Dear Prof. Gavin, Thanks a lot for your help. It is working now. However, I have another query. After x optimize with the struct file a message comes as: SPACE GROUP CONTAINS INVERSION * alpha(3) .gt. 91.0; reset to 90.1. *However, the struct file remains the same after this message. Hence, should we ignore the message?
with regards, On Tue, 25 Aug 2020 at 11:57, Gavin Abo <gs...@crimson.ua.edu> wrote: > I took your attached Nb2Se3_all_min_initial.struct at [1], kept the > structure the same but swapped the lattice angles (beta<->gamma), lattice > constants (b<->c), and atomic positions (y<->z) in StructGen of w2web and > generated the new symmetry operations for it with "x symmetry" which gave > the attached Nb2Se3_all_min.struct following the advice at: > > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html > <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$> > > I then ran the 4D "x optimize" on it using WIEN2k 19.2 as given below. > I'm not able to reproduce what you have described as instead it looks like > the "x optimize" script changes the gamma angle just fine from the original > 104.153240 degrees to other angles such as 102.070175 and 106.236305 in > some of the .struct files. > > username@computername:~/wiendata/Nb2Se3_all_min$ ls > Nb2Se3_all_min.struct > username@computername:~/wiendata/Nb2Se3_all_min$ x optimize > ******************************************** > GENERATES STRUCT-FILES AND optimize.job > PLEASE CHOOSE ONE OF THE FOLLOWING FEATURES: > > [1] VARY VOLUME with CONSTANT RATIO A:B:C > [2] VARY C/A RATIO with CONSTANT VOLUME (tetr and hex lattices) > [3] VARY C/A RATIO with CONSTANT VOLUME and B/A (orthorh lattice) > [4] VARY B/A RATIO with CONSTANT VOLUME and C/A (orthorh lattice) > [5] VARY A and C (2D-case) (tetragonal or hexagonal lattice) > [6] VARY A, B and C (3D-case) (orthorhombic lattice) > [7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice) > [8] VARY C/A RATIO and VOLUME (2D-case) (tetr and hex lattices) > > ******************************************** > > 7 > > *************************************************** > Generating > Nb2Se3_all_min_initial.struct > > next time this file will be used as template unless you remove it > explicitly. > *************************************************** > number of structures: 15, 81 (3x3x3x3), 256 (4x4x4x4) > 15 > PLEASE enter a percentage change of a > 2 > Nb2Se3_all_min_mon____1.00.struct > > 12.153492 17.398148 6.478929104.153240 > Nb2Se3_all_min_mon____2.00.struct > > 12.401522 17.398148 6.478929104.153240 > Nb2Se3_all_min_mon____3.00.struct > > 12.649552 17.398148 6.478929104.153240 > Nb2Se3_all_min_mon____4.00.struct > > 12.401522 17.050185 6.478929104.153240 > Nb2Se3_all_min_mon____5.00.struct > > 12.401522 17.746111 6.478929104.153240 > Nb2Se3_all_min_mon____6.00.struct > > 12.401522 17.398148 6.349350104.153240 > Nb2Se3_all_min_mon____7.00.struct > > 12.401522 17.398148 6.608508104.153240 > Nb2Se3_all_min_mon____8.00.struct > > 12.153492 17.050185 6.478929104.153240 > Nb2Se3_all_min_mon____9.00.struct > > 12.153492 17.398148 6.349350104.153240 > Nb2Se3_all_min_mon___10.00.struct > > 12.401522 17.050185 6.349350104.153240 > Nb2Se3_all_min_mon___11.00.struct > > 12.401522 17.398148 6.478929102.070175 > Nb2Se3_all_min_mon___12.00.struct > > 12.401522 17.398148 6.478929106.236305 > Nb2Se3_all_min_mon___13.00.struct > > 12.153492 17.398148 6.478929102.070175 > Nb2Se3_all_min_mon___14.00.struct > > 12.401522 17.050185 6.478929102.070175 > Nb2Se3_all_min_mon___15.00.struct > > 12.401522 17.398148 6.349350102.070175 > Now run optimize.job > 0.0u 0.0s 0:09.80 0.0% 0+0k 0+264io 0pf+0w > > username@computername:~/wiendata/Nb2Se3_all_min$ awk 'FNR==4 {print > FILENAME, substr($5, length($5)-9, length($5))}' *.struct > Nb2Se3_all_min_initial.struct 104.153240 > Nb2Se3_all_min_mon___10.00.struct 104.153240 > Nb2Se3_all_min_mon____1.00.struct 104.153240 > Nb2Se3_all_min_mon___11.00.struct 102.070175 > Nb2Se3_all_min_mon___12.00.struct 106.236305 > Nb2Se3_all_min_mon___13.00.struct 102.070175 > Nb2Se3_all_min_mon___14.00.struct 102.070175 > Nb2Se3_all_min_mon___15.00.struct 102.070175 > Nb2Se3_all_min_mon____2.00.struct 104.153240 > Nb2Se3_all_min_mon____3.00.struct 104.153240 > Nb2Se3_all_min_mon____4.00.struct 104.153240 > Nb2Se3_all_min_mon____5.00.struct 104.153240 > Nb2Se3_all_min_mon____6.00.struct 104.153240 > Nb2Se3_all_min_mon____7.00.struct 104.153240 > Nb2Se3_all_min_mon____8.00.struct 104.153240 > Nb2Se3_all_min_mon____9.00.struct 104.153240 > Nb2Se3_all_min.struct 104.153240 > > [1] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20403.html > On 8/24/2020 11:25 AM, shamik chakrabarti wrote: > > Dear Prof. Laurence Marks Sir, > > I have changed the atomic > coordinates & reduced the symmetry to 1_P with the help of the Bilbao > crystallographic server. The calculation is still running & 3 structures > are already generated without showing any error. However, the value of > Gamma is still not changing. Why so? > > Thanks & Regards, > > On Mon, 24 Aug 2020 at 18:03, Laurence Marks <laurence.ma...@gmail.com> > wrote: > >> You have to also change the positions, and symmetry of course! >> >> _____ >> Professor Laurence Marks >> "Research is to see what everybody else has seen, and to think what >> nobody else has thought", Albert Szent-Gyorgi >> www.numis.northwestern.edu >> >> On Mon, Aug 24, 2020, 07:29 shamik chakrabarti <shamik15041...@gmail.com> >> wrote: >> >>> Dear Prof. Gavin, >>> >>> If I change a to b, b to c & c to a to make alpha >>> to beta, beta to gamma & gamma to alpha the produced structure shows >>> unphysical RMTs for all the atoms.: 1 for Nb & 0.51 for Se. What to do? >>> >>> with regards, >>> >>> On Mon, 24 Aug 2020 at 16:07, Gavin Abo <gs...@crimson.ua.edu> wrote: >>> >>>> The 4D is option 7 [ >>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html >>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvLE6WOCw$> >>>> , >>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html >>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btgMniYYw$> >>>> ]: >>>> >>>> [7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice) >>>> >>>> I think that only worked correctly when the gamma angle was the one >>>> that was greater than 90 (e.g., in your case it would likely need to be >>>> alpha=90 degrees, beta = 90 degrees, Gamma=104.15 degrees), refer to: >>>> >>>> >>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html >>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$> >>>> >>>> >>>> On 8/23/2020 11:42 AM, shamik chakrabarti wrote: >>>> >>>> Dear wien2k users, >>>> >>>> During 4D optimization of a monoclinic system >>>> (file attached) I have obtained an error as described below; >>>> >>>> 'FERMI' - EFERMI OUT OF ENERGY RANGE >>>> 'FERMI' - STOP IN EFI >>>> 'FERMI' - ENERGY OF LOWER BOUND : -4.50517 >>>> >>>> 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.00000 >>>> >>>> 'FERMI' - ENERGY OF UPPER BOUND :3003.00451 >>>> >>>> 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 112.00000 >>>> >>>> 'FERMI' - ADD 112.00000 >>>> >>>> 'FERMI' - SOS 0.0000.0000.0000.0000.0000.0000.0000.0000.0003.156 >>>> >>>> 'FERMI' - NOS ************************************************** >>>> >>>> What is the meaning of this error & how to get out of it? >>>> >>>> I have two more queries: >>>> (1) During 4D optimization, I am also expecting the change in the value >>>> of Gamma, but it remains the same along with all structures produced by x >>>> optimize & also in the case_default.struct the Gamma is not changing. why >>>> so? >>>> >>>> (2) In my structure, I have alpha=90 degree, beta = 104.15 degrees, >>>> Gamma=90 degree. Whether the code will change the beta of my structure or I >>>> have to change the lattice parameter a to b, b to c & c to a to produce >>>> alpha to beta, beta to gamma & gamma to alpha? >>>> >>>> Looking forward to your reply in this regard. Thanks in advance. >>>> >>>> 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 >>>> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bunRXl53g$> >>>> SEARCH the MAILING-LIST at: >>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>>> <https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btS5vJXnA$> >>>> >>> >>> >>> -- >>> 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 >>> >>> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bunRXl53g$ >>> SEARCH the MAILING-LIST at: >>> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btS5vJXnA$ >>> >> _______________________________________________ >> 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