bas geobas build error message while running a calculation using ZORA feature
Clicked A Few Times
9:17:21 PM PDT - Fri, Jun 26th 2015
Hi,

I ended with the below error message, when I was running NWChem using ZORA feature.

NWChem DFT Module
                                -----------------




                             B3LYP/cc-pVDZ-pp/zora"


0:bas_geobas_build: basis/geometry mismatch:Received an Error in Communication

ERROR: geometry tag C2 (Carbon) is an atom but has no functions in basis "ao basis"

ERROR: only bq* centers can have no functions

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

bas_geobas_build: basis/geometry mismatch                   0

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

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

 current input line :

   96: task DFT energy

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

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

There is an error in the specified basis set

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

For more information see the NWChem manual at http://nwchemgit.github.io/index.php/NWChem_Documentation




For further details see manual section:

MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.


mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

 Process name: [[6093,1],0]

 Exit code:    255


INPUT File:

title B3LYP/cc-pvdz/zora"
memory total 400 mb
echo
geometry units angstroms
symmetry c1
Ir1 0.0429710000000 0.0037150000000 -0.0518300000000
C2 2.0837130000000 0.2858480000000 -0.1881780000000
C3 2.4110990000000 0.4583120000000 -1.5657240000000
C4 3.7831340000000 0.7080860000000 -1.8802690000000
C5 4.7652080000000 0.7909470000000 -0.8775270000000
C6 4.4188390000000 0.6383280000000 0.4682270000000
C7 3.0821370000000 0.3980000000000 0.8086920000000
C8 1.3356020000000 0.3528330000000 -2.5939620000000
N9 0.0902830000000 0.1007240000000 -2.1018020000000
C10 -0.9315740000000 -0.0265630000000 -2.9795080000000
C11 -0.7944140000000 0.0858860000000 -4.3656600000000
C12 0.4758120000000 0.3496930000000 -4.8824170000000
C13 1.5449290000000 0.4823910000000 -3.9873640000000
F14 4.2182270000000 0.8801900000000 -3.1493910000000
F15 5.3640050000000 0.7268600000000 1.4331450000000
H16 5.7932200000000 0.9774600000000 -1.1474910000000
H17 2.8390300000000 0.3019010000000 1.8546090000000
H18 -1.9117540000000 -0.2336030000000 -2.5860150000000
H19 -1.6494290000000 -0.0259470000000 -5.0157220000000
H20 0.6310880000000 0.4470350000000 -5.9469250000000
H21 2.5094620000000 0.6794230000000 -4.4187700000000
C22 -0.1830850000000 2.0442310000000 0.1045180000000
C23 -1.5781820000000 2.3288620000000 0.0993620000000
C24 -1.9585370000000 3.6954000000000 0.2772130000000
C25 -0.9993590000000 4.7154180000000 0.4130310000000
C26 0.3657590000000 4.4129920000000 0.3894330000000
C27 0.7691740000000 3.0808140000000 0.2396900000000
C28 -2.5566280000000 1.2145890000000 -0.0627220000000
N29 -2.0189890000000 -0.0395580000000 -0.0978640000000
C30 -2.8690300000000 -1.0866580000000 -0.2205200000000
C31 -4.2529320000000 -0.9701620000000 -0.3713210000000
C32 -4.8073170000000 0.3107770000000 -0.3786320000000
C33 -3.9491100000000 1.4065250000000 -0.2289280000000
F34 -3.2518690000000 4.0885700000000 0.3340970000000
F35 1.2873660000000 5.3963330000000 0.5163360000000
H36 -1.3180120000000 5.7383570000000 0.5413570000000
H37 1.8267330000000 2.8678250000000 0.2396730000000
H38 -2.4569190000000 -2.0787580000000 -0.2021350000000
H39 -4.8739190000000 -1.8483140000000 -0.4695330000000
H40 -5.8716690000000 0.4537060000000 -0.4945890000000
H41 -4.4049260000000 2.3798190000000 -0.2461500000000
N42 -0.9813790000000 -0.0040710000000 2.5276970000000
C43 -1.3246040000000 -1.2770580000000 2.7381330000000
C44 -0.1902840000000 -2.0557810000000 2.3540030000000
C45 0.8059810000000 -1.1904620000000 2.6895770000000
N46 0.2519230000000 -0.1617770000000 1.9924980000000
C47 -0.1441430000000 -3.1927370000000 1.3714000000000
P48 0.1323950000000 -2.3547690000000 -0.2818950000000
C49 1.9693860000000 -2.6539570000000 -0.5927470000000
C50 2.4214350000000 -2.7557740000000 -1.9272970000000
C51 3.7788860000000 -2.9869860000000 -2.2198140000000
C52 4.7073060000000 -3.1327180000000 -1.1734450000000
C53 4.2709370000000 -3.0543430000000 0.1616210000000
C54 2.9115260000000 -2.8223340000000 0.4479190000000
C55 -0.4069850000000 -3.8716860000000 -1.2436460000000
C56 0.1571880000000 -5.1490670000000 -1.0244340000000
C57 -0.2773710000000 -6.2638230000000 -1.7671470000000
C58 -1.2807100000000 -6.1128480000000 -2.7420770000000
C59 -1.8417500000000 -4.8440320000000 -2.9769870000000
C60 -1.4023530000000 -3.7322200000000 -2.2331360000000
C61 -2.7535400000000 -1.6731700000000 3.0743240000000
F62 -3.6253030000000 -0.7042600000000 2.7905580000000
F63 -3.1036280000000 -2.7695610000000 2.4001890000000
F64 -2.8303670000000 -1.9423480000000 4.3776610000000
H65 1.0177680000000 -0.8664360000000 3.7023820000000
H66 0.6443870000000 -3.9042810000000 1.6107400000000
H67 -1.0734030000000 -3.7610140000000 1.3602710000000
H68 1.7140160000000 -2.6495550000000 -2.7375240000000
H69 4.1052790000000 -3.0524600000000 -3.2475680000000
H70 5.7503060000000 -3.3082870000000 -1.3942070000000
H71 4.9805190000000 -3.1682590000000 0.9685000000000
H72 2.6081800000000 -2.7591280000000 1.4802430000000
H73 0.9409870000000 -5.2791660000000 -0.2928640000000
H74 0.1648930000000 -7.2338920000000 -1.5926800000000
H75 -1.6135570000000 -6.9671120000000 -3.3136690000000
H76 -2.6061670000000 -4.7226800000000 -3.7306450000000
H77 -1.8314840000000 -2.7614180000000 -2.4283110000000
end
basis
iridium library cc-pvdz rel
end

DFT
XC B3LYP
END

RELATIVISTIC
ZORA ON
END

task DFT energy

Thanks,
-Tatireddy

Gets Around
3:01:06 PM PDT - Sat, Jun 27th 2015
It appears that you have assigned a basis set for iridium only. You need to assign basis set data for your other elements too.

Clicked A Few Times
9:44:17 PM PDT - Sun, Jun 28th 2015
Hi Mernst,

Thank you for the suggestion. I have modified the input file by assigning the basis set data for other elements.
Still I end up with the above mentioned error.

Modified Input file
{only basis set section information}

basis
Ir library cc-pVDZ-pp rel
end

basis
C library 6-31G**
end

basis
H library 6-31G**
end

basis
F library 6-31G**
end

basis
N library 6-31G**
end

Output

0:bas_geobas_build: basis/geometry mismatch:Received an Error in Communication

ERROR: geometry tag Ir1 (Iridium) is an atom but has no functions in basis "ao basis"

ERROR: only bq* centers can have no functions

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

bas_geobas_build: basis/geometry mismatch                   0

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

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

 current input line :

  112: task DFT energy

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

Am I doing something wrong here?

-Tati

Gets Around
11:09:56 PM PDT - Sun, Jun 28th 2015
Ah, yes, I forgot. Basis sets are assigned by geometry tag rather than element. This is so you can e.g. assign different basis sets to two different groups of oxygen atoms. You should get rid of the numbers after the element symbols since you just want one basis set assignment per element. That is, instead of

Ir1 0.0429710000000 0.0037150000000 -0.0518300000000
C2 2.0837130000000 0.2858480000000 -0.1881780000000
C3 2.4110990000000 0.4583120000000 -1.5657240000000
...


you want

Ir 0.0429710000000 0.0037150000000 -0.0518300000000
C 2.0837130000000 0.2858480000000 -0.1881780000000
C 2.4110990000000 0.4583120000000 -1.5657240000000
...

Clicked A Few Times
2:40:02 AM PDT - Mon, Jun 29th 2015
Hi Mernst,

I have removed the numbers after the elements and gave a shot, still I end up with the below message.

0:bas_geobas_build: basis/geometry mismatch:Received an Error in Communication

ERROR: geometry tag Ir (Iridium) is an atom but has no functions in basis "ao basis"

ERROR: only bq* centers can have no functions

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

bas_geobas_build: basis/geometry mismatch                   0

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

-Tatireddy

Gets Around
9:49:20 AM PDT - Mon, Jun 29th 2015
Can you post your input file that you are trying to use now?

Forum Regular
10:02:34 AM PDT - Mon, Jun 29th 2015
You need to combine your basis input into one block.
Instead of

basis
Ir library cc-pVDZ-pp rel
end

basis
C library 6-31G**
end

basis
H library 6-31G**
end

basis
F library 6-31G**
end

basis
N library 6-31G**
end

do

basis
Ir library cc-pVDZ-pp rel
C library 6-31G**
H library 6-31G**
F library 6-31G**
N library 6-31G**
end

Best,
Sean

Clicked A Few Times
8:49:45 PM PDT - Mon, Jun 29th 2015
Hi Sean,

Thank you for the suggestion. After editing the input file I gave a shot at the calculation this time it ended up saying the below error message.

Input file:

title B3LYP/cc-pvdz/zora"
memory total 400 mb

echo

geometry units angstroms

symmetry c1

Ir 0.0429710000000 0.0037150000000 -0.0518300000000

C 2.0837130000000 0.2858480000000 -0.1881780000000

C 2.4110990000000 0.4583120000000 -1.5657240000000

C 3.7831340000000 0.7080860000000 -1.8802690000000

C 4.7652080000000 0.7909470000000 -0.8775270000000

C 4.4188390000000 0.6383280000000 0.4682270000000

C 3.0821370000000 0.3980000000000 0.8086920000000

C 1.3356020000000 0.3528330000000 -2.5939620000000

N 0.0902830000000 0.1007240000000 -2.1018020000000

C -0.9315740000000 -0.0265630000000 -2.9795080000000

C -0.7944140000000 0.0858860000000 -4.3656600000000

C 0.4758120000000 0.3496930000000 -4.8824170000000

C 1.5449290000000 0.4823910000000 -3.9873640000000

F 4.2182270000000 0.8801900000000 -3.1493910000000

F 5.3640050000000 0.7268600000000 1.4331450000000

H 5.7932200000000 0.9774600000000 -1.1474910000000

H 2.8390300000000 0.3019010000000 1.8546090000000

H -1.9117540000000 -0.2336030000000 -2.5860150000000

H -1.6494290000000 -0.0259470000000 -5.0157220000000

H 0.6310880000000 0.4470350000000 -5.9469250000000

H 2.5094620000000 0.6794230000000 -4.4187700000000

C -0.1830850000000 2.0442310000000 0.1045180000000

C -1.5781820000000 2.3288620000000 0.0993620000000

C -1.9585370000000 3.6954000000000 0.2772130000000

C -0.9993590000000 4.7154180000000 0.4130310000000

C 0.3657590000000 4.4129920000000 0.3894330000000

C 0.7691740000000 3.0808140000000 0.2396900000000

C -2.5566280000000 1.2145890000000 -0.0627220000000

N -2.0189890000000 -0.0395580000000 -0.0978640000000

C -2.8690300000000 -1.0866580000000 -0.2205200000000

C -4.2529320000000 -0.9701620000000 -0.3713210000000

C -4.8073170000000 0.3107770000000 -0.3786320000000

C -3.9491100000000 1.4065250000000 -0.2289280000000

F -3.2518690000000 4.0885700000000 0.3340970000000

F 1.2873660000000 5.3963330000000 0.5163360000000

H -1.3180120000000 5.7383570000000 0.5413570000000

H 1.8267330000000 2.8678250000000 0.2396730000000

H -2.4569190000000 -2.0787580000000 -0.2021350000000

H -4.8739190000000 -1.8483140000000 -0.4695330000000

H -5.8716690000000 0.4537060000000 -0.4945890000000

H -4.4049260000000 2.3798190000000 -0.2461500000000

N -0.9813790000000 -0.0040710000000 2.5276970000000

C -1.3246040000000 -1.2770580000000 2.7381330000000

C -0.1902840000000 -2.0557810000000 2.3540030000000

C 0.8059810000000 -1.1904620000000 2.6895770000000

N 0.2519230000000 -0.1617770000000 1.9924980000000

C -0.1441430000000 -3.1927370000000 1.3714000000000

P 0.1323950000000 -2.3547690000000 -0.2818950000000

C 1.9693860000000 -2.6539570000000 -0.5927470000000

C 2.4214350000000 -2.7557740000000 -1.9272970000000

C 3.7788860000000 -2.9869860000000 -2.2198140000000

C 4.7073060000000 -3.1327180000000 -1.1734450000000

C 4.2709370000000 -3.0543430000000 0.1616210000000

C 2.9115260000000 -2.8223340000000 0.4479190000000

C -0.4069850000000 -3.8716860000000 -1.2436460000000

C 0.1571880000000 -5.1490670000000 -1.0244340000000

C -0.2773710000000 -6.2638230000000 -1.7671470000000

C -1.2807100000000 -6.1128480000000 -2.7420770000000

C -1.8417500000000 -4.8440320000000 -2.9769870000000

C -1.4023530000000 -3.7322200000000 -2.2331360000000

C -2.7535400000000 -1.6731700000000 3.0743240000000

F -3.6253030000000 -0.7042600000000 2.7905580000000

F -3.1036280000000 -2.7695610000000 2.4001890000000

F -2.8303670000000 -1.9423480000000 4.3776610000000

H 1.0177680000000 -0.8664360000000 3.7023820000000

H 0.6443870000000 -3.9042810000000 1.6107400000000

H -1.0734030000000 -3.7610140000000 1.3602710000000

H 1.7140160000000 -2.6495550000000 -2.7375240000000

H 4.1052790000000 -3.0524600000000 -3.2475680000000

H 5.7503060000000 -3.3082870000000 -1.3942070000000

H 4.9805190000000 -3.1682590000000 0.9685000000000

H 2.6081800000000 -2.7591280000000 1.4802430000000

H 0.9409870000000 -5.2791660000000 -0.2928640000000

H 0.1648930000000 -7.2338920000000 -1.5926800000000

H -1.6135570000000 -6.9671120000000 -3.3136690000000

H -2.6061670000000 -4.7226800000000 -3.7306450000000

H -1.8314840000000 -2.7614180000000 -2.4283110000000

end

basis
Ir library cc-pVDZ-pp rel
P library 6-31G**
C library 6-31G**
F library 6-31G**
H library 6-31G**
N library 6-31G**
end

DFT
XC B3LYP
END

RELATIVISTIC
ZORA ON
END

task DFT energy

Error Message:

Superposition of Atomic Density Guess
     -------------------------------------




     charge =      77.0 Ir (Iridium)



     symmetry species            s     p     d     f

     number of basis functions =22    19    11     1

     number of cont. functions = 4     4     3     1

     number of closed shells   = 6     4     2     1

     number of open shells     = 0     0     1     0

     open shell occupation     = 0     0     7     0

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

atomscf:atomd: error in atom scf                   0

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

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

 current input line :

  101: task DFT energy

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

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

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:atomscf:atomd: error in atom scf:Received an Error in Communication

MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.


mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

 Process name: [[8875,1],0]

 Exit code:    255

Forum Regular
9:20:00 AM PDT - Tue, Jun 30th 2015
Your problem is that you have specified a basis set for iridium that is designed for a pseudo-potential but have not included a pseudo-potential in your input. If you want to use cc-pVDZ-pp then you need to add

ecp
Ir library cc-pVDZ-pp
end

to your input. Otherwise you need to select an all-electron basis set for iridium.

Best,
Sean

Clicked A Few Times
12:02:32 AM PDT - Wed, Jul 1st 2015
Hi Sean,

Thank you for the suggestion.

-Tatireddy


Forum >> NWChem's corner >> Running NWChem