Hello,
I am trying your new DOS code , in cojunction with the bader 0.27. If only a surfce is invloved in the slab, both the two codes work fine in a preliminary calculation. However, If adsorbates (e.g., a propylene molecule) are introduced, DOS projection in Bader volume fails to run.
The standard output is as follows, and the OUTCAR file is also attached.
Can you give me any suggestions?
Thanks.
Yi-An
P.S.: I have set "ulimit -s unlimited" in my submission script. All other calculations such as geometry optimization and TS search work fine.
=========================================
Starting job 3889395 ("Catalysis") on compute-0-0 at Mon Jul 26 13:24:51 CEST 2010
running on 32 nodes
distr: one band on 32 nodes, 1 groups
vasp.5.2.2 15Apr09 complex
POSCAR found type information on POSCAR Ir Pt C H
POSCAR found : 4 types and 54 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...( 1 )
reading WAVECAR
entering main loop
N E dE d eps ncg rms rms(c)
RMM: 1 0.472270252153E+04 0.47227E+04 -0.13682E+05 3367 0.112E+03
RMM: 2 0.103118350028E+04 -0.36915E+04 -0.40087E+04 3367 0.328E+02
RMM: 3 0.145330400519E+03 -0.88585E+03 -0.98933E+03 3367 0.155E+02
RMM: 4 -0.176255401388E+03 -0.32159E+03 -0.27020E+03 3367 0.121E+02
RMM: 5 -0.295615425147E+03 -0.11936E+03 -0.10529E+03 3367 0.740E+01
RMM: 6 -0.353853352774E+03 -0.58238E+02 -0.51010E+02 3367 0.588E+01
RMM: 7 -0.385459151422E+03 -0.31606E+02 -0.28836E+02 3367 0.392E+01
RMM: 8 -0.404552781532E+03 -0.19094E+02 -0.17176E+02 3367 0.337E+01
RMM: 9 -0.434029444067E+03 -0.29477E+02 -0.28680E+02 10246 0.236E+01
RMM: 10 -0.439477181164E+03 -0.54477E+01 -0.51725E+01 10807 0.604E+00
RMM: 11 -0.440738581909E+03 -0.12614E+01 -0.98156E+00 10300 0.208E+00
RMM: 12 -0.440995226770E+03 -0.25664E+00 -0.18111E+00 10520 0.729E-01 0.326E+01
RMM: 13 -0.418725973110E+03 0.22269E+02 -0.75504E+01 7539 0.222E+01 0.183E+01
RMM: 14 -0.451300002715E+03 -0.32574E+02 -0.93580E+01 8814 0.150E+01 0.330E+01
RMM: 15 -0.434559637842E+03 0.16740E+02 -0.31619E+01 8349 0.903E+00 0.286E+01
RMM: 16 -0.411104065526E+03 0.23456E+02 -0.10613E+01 7942 0.594E+00 0.818E+00
RMM: 17 -0.410633250118E+03 0.47082E+00 -0.44937E+00 8826 0.328E+00 0.605E+00
RMM: 18 -0.410040975572E+03 0.59227E+00 -0.17721E+00 8381 0.241E+00 0.303E+00
RMM: 19 -0.409882471850E+03 0.15850E+00 -0.59990E-01 8374 0.142E+00 0.191E+00
RMM: 20 -0.409828386753E+03 0.54085E-01 -0.21545E-01 7868 0.890E-01 0.127E+00
RMM: 21 -0.409810156716E+03 0.18230E-01 -0.67574E-02 8127 0.462E-01 0.100E+00
RMM: 22 -0.409792175398E+03 0.17981E-01 -0.24756E-02 8342 0.262E-01 0.431E-01
RMM: 23 -0.409788403471E+03 0.37719E-02 -0.13228E-02 8562 0.168E-01 0.303E-01
RMM: 24 -0.409786974126E+03 0.14293E-02 -0.42590E-03 8334 0.103E-01 0.212E-01
RMM: 25 -0.409786640474E+03 0.33365E-03 -0.29494E-03 7892 0.100E-01 0.197E-01
RMM: 26 -0.409786366424E+03 0.27405E-03 -0.14300E-03 7788 0.611E-02 0.123E-01
RMM: 27 -0.409787169682E+03 -0.80326E-03 -0.14345E-03 7705 0.612E-02 0.107E-01
RMM: 28 -0.409788057263E+03 -0.88758E-03 -0.61680E-04 6163 0.441E-02 0.104E-01
RMM: 29 -0.409788691429E+03 -0.63417E-03 -0.27826E-04 4576 0.365E-02 0.385E-02
RMM: 30 -0.409789135490E+03 -0.44406E-03 -0.12984E-04 4062 0.288E-02 0.258E-02
RMM: 31 -0.409789734571E+03 -0.59908E-03 -0.12042E-04 4002 0.258E-02 0.245E-02
RMM: 32 -0.409789913802E+03 -0.17923E-03 -0.51594E-05 3843 0.184E-02 0.127E-02
RMM: 33 -0.409790059151E+03 -0.14535E-03 -0.26607E-05 3566 0.125E-02 0.674E-03
RMM: 34 -0.409790166866E+03 -0.10772E-03 -0.17343E-05 3321 0.986E-03 0.866E-03
RMM: 35 -0.409790221648E+03 -0.54781E-04 -0.13235E-05 2976 0.792E-03
1 F= -.40979022E+03 E0= -.40929334E+03 d E =-.993766E+00
writing wavefunctions
START DOS PROJECTION IN BADER VOLUMES
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
vasp5-titan-9 00000000005AB95F Unknown Unknown Unknown
vasp5-titan-9 0000000000725DDC Unknown Unknown Unknown
vasp5-titan-9 000000000046A41A Unknown Unknown Unknown
vasp5-titan-9 000000000043886C Unknown Unknown Unknown
libc.so.6 000000322D41D8B4 Unknown Unknown Unknown
vasp5-titan-9 0000000000438779 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libopen-pal.so.0 00002AC27062463E Unknown Unknown Unknown
libopen-pal.so.0 00002AC270626633 Unknown Unknown Unknown
libc.so.6 000000322D42E94C Unknown Unknown Unknown
vasp5-titan-9 0000000000D16F8C Unknown Unknown Unknown
vasp5-titan-9 0000000000D1B563 Unknown Unknown Unknown
libpthread.so.0 000000322DC0DE80 Unknown Unknown Unknown
vasp5-titan-9 00000000005AB95F Unknown Unknown Unknown
vasp5-titan-9 0000000000725DDC Unknown Unknown Unknown
vasp5-titan-9 000000000046A41A Unknown Unknown Unknown
vasp5-titan-9 000000000043886C Unknown Unknown Unknown
libc.so.6 000000322D41D8B4 Unknown Unknown Unknown
vasp5-titan-9 0000000000438779 Unknown Unknown Unknown
--------------------------------------------------------------------------
mpiexec has exited due to process rank 7 with PID 9299 on
node compute-0-0.local exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
Job 3889395 ("Catalysis") completed on compute-0-0 at Mon Jul 26 22:05:22 CEST 2010
problems with the inclusion of adsorbates
Moderator: moderators
problems with the inclusion of adsorbates
- Attachments
-
- OUTCAR.rar
- (35.87 KiB) Downloaded 16887 times
Re: problems with the inclusion of adsorbates
From the OUTCAR, it seems the projection had finished. After that, the code died.
I may still need to see other files of the calculation, including the INCAR, KPOINT, POSCAR, POTCAR and BDRCAR.
Please put them in a web sever that I can download from (don't send them in email).
Wenjie
I may still need to see other files of the calculation, including the INCAR, KPOINT, POSCAR, POTCAR and BDRCAR.
Please put them in a web sever that I can download from (don't send them in email).
Wenjie
Re: problems with the inclusion of adsorbates
Hello wenjie,
Enclosed you can find the files.
Looking forward to hearing from you soon.
Thank you.
Yi-An
Enclosed you can find the files.
Looking forward to hearing from you soon.
Thank you.
Yi-An
Last edited by hlzya on Thu Aug 05, 2010 4:03 pm, edited 1 time in total.
Re: problems with the inclusion of adsorbates
Update:
I have tried the same mession using Vasp.4.6.36, and no grogress was found.
Yi-An
I have tried the same mession using Vasp.4.6.36, and no grogress was found.
Yi-An
Re: problems with the inclusion of adsorbates
Update again:
I added the option of "-heap-arrays 64" in the line of "FFLAG" in the makefile and compiled the code again. It was found the standard output became as follows:
======================
Starting job 3975221 ("Catalysis") on compute-10-23,compute-11-[21,28],compute-12-[1,3,26],compute-14-[3,19] at Thu Aug 5 18:15:14 CEST 2010
running on 64 nodes
distr: one band on 64 nodes, 1 groups
vasp.5.2.2 15Apr09 complex
POSCAR found type information on POSCAR Ir Pt C H
POSCAR found : 4 types and 54 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...( 1 )
reading WAVECAR
entering main loop
N E dE d eps ncg rms rms(c)
RMM: 1 0.472270252152E+04 0.47227E+04 -0.13682E+05 3367 0.112E+03
RMM: 2 0.103118350028E+04 -0.36915E+04 -0.40087E+04 3367 0.328E+02
RMM: 3 0.145330400516E+03 -0.88585E+03 -0.98933E+03 3367 0.155E+02
RMM: 4 -0.176255401391E+03 -0.32159E+03 -0.27020E+03 3367 0.121E+02
RMM: 5 -0.295615425151E+03 -0.11936E+03 -0.10529E+03 3367 0.740E+01
RMM: 6 -0.353853352778E+03 -0.58238E+02 -0.51010E+02 3367 0.588E+01
RMM: 7 -0.385459151426E+03 -0.31606E+02 -0.28836E+02 3367 0.392E+01
RMM: 8 -0.404552781536E+03 -0.19094E+02 -0.17176E+02 3367 0.337E+01
RMM: 9 -0.434029444071E+03 -0.29477E+02 -0.28680E+02 10246 0.236E+01
RMM: 10 -0.439477181168E+03 -0.54477E+01 -0.51725E+01 10807 0.604E+00
RMM: 11 -0.440738581913E+03 -0.12614E+01 -0.98156E+00 10300 0.208E+00
RMM: 12 -0.440995226774E+03 -0.25664E+00 -0.18111E+00 10520 0.729E-01 0.326E+01
RMM: 13 -0.418725973113E+03 0.22269E+02 -0.75504E+01 7539 0.222E+01 0.183E+01
RMM: 14 -0.451300002719E+03 -0.32574E+02 -0.93580E+01 8814 0.150E+01 0.330E+01
RMM: 15 -0.434559637846E+03 0.16740E+02 -0.31619E+01 8349 0.903E+00 0.286E+01
RMM: 16 -0.411104065530E+03 0.23456E+02 -0.10613E+01 7942 0.594E+00 0.818E+00
RMM: 17 -0.410633250122E+03 0.47082E+00 -0.44937E+00 8826 0.328E+00 0.605E+00
RMM: 18 -0.410040975577E+03 0.59227E+00 -0.17721E+00 8381 0.241E+00 0.303E+00
RMM: 19 -0.409882471855E+03 0.15850E+00 -0.59990E-01 8374 0.142E+00 0.191E+00
RMM: 20 -0.409828386757E+03 0.54085E-01 -0.21545E-01 7868 0.890E-01 0.127E+00
RMM: 21 -0.409810156720E+03 0.18230E-01 -0.67574E-02 8127 0.462E-01 0.100E+00
RMM: 22 -0.409792175403E+03 0.17981E-01 -0.24756E-02 8342 0.262E-01 0.431E-01
RMM: 23 -0.409788403475E+03 0.37719E-02 -0.13228E-02 8562 0.168E-01 0.303E-01
RMM: 24 -0.409786974130E+03 0.14293E-02 -0.42590E-03 8334 0.103E-01 0.212E-01
RMM: 25 -0.409786640479E+03 0.33365E-03 -0.29494E-03 7892 0.100E-01 0.197E-01
RMM: 26 -0.409786366428E+03 0.27405E-03 -0.14300E-03 7788 0.611E-02 0.123E-01
RMM: 27 -0.409787169686E+03 -0.80326E-03 -0.14345E-03 7705 0.612E-02 0.107E-01
RMM: 28 -0.409788057267E+03 -0.88758E-03 -0.61680E-04 6163 0.441E-02 0.104E-01
RMM: 29 -0.409788691434E+03 -0.63417E-03 -0.27826E-04 4576 0.365E-02 0.385E-02
RMM: 30 -0.409789135494E+03 -0.44406E-03 -0.12984E-04 4062 0.288E-02 0.258E-02
RMM: 31 -0.409789734574E+03 -0.59908E-03 -0.12042E-04 4002 0.258E-02 0.245E-02
RMM: 32 -0.409789913806E+03 -0.17923E-03 -0.51594E-05 3843 0.184E-02 0.127E-02
RMM: 33 -0.409790059155E+03 -0.14535E-03 -0.26607E-05 3566 0.125E-02 0.674E-03
RMM: 34 -0.409790166871E+03 -0.10772E-03 -0.17343E-05 3321 0.986E-03 0.866E-03
RMM: 35 -0.409790221652E+03 -0.54781E-04 -0.13235E-05 2976 0.792E-03
1 F= -.40979022E+03 E0= -.40929334E+03 d E =-.993766E+00
writing wavefunctions
START DOS PROJECTION IN BADER VOLUMES
===========================
In other words, there is no stack size error any more. However, I found the OUTCAR file was alomost the same as the attached one. The code is now still running on the computational node. The OUTCAR file, however, has not been updated for about 6 hours.
Thank you.
Yi-An
I added the option of "-heap-arrays 64" in the line of "FFLAG" in the makefile and compiled the code again. It was found the standard output became as follows:
======================
Starting job 3975221 ("Catalysis") on compute-10-23,compute-11-[21,28],compute-12-[1,3,26],compute-14-[3,19] at Thu Aug 5 18:15:14 CEST 2010
running on 64 nodes
distr: one band on 64 nodes, 1 groups
vasp.5.2.2 15Apr09 complex
POSCAR found type information on POSCAR Ir Pt C H
POSCAR found : 4 types and 54 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...( 1 )
reading WAVECAR
entering main loop
N E dE d eps ncg rms rms(c)
RMM: 1 0.472270252152E+04 0.47227E+04 -0.13682E+05 3367 0.112E+03
RMM: 2 0.103118350028E+04 -0.36915E+04 -0.40087E+04 3367 0.328E+02
RMM: 3 0.145330400516E+03 -0.88585E+03 -0.98933E+03 3367 0.155E+02
RMM: 4 -0.176255401391E+03 -0.32159E+03 -0.27020E+03 3367 0.121E+02
RMM: 5 -0.295615425151E+03 -0.11936E+03 -0.10529E+03 3367 0.740E+01
RMM: 6 -0.353853352778E+03 -0.58238E+02 -0.51010E+02 3367 0.588E+01
RMM: 7 -0.385459151426E+03 -0.31606E+02 -0.28836E+02 3367 0.392E+01
RMM: 8 -0.404552781536E+03 -0.19094E+02 -0.17176E+02 3367 0.337E+01
RMM: 9 -0.434029444071E+03 -0.29477E+02 -0.28680E+02 10246 0.236E+01
RMM: 10 -0.439477181168E+03 -0.54477E+01 -0.51725E+01 10807 0.604E+00
RMM: 11 -0.440738581913E+03 -0.12614E+01 -0.98156E+00 10300 0.208E+00
RMM: 12 -0.440995226774E+03 -0.25664E+00 -0.18111E+00 10520 0.729E-01 0.326E+01
RMM: 13 -0.418725973113E+03 0.22269E+02 -0.75504E+01 7539 0.222E+01 0.183E+01
RMM: 14 -0.451300002719E+03 -0.32574E+02 -0.93580E+01 8814 0.150E+01 0.330E+01
RMM: 15 -0.434559637846E+03 0.16740E+02 -0.31619E+01 8349 0.903E+00 0.286E+01
RMM: 16 -0.411104065530E+03 0.23456E+02 -0.10613E+01 7942 0.594E+00 0.818E+00
RMM: 17 -0.410633250122E+03 0.47082E+00 -0.44937E+00 8826 0.328E+00 0.605E+00
RMM: 18 -0.410040975577E+03 0.59227E+00 -0.17721E+00 8381 0.241E+00 0.303E+00
RMM: 19 -0.409882471855E+03 0.15850E+00 -0.59990E-01 8374 0.142E+00 0.191E+00
RMM: 20 -0.409828386757E+03 0.54085E-01 -0.21545E-01 7868 0.890E-01 0.127E+00
RMM: 21 -0.409810156720E+03 0.18230E-01 -0.67574E-02 8127 0.462E-01 0.100E+00
RMM: 22 -0.409792175403E+03 0.17981E-01 -0.24756E-02 8342 0.262E-01 0.431E-01
RMM: 23 -0.409788403475E+03 0.37719E-02 -0.13228E-02 8562 0.168E-01 0.303E-01
RMM: 24 -0.409786974130E+03 0.14293E-02 -0.42590E-03 8334 0.103E-01 0.212E-01
RMM: 25 -0.409786640479E+03 0.33365E-03 -0.29494E-03 7892 0.100E-01 0.197E-01
RMM: 26 -0.409786366428E+03 0.27405E-03 -0.14300E-03 7788 0.611E-02 0.123E-01
RMM: 27 -0.409787169686E+03 -0.80326E-03 -0.14345E-03 7705 0.612E-02 0.107E-01
RMM: 28 -0.409788057267E+03 -0.88758E-03 -0.61680E-04 6163 0.441E-02 0.104E-01
RMM: 29 -0.409788691434E+03 -0.63417E-03 -0.27826E-04 4576 0.365E-02 0.385E-02
RMM: 30 -0.409789135494E+03 -0.44406E-03 -0.12984E-04 4062 0.288E-02 0.258E-02
RMM: 31 -0.409789734574E+03 -0.59908E-03 -0.12042E-04 4002 0.258E-02 0.245E-02
RMM: 32 -0.409789913806E+03 -0.17923E-03 -0.51594E-05 3843 0.184E-02 0.127E-02
RMM: 33 -0.409790059155E+03 -0.14535E-03 -0.26607E-05 3566 0.125E-02 0.674E-03
RMM: 34 -0.409790166871E+03 -0.10772E-03 -0.17343E-05 3321 0.986E-03 0.866E-03
RMM: 35 -0.409790221652E+03 -0.54781E-04 -0.13235E-05 2976 0.792E-03
1 F= -.40979022E+03 E0= -.40929334E+03 d E =-.993766E+00
writing wavefunctions
START DOS PROJECTION IN BADER VOLUMES
===========================
In other words, there is no stack size error any more. However, I found the OUTCAR file was alomost the same as the attached one. The code is now still running on the computational node. The OUTCAR file, however, has not been updated for about 6 hours.
Thank you.
Yi-An