A error about: task sodft energy
Clicked A Few Times
1:07:54 AM PDT - Tue, Sep 10th 2013
Hi, all
I've got the following error while running a sodft calculation:


     Superposition of Atomic Density Guess

     -------------------------------------



Sum of atomic energies:       -9154.38972369



Renormalizing density from    1102.00 to   1103



Integral file          = ./Au58.aoints.000

Record size in doubles =    65536    No. of integs per rec  =    43688

Max. records in memory =        0    Max. records in file   =  1484374

No. of bits per label  =       16    No. of bits per value  =       32




#quartets = 1.003D+10 #integrals = 5.969D+11 #direct =  0.0% #cached =100.0%


File balance: exchanges= 383 moved=****** time=5690.9



     Non-variational initial energy

     ------------------------------



Total energy =   -7848.438010

1-e energy   = -126811.910551

2-e energy   =   62492.511107

HOMO         =      -0.118892

LUMO         =      -0.108705



------------------------------------------------------------------------

ga_orthog: hard zero     5067

------------------------------------------------------------------------

This error has not yet been assigned to a category

------------------------------------------------------------------------

For more information see the NWChem manual at 

http://nwchemgit.github.io/index.php/NWChem_Documentation




For further details see manual section: 

No section for this category
0:0:ga_orthog: hard zero:: 5067
Last System Error Message from Task 0:: Inappropriate ioctl for device
ga_orthog: hard zero     5067

------------------------------------------------------------------------

This error has not yet been assigned to a category

------------------------------------------------------------------------

For more information see the NWChem manual at 

http://nwchemgit.github.io/index.php/NWChem_Documentation




For further details see manual section: 

No section for this category




The inputfile is:
echo
start Au58

title "tutorial demonstrating the use of a ecp"

memory total 1500 mb

charge -1

geometry
Au -4.98544600 -0.98923700 2.30981600
Au -0.66274400 -4.18034800 3.01643800
Au 2.71783000 2.25122700 3.75253300
Au -1.77135600 2.89784900 3.96533800
Au -4.23659800 -1.60923500 -3.28153700
Au 5.12739700 0.07880400 0.22656300
Au -2.71251600 -2.32859300 3.43227400
Au 2.00832400 4.28713600 1.91235200
Au -4.32049200 3.48343300 -1.10087700
Au 4.93343700 0.52383500 3.07552100
Au 4.25324700 2.12898600 -1.63909300
Au -1.98939900 4.91181000 -0.73756800
Au 0.18067800 1.98701400 2.23581500
Au 4.33925700 -2.49802300 -0.85146700
Au -3.22418900 -3.54293000 -1.47330400
Au -0.38867200 4.71941000 -3.07478200
Au 0.43882200 -0.82334500 -4.60311400
Au 0.43805400 1.07164200 4.90607900
Au -1.31641800 -2.55130400 0.70832300
Au 2.56747100 -0.73001700 4.28807600
Au -4.24126700 1.55062600 3.35867800
Au 4.96036800 -0.36068800 -2.63657400
Au 1.66252300 -2.34383300 0.68329700
Au -3.37325900 3.59039300 1.60008200
Au 2.01442700 -3.38164900 3.30321700
Au -4.83819400 1.28457500 0.56301700
Au 2.07570000 3.47923100 -2.90458800
Au 2.20753900 -4.25171900 -1.61478200
Au -0.00819200 -1.26170200 3.15051800
Au 2.47098200 0.30128600 1.64238500
Au 2.60443300 0.87995400 -3.88592200
Au 4.26509000 -2.01001700 2.09986700
Au 2.49074700 -0.20361400 -1.17796200
Au 0.05764600 2.22844900 -4.64637600
Au 0.02080300 -0.08837000 0.34878100
Au -4.11989800 -3.39323000 1.20155500
Au -2.38979100 2.81262300 -3.08082100
Au 0.26873900 -1.97542300 -1.81803100
Au -2.17291400 0.22238500 -4.15239800
Au -4.41562700 0.97347200 -2.28858000
Au -5.02377100 -1.32760400 -0.54389200
Au -1.73783400 -2.64626000 -3.78989000
Au 2.89259100 -2.01783100 -3.44758500
Au 0.73499200 5.19709400 -0.51760500
Au -2.14875700 0.12445400 4.67530700
Au -2.29161700 -0.65739400 -1.24146200
Au -0.01666800 0.95957500 -2.26623300
Au 3.44428900 4.59843800 -0.61830200
Au 4.27018700 2.63868300 1.25813100
Au -2.34548900 0.09932300 1.78174600
Au -2.09049300 -5.23968500 0.63928700
Au 0.74358400 -5.09420900 0.73725800
Au -0.79338100 4.64768100 1.87123600
Au -0.65043800 -4.70008700 -1.78805500
Au 0.79829300 -3.71041500 -4.06584600
Au -1.71905400 2.09360700 -0.22041300
Au 1.49571700 2.38091000 -0.27899500
Au 3.50130800 -4.48714400 1.00256400
end

basis
Au S 
     2.4651000              1.0000000
Au S 
     1.9431000              1.0000000
Au S 
     0.5613000              1.0000000
Au S 
     0.1452000              1.0000000
Au S 
     0.0503900              1.0000000
Au P 
     3.5306000              1.0000000
Au P 
     2.6122000              1.0000000
Au P 
     0.9813000              1.0000000
Au P 
     0.4266000              1.0000000
Au P 
     0.1475000              1.0000000
Au D 
     1.3366000              1.0000000
Au D 
     0.5035000              1.0000000
Au D 
     0.1940000              1.0000000
Au D 
     0.0756000              1.0000000
end

ECP
Au nelec 60
Au ul
2 2.07069993 -0.90820301
2 5.28779984 -13.97286034
2 13.28610039 -78.04593658
2 38.22499847 -150.67013550
2 120.82949829 -433.79324341
1 415.27328491 -53.92461777
Au S
2 2.81620002 -45.11843872
2 3.12030005 109.24782562
2 4.16239977 -184.75865173
2 6.38819981 436.13348389
2 10.11999989 -356.46279907
2 17.04649925 411.84240723
1 50.50329971 31.95258903
0 39.28239822 6.79167795
Au P
2 2.41569996 -30.62415695
2 2.79209995 101.11966705
2 3.67700005 -210.51446533
2 5.37360001 435.37313843
2 8.36999989 -396.14450073
2 13.32330036 368.87313843
1 37.15980148 31.59367371
0 37.42219925 5.83880520
Au D
2 1.87390006 -34.10911942
2 2.11870003 100.58750153
2 2.69359994 -172.30566406
2 3.81640005 290.82238770
2 5.69740009 -292.96429443
2 8.62959957 275.67791748
1 19.68020058 30.37005806
0 25.98660088 7.86203289
Au F
2 1.43149996 40.06137466
2 1.65450001 -128.38630676
2 2.16300011 247.77139282
2 3.08719993 -342.54879761
2 4.65740013 359.27548218
2 6.90420008 -182.27494812
1 10.14780045 53.49130630
0 47.02579880 4.28036213
END 
SO                                    

  	Au p                               

    2       2.415700       20.831138  

    2       2.792100      -55.173904  

    2       3.677000       67.313564  

    2       5.373600      -17.020942  

    2       8.370000      -45.124680  

    2      13.323300       23.440232  

    1      37.159800       -5.458496  

    0      37.422200         .156970  

   Au d                            

   2       1.873900        1.020373

   2       2.118700       -1.781020

   2       2.693600        -.987213

   2       3.816400       10.584266

   2       5.697400      -18.154486

   2       8.629600       10.498401

   1      19.680200        -.745309

   0      25.986600         .038670

 	Au f                            

   2       1.431500        1.100953

   2       1.654500       -3.519561

   2       2.163000        6.730668

   2       3.087200       -9.073041

   2       4.657400        7.478326

   2       6.904200       -3.261827

   1      10.147800         .076227

   0      47.025800        -.007474

   Au g                            

   2       2.070700        -.006998

   2       5.287800         .008684

   2      13.286100         .074875

   2      38.225000         .601742

   2     120.829500        1.616524

   1     415.273300        2.676910

END

dft 
 mult 2

 xc pbe0

 semidirect memsize 100000000 

 iterations 1000
end
task sodft energy

I run the sodft calculation in nwchem6.3.
The settings/commands used to compile NWChem is:


export NWCHEM_TOP=/opt/nwchem/nwchem-src-2013-07-19
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export LARGE_FILES=TRUE

export IB_HOME=/usr
export IB_INCLUDE=$IB_HOME/include
export IB_LIB=$IB_HOME/lib
export IB_LIB_NAME="-libcm -lpthread -libverbs -libumad -lpthread -lrt"
  1. export IB_LIB_NAME="-libcm -lpthread"
export ARMCI_NETWORK=OPENIB
export MSG_COMMS=MPI
export ARMCI_DEFAULT_SHMMAX=8192

export MRCC_THEORY=TRUE

export USE_NOFSCHECK=TRUE
export LIB_DEFINES="-DDFLT_TOT_MEM=171349760"
export TCGRSH=/usr/bin/ssh
cd $NWCHEM_TOP/src
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/home/scc/intel/impi/4.1.0.024
export MPI_LIB=$MPI_LOC/lib64
export MPI_INCLUDE=$MPI_LOC/include64
export LIBMPI="-L/home/scc/intel/impi/4.1.0.024/lib64 -lmpigf -lmpigi -lmpi_ilp64 -lmpi"

export PYTHONHOME=/usr
export PYTHONVERSION=2.6
export USE_PYTHON64=y
export PYTHONLIBTYPE=so
  1. source /opt/intel/composerxe/bin/compilervars.sh intel64
  2. source /opt/intel/impi/4.0.3/bin64/mpivars.sh
  3. source /opt/intel/composerxe/mkl/bin/intel64/mklvars_intel64.sh

source /home/scc/intel/composerxe/bin/compilervars.sh intel64
source /home/scc/intel/impi/4.1.0.024/intel64/bin/mpivars.sh
source /home/scc/intel/mkl/bin/mklvars.sh intel64

  1. intel MKL
export MKLLIB=/home/scc/intel/mkl/lib/intel64
export MKLINC=/home/scc/intel/mkl/include
export MKLLINK1="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_blacs_ilp64 -lmkl_blacs_intelmpi_ilp64 -lmkl_blacs_intelmpi_lp64 -lmkl_blacs_lp64 -lmkl_blas95_ilp64 -lmkl_blas95_lp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_scalapack_ilp64 -lmkl_scalapack_lp64 "
export MKLLINK2=" -lmkl_core -lmkl_lapack95_lp64 -liomp5 -lpthread"
export BLASOPT="-L${MKLLIB} $MKLLINK1 $MKLLINK2 "
export MKLROOT=/opt/intel/composerxe/mkl
  1. export BLASOPT="-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"

export FC="ifort -i8 -I${MKLROOT}/include"
export CC="icc -DMKL_ILP64 -I${MKLROOT}/include"
make nwchem_config
make -j 6 FC=ifort CC=icc > nwchem_config_ib_intel.log


Any help with this problem would be appreciated!

Forum Vet
4:25:13 PM PDT - Tue, Sep 10th 2013
Hugh
The Spin-orbit code is a bit more numerical sensitive than the regular DFT code.
I did a quick run on your gold cluster geometry with LDA and I noticed a pretty large gradient.
Has your geometry been optimized? If this is not the case, I would first optimize it,
and then run spin-orbit on it.

Cheers, Edo

Clicked A Few Times
6:12:58 PM PDT - Tue, Sep 10th 2013
Dear Dr.Edo,
Thanks for your reply.
The geometry of Au58 cluster has been optimized by Dmol3 at PBE/DNP+ level. I want to calculate its single point energy using sodft at PBE0/CRENBL+SO basis set based on the geometry. I calculate several times, but failed. I test the Au20 at PBE0/CRENBL+SO level. It can be calculated. Whether the CRENBL+SO basis set is very large for Au58 cluster at PBE0 functional?

best wishes,
    Hugh

Forum Vet
1:17:02 PM PDT - Wed, Sep 11th 2013
Dear Hugh,
I missed one important detail, that is the linear dependence exhibited by you input.
Unfortunately, the spin-orbit code is not able to deal with linear dependencies (while the regular DFT code is).
A way to circumvent this problem is to force NWChem to set the number of linear dependencies to zero (however,
by doing so you might have convergence problems). To achieve this, please insert the following line before the task line

set lindep:n_dep 0

Cheers, Edo

Clicked A Few Times
5:42:12 PM PDT - Wed, Sep 11th 2013
Dear Edo,
Thanks for your suggestion. I will try it!



best wishes,
    Hugh

Clicked A Few Times
12:49:15 AM PDT - Fri, Sep 20th 2013
Dear Edo,
I tested the "set lindep: n_dep 0" in input file. It's work with SCF calculation. But another problem arises. The shock appears in scf calculation. I don't know what lead to it.

The input file is:

echo
start Au58

title "tutorial demonstrating the use of a ecp"

memory total 5000 mb

charge -1

geometry
Au -4.98544600 -0.98923700 2.30981600
Au -0.66274400 -4.18034800 3.01643800
Au 2.71783000 2.25122700 3.75253300
Au -1.77135600 2.89784900 3.96533800
Au -4.23659800 -1.60923500 -3.28153700
Au 5.12739700 0.07880400 0.22656300
Au -2.71251600 -2.32859300 3.43227400
Au 2.00832400 4.28713600 1.91235200
Au -4.32049200 3.48343300 -1.10087700
Au 4.93343700 0.52383500 3.07552100
Au 4.25324700 2.12898600 -1.63909300
Au -1.98939900 4.91181000 -0.73756800
Au 0.18067800 1.98701400 2.23581500
Au 4.33925700 -2.49802300 -0.85146700
Au -3.22418900 -3.54293000 -1.47330400
Au -0.38867200 4.71941000 -3.07478200
Au 0.43882200 -0.82334500 -4.60311400
Au 0.43805400 1.07164200 4.90607900
Au -1.31641800 -2.55130400 0.70832300
Au 2.56747100 -0.73001700 4.28807600
Au -4.24126700 1.55062600 3.35867800
Au 4.96036800 -0.36068800 -2.63657400
Au 1.66252300 -2.34383300 0.68329700
Au -3.37325900 3.59039300 1.60008200
Au 2.01442700 -3.38164900 3.30321700
Au -4.83819400 1.28457500 0.56301700
Au 2.07570000 3.47923100 -2.90458800
Au 2.20753900 -4.25171900 -1.61478200
Au -0.00819200 -1.26170200 3.15051800
Au 2.47098200 0.30128600 1.64238500
Au 2.60443300 0.87995400 -3.88592200
Au 4.26509000 -2.01001700 2.09986700
Au 2.49074700 -0.20361400 -1.17796200
Au 0.05764600 2.22844900 -4.64637600
Au 0.02080300 -0.08837000 0.34878100
Au -4.11989800 -3.39323000 1.20155500
Au -2.38979100 2.81262300 -3.08082100
Au 0.26873900 -1.97542300 -1.81803100
Au -2.17291400 0.22238500 -4.15239800
Au -4.41562700 0.97347200 -2.28858000
Au -5.02377100 -1.32760400 -0.54389200
Au -1.73783400 -2.64626000 -3.78989000
Au 2.89259100 -2.01783100 -3.44758500
Au 0.73499200 5.19709400 -0.51760500
Au -2.14875700 0.12445400 4.67530700
Au -2.29161700 -0.65739400 -1.24146200
Au -0.01666800 0.95957500 -2.26623300
Au 3.44428900 4.59843800 -0.61830200
Au 4.27018700 2.63868300 1.25813100
Au -2.34548900 0.09932300 1.78174600
Au -2.09049300 -5.23968500 0.63928700
Au 0.74358400 -5.09420900 0.73725800
Au -0.79338100 4.64768100 1.87123600
Au -0.65043800 -4.70008700 -1.78805500
Au 0.79829300 -3.71041500 -4.06584600
Au -1.71905400 2.09360700 -0.22041300
Au 1.49571700 2.38091000 -0.27899500
Au 3.50130800 -4.48714400 1.00256400
end

basis
Au S 
     2.4651000              1.0000000
Au S 
     1.9431000              1.0000000
Au S 
     0.5613000              1.0000000
Au S 
     0.1452000              1.0000000
Au S 
     0.0503900              1.0000000
Au P 
     3.5306000              1.0000000
Au P 
     2.6122000              1.0000000
Au P 
     0.9813000              1.0000000
Au P 
     0.4266000              1.0000000
Au P 
     0.1475000              1.0000000
Au D 
     1.3366000              1.0000000
Au D 
     0.5035000              1.0000000
Au D 
     0.1940000              1.0000000
Au D 
     0.0756000              1.0000000
end

ECP
Au nelec 60
Au ul
2 2.07069993 -0.90820301
2 5.28779984 -13.97286034
2 13.28610039 -78.04593658
2 38.22499847 -150.67013550
2 120.82949829 -433.79324341
1 415.27328491 -53.92461777
Au S
2 2.81620002 -45.11843872
2 3.12030005 109.24782562
2 4.16239977 -184.75865173
2 6.38819981 436.13348389
2 10.11999989 -356.46279907
2 17.04649925 411.84240723
1 50.50329971 31.95258903
0 39.28239822 6.79167795
Au P
2 2.41569996 -30.62415695
2 2.79209995 101.11966705
2 3.67700005 -210.51446533
2 5.37360001 435.37313843
2 8.36999989 -396.14450073
2 13.32330036 368.87313843
1 37.15980148 31.59367371
0 37.42219925 5.83880520
Au D
2 1.87390006 -34.10911942
2 2.11870003 100.58750153
2 2.69359994 -172.30566406
2 3.81640005 290.82238770
2 5.69740009 -292.96429443
2 8.62959957 275.67791748
1 19.68020058 30.37005806
0 25.98660088 7.86203289
Au F
2 1.43149996 40.06137466
2 1.65450001 -128.38630676
2 2.16300011 247.77139282
2 3.08719993 -342.54879761
2 4.65740013 359.27548218
2 6.90420008 -182.27494812
1 10.14780045 53.49130630
0 47.02579880 4.28036213
END 
SO                                    

  	Au p                               

    2       2.415700       20.831138  

    2       2.792100      -55.173904  

    2       3.677000       67.313564  

    2       5.373600      -17.020942  

    2       8.370000      -45.124680  

    2      13.323300       23.440232  

    1      37.159800       -5.458496  

    0      37.422200         .156970  

   Au d                            

   2       1.873900        1.020373

   2       2.118700       -1.781020

   2       2.693600        -.987213

   2       3.816400       10.584266

   2       5.697400      -18.154486

   2       8.629600       10.498401

   1      19.680200        -.745309

   0      25.986600         .038670

 	Au f                            

   2       1.431500        1.100953

   2       1.654500       -3.519561

   2       2.163000        6.730668

   2       3.087200       -9.073041

   2       4.657400        7.478326

   2       6.904200       -3.261827

   1      10.147800         .076227

   0      47.025800        -.007474

   Au g                            

   2       2.070700        -.006998

   2       5.287800         .008684

   2      13.286100         .074875

   2      38.225000         .601742

   2     120.829500        1.616524

   1     415.273300        2.676910

END

dft 
 mult 2

 xc pbe0

 direct

 convergence diis 2

 convergence nolevelshifting
  1. semidirect memsize 100000000 
 iterations 1000
end
set lindep:n_dep 0
  1. set lindep:tol 1.0d-6
task sodft energy

The output file is:

          Memory utilization after 1st SCF pass:                                        

          Heap Space remaining (MW):      163.54           163540250                    

         Stack Space remaining (MW):      111.66           111660032                    

                                                                                        

  convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time           

---------------- ----- ----------------- --------- --------- ---------  ------          

d= 0,ls=0.0,diis     1  -7884.5863206700 -6.44D+04  2.98D+01  8.94D+01  6334.7          

                                                    1.69D-01  8.94D+01                  

d= 0,ls=0.0,diis     2  -7891.9981962670 -7.41D+00  6.89D+02  1.25D+01 12275.9          

                                                    6.76D+02  1.25D+01                  

d= 0,ls=0.0,diis     3  -6930.9339644882  9.61D+02  7.68D+01  5.41D+05 21069.9          

                                                    9.15D+01  5.41D+05                  

d= 0,ls=0.0,diis     4  -6687.3234788920  2.44D+02  1.04D+03  7.06D+05 30131.9          

                                                    1.04D+03  7.06D+05                  

d= 0,ls=0.0,diis     5   3967.3284565419  1.07D+04  8.79D+02  2.86D+05 38647.1          

                                                    8.78D+02  2.86D+05                  

d= 0,ls=0.0,diis     6  19803.8589373688  1.58D+04  5.16D+02  6.55D+05 46846.8          

                                                    5.16D+02  6.55D+05                  

d= 0,ls=0.0,diis     7   1860.5124113727 -1.79D+04  6.37D+02  5.01D+05 55291.2          

                                                    6.37D+02  5.01D+05                  

d= 0,ls=0.0,diis     8  17618.2307018081  1.58D+04  3.24D+02  3.24D+05 63667.0          

                                                    3.24D+02  3.24D+05                  

d= 0,ls=0.0,diis     9  22353.0393877535  4.73D+03  2.66D+02  9.29D+04 72428.4          

                                                    2.66D+02  9.29D+04                  

d= 0,ls=0.0,diis    10   6648.7050728123 -1.57D+04  1.61D+02  9.48D+04 80767.0          

                                                    1.61D+02  9.48D+04                  

d= 0,ls=0.0,diis    11   1688.8423437193 -4.96D+03  1.44D+02  4.62D+04 89204.5          

                                                    1.44D+02  4.62D+04                  

d= 0,ls=0.0,diis    12  22821.3011819762  2.11D+04  1.51D+02  7.85D+04 97802.3          

                                                    1.51D+02  7.85D+04                  

d= 0,ls=0.0,diis    13  17166.4101493446 -5.65D+03  1.48D+02  7.24D+04106162.9          

                                                    1.48D+02  7.24D+04

best wishes,
   Hugh

Forum Vet
6:21:31 PM PDT - Fri, Sep 20th 2013
Hugh
Given the current limitation of the DFT code (until we fix the treatment of linear dependencies),
the only suggestion I can give you is to modify by hand the basis set in order to avoid the
occurrence of linear dependencies.
For example, I would first remove all the smallest exponents for s, p and d functions and see if you can converge in these conditions. Next, I would re-introduce the smallest s, and so on ...


Forum >> NWChem's corner >> General Topics