Re: [Wien] Structure optimization of Beta -Sn
As far as I know, cif2struct supports only the official names of the 230 space groups as listed eg. at the Bilbao cryst. server, but not the (older ??) _space_group_name_H-M_altconvention. For SG # 141 only I41/amd is supported. Only for low symmetry SGs with different setting, more than one name is supported, eg. 50, 8,3,'Pban','-P-2zab;-2xb ', & 50, 8,3,'Pncb','-P-2xbc;-2yc ', & 50, 8,3,'Pcna','-P-2yca;-2za '/ As far as I know, for parsing the cif files official subroutines from IUCR were used, but maybe they have been updated by now or only a subset was used or this cif file does not obey the standard. Am 04.06.2020 um 10:00 schrieb Tran, Fabien: With your modified cif file, I obtain at the end of init_lapw a struct file which has two atoms per cell. Since there is no atoms at the corners, it is visually not 100% clear that it is the correct beta-Sn, but I guess it is (?). I am wondering where the problem with original cif file comes from. From cif2struct or a non-conventional format of the cif file? Maybe Peter knows. From: Wien on behalf of Xavier Rocquefelte Sent: Thursday, June 4, 2020 9:28 AM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Structure optimization of Beta -Sn Indeed, I used the one from VESTA! Yesteray night I was working in parallel ;) Here is the file I previously sent with modification by hand ... the cif format was not totally supported by cif2struct. Regards Xavier ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier Sir, Thank you so much for your time & suggestions. with regards, On Thu, 4 Jun 2020 at 14:55, Xavier Rocquefelte < xavier.rocquefe...@univ-rennes1.fr> wrote: > This last input file leads to a correct structure. > > Best regards > > Xavier > Le 04/06/2020 à 11:11, shamik chakrabarti a écrit : > > Dear Xavier Sir, > > With the modified cif file & origin choice one, I get > the structure as attached herewith this mail. Kindly let me know if it is > the structure you are asking for. I am using wien2k 19.1. > > with regards > > On Thu, 4 Jun 2020 at 13:30, Tran, Fabien > wrote: > >> With your modified cif file, I obtain at the end of init_lapw a struct >> file which has two atoms per cell. Since there is no atoms at the corners, >> it is visually not 100% clear that it is the correct beta-Sn, but I guess >> it is (?). >> >> I am wondering where the problem with original cif file comes from. From >> cif2struct or a non-conventional format of the cif file? Maybe Peter knows. >> >> >> From: Wien on behalf of Xavier >> Rocquefelte >> Sent: Thursday, June 4, 2020 9:28 AM >> To: wien@zeus.theochem.tuwien.ac.at >> Subject: Re: [Wien] Structure optimization of Beta -Sn >> >> Indeed, I used the one from VESTA! Yesteray night I was working in >> parallel ;) >> >> Here is the file I previously sent with modification by hand ... the cif >> format was not totally supported by cif2struct. >> >> Regards >> >> Xavier >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >> > > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > > ___ > Wien mailing > listw...@zeus.theochem.tuwien.ac.athttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > -- > > Institut des Sciences Chimiques de Rennes (ISCR) > Univ Rennes - CNRS - UMR6226, > Francehttps://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier > > ICAMM2019 : VASP Workshop and International Materials Modelling Conf > June 26-July 3 2019, Rennes Franceicamm2019.sciencesconf.org : Registration > opening soon, see you there! > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
This last input file leads to a correct structure. Best regards Xavier Le 04/06/2020 à 11:11, shamik chakrabarti a écrit : Dear Xavier Sir, With the modified cif file & origin choice one, I get the structure as attached herewith this mail. Kindly let me know if it is the structure you are asking for. I am using wien2k 19.1. with regards On Thu, 4 Jun 2020 at 13:30, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: With your modified cif file, I obtain at the end of init_lapw a struct file which has two atoms per cell. Since there is no atoms at the corners, it is visually not 100% clear that it is the correct beta-Sn, but I guess it is (?). I am wondering where the problem with original cif file comes from. From cif2struct or a non-conventional format of the cif file? Maybe Peter knows. From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Xavier Rocquefelte mailto:xavier.rocquefe...@univ-rennes1.fr>> Sent: Thursday, June 4, 2020 9:28 AM To: wien@zeus.theochem.tuwien.ac.at <mailto:wien@zeus.theochem.tuwien.ac.at> Subject: Re: [Wien] Structure optimization of Beta -Sn Indeed, I used the one from VESTA! Yesteray night I was working in parallel ;) Here is the file I previously sent with modification by hand ... the cif format was not totally supported by cif2struct. Regards Xavier ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at <mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Institut des Sciences Chimiques de Rennes (ISCR) Univ Rennes - CNRS - UMR6226, France https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier ICAMM2019 : VASP Workshop and International Materials Modelling Conf June 26-July 3 2019, Rennes France icamm2019.sciencesconf.org : Registration opening soon, see you there! ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier Sir, With the modified cif file & origin choice one, I get the structure as attached herewith this mail. Kindly let me know if it is the structure you are asking for. I am using wien2k 19.1. with regards On Thu, 4 Jun 2020 at 13:30, Tran, Fabien wrote: > With your modified cif file, I obtain at the end of init_lapw a struct > file which has two atoms per cell. Since there is no atoms at the corners, > it is visually not 100% clear that it is the correct beta-Sn, but I guess > it is (?). > > I am wondering where the problem with original cif file comes from. From > cif2struct or a non-conventional format of the cif file? Maybe Peter knows. > > > From: Wien on behalf of Xavier > Rocquefelte > Sent: Thursday, June 4, 2020 9:28 AM > To: wien@zeus.theochem.tuwien.ac.at > Subject: Re: [Wien] Structure optimization of Beta -Sn > > Indeed, I used the one from VESTA! Yesteray night I was working in > parallel ;) > > Here is the file I previously sent with modification by hand ... the cif > format was not totally supported by cif2struct. > > Regards > > Xavier > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India Beta_Sn_final_V.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
With your modified cif file, I obtain at the end of init_lapw a struct file which has two atoms per cell. Since there is no atoms at the corners, it is visually not 100% clear that it is the correct beta-Sn, but I guess it is (?). I am wondering where the problem with original cif file comes from. From cif2struct or a non-conventional format of the cif file? Maybe Peter knows. From: Wien on behalf of Xavier Rocquefelte Sent: Thursday, June 4, 2020 9:28 AM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Structure optimization of Beta -Sn Indeed, I used the one from VESTA! Yesteray night I was working in parallel ;) Here is the file I previously sent with modification by hand ... the cif format was not totally supported by cif2struct. Regards Xavier ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
I have to remove "s" as you did and rewrite the loop with the symmetry operations. It is a problem with the origin choice! Regards Xavier Le 04/06/2020 à 09:33, Tran, Fabien a écrit : Dear Xavier, Your cif file can be converted to struct, but only if I remove "s" as suggested by Shamik. I tried with cif2struct from old and new versions of cWIEN2k. But, I still get the wrong structure at the end of init_lapw (4 equivalent atoms). If I understood correctly, you did not have these two problems with your cif file? *From:* Wien on behalf of Xavier Rocquefelte *Sent:* Thursday, June 4, 2020 9:13 AM *To:* wien@zeus.theochem.tuwien.ac.at *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Fabien This is strange... Perhaps a conversion problem. Yes I have used the following cif file and cif2struct works for me! Regards Xavier Le 04/06/2020 à 09:10, Tran, Fabien a écrit : Dear Xavier, I read your email from yesterday, but I thought that his struct filewas correct, because I got the same struct file from this cif file: http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif But you are right; if I visualize it, I can see that it is not beta-Sn. Besides, I can not convert cif to struct other cif files like the one that you sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct file is generated. Did cif2struct work for you? *From:* Wien on behalf of Xavier Rocquefelte *Sent:* Wednesday, June 3, 2020 11:54 PM *To:* wien@zeus.theochem.tuwien.ac.at *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1 NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? *From:* Wien on behalf of shamik chakrabarti *Sent:* Wednesday, June 3, 2020 8:40 PM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 *From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on beh
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier, Your cif file can be converted to struct, but only if I remove "s" as suggested by Shamik. I tried with cif2struct from old and new versions of cWIEN2k. But, I still get the wrong structure at the end of init_lapw (4 equivalent atoms). If I understood correctly, you did not have these two problems with your cif file? From: Wien on behalf of Xavier Rocquefelte Sent: Thursday, June 4, 2020 9:13 AM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Fabien This is strange... Perhaps a conversion problem. Yes I have used the following cif file and cif2struct works for me! Regards Xavier Le 04/06/2020 à 09:10, Tran, Fabien a écrit : Dear Xavier, I read your email from yesterday, but I thought that his struct file was correct, because I got the same struct file from this cif file: http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif But you are right; if I visualize it, I can see that it is not beta-Sn. Besides, I can not convert cif to struct other cif files like the one that you sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct file is generated. Did cif2struct work for you? From: Wien <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Xavier Rocquefelte <mailto:xavier.rocquefe...@univ-rennes1.fr> Sent: Wednesday, June 3, 2020 11:54 PM To: wien@zeus.theochem.tuwien.ac.at<mailto:wien@zeus.theochem.tuwien.ac.at> Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? From: Wien <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of shamik chakrabarti <mailto:shamik15041...@gmail.com> Sent: Wednesday, June 3, 2020 8:40 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> Sent: Wednesday, June 3, 2020 8:06 PM To: A Mailing list for WIEN2k users Subject: [Wien] Structure optimizat
Re: [Wien] Structure optimization of Beta -Sn
Indeed, I used the one from VESTA! Yesteray night I was working in parallel ;) Here is the file I previously sent with modification by hand ... the cif format was not totally supported by cif2struct. Regards Xavier ) 2020 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure. All rights reserved. data_106072-ICSD _database_code_ICSD 106072 _audit_creation_date 2004-10-01 _audit_update_record 2017-08-01 _chemical_name_common Tin _chemical_formula_structural Sn _chemical_formula_sum Sn1 _chemical_name_structure_type Sn(tI4) _exptl_crystal_density_diffrn 7.29 _diffrn_ambient_temperature 296. _citation_title ; X-ray investigation of thermal expansion and atomic thermal vibrations of tin, indium, and their alloys ; loop_ _citation_id _citation_journal_full _citation_year _citation_journal_volume _citation_page_first _citation_page_last _citation_journal_id_ASTM primary 'Physica Status Solidi B: Basic Solid State Physics' 1981 107 245 253 PSSBBD loop_ _citation_author_citation_id _citation_author_name primary 'Wolcyrz, M.' primary 'Kubiak, R.' primary 'Maciejewski, S.' _cell_length_a 5.8308(2) _cell_length_b 5.8308(2) _cell_length_c 3.1810(2) _cell_angle_alpha 90. _cell_angle_beta 90. _cell_angle_gamma 90. _cell_volume 108.15 _cell_formula_units_Z 4 _symmetry_space_group_name_H-M 'I 41/a m d' _symmetry_Int_Tables_number 141 loop_ loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, -y+1/2, z+1/2' '-y, x+1/2, z+1/4' 'y+1/2, -x, z+3/4' '-x+1/2, y, -z+3/4' 'x, -y+1/2, -z+1/4' 'y+1/2, x+1/2, -z+1/2' '-y, -x, -z' '-x, -y+1/2, -z+1/4' 'x+1/2, y, -z+3/4' 'y, -x, -z' '-y+1/2, x+1/2, -z+1/2' 'x+1/2, -y+1/2, z+1/2' '-x, y, z' '-y+1/2, -x, z+3/4' 'y, x+1/2, z+1/4' 'x+1/2, y+1/2, z+1/2' '-x, -y, z' '-y+1/2, x, z+3/4' 'y, -x+1/2, z+1/4' '-x, y+1/2, -z+1/4' 'x+1/2, -y, -z+3/4' 'y, x, -z' '-y+1/2, -x+1/2, -z+1/2' '-x+1/2, -y, -z+3/4' 'x, y+1/2, -z+1/4' 'y+1/2, -x+1/2, -z+1/2' '-y, x, -z' 'x, -y, z' '-x+1/2, y+1/2, z+1/2' '-y, -x+1/2, z+1/4' 'y+1/2, x, z+3/4' loop_ _atom_type_symbol _atom_type_oxidation_number Sn0+ 0 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_B_iso_or_equiv _atom_site_occupancy Sn1 Sn0+ 4 a 0 0 0 . 1. loop_ _atom_site_aniso_label _atom_site_aniso_type_symbol _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Sn1 Sn0+ 0.0200(2) 0.0200(2) 0.0241(2) 0. 0. 0. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
hii Shamik, open the cif file in VESTA and then export it again as a cif file. This new cif file should work. Regards Bhamu On Thu, Jun 4, 2020 at 12:43 PM Xavier Rocquefelte < xavier.rocquefe...@univ-rennes1.fr> wrote: > Dear Fabien > > This is strange... Perhaps a conversion problem. Yes I have used the > following cif file and cif2struct works for me! > > Regards > > Xavier > > > > Le 04/06/2020 à 09:10, Tran, Fabien a écrit : > > Dear Xavier, > > I read your email from yesterday, but I thought that his struct file was > correct, because I got the same struct file from this cif file: > > http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif > > But you are right; if I visualize it, I can see that it is not beta-Sn. > Besides, I can not convert cif to struct other cif files like the one that > you sent. With cif2struct, I get "unknown space group name: I41/amds" and > no struct file is generated. > > Did cif2struct work for you? > > > > -- > *From:* Wien > on behalf of Xavier Rocquefelte > > *Sent:* Wednesday, June 3, 2020 11:54 PM > *To:* wien@zeus.theochem.tuwien.ac.at > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > > Dear Fabien, > > I explained to Shamik that the structure he was using was not correct. > > I also sent cif and struct file. > > See below a proper case.struct file. > > Shamik could you please send email only to the wienlist to avoid multiple > answers from the list and many people trying to help you without having all > the details? > > > blebleble > B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd > MODE OF CALC=RELA unit=bohr > 11.019938 11.019938 6.011975 90.00 90.00 90.00 > ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 > MULT= 2 ISPLIT=-2 >1: X=0. Y=0.2500 Z=0.3750 > Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. > LOCAL ROT MATRIX:1.000 0.000 0.000 > 0.000 1.000 0.000 > 0.000 0.000 1.000 > 16 NUMBER OF SYMMETRY OPERATIONS > 1 0 0 0. > 0 1 0 0. > 0 0 1 0. >1 > -1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 >2 > 0-1 0 0.2500 > 1 0 0 0.7500 > 0 0 1 0.2500 >3 > 0 1 0 0.2500 > -1 0 0 0.2500 > 0 0 1 0.7500 >4 > -1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 >5 > 1 0 0 0. > 0-1 0 0. > 0 0-1 0. >6 > 0 1 0 0.2500 > 1 0 0 0.7500 > 0 0-1 0.2500 >7 > 0-1 0 0.2500 > -1 0 0 0.2500 > 0 0-1 0.7500 >8 > -1 0 0 0. > 0-1 0 0. > 0 0-1 0. >9 > 1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 > 10 > 0 1 0 0.7500 > -1 0 0 0.2500 > 0 0-1 0.7500 > 11 > 0-1 0 0.7500 > 1 0 0 0.7500 > 0 0-1 0.2500 > 12 > 1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 > 13 > -1 0 0 0. > 0 1 0 0. > 0 0 1 0. > 14 > 0-1 0 0.7500 > -1 0 0 0.2500 > 0 0 1 0.7500 > 15 > 0 1 0 0.7500 > 1 0 0 0.7500 > 0 0 1 0.2500 > 16 > > > > > > Le 03/06/2020 à 21:38, Tran, Fabien a écrit : > > Using a RKmax above 7 should not lead to completely wrong results. > One important point is how the lattice constants a and c were varied. In a > meaningful way? > > > -- > *From:* Wien > on behalf of shamik chakrabarti > > *Sent:* Wednesday, June 3, 2020 8:40 PM > *To:* A Mailing list for WIEN2k users > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > Dear Dr. Tran, > > I have used both plain GGA & nlvdw independently & in > both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for > GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am > currently going through the literature you have sent.. > > with regards, > > On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote: > >> At first sight you struct file seems ok, but this is difficult to help >> you without more details. For instance: Which functional have you used? Are >> you keeping the c/a ratio fixed? Have you looked into the literature: >> >> https://aip.scitation.org/doi/abs/10.1063/1.4948434 >> >> >> -- >> *From:* Wien on behalf o
Re: [Wien] Structure optimization of Beta -Sn
Dear Dr. Tran, You have to remove the "s" from "I41/amds" & then you will get the struct. However, the struct file is always giving 4 equivalent atoms/unit cell. with regards, On Thu, 4 Jun 2020 at 12:40, Tran, Fabien wrote: > Dear Xavier, > > I read your email from yesterday, but I thought that his struct file was > correct, because I got the same struct file from this cif file: > > http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif > > But you are right; if I visualize it, I can see that it is not beta-Sn. > Besides, I can not convert cif to struct other cif files like the one that > you sent. With cif2struct, I get "unknown space group name: I41/amds" and > no struct file is generated. > > Did cif2struct work for you? > > > > -- > *From:* Wien on behalf of > Xavier Rocquefelte > *Sent:* Wednesday, June 3, 2020 11:54 PM > *To:* wien@zeus.theochem.tuwien.ac.at > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > > Dear Fabien, > > I explained to Shamik that the structure he was using was not correct. > > I also sent cif and struct file. > > See below a proper case.struct file. > > Shamik could you please send email only to the wienlist to avoid multiple > answers from the list and many people trying to help you without having all > the details? > > > blebleble > B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd > MODE OF CALC=RELA unit=bohr > 11.019938 11.019938 6.011975 90.00 90.00 90.00 > ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 > MULT= 2 ISPLIT=-2 >1: X=0. Y=0.2500 Z=0.3750 > Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. > LOCAL ROT MATRIX:1.000 0.000 0.000 > 0.000 1.000 0.000 > 0.000 0.000 1.000 > 16 NUMBER OF SYMMETRY OPERATIONS > 1 0 0 0. > 0 1 0 0. > 0 0 1 0. >1 > -1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 >2 > 0-1 0 0.2500 > 1 0 0 0.7500 > 0 0 1 0.2500 >3 > 0 1 0 0.2500 > -1 0 0 0.2500 > 0 0 1 0.7500 >4 > -1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 >5 > 1 0 0 0. > 0-1 0 0. > 0 0-1 0. >6 > 0 1 0 0.2500 > 1 0 0 0.7500 > 0 0-1 0.2500 >7 > 0-1 0 0.2500 > -1 0 0 0.2500 > 0 0-1 0.7500 >8 > -1 0 0 0. > 0-1 0 0. > 0 0-1 0. >9 > 1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 > 10 > 0 1 0 0.7500 > -1 0 0 0.2500 > 0 0-1 0.7500 > 11 > 0-1 0 0.7500 > 1 0 0 0.7500 > 0 0-1 0.2500 > 12 > 1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 > 13 > -1 0 0 0. > 0 1 0 0. > 0 0 1 0. > 14 > 0-1 0 0.7500 > -1 0 0 0.2500 > 0 0 1 0.7500 > 15 > 0 1 0 0.7500 > 1 0 0 0.7500 > 0 0 1 0.2500 > 16 > > > > > > Le 03/06/2020 à 21:38, Tran, Fabien a écrit : > > Using a RKmax above 7 should not lead to completely wrong results. > One important point is how the lattice constants a and c were varied. In a > meaningful way? > > > -- > *From:* Wien > on behalf of shamik chakrabarti > > *Sent:* Wednesday, June 3, 2020 8:40 PM > *To:* A Mailing list for WIEN2k users > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > Dear Dr. Tran, > > I have used both plain GGA & nlvdw independently & in > both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for > GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am > currently going through the literature you have sent.. > > with regards, > > On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote: > >> At first sight you struct file seems ok, but this is difficult to help >> you without more details. For instance: Which functional have you used? Are >> you keeping the c/a ratio fixed? Have you looked into the literature: >> >> https://aip.scitation.org/doi/abs/10.1063/1.4948434 >> >> >> -- >> *From:* Wien on behalf of >> shamik chakrabarti >> *Sent:* Wednesday, June 3, 2020 8:06 PM >> *To:* A Mailing list for WIEN2k users >> *Subject:* [Wien] Structure optimization of Beta -Sn >> >> Dea
Re: [Wien] Structure optimization of Beta -Sn
Dear Fabien This is strange... Perhaps a conversion problem. Yes I have used the following cif file and cif2struct works for me! Regards Xavier Le 04/06/2020 à 09:10, Tran, Fabien a écrit : Dear Xavier, I read your email from yesterday, but I thought that his struct filewas correct, because I got the same struct file from this cif file: http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif But you are right; if I visualize it, I can see that it is not beta-Sn. Besides, I can not convert cif to struct other cif files like the one that you sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct file is generated. Did cif2struct work for you? *From:* Wien on behalf of Xavier Rocquefelte *Sent:* Wednesday, June 3, 2020 11:54 PM *To:* wien@zeus.theochem.tuwien.ac.at *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1 NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? *From:* Wien on behalf of shamik chakrabarti *Sent:* Wednesday, June 3, 2020 8:40 PM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 *From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> *Sent:* Wednesday, June 3, 2020 8:06 PM *To:* A Mailing list for WIEN2k users *Subject:* [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list W
Re: [Wien] Structure optimization of Beta -Sn
Dear Xacier Sir, Thank you for your precious time to solve my problem. The problem I was having, is that after doing cif2struct I am always getting the struct file attached herewith. Please advise me the needful. with regards, On Thu, 4 Jun 2020 at 12:28, Xavier Rocquefelte < xavier.rocquefe...@univ-rennes1.fr> wrote: > Dear Shamik > > I will do as I do with my colleagues who are learning how to use WIEN2k ;) > > Use the cif file I previously sent. If you directory is named Beta-Sn, > rename the cif file Beta-Sn.cif. > > Then use cif2struct in this way: cif2struct Beta-Sn.cif. It will > generate Beta-Sn.struct > > Then initialize the calculation and read carefully what WIEN2k is saying. > > You will see this message when doing sgroup: > > > sgroup(08:56:30) 0.000u 0.000s 0:00.00 0.0%0+0k 0+8io 0pf+0w >Names of point group: -4m2 -4m2 D2d > warning: !!! Struct file is not consistent with space group found. > Number and name of space group: 141 (I 41/a m d) [origin choice 2] > warning: !!! Struct file is not consistent with space group found. > -> check in TT.outputsgroup for proper symmetry, compare > with your struct file and later with TT.outputs > sgroup has also produced a new struct file based on your old one. > If you see warnings above, consider to use the newly generated > struct file, which you can view (edit) now. > -> continue with symmetry (old case.struct) or use/edit > TT.struct_sgroup ? (c/e) > e > > You see that WIEN2k is not happy with this setting and more specifically > WIEN2k has only one origin choice for this space group (the second one) > while the structure I sent you and the one you were using is based on > the origin choice 1. But WIEN2k helps you and proposes to generate the > structure file with the origin choice 2. > > Thus you must use the new file. > > e > -> Do you want to use the new struct file ? (y/n) > y > next is nn > > nn(08:57:51) specify nn-bondlength factor: (usually=2) [and > optionally dlimit, dstmax (about >1.d-5, 20)] > 2 > DSTMAX: 22.004768372 > iix,iiy,iiz 5 5 5 55.09969 > 55.0996930.059875000 > NAMED ATOM: Sn1 Z changed to IATNR+999 to determine equivalency > > ATOM 1 Sn1ATOM 1 Sn1 > RMT( 1)=2.5 AND RMT( 1)=2.5 > SUMS TO 5.0 LT. NN-DIST= 5.71128 > NN ENDS > 0.004u 0.000s 0:01.51 0.0%0+0k 0+32io 0pf+0w > -> check in TT.outputnn for overlapping spheres, > coordination and nearest neighbor distances > -> continue with sgroup or edit the TT.struct file (c/e) > c > next is sgroup > > sgroup(08:58:02) 0.000u 0.000s 0:00.00 0.0%0+0k 0+8io 0pf+0w >Names of point group: -4m2 -4m2 D2d > Number and name of space group: 141 (I 41/a m d) [origin choice 2] > -> check in TT.outputsgroup for proper symmetry, compare > with your struct file and later with TT.outputs > sgroup has also produced a new struct file based on your old one. > If you see warnings above, consider to use the newly generated > struct file, which you can view (edit) now. > -> continue with symmetry (old case.struct) or use/edit > TT.struct_sgroup ? (c/e) > c > > And as you can see you have no more warnings. > > Best regards, > > Xavier > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India Beta_Sn_struct.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier, I read your email from yesterday, but I thought that his struct file was correct, because I got the same struct file from this cif file: http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif But you are right; if I visualize it, I can see that it is not beta-Sn. Besides, I can not convert cif to struct other cif files like the one that you sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct file is generated. Did cif2struct work for you? From: Wien on behalf of Xavier Rocquefelte Sent: Wednesday, June 3, 2020 11:54 PM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? From: Wien <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of shamik chakrabarti <mailto:shamik15041...@gmail.com> Sent: Wednesday, June 3, 2020 8:40 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> Sent: Wednesday, June 3, 2020 8:06 PM To: A Mailing list for WIEN2k users Subject: [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___
Re: [Wien] Structure optimization of Beta -Sn
Dear Shamik I will do as I do with my colleagues who are learning how to use WIEN2k ;) Use the cif file I previously sent. If you directory is named Beta-Sn, rename the cif file Beta-Sn.cif. Then use cif2struct in this way: cif2struct Beta-Sn.cif. It will generate Beta-Sn.struct Then initialize the calculation and read carefully what WIEN2k is saying. You will see this message when doing sgroup: > sgroup (08:56:30) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w Names of point group: -4m2 -4m2 D2d warning: !!! Struct file is not consistent with space group found. Number and name of space group: 141 (I 41/a m d) [origin choice 2] warning: !!! Struct file is not consistent with space group found. -> check in TT.outputsgroup for proper symmetry, compare with your struct file and later with TT.outputs sgroup has also produced a new struct file based on your old one. If you see warnings above, consider to use the newly generated struct file, which you can view (edit) now. -> continue with symmetry (old case.struct) or use/edit TT.struct_sgroup ? (c/e) e You see that WIEN2k is not happy with this setting and more specifically WIEN2k has only one origin choice for this space group (the second one) while the structure I sent you and the one you were using is based on the origin choice 1. But WIEN2k helps you and proposes to generate the structure file with the origin choice 2. Thus you must use the new file. e -> Do you want to use the new struct file ? (y/n) y next is nn > nn (08:57:51) specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about 1.d-5, 20)] 2 DSTMAX: 22.004768372 iix,iiy,iiz 5 5 5 55.09969 55.09969 30.059875000 NAMED ATOM: Sn1 Z changed to IATNR+999 to determine equivalency ATOM 1 Sn1 ATOM 1 Sn1 RMT( 1)=2.5 AND RMT( 1)=2.5 SUMS TO 5.0 LT. NN-DIST= 5.71128 NN ENDS 0.004u 0.000s 0:01.51 0.0% 0+0k 0+32io 0pf+0w -> check in TT.outputnn for overlapping spheres, coordination and nearest neighbor distances -> continue with sgroup or edit the TT.struct file (c/e) c next is sgroup > sgroup (08:58:02) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w Names of point group: -4m2 -4m2 D2d Number and name of space group: 141 (I 41/a m d) [origin choice 2] -> check in TT.outputsgroup for proper symmetry, compare with your struct file and later with TT.outputs sgroup has also produced a new struct file based on your old one. If you see warnings above, consider to use the newly generated struct file, which you can view (edit) now. -> continue with symmetry (old case.struct) or use/edit TT.struct_sgroup ? (c/e) c And as you can see you have no more warnings. Best regards, Xavier ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier Sir, I have a request. Could you please send me the struct file in case.struct format as an attached file to this mail. with kind regards, On Thu, 4 Jun 2020 at 11:43, shamik chakrabarti wrote: > Dear Xavier Sir, > >Please excuse me to resolve a confusion. I have not > sent any mail to anybody's personal mail & has sent the mail only to the > wien2k mailing list. Dr. Tran answers my query as he was the first one to > answer my query through a mail sent to the mailing list only. > > with regards, > > On Thu, 4 Jun 2020 at 11:15, shamik chakrabarti > wrote: > >> Dear Xavier Sir, >> >> Thank you so much for your suggestions. I will >> strictly follow it. >> >> with kind regards, >> >> On Thu, 4 Jun 2020 at 03:39, Xavier Rocquefelte < >> xavier.rocquefe...@univ-rennes1.fr> wrote: >> >>> Here is a cif file. You can see that Sn is on a Wyckoff position 4a, >>> which means that you have 4 equivalent positions in the space group I 41/a >>> m d. >>> >>> In WIEN2k, it leads to a case.struct file having only 2 equivalent >>> positions, because only the positions in the primitive cell are shown in >>> the case.struct file and here the cell is body-centered (I). >>> >>> >>> The fact that you have 4 equivalent position in the case.struct file you >>> sent to the list is clearly an indication that the structure is not >>> correct. >>> >>> In addition, when starting a calculation you should first check the bond >>> distances from the litterature, which is about 3.02 angtström for Sn-Sn. >>> More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn >>> distance. >>> >>> >>> In the structure you sent to the list the Sn-Sn distances were 2.2 >>> angström!!! It is too small for such an element. It is why the geometry >>> optimization goes wrong. Thus, the first thing to due before doing >>> "run_lapw" is to check your data. To do so, you must check carefully: >>> >>> >>> - case.outputnn --> bond distances and coordination >>> >>> - case.outputs --> point group for each inequivalent atoms >>> >>> ... >>> >>> >>> Regards >>> >>> Xavier >>> >>> >>> >>> >>> >>> >>> Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit : >>> >>> Dear Fabien, >>> >>> I explained to Shamik that the structure he was using was not correct. >>> >>> I also sent cif and struct file. >>> >>> See below a proper case.struct file. >>> >>> Shamik could you please send email only to the wienlist to avoid >>> multiple answers from the list and many people trying to help you without >>> having all the details? >>> >>> >>> blebleble >>> B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd >>> MODE OF CALC=RELA unit=bohr >>> 11.019938 11.019938 6.011975 90.00 90.00 90.00 >>> ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 >>> MULT= 2 ISPLIT=-2 >>>1: X=0. Y=0.2500 Z=0.3750 >>> Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. >>> LOCAL ROT MATRIX:1.000 0.000 0.000 >>> 0.000 1.000 0.000 >>> 0.000 0.000 1.000 >>> 16 NUMBER OF SYMMETRY OPERATIONS >>> 1 0 0 0. >>> 0 1 0 0. >>> 0 0 1 0. >>>1 >>> -1 0 0 0.5000 >>> 0-1 0 0. >>> 0 0 1 0.5000 >>>2 >>> 0-1 0 0.2500 >>> 1 0 0 0.7500 >>> 0 0 1 0.2500 >>>3 >>> 0 1 0 0.2500 >>> -1 0 0 0.2500 >>> 0 0 1 0.7500 >>>4 >>> -1 0 0 0.5000 >>> 0 1 0 0. >>> 0 0-1 0.5000 >>>5 >>> 1 0 0 0. >>> 0-1 0 0. >>> 0 0-1 0. >>>6 >>> 0 1 0 0.2500 >>> 1 0 0 0.7500 >>> 0 0-1 0.2500 >>>7 >>> 0-1 0 0.2500 >>> -1 0 0 0.2500 >>> 0 0-1 0.7500 >>>8 >>> -1 0 0 0. >>> 0-1 0 0.0000 >>> 0 0-1 0.00000000 >>>9 >>> 1 0 0 0.5000 >>&
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier Sir, Please excuse me to resolve a confusion. I have not sent any mail to anybody's personal mail & has sent the mail only to the wien2k mailing list. Dr. Tran answers my query as he was the first one to answer my query through a mail sent to the mailing list only. with regards, On Thu, 4 Jun 2020 at 11:15, shamik chakrabarti wrote: > Dear Xavier Sir, > > Thank you so much for your suggestions. I will > strictly follow it. > > with kind regards, > > On Thu, 4 Jun 2020 at 03:39, Xavier Rocquefelte < > xavier.rocquefe...@univ-rennes1.fr> wrote: > >> Here is a cif file. You can see that Sn is on a Wyckoff position 4a, >> which means that you have 4 equivalent positions in the space group I 41/a >> m d. >> >> In WIEN2k, it leads to a case.struct file having only 2 equivalent >> positions, because only the positions in the primitive cell are shown in >> the case.struct file and here the cell is body-centered (I). >> >> >> The fact that you have 4 equivalent position in the case.struct file you >> sent to the list is clearly an indication that the structure is not >> correct. >> >> In addition, when starting a calculation you should first check the bond >> distances from the litterature, which is about 3.02 angtström for Sn-Sn. >> More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn >> distance. >> >> >> In the structure you sent to the list the Sn-Sn distances were 2.2 >> angström!!! It is too small for such an element. It is why the geometry >> optimization goes wrong. Thus, the first thing to due before doing >> "run_lapw" is to check your data. To do so, you must check carefully: >> >> >> - case.outputnn --> bond distances and coordination >> >> - case.outputs --> point group for each inequivalent atoms >> >> ... >> >> >> Regards >> >> Xavier >> >> >> >> >> >> >> Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit : >> >> Dear Fabien, >> >> I explained to Shamik that the structure he was using was not correct. >> >> I also sent cif and struct file. >> >> See below a proper case.struct file. >> >> Shamik could you please send email only to the wienlist to avoid multiple >> answers from the list and many people trying to help you without having all >> the details? >> >> >> blebleble >> B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd >> MODE OF CALC=RELA unit=bohr >> 11.019938 11.019938 6.011975 90.00 90.00 90.00 >> ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 >> MULT= 2 ISPLIT=-2 >>1: X=0. Y=0.2500 Z=0.3750 >> Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. >> LOCAL ROT MATRIX:1.000 0.000 0.000 >> 0.000 1.000 0.000 >> 0.000 0.000 1.000 >> 16 NUMBER OF SYMMETRY OPERATIONS >> 1 0 0 0. >> 0 1 0 0. >> 0 0 1 0. >>1 >> -1 0 0 0.5000 >> 0-1 0 0. >> 0 0 1 0.5000 >>2 >> 0-1 0 0.2500 >> 1 0 0 0.7500 >> 0 0 1 0.2500 >>3 >> 0 1 0 0.2500 >> -1 0 0 0.2500 >> 0 0 1 0.7500 >>4 >> -1 0 0 0.5000 >> 0 1 0 0. >> 0 0-1 0.5000 >>5 >> 1 0 0 0. >> 0-1 0 0. >> 0 0-1 0. >>6 >> 0 1 0 0.2500 >> 1 0 0 0.7500 >> 0 0-1 0.2500 >>7 >> 0-1 0 0.2500 >> -1 0 0 0.2500 >> 0 0-1 0.7500 >>8 >> -1 0 0 0. >> 0-1 0 0. >> 0 0-1 0. >>9 >> 1 0 0 0.5000 >> 0 1 0 0. >> 0 0-1 0.5000 >> 10 >> 0 1 0 0.7500 >> -1 0 0 0.2500 >> 0 0-1 0.7500 >> 11 >> 0-1 0 0.7500 >> 1 0 0 0.7500 >> 0 0-1 0.25000000 >> 12 >> 1 0 0 0.5000 >> 0-1 0 0. >> 0 0 1 0.5000 >> 13 >> -1 0 0 0. >> 0 1 0 0. >> 0 0 1 0. >> 14 >> 0-1 0 0.7500 >> -1 0 0 0.2500 >> 0 0 1 0.7500 >> 15 >> 0 1 0 0.7500 >> 1 0 0 0.7500 >> 0 0 1 0.2500 >> 16 >> >> >> >> >> >> Le 03/06/2020 à 21:38, Tran, Fabie
Re: [Wien] Structure optimization of Beta -Sn
Dear Xavier Sir, Thank you so much for your suggestions. I will strictly follow it. with kind regards, On Thu, 4 Jun 2020 at 03:39, Xavier Rocquefelte < xavier.rocquefe...@univ-rennes1.fr> wrote: > Here is a cif file. You can see that Sn is on a Wyckoff position 4a, which > means that you have 4 equivalent positions in the space group I 41/a m d. > > In WIEN2k, it leads to a case.struct file having only 2 equivalent > positions, because only the positions in the primitive cell are shown in > the case.struct file and here the cell is body-centered (I). > > > The fact that you have 4 equivalent position in the case.struct file you > sent to the list is clearly an indication that the structure is not > correct. > > In addition, when starting a calculation you should first check the bond > distances from the litterature, which is about 3.02 angtström for Sn-Sn. > More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn > distance. > > > In the structure you sent to the list the Sn-Sn distances were 2.2 > angström!!! It is too small for such an element. It is why the geometry > optimization goes wrong. Thus, the first thing to due before doing > "run_lapw" is to check your data. To do so, you must check carefully: > > > - case.outputnn --> bond distances and coordination > > - case.outputs --> point group for each inequivalent atoms > > ... > > > Regards > > Xavier > > > > > > > Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit : > > Dear Fabien, > > I explained to Shamik that the structure he was using was not correct. > > I also sent cif and struct file. > > See below a proper case.struct file. > > Shamik could you please send email only to the wienlist to avoid multiple > answers from the list and many people trying to help you without having all > the details? > > > blebleble > B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd > MODE OF CALC=RELA unit=bohr > 11.019938 11.019938 6.011975 90.00 90.00 90.00 > ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 > MULT= 2 ISPLIT=-2 >1: X=0. Y=0.2500 Z=0.3750 > Sn1NPT= 781 R0=.1 RMT= 2.5 Z: 50. > LOCAL ROT MATRIX:1.000 0.000 0.000 > 0.000 1.000 0.000 > 0.000 0.000 1.000 > 16 NUMBER OF SYMMETRY OPERATIONS > 1 0 0 0. > 0 1 0 0. > 0 0 1 0. >1 > -1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 >2 > 0-1 0 0.2500 > 1 0 0 0.7500 > 0 0 1 0.2500 >3 > 0 1 0 0.2500 > -1 0 0 0.2500 > 0 0 1 0.7500 >4 > -1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 >5 > 1 0 0 0. > 0-1 0 0. > 0 0-1 0. >6 > 0 1 0 0.2500 > 1 0 0 0.7500 > 0 0-1 0.2500 >7 > 0-1 0 0.2500 > -1 0 0 0.2500 > 0 0-1 0.7500 >8 > -1 0 0 0. > 0-1 0 0. > 0 0-1 0. >9 > 1 0 0 0.5000 > 0 1 0 0. > 0 0-1 0.5000 > 10 > 0 1 0 0.7500 > -1 0 0 0.2500 > 0 0-1 0.7500 > 11 > 0-1 0 0.7500 > 1 0 0 0.7500 > 0 0-1 0.2500 > 12 > 1 0 0 0.5000 > 0-1 0 0. > 0 0 1 0.5000 > 13 > -1 0 0 0. > 0 1 0 0. > 0 0 1 0. > 14 > 0-1 0 0.7500 > -1 0 0 0.2500 > 0 0 1 0.7500 > 15 > 0 1 0 0.7500 > 1 0 0 0.7500 > 0 0 1 0.2500 > 16 > > > > > > Le 03/06/2020 à 21:38, Tran, Fabien a écrit : > > Using a RKmax above 7 should not lead to completely wrong results. > One important point is how the lattice constants a and c were varied. In a > meaningful way? > > > -- > *From:* Wien > on behalf of shamik chakrabarti > > *Sent:* Wednesday, June 3, 2020 8:40 PM > *To:* A Mailing list for WIEN2k users > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > Dear Dr. Tran, > > I have used both plain GGA & nlvdw independently & in > both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for > GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am > currently going through the literature you have sent.. > > with regards, > > On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote: > >> At first sight you struct file seems ok, but this is difficult to help >> you without more detai
Re: [Wien] Structure optimization of Beta -Sn
Here is a cif file. You can see that Sn is on a Wyckoff position 4a, which means that you have 4 equivalent positions in the space group I 41/a m d. In WIEN2k, it leads to a case.struct file having only 2 equivalent positions, because only the positions in the primitive cell are shown in the case.struct file and here the cell is body-centered (I). The fact that you have 4 equivalent position in the case.struct file you sent to the list is clearly an indication that the structure is not correct. In addition, when starting a calculation you should first check the bond distances from the litterature, which is about 3.02 angtström for Sn-Sn. More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn distance. In the structure you sent to the list the Sn-Sn distances were 2.2 angström!!! It is too small for such an element. It is why the geometry optimization goes wrong. Thus, the first thing to due before doing "run_lapw" is to check your data. To do so, you must check carefully: - case.outputnn --> bond distances and coordination - case.outputs --> point group for each inequivalent atoms ... Regards Xavier Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit : Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1 NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? *From:* Wien on behalf of shamik chakrabarti *Sent:* Wednesday, June 3, 2020 8:40 PM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 *From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> *Sent:* Wednesday, June 3, 2020 8:06 PM *To:* A Mailing list for WIEN2k users *Subject:* [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards,
Re: [Wien] Structure optimization of Beta -Sn
Dear Fabien, I explained to Shamik that the structure he was using was not correct. I also sent cif and struct file. See below a proper case.struct file. Shamik could you please send email only to the wienlist to avoid multiple answers from the list and many people trying to help you without having all the details? blebleble B LATTICE,NONEQUIV.ATOMS: 1 141 I41/amd MODE OF CALC=RELA unit=bohr 11.019938 11.019938 6.011975 90.00 90.00 90.00 ATOM 1: X=0.5000 Y=0.2500 Z=0.1250 MULT= 2 ISPLIT=-2 1: X=0. Y=0.2500 Z=0.3750 Sn1 NPT= 781 R0=.1 RMT= 2.5 Z: 50. LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 16 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 -1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 2 0-1 0 0.2500 1 0 0 0.7500 0 0 1 0.2500 3 0 1 0 0.2500 -1 0 0 0.2500 0 0 1 0.7500 4 -1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 5 1 0 0 0. 0-1 0 0. 0 0-1 0. 6 0 1 0 0.2500 1 0 0 0.7500 0 0-1 0.2500 7 0-1 0 0.2500 -1 0 0 0.2500 0 0-1 0.7500 8 -1 0 0 0. 0-1 0 0. 0 0-1 0. 9 1 0 0 0.5000 0 1 0 0. 0 0-1 0.5000 10 0 1 0 0.7500 -1 0 0 0.2500 0 0-1 0.7500 11 0-1 0 0.7500 1 0 0 0.7500 0 0-1 0.2500 12 1 0 0 0.5000 0-1 0 0. 0 0 1 0.5000 13 -1 0 0 0. 0 1 0 0. 0 0 1 0. 14 0-1 0 0.7500 -1 0 0 0.2500 0 0 1 0.7500 15 0 1 0 0.7500 1 0 0 0.7500 0 0 1 0.2500 16 Le 03/06/2020 à 21:38, Tran, Fabien a écrit : Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? *From:* Wien on behalf of shamik chakrabarti *Sent:* Wednesday, June 3, 2020 8:40 PM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 *From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> *Sent:* Wednesday, June 3, 2020 8:06 PM *To:* A Mailing list for WIEN2k users *Subject:* [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at <mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Institut des Sciences Chimiques de Rennes (ISCR) Univ Rennes - CNRS - UMR6226, France https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier ICAMM2019 : VASP Workshop and International Materials Modelling Conf June 26-July 3 2019, Rennes France icamm2019.sciencesconf.org : R
Re: [Wien] Structure optimization of Beta -Sn
A suggestion is to put in the struct file the PBE lattice constant?s from the paper (after conversion in bohr), and then use option [5] of "x optimize". If you do not see some minimum (use only PBE without vdW), then something else is wrong in your files. From: Wien on behalf of shamik chakrabarti Sent: Wednesday, June 3, 2020 9:42 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Structure optimization of Beta -Sn I have used change in volume with a:b:c = constant as a primary optimization. After optimization of volume I will move to c/a variation with constant volume for tetragonal lattice On Thu, 4 Jun 2020 at 01:08, Tran, Fabien mailto:fabien.t...@tuwien.ac.at>> wrote: Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> Sent: Wednesday, June 3, 2020 8:40 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> Sent: Wednesday, June 3, 2020 8:06 PM To: A Mailing list for WIEN2k users Subject: [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
I have used change in volume with a:b:c = constant as a primary optimization. After optimization of volume I will move to c/a variation with constant volume for tetragonal lattice On Thu, 4 Jun 2020 at 01:08, Tran, Fabien wrote: > Using a RKmax above 7 should not lead to completely wrong results. > One important point is how the lattice constants a and c were varied. In a > meaningful way? > > > -- > *From:* Wien on behalf of > shamik chakrabarti > *Sent:* Wednesday, June 3, 2020 8:40 PM > *To:* A Mailing list for WIEN2k users > *Subject:* Re: [Wien] Structure optimization of Beta -Sn > > Dear Dr. Tran, > > I have used both plain GGA & nlvdw independently & in > both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for > GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am > currently going through the literature you have sent.. > > with regards, > > On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote: > >> At first sight you struct file seems ok, but this is difficult to help >> you without more details. For instance: Which functional have you used? Are >> you keeping the c/a ratio fixed? Have you looked into the literature: >> >> https://aip.scitation.org/doi/abs/10.1063/1.4948434 >> >> >> -- >> *From:* Wien on behalf of >> shamik chakrabarti >> *Sent:* Wednesday, June 3, 2020 8:06 PM >> *To:* A Mailing list for WIEN2k users >> *Subject:* [Wien] Structure optimization of Beta -Sn >> >> Dear wien2k users, >> >> I am trying to optimize the structure of >> Beta - Sn. However, even after 20% increment of the volume there is no sign >> of energy minima. I am attaching the struct file herewith this mail >> for your consideration. >> >> Looking forward to hearing from you. >> >> with regards, >> >> -- >> Dr. Shamik Chakrabarti >> Research Fellow >> Department of Physics >> Indian Institute of Technology Patna >> Bihta-801103 >> Patna >> Bihar, India >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >> > > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Using a RKmax above 7 should not lead to completely wrong results. One important point is how the lattice constants a and c were varied. In a meaningful way? From: Wien on behalf of shamik chakrabarti Sent: Wednesday, June 3, 2020 8:40 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Structure optimization of Beta -Sn Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> Sent: Wednesday, June 3, 2020 8:06 PM To: A Mailing list for WIEN2k users Subject: [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Your structure file seems to be not correct! You should have only one inequivalent position and the space group is I 41/a m d. Here is the structure: http://som.web.cmu.edu/structures/S018-beta-Sn.html Le 03/06/2020 à 20:40, shamik chakrabarti a écrit : Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <mailto:fabien.t...@tuwien.ac.at>> wrote: At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 *From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of shamik chakrabarti mailto:shamik15041...@gmail.com>> *Sent:* Wednesday, June 3, 2020 8:06 PM *To:* A Mailing list for WIEN2k users *Subject:* [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at <mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Institut des Sciences Chimiques de Rennes (ISCR) Univ Rennes - CNRS - UMR6226, France https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier ICAMM2019 : VASP Workshop and International Materials Modelling Conf June 26-July 3 2019, Rennes France icamm2019.sciencesconf.org : Registration opening soon, see you there! ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
Dear Dr. Tran, I have used both plain GGA & nlvdw independently & in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am currently going through the literature you have sent.. with regards, On Wed, 3 Jun 2020 at 23:53, Tran, Fabien wrote: > At first sight you struct file seems ok, but this is difficult to help you > without more details. For instance: Which functional have you used? Are you > keeping the c/a ratio fixed? Have you looked into the literature: > > https://aip.scitation.org/doi/abs/10.1063/1.4948434 > > > -- > *From:* Wien on behalf of > shamik chakrabarti > *Sent:* Wednesday, June 3, 2020 8:06 PM > *To:* A Mailing list for WIEN2k users > *Subject:* [Wien] Structure optimization of Beta -Sn > > Dear wien2k users, > > I am trying to optimize the structure of > Beta - Sn. However, even after 20% increment of the volume there is no sign > of energy minima. I am attaching the struct file herewith this mail > for your consideration. > > Looking forward to hearing from you. > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Structure optimization of Beta -Sn
At first sight you struct file seems ok, but this is difficult to help you without more details. For instance: Which functional have you used? Are you keeping the c/a ratio fixed? Have you looked into the literature: https://aip.scitation.org/doi/abs/10.1063/1.4948434 From: Wien on behalf of shamik chakrabarti Sent: Wednesday, June 3, 2020 8:06 PM To: A Mailing list for WIEN2k users Subject: [Wien] Structure optimization of Beta -Sn Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Structure optimization of Beta -Sn
Dear wien2k users, I am trying to optimize the structure of Beta - Sn. However, even after 20% increment of the volume there is no sign of energy minima. I am attaching the struct file herewith this mail for your consideration. Looking forward to hearing from you. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India beta_Sn_V_initial.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html