[Wien] geometry optimization with spin-orbit interaction
Dear All, I have a few questions about geometry optimization. Is it possible to do geometry optimization with spin-orbit interaction? If so how do I set it up? I tried the following: min_lapw -p -I -sp -i 160 -ec 0.0001 -cc 0.0001 -in1ef But it didn't work. I would like to do a geometry optimization with the following scf options: runsp_lapw -p -i 160 -ec 0.0001 -cc 0.0001 -in1ef -so -I I can only make the optimization working with the following options though min_lapw -p -I -sp -i 160 It seems like that I can't (1) specify the s.o. option for geometry optimizations and (2) set the convergence criteria for energy and charge other than the default for geometry optimization. Thanks a lot for any help! Zhiyong
[Wien] x symmetso issue
Dear All, I am running initso_lapw after initialization of the scf calculation. I got the following error when running x symmetso -up: Does anybody have encountered similar issues? Where could I look for errors for this problem? Thanks! Zhiyong forrtl: severe (153): allocatable array or pointer is not allocated Image PCRoutineLineSource symmetso 004BB4CD Unknown Unknown Unknown symmetso 004B9FD5 Unknown Unknown Unknown symmetso 00487D00 Unknown Unknown Unknown symmetso 0047CD6A Unknown Unknown Unknown symmetso 00448581 Unknown Unknown Unknown symmetso 0040EA90 clmchange_ 69 clmchange.f symmetso 00421938 symso_427 symso.f symmetso 00403E44 MAIN__ 72 symmetso.f symmetso 004036DC Unknown Unknown Unknown libc.so.6 003E1251C40B Unknown Unknown Unknown symmetso 0040360A Unknown Unknown Unknown 0.076u 0.056s 0:00.13 92.3% 0+0k 0+0io 0pf+0w error: command /home/apps/wien2k_10/symmetso symmetso.def failed
[Wien] core electron leaking issue
Dear All, I am trying to initialize the calculation with lstart WARNING: R0 for atom -4 Z= 83.00 too big With that I reduced the muffin tin radius for that atom but eventually I got the 0.010 Bi CORE electrons leak out of MT-sphere as well as the following error: R0 for atom -4 Z= 83.00 too big How could I resolve this problem? Thanks a lot! Zhiyong
[Wien] absoption coefficients calculation
Deal All, I have a few questions about the calculation of absorption coefficients with spin-orbit interactions. With the converged spin-orbit calculations, I ran (1)x lapw2 -fermi -up (2)x optic -up; (3) x joint -up; (4) then copied case.jointup to case.joint; (5)x kram, all with spin-orbit options. Since it is a spin-orbit calculations, I chose 9 for the number of choices (columns in *outmat) in case.inop and also 9 for NUMBER OF COLUMNS in case.injoint. The system has 3-fold and inversion symmetry in hcp lattice. For the absorption coefficients, there are 9 components, with large contributions with xy xx=yyzz and all the other components are essentially zero. Here are some of my questions: (1)Are there any good references for the symmetry properties of the absorption coefficients? (2)To get the total absorption coefficients do I simply sum up all the xx, yy, ... components? (3)As noticed, the xx and yy components are degenerate, which is expected (correct me if I am wrong here). However the yx component is large but the xy components are almost zero. Should I also expect degeneracy in xy and yx components? (4)Is there a general selection based on symmetry for these components? How do I interpret each component physically? (5)The energy window I selected for the momentum matrix calculation is large, from -5.0 to 8 eV. So I wuold not expect that this will break the symmetry for the absorption coefficients. Any comments and suggestions would be greatly appreciated. Thank you very much fro your attention. Zhiyong
[Wien] xyz2struct input format
Dear All, I am trying to convert xyz files to wien.struct files using xyz2struct. I tried to read the manual but I am still not so sure about the input file format. Here is the xyz file I used but it seems like that the generated .struct file is wrong. This is supposed to be a hexagonal cell and the parameters are 4.143, 4.143, 28.636, 90, 90, 120. Could somebody kindly let me know what is the correct xyz file format for xyz2struct? Thank you very much, Zhiyong ang C L 1. 3.5879 -2.0715 0. 0. 4.1430 0. 0. 0. 28.636 Bi 0.00 0.0011.4773088271 Bi 1.1959810132 2.071499879721.0226421830 Bi 2.3919620265 0.00 1.9319754711 Bi 0.00 0.00 -11.4773088271 Bi 1.1959810132 2.0714998797-1.9319754711 Bi 2.3919620265 0.00 7.6133578848 Se 0.00 0.00 6.0622412142 Se 1.1959810132 2.071499879715.6075745701 Se 2.3919620265 0.0025.1529079260 Se 0.00 0.00-6.0622412142 Se 1.1959810132 2.0714998797 3.4830921417 Se 2.3919620265 0.0013.0284254977 Se 0.00 0.00 0.00 Se 1.1959810132 2.0714998797 9.545559 Se 2.3919620265 0.0019.0906667118
[Wien] Overlapping spheres error
Dear All, I am running a calculation for Bi2Se3 and got the overlapping sphere error. By default, the StructGen set all the RMT to 2.09, for both Bi and Se. The RMT of Bi resulted in leaking core electrons of ca. 0.023 and I got a warning message. I then increased the RMT for Bi to 2.3 to get rid of the leaking core electrons. When I run the lapw0 I got the following error, since the sum of the RMT is greater then the nearest neigbors. How should I fix this problem? Do I need to try and test differetn values for the RMT for the individual atoms until I satisfy the requirements? Are there a utility program in wien-2k that allows automatic adjustment of the RMT parameters? Thanks a lot! Zhiyong 'NN' - overlapping spheres 'NN' - RMT( 9)=2.09000 AND RMT(15)=2.3 'NN' - SUMS TO 4.39000 GT NNN-DIST= 4.34299
[Wien] w2web, StructGen
Dear All, I am trying to use w2web to generate structures for Bi2Se3. I chose the space group R-3m and entered the three non-equivalent atoms. However, the generated structure seem to be incorrect as only one of the three equivalent positions of Atom 3 are generated. Even if I use and upload the the cif file I still got the same structure file. I have included the generated structures below. Thanks a lot, Zhiyong blebleble R LATTICE,NONEQUIV.ATOMS: 3166_R-3m MODE OF CALC=RELA unit=bohr 7.829135 7.829135 54.114198 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0.4008 MULT= 6 ISPLIT= 8 ATOM -1:X= 0. Y=0. Z=0.5992 ATOM -1:X= 0. Y=0.4008 Z=0. ATOM -1:X= 0. Y=0.5992 Z=0. ATOM -1:X= 0.4008 Y=0. Z=0. ATOM -1:X= 0.5992 Y=0. Z=0. Bi NPT= 781 R0=0.0500 RMT=1.5100 Z: 83.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.0001 Y=0. Z=0.2117 MULT= 6 ISPLIT= 8 ATOM -2:X= 0. Y=0. Z=0.7883 ATOM -2:X= 0. Y=0.2117 Z=0.0001 ATOM -2:X= 0. Y=0.7883 Z=0. ATOM -2:X= 0.2117 Y=0.0001 Z=0. ATOM -2:X= 0.7883 Y=0. Z=0. Se NPT= 781 R0=0.5000 RMT=0.8000 Z: 34.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -3: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 8 Se NPT= 781 R0=0.5000 RMT=0.8000 Z: 34.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0 NUMBER OF SYMMETRY OPERATIONS
[Wien] parallel wien2k
Dear All, I think I have problem with the compiler options/libraries for the parallel wien2k. I can run lapw0/1_mpi with k-point parallel mode but not with mpi. Here are the options and libraries with which I built the wien2k: RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_lp64 -Wl,--end-group -lpthread -L/home/zzhang/fftw/fftw-2.1.5/lib -lfftw_mpi -lfftw FPOPT(par.comp.options): FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback I used fftw-2.1.5 for the parallel fftw. Does anybody see a problem with the options I used? Does anybody have a set of compiler options and libraries for working lapw0_mpi? I used mpich2 to compile the code and the architecture is Intel x86_64. Thanks in advance! Zhiyong - Original Message - From: Zhiyong Zhang zyzh...@stanford.edu To: A Mailing list for WIEN2k users wien at zeus.theochem.tuwien.ac.at Sent: Wednesday, February 24, 2010 5:16:23 PM GMT -08:00 US/Canada Pacific Subject: Re: [Wien] parallel wien2k Dear Laurence and All, Thank you very much for the information. It has been very helpful in clarifying some of the issues. Based on your input, I was able to prepare the .machines in the correct format, I believe: .machines: # lapw0: nx59:2 nx58:2 1:nx59 1:nx59 1:nx58 1:nx58 granularity:1 extrafine:1 and .machine0 nx59 nx59 nx58 nx58 However, I still got the same problem in TiC.vns, which presumably resulted in the crash in lapw1para. Are there any places in the output files that I can look for clues of problem? For the same calculation, I can run the lapw0 in serial mode and lapw1 in k-point parallel mode successfully. Thanks in advance, Zhiyong - Original Message - From: Laurence Marks l-ma...@northwestern.edu To: A Mailing list for WIEN2k users wien at zeus.theochem.tuwien.ac.at Sent: Tuesday, February 23, 2010 4:55:19 AM GMT -08:00 US/Canada Pacific Subject: Re: [Wien] parallel wien2k Several points: 1) You only use -fc X for a structure with variable atomic positions, and the TiC example has none so it will report that there are no forces (but this should not stop the calculation). 2) The NaN in your case.vns file means that something went wrong in the lapw0 call, which is why lapw1 is crashing. It is safer to delete the case.vns file. 3) Are you using single core CPU's or multicore? The normal format for a parallel lapw0 call (using mpi) is lapw0: nx1:2 nx62:2 -- please note the space after the :, it often matters To do this you have to have mpi installed and have compiled lapw0_mpi. If you do not have it you can use lapw0: nx1 This will run a serial lapw0 on nx1 4) All the above assumes that you have local control of what nodes you can use rather than this being controlled by a queuing system such as pbs. If you are using pbs or similar then you have to have a script to generate the .machines file since you do not know what machines to use (unless you are running interactively). 5) The script you have will run serial (i.e. not mpi) lapw1, 2 k-vectors on nx1 and 2 on nx62. If you want to have these run using the parallel versions (i.e. lapw1_mpi) you would need to use 1:nx1:2 1:nx62:2 (Note no space after the :). Whether it is faster to run with 2 processors on nx1, as against 2 different k-points will depend upon your cpu's. For a simple calculation such as TiC it will be hard to see much difference, but this can matter for larger ones. Be aware that if (for instance) you had 4 processors on nx1 it may be a bad idea to use 1:nx1:2 1:nx1:2 because some variants of mpi will launch both lapw1_mpi jobs on the same cores (CPU_AFFINITY is often the relevant flag, but this varies with mpi flavor). 2010/2/22 zyzhang zyzhang at stanford.edu: Dear All, I am trying to test wien2k in parallel mode and I got into some problem. I am using run_lapw -p -i 40 -fc 0.001 ?I If I use a number of 0.001 for the option fc above, I got the following error: Force-convergence not possible. Forces not present. If I do not use a number for the ?fc option, but use ?run_lapw -p -i 40 -fc ?I? instead Then lapw0 finishes without a problem but the program doesn?t branch to lapw1. An error message is generated when doing the test ?if ($fcut == 0) goto lapw1 I was able to do ?run_lapw -p -i 40 ?I?, without the ?-fc? option at all and was able to finish ?lapw0 ?p? and then start ?lapw1 ?p? but got into the following error: error: command?? /home/zzhang/wien2k/lapw1para lapw1.def?? failed Does anybody have similar problems and know how to fix this? It does the following: running LAPW1 in parallel mode (using .machines) and the .machines file is as follows: # lapw0:nx1? nx1? nx62? nx62 lapw1:nx1? nx1? nx62? nx62 lapw2:nx1? nx1? nx62? nx62 1:nx1 1:nx1 1:nx62 1:nx62 granularity:1 extrafine:1 Thanks, Zhiyong
[Wien] parallel wien2k
Dear Laurence and All, Thank you very much for the information. It has been very helpful in clarifying some of the issues. Based on your input, I was able to prepare the .machines in the correct format, I believe: .machines: # lapw0: nx59:2 nx58:2 1:nx59 1:nx59 1:nx58 1:nx58 granularity:1 extrafine:1 and .machine0 nx59 nx59 nx58 nx58 However, I still got the same problem in TiC.vns, which presumably resulted in the crash in lapw1para. Are there any places in the output files that I can look for clues of problem? For the same calculation, I can run the lapw0 in serial mode and lapw1 in k-point parallel mode successfully. Thanks in advance, Zhiyong - Original Message - From: Laurence Marks l-ma...@northwestern.edu To: A Mailing list for WIEN2k users wien at zeus.theochem.tuwien.ac.at Sent: Tuesday, February 23, 2010 4:55:19 AM GMT -08:00 US/Canada Pacific Subject: Re: [Wien] parallel wien2k Several points: 1) You only use -fc X for a structure with variable atomic positions, and the TiC example has none so it will report that there are no forces (but this should not stop the calculation). 2) The NaN in your case.vns file means that something went wrong in the lapw0 call, which is why lapw1 is crashing. It is safer to delete the case.vns file. 3) Are you using single core CPU's or multicore? The normal format for a parallel lapw0 call (using mpi) is lapw0: nx1:2 nx62:2 -- please note the space after the :, it often matters To do this you have to have mpi installed and have compiled lapw0_mpi. If you do not have it you can use lapw0: nx1 This will run a serial lapw0 on nx1 4) All the above assumes that you have local control of what nodes you can use rather than this being controlled by a queuing system such as pbs. If you are using pbs or similar then you have to have a script to generate the .machines file since you do not know what machines to use (unless you are running interactively). 5) The script you have will run serial (i.e. not mpi) lapw1, 2 k-vectors on nx1 and 2 on nx62. If you want to have these run using the parallel versions (i.e. lapw1_mpi) you would need to use 1:nx1:2 1:nx62:2 (Note no space after the :). Whether it is faster to run with 2 processors on nx1, as against 2 different k-points will depend upon your cpu's. For a simple calculation such as TiC it will be hard to see much difference, but this can matter for larger ones. Be aware that if (for instance) you had 4 processors on nx1 it may be a bad idea to use 1:nx1:2 1:nx1:2 because some variants of mpi will launch both lapw1_mpi jobs on the same cores (CPU_AFFINITY is often the relevant flag, but this varies with mpi flavor). 2010/2/22 zyzhang zyzhang at stanford.edu: Dear All, I am trying to test wien2k in parallel mode and I got into some problem. I am using run_lapw -p -i 40 -fc 0.001 ?I If I use a number of 0.001 for the option fc above, I got the following error: Force-convergence not possible. Forces not present. If I do not use a number for the ?fc option, but use ?run_lapw -p -i 40 -fc ?I? instead Then lapw0 finishes without a problem but the program doesn?t branch to lapw1. An error message is generated when doing the test ?if ($fcut == 0) goto lapw1 I was able to do ?run_lapw -p -i 40 ?I?, without the ?-fc? option at all and was able to finish ?lapw0 ?p? and then start ?lapw1 ?p? but got into the following error: error: command?? /home/zzhang/wien2k/lapw1para lapw1.def?? failed Does anybody have similar problems and know how to fix this? It does the following: running LAPW1 in parallel mode (using .machines) and the .machines file is as follows: # lapw0:nx1? nx1? nx62? nx62 lapw1:nx1? nx1? nx62? nx62 lapw2:nx1? nx1? nx62? nx62 1:nx1 1:nx1 1:nx62 1:nx62 granularity:1 extrafine:1 Thanks, Zhiyong ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
