From cy22resch11027 at iith.ac.in Tue Nov 1 06:10:15 2022 From: cy22resch11027 at iith.ac.in (Ibtesham Tarannum) Date: Tue, 1 Nov 2022 10:40:15 +0530 Subject: [ADF-LIST] ADFlist Digest, Vol 94, Issue 2 In-Reply-To: <6750E703-E480-4397-9361-34A5B0D79F6E@gmail.com> References: <6750E703-E480-4397-9361-34A5B0D79F6E@gmail.com> Message-ID: Respected Sir, I beg to state that I have followed the above-mentioned methods but still do not converge. Here is the log file attached. Please have a look. Thank you Sincerely Ibtesham On Sat, Oct 29, 2022 at 12:11 PM Marcel Swart via ADFlist wrote: > Dear Ibtesham, > > Please try with the following settings: > > SCF > Converge 1.0e-6 1.0e-4 > DIIS > Ok 0.01 > End > Mixing 0.20 > Mixing1 0.10 > Iterations 199 > End > Occupations Smear=0.0 > > And if not converged still, reduce the mixing and mixing1 parameters: > > SCF > Converge 1.0e-6 1.0e-4 > DIIS > Ok 0.01 > End > Mixing 0.15 > Mixing1 0.05 > Iterations 199 > End > Occupations Smear=0.0 > > If still not converged, please send me the logfile with the ErrMat lines. > > Marcel Swart > ICREA Research Professor at University of Girona (UdG) > Director of Institut de Qu?mica Computacional i Cat?lisi, UdG > > Univ. Girona, Campus Montilivi (Ci?ncies) > c/ M.A. Capmany i Farn?s, 69 > 17003 Girona, Spain > > www.marcelswart.eu > marcel.swart at gmail.com > > > On 28 Oct 2022, at 19:52, adflist-request at scm.com wrote: > > Dear Ibtesham Tarannum, > > It looks like one of your fragment calculations did not converge fully. > I suspect using more than 1000 iterations will not help you much here. > It may be tough to converge this system with 5 unpaired electrons. > > Perhaps your EDA will still give sensible results though? > > Kind regards, > > Fedor > > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist > -- Disclaimer:- This?footer text is to convey that this email is sent by one of the?users of IITH. So, do not mark it as SPAM. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Dy66.out Type: application/octet-stream Size: 580517 bytes Desc: not available URL: From marcel.swart at gmail.com Tue Nov 1 10:57:38 2022 From: marcel.swart at gmail.com (Marcel Swart) Date: Tue, 1 Nov 2022 10:57:38 +0100 Subject: [ADF-LIST] ADFlist Digest, Vol 95, Issue 1 In-Reply-To: References: Message-ID: <41FEC028-E488-4681-BE81-D89256F71F9A@gmail.com> > Respected Sir, > I beg to state that I have followed the above-mentioned methods but still > do not converge. > Here is the log file attached. Please have a look. > > Thank you > > Sincerely > > Ibtesham A 27 27 1.000 -2.076 au Region_2 1.00 27 A 1 ( -56.492 eV) B 1.000 -2.012 au ( -54.762 eV) A 28 28 1.000 -1.466 au Region_2 1.00 28 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 29 29 1.000 -1.466 au Region_2 1.00 29 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 30 30 1.000 -1.466 au Region_2 1.00 30 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 31 31 1.000 -1.466 au Region_2 1.00 31 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 32 32 1.000 -1.466 au Region_2 1.00 32 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 33 33 1.000 -1.466 au Region_2 1.00 33 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) A 34 34 1.000 -1.466 au Region_2 1.00 34 A 1 ( -39.889 eV) B 0.286 -1.100 au ( -29.941 eV) If I understand it correctly, you have first prepared a fragment for Dy(III) with NOSYM, and where you occupied all f-orbitals by 2/7? Why? I would use symmetry of some sort (D2h, C2v) and then use the IrrepOccupations block to assign electrons to specific irreps https://www.scm.com/doc/ADF/Input/Electronic_Configuration.html#keyscheme-irrepoccupations I.e. something like this if you?re using Core Small: IrrepOccupations A.g 1.0 // 1.0 B1.g 0.0 // 0.0 B2.g 0.0 // 0.0 B3.g 0.0 // 0.0 A.u 1.0 // 0.0 B1.u 3.0 // 2.0 B2.u 3.0 // 2.0 B3.u 3.0 // 1.0 End MS From sachinadityaramesh at gmail.com Wed Nov 2 09:13:00 2022 From: sachinadityaramesh at gmail.com (Sachin Ramesh) Date: Wed, 2 Nov 2022 13:43:00 +0530 Subject: [ADF-LIST] Unusual Results in EDA Message-ID: Dear all, We are interested in certain europium complexes, in this regard I have done an EDA of a complex of Europium(III). The complex: Eu(NO3)3.3L Oxidation state of metal: 3+ No. of unpaired electrons: 6 Net charge on the complex: 0 Fragment 1: Eu(NO3)3 Fragment 2: Ligand1 Fragment 3: Ligand2 Fragment 4: Ligand3 To the best of our knowledge the input is accurate. We have obtained the following results, ---------------------------------------------------------------------------- Pauli Repulsion = 5.5217 eV Electrostatic Interaction = -5.6441 eV Total Steric Interaction = -0.1224 eV --------------------------------------------------------------------------- All computations are performed using ADF2016 Are my results valid or am I missing something? This seems unusual only because the systems we have worked with have always resulted in +ve steric interaction (as defined in Baerends-Bickelhaupt paper) Kindly advice -Sachin -------------- next part -------------- An HTML attachment was scrubbed... URL: From ism45 at yahoo.com Thu Nov 3 07:53:07 2022 From: ism45 at yahoo.com (Ismail Badran) Date: Thu, 3 Nov 2022 06:53:07 +0000 (UTC) Subject: [ADF-LIST] Memory problem References: <1516387834.800813.1667458387990.ref@mail.yahoo.com> Message-ID: <1516387834.800813.1667458387990@mail.yahoo.com> Hello all,? I am facing troubles with some band jobs, it is very surprising that the jobs fail with memory allocation errors, although I am running the jobs on an HPC server with 32 cpu and 256 GB I already contacted the server admin and they failed to solve the problem. Any idea on such error ! I am attaching the input and output files for your reference? Note: mem=0 means request all memory on node, which is 256 GB Ismail Dr. Ismail Badran?PhD in Physical Chemistry -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Graph_Amine_08.run Type: application/octet-stream Size: 65014 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AMS_Ismail_64.sh Type: text/x-sh Size: 370 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Graph_Amine_08.run.log Type: application/octet-stream Size: 153024 bytes Desc: not available URL: From vanschoot at scm.com Thu Nov 3 10:03:27 2022 From: vanschoot at scm.com (Hans van Schoot) Date: Thu, 3 Nov 2022 10:03:27 +0100 Subject: [ADF-LIST] Memory problem In-Reply-To: <1516387834.800813.1667458387990@mail.yahoo.com> References: <1516387834.800813.1667458387990.ref@mail.yahoo.com> <1516387834.800813.1667458387990@mail.yahoo.com> Message-ID: Dear Ismail, Please check the following documentation item, it could be that the SLURM batch system is incorrectly monitoring shared memory: https://www.scm.com/doc/Installation/Additional_Information_and_Known_Issues.html#shared-memory-and-batch-systems-slurm best regards, Hans van Schoot On 03-11-2022 07:53, Ismail Badran via ADFlist wrote: > Hello all, > > I am facing troubles with some band jobs, it is very surprising that > the jobs fail with memory allocation errors, although I am running the > jobs on an HPC server with 32 cpu and 256 GB > > I already contacted the server admin and they failed to solve the > problem. Any idea on such error ! > > I am attaching the input and output files for your reference > > Note: mem=0 means request all memory on node, which is 256 GB > > Ismail > > > Dr. Ismail Badran > PhD in Physical Chemistry > > > _______________________________________________ > ADFlist mailing list > ADFlist at scm.com > https://lists.scm.com/mailman/listinfo/adflist -------------- next part -------------- An HTML attachment was scrubbed... URL: From philipse at scm.com Thu Nov 3 10:25:55 2022 From: philipse at scm.com (Pier Philipsen) Date: Thu, 3 Nov 2022 10:25:55 +0100 Subject: [ADF-LIST] Memory problem In-Reply-To: References: <1516387834.800813.1667458387990.ref@mail.yahoo.com> <1516387834.800813.1667458387990@mail.yahoo.com> Message-ID: <374b246d-e463-8a2b-1932-028cecb9b11a@scm.com> Dear Ismael, It is a big job with ~600 atoms. You could try to submit on more nodes, if disk usage were to be the issue. The number of basis functions is 8000 and that sounds like it should be doable. You could also try to use a frozen core, which will work well, but only saves you a few 1s functions for this organic system. Best regards, Pier On 03-11-2022 10:03, Hans van Schoot via ADFlist wrote: > Dear Ismail, > > Please check the following documentation item, it could be that the > SLURM batch system is incorrectly monitoring shared memory: > https://www.scm.com/doc/Installation/Additional_Information_and_Known_Issues.html#shared-memory-and-batch-systems-slurm > > best regards, > Hans van Schoot > > On 03-11-2022 07:53, Ismail Badran via ADFlist wrote: >> Hello all, >> >> I am facing troubles with some band jobs, it is very surprising that >> the jobs fail with memory allocation errors, although I am running >> the jobs on an HPC server with 32 cpu and 256 GB >> >> I already contacted the server admin and they failed to solve the >> problem. Any idea on such error ! >> >> I am attaching the input and output files for your reference >> >> Note: mem=0 means request all memory on node, which is 256 GB >> >> Ismail >> >> >> Dr. Ismail Badran >> PhD in Physical Chemistry >> >> >> _______________________________________________ >> ADFlist mailing list >> ADFlist at scm.com >> https://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: From ism45 at yahoo.com Fri Nov 4 14:28:29 2022 From: ism45 at yahoo.com (Ismail Badran) Date: Fri, 4 Nov 2022 13:28:29 +0000 (UTC) Subject: [ADF-LIST] Memory problem In-Reply-To: <374b246d-e463-8a2b-1932-028cecb9b11a@scm.com> References: <1516387834.800813.1667458387990.ref@mail.yahoo.com> <1516387834.800813.1667458387990@mail.yahoo.com> <374b246d-e463-8a2b-1932-028cecb9b11a@scm.com> Message-ID: <879353964.1478520.1667568509195@mail.yahoo.com> I have just received an email from the HPC in Canada telling me that my jobs did not fail because of memory problems, They looked at the memory used and it was much less than what I asked for.? Looks like an issue with the BAND itself? Any further ideas would help here please? Dr. Ismail Badran?PhD in Physical Chemistry On Thursday, November 3, 2022 at 11:26:14 a.m. GMT+2, Pier Philipsen via ADFlist wrote: Dear Ismael, It is a big job with ~600 atoms. You could try to submit on more nodes, if disk usage were to be the issue. The number of basis functions is 8000 and that sounds like it should be doable. You could also try to use a frozen core, which will work well, but only saves you a few 1s functions for this organic system. Best regards, Pier On 03-11-2022 10:03, Hans van Schoot via ADFlist wrote: Dear Ismail, Please check the following documentation item, it could be that the SLURM batch system is incorrectly monitoring shared memory: https://www.scm.com/doc/Installation/Additional_Information_and_Known_Issues.html#shared-memory-and-batch-systems-slurm best regards, Hans van Schoot On 03-11-2022 07:53, Ismail Badran via ADFlist wrote: Hello all,? I am facing troubles with some band jobs, it is very surprising that the jobs fail with memory allocation errors, although I am running the jobs on an HPC server with 32 cpu and 256 GB I already contacted the server admin and they failed to solve the problem. Any idea on such error ! I am attaching the input and output files for your reference? Note: mem=0 means request all memory on node, which is 256 GB Ismail Dr. Ismail Badran? PhD in Physical Chemistry _______________________________________________ ADFlist mailing list ADFlist at scm.com https://lists.scm.com/mailman/listinfo/adflist _______________________________________________ ADFlist mailing list ADFlist at scm.com https://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: From ism45 at yahoo.com Wed Nov 9 16:34:13 2022 From: ism45 at yahoo.com (Ismail Badran) Date: Wed, 9 Nov 2022 15:34:13 +0000 (UTC) Subject: [ADF-LIST] Memory problem In-Reply-To: <374b246d-e463-8a2b-1932-028cecb9b11a@scm.com> References: <1516387834.800813.1667458387990.ref@mail.yahoo.com> <1516387834.800813.1667458387990@mail.yahoo.com> <374b246d-e463-8a2b-1932-028cecb9b11a@scm.com> Message-ID: <2046512546.306859.1668008053842@mail.yahoo.com> Hello all,? looks like removing the shared memory option can solve the problem after all? Engine BAND? ? Programmer? ? ? ? Usesharedmemory No? ? End Thanks? Dr. Ismail Badran?PhD in Physical Chemistry On Thursday, November 3, 2022 at 11:26:14 a.m. GMT+2, Pier Philipsen via ADFlist wrote: Dear Ismael, It is a big job with ~600 atoms. You could try to submit on more nodes, if disk usage were to be the issue. The number of basis functions is 8000 and that sounds like it should be doable. You could also try to use a frozen core, which will work well, but only saves you a few 1s functions for this organic system. Best regards, Pier On 03-11-2022 10:03, Hans van Schoot via ADFlist wrote: Dear Ismail, Please check the following documentation item, it could be that the SLURM batch system is incorrectly monitoring shared memory: https://www.scm.com/doc/Installation/Additional_Information_and_Known_Issues.html#shared-memory-and-batch-systems-slurm best regards, Hans van Schoot On 03-11-2022 07:53, Ismail Badran via ADFlist wrote: Hello all,? I am facing troubles with some band jobs, it is very surprising that the jobs fail with memory allocation errors, although I am running the jobs on an HPC server with 32 cpu and 256 GB I already contacted the server admin and they failed to solve the problem. Any idea on such error ! I am attaching the input and output files for your reference? Note: mem=0 means request all memory on node, which is 256 GB Ismail Dr. Ismail Badran? PhD in Physical Chemistry _______________________________________________ ADFlist mailing list ADFlist at scm.com https://lists.scm.com/mailman/listinfo/adflist _______________________________________________ ADFlist mailing list ADFlist at scm.com https://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: From cristina.moliner at unige.it Mon Nov 28 19:51:15 2022 From: cristina.moliner at unige.it (Cristina Moliner) Date: Mon, 28 Nov 2022 19:51:15 +0100 Subject: [ADF-LIST] Simulation of plasma-assisted oxidation reactions Message-ID: <835c7e3a-199e-fbd6-5467-94113eb9044b@unige.it> Hi all, I am trying to simulate the plasma-assisted oxidation of hydrogen at low temperatures with REAXFF and eREAXFF. I thought that I could first carry out the reactions using the reactive force field (REAXFF) and then export those results to eREAXFF and apply an electrical stimulus but i am not sure of how to do it, if it can be done anyhow. The other option would be to try adding electrons directly to my H2/O2 system on REAXFF but again, i am not sure of how to do it properly. Any indication on how to simulate plasma-assisted oxidation reactions would be much appreciated, if possible using REAXFF. Thank you and best regards, Cristina Moliner -- **************************************************** Cristina Moliner PERT - Process Engineering Research Team Department of Civil, Chemical and Environmental Engineering DICCA University of Genova Via Opera Pia, 15a 16145, Genova, Italy tel: +39 010 335 2912 Mob: +39 366 5029287 E-mail cristina.moliner at unige.it http://www3.dicca.unige.it/pert/ Skype contact: cristina.moliner *****************************************************