scm.com (Pier Philipsen) Date: Fri, 22 Apr 2022 11:19:45 +0200 Subject: [ADF-LIST] Help with Fe3O4 In-Reply-To: <9942247450a94449bad34cd1603fdc54@qu.edu.qa> References: <8bb58802.AU4AAFNG32IAAAAAAAAAAP-XPaYAASKLT0kAAAAAAAm5ZgBiMvmu@mailjet.com> <2b53e37b-fcd6-5d88-d987-b71c2019a688@scm.com> <164212a5a6174830a2935467c197063d@qu.edu.qa> <1090172f-001a-78c2-6e38-49e869ea3cec@scm.com> <284ab87aa4b945f9b35c05fa0b9f86f9@qu.edu.qa> <78c3fcd1-2a61-79c7-3226-2d9e371ca450@scm.com> <9942247450a94449bad34cd1603fdc54@qu.edu.qa> Message-ID: <157ee01f-ad55-7ebc-8aa9-139b061fa99e@scm.com> Dear Ismail, It is not possible to control/constrain spin polarizations for atoms.? Not using spin, your job works fine, except for using rather a lot of SCF iterations per geometry step (~80) which can be improved a bit (~60) by using a finite electronic temperature ??? Convergence ElectronicTemperature=0.003 ?I assume that when starting to use spin more iterations are required, especially when the system is quite far from the optimum geometry. It makes sense to first optimize not using spin. Best regards, Pier On 21-04-2022 18:19, Ismail Badran wrote: >>> >>> Over the last week, I was attempting to work with an Fe3O4 lattice. >>> All jobs I summitted using the BAND engine have failed. I guess now >>> the problem is with setting the correct spin polarization to?the >>> different Fe2+ and Fe3+ atoms. Have anyone worked with Fe3O4 (111) >>> slabs? Any successwith BAND? >>> >>> >>> *Dr. Ismail Badran* >>> >>> * >>> **Associate?Professor of Physical Chemistry >>> *Department of Chemistry and Earth Sciences, Qatar University >>> >>> BCR, Corridor E, ROOM E121 >>> P.O. Box: 2713, Doha, Qatar >>> >>> ibadran at qu.edu.qa >>> >>> Profile: http://qufaculty.qu.edu.qa/ibadran >>> >>> >>> >>> > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist -------------- next part -------------- An HTML attachment was scrubbed... URL: