Error calculating polarizability for hydrogen α (i ω) exit code 139

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etorres
Posts: 7
Joined: 26 Sep 2018, 13:00
First name(s): Estefania
Last name(s): Torres Avila
Affiliation: University of Cadiz
Country: Spain

Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by etorres » 15 Oct 2018, 13:10

Hi,

I am interested in calculating polarizability at imaginary frequencies for free atoms. I had no problem with carbon, oxygen, helium, ... but when I use the same procedure for the hydrogen atom, I get the following error on terminal:

*******************************************
**** OUTPUT FROM DALTON SHELL SCRIPT
*******************************************

DALTON release Dalton2016.2 (2016)

Invocation: /home/software/dalton/build/dalton calculation_alpha.dal hydrogen _aug-cc-pvqz.mol

lun oct 15 14:18:35 CEST 2018

Calculation: calculation_alpha_hydrogen_aug-cc-pvqz (input files: calculatio n_alpha.dal and hydrogen_aug-cc-pvqz.mol)
PID : 8716
Input dir : /home/fany/calculos/daltoncalc/oxigeno_O4
Scratch dir: /tmp/DALTON_scratch_fany/calculation_alpha_hydrogen_aug-cc-pvqz_ 8716


INFO : OMP_NUM_THREADS is not defined by the user, and default values will be a ssumed:
INFO : gnu and intel compilers defaults to all available cores,
INFO : whereas portland compilers defaults to one


DALTON: default work memory size used. 64000000

Work memory size (LMWORK+2): 64000002 = 488.28 megabytes; node 0

0: Directories for basis set searches:
/home/fany/calculos/daltoncalc/oxigeno_O4:/home/software/dalton/build/basis

NOTE: 1 informational messages have been issued.
Check output, result, and error files for "INFO".

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x14c23fd972da in ???
#1 0x14c23fd96503 in ???
#2 0x14c23f1e9f1f in ???
#3 0x14c240a2b518 in ???
#4 0x55f8d0c2c2f7 in ???
#5 0xffffffffffffffff in ???
/home/software/dalton/build/dalton: línea 722: 8740 Violación de segmento (`core' generado) $DALTON_EXE
Error in /home/software/dalton/build/dalton.x, exit code 139

SERIOUS ERROR:
DALTON finished with non-zero exit code: 139

File list in scratch directory:

total 3456
-rw-rw-r-- 1 fany fany 176 oct 15 14:18 RSP_DIAG
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_AB
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_AS
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_E1RED
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_E2RED
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_SB
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_SRED
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 ABS_SS
-rw-rw-r-- 1 fany fany 16 oct 15 14:18 ABSVECS
-rw-rw-r-- 1 fany fany 40748 oct 15 14:18 DALTON.OUT
-rw-rw-r-- 1 fany fany 17036 oct 15 14:18 MODRCINT
-rw-rw-r-- 1 fany fany 210924 oct 15 14:18 MOTWOINT
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 RSP_BVEC
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 RSP_SVEC
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 RSPVEC
-rw-rw-r-- 1 fany fany 3000 oct 15 14:18 LUINDF
-rw-rw-r-- 1 fany fany 145 oct 15 14:18 DALTON.STAT
-rw-rw-r-- 1 fany fany 2473 oct 15 14:18 molden.inp
-rw-rw-r-- 1 fany fany 187 oct 15 14:18 molden_MOS.tmp
-rw-rw-r-- 1 fany fany 19816 oct 15 14:18 SIRIFC
-rw-rw-r-- 1 fany fany 4456 oct 15 14:18 SIRIUS.RST
-rw-rw-r-- 1 fany fany 980600 oct 15 14:18 DALTON.QUAD
-rw-rw-r-- 1 fany fany 185968 oct 15 14:18 AOPROPER
-rw-rw-r-- 1 fany fany 1904108 oct 15 14:18 AOTWOINT
-rw-rw-r-- 1 fany fany 3059 oct 15 14:18 DALTON.CM
-rw-rw-r-- 1 fany fany 91340 oct 15 14:18 AOONEINT
-rw-rw-r-- 1 fany fany 1990 oct 15 14:18 AMFI_MNF.INP
-rw-rw-r-- 1 fany fany 2441 oct 15 14:18 AMFI_SYMINFO.TXT
-rw-rw-r-- 1 fany fany 2455 oct 15 14:18 DALTON.BAS
-rw-rw-r-- 1 fany fany 3077 oct 15 14:18 LUSH.BAS
-rw-rw-r-- 1 fany fany 105 oct 15 14:18 midasifc.cartrot
-rw-rw-r-- 1 fany fany 332 oct 15 14:18 firstsym.wrl
-rw-rw-r-- 1 fany fany 82 oct 15 14:18 midasifc.cartorig
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 DALTON.PROP
-rw-rw-r-- 1 fany fany 0 oct 15 14:18 midasifc.prop
-rw-rw-r-- 1 fany fany 156 oct 15 14:18 DALTON.INP
-rw-rw-r-- 1 fany fany 111 oct 15 14:18 MOLECULE.INP
3,4M .
calculation_alpha_hydrogen_aug-cc-pvqz.tar.gz has been copied to /home/fany/calculos/daltoncalc/oxigeno_O4
----------------------------------------------------------
WARNING for ERROR (DALTON program stopped with exit code 139)
- THEREFORE scratch directory /tmp/DALTON_scratch_fany/calculation_alpha_hydrogen_aug-cc-pvqz_8716 is not deleted
by this script so you may restart the calculation, if possible
( /tmp/DALTON_scratch_fany/calculation_alpha_hydrogen_aug-cc-pvqz_8716 may be deleted by your queueing system )
- REMEMBER to delete /tmp/DALTON_scratch_fany/calculation_alpha_hydrogen_aug-cc-pvqz_8716 yourself !!!

----------------------------------------------------------
2 informational messages have been issued by DALTON,
output from 'grep -n INFO' (max 10 lines):
693: INFO: E(LUMO) - E(HOMO) small or negative.
724: INFO: Sorry, plot of MOs with Molden is only implemented for spherical GTOs

lun oct 15 14:18:38 CEST 2018
*****************************************
I attach the input and output files, and also the scratch directory.

Thank you in advance for the help.
Attachments
calculation_alpha_hydrogen_aug-cc-pvqz.tar.gz
(8.85 KiB) Downloaded 43 times
calculation_alpha_hydrogen_aug-cc-pvqz.out
(39.79 KiB) Downloaded 53 times
hydrogen_aug-cc-pvqz.mol
(111 Bytes) Downloaded 47 times
calculation_alpha_hydrogen_aug-cc-pvqz_8716.rar
(459.69 KiB) Downloaded 46 times
calculation_alpha.dal
(156 Bytes) Downloaded 48 times

kennethruud
Posts: 253
Joined: 27 Aug 2013, 16:42
First name(s): Kenneth
Last name(s): Ruud
Affiliation: UiT The Arctic University of Norway
Country: Norway

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by kennethruud » 15 Oct 2018, 14:24

The reason for the crash is no doubt that your trying to calculate an open-shell system. However, this also suggests that the calculations you have done for oxygen and carbon are probably been calculated as closed-shell system, thus not representative of the atoms you want to study. Dalton has limited functionality for open-shell systems.


Best regards,

Kenneth

hjaaj
Posts: 317
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by hjaaj » 15 Oct 2018, 15:49

I think that this is a specific problem for a one-electron system with no doubly-occupied orbitals - a special case which has not been thoroughly tested.

-- Hans Jørgen.

etorres
Posts: 7
Joined: 26 Sep 2018, 13:00
First name(s): Estefania
Last name(s): Torres Avila
Affiliation: University of Cadiz
Country: Spain

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by etorres » 17 Oct 2018, 10:58

Thank you for your fast and helpful answers.

From your answers and another topic in the forum (viewtopic.php?f=9&t=609), I understand that currently it is not possible to perform a DFT calculation for an open-shell system. Is this correct?

I have tried to run it with MP2 method, and I got reasonable results for the hydrogen atom (I attach output file in case you would like to check it). I could use this method for my research, but as Kenneth pointed me out, I hadn't realized my calculations for oxygen and carbon were for a closed-shell system. I have been reading the manual about this issue, but I don't get to run a calculation with the spin multiplicity that I want. I checked that this input.dal file works:
**DALTON INPUT
.RUN RESPONSE
**WAVE FUNCTIONS
.HF
.MP2
*CONFIGURATION INPUT
.SPIN MULTIPLICITY
1

**RESPONSE
*ABSORP
.ALPHA
.IMAG F
.FREQ I
0.0 3.00 0.10
**END OF DALTON INPUT
But, when I change to the spin multiplicity for a free oxygen atom:
**DALTON INPUT
.RUN RESPONSE
**WAVE FUNCTIONS
.HF
.MP2
*CONFIGURATION INPUT
.SPIN MULTIPLICITY
3

**RESPONSE
*ABSORP
.ALPHA
.IMAG F
.FREQ I
0.0 3.00 0.10
**END OF DALTON INPUT
I get the following error message in console:

Code: Select all

   *******************************************
   **** OUTPUT FROM DALTON SHELL SCRIPT
   *******************************************

   DALTON release Dalton2016.2 (2016)

   Invocation: /home/software/dalton/build/dalton calculation_alpha.dal oxygen_aug-cc-pvqz.mol

   mié oct 17 11:33:22 CEST 2018

   Calculation: calculation_alpha_oxygen_aug-cc-pvqz  (input files: calculation_alpha.dal and oxygen_aug-cc-pvqz.mol)
   PID        : 19308
   Input dir  : /home/fany/calculos/daltoncalc/oxigeno_O4_multiplicidad3
   Scratch dir: /tmp/DALTON_scratch_fany/calculation_alpha_oxygen_aug-cc-pvqz_19308


 INFO : OMP_NUM_THREADS is not defined by the user, and default values will be assumed:
 INFO : gnu and intel compilers defaults to all available cores,
 INFO : whereas portland compilers defaults to one


 DALTON: default work memory size used.            64000000

 Work memory size (LMWORK+2):    64000002 =  488.28 megabytes; node   0

   0: Directories for basis set searches:
     /home/fany/calculos/daltoncalc/oxigeno_O4_multiplicidad3:/home/software/dalton/build/basis


                        1 ERROR(s) occured in SIRIUS input processing.
                    Program cannot continue.
                    Correct ERROR(s) and be welcome back

 Node      0:  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
 *** ERROR *** SIRIUS input errors.

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x14b094b5f2da in ???
#1  0x14b094b5e503 in ???
#2  0x14b093fb1f1f in ???
#3  0x5601a7e929b0 in ???
#4  0x5601a7eb466f in ???
#5  0x5601a816c5b9 in ???
#6  0x5601a8170f12 in ???
#7  0x5601a8106783 in ???
#8  0x5601a75f440d in ???
#9  0x5601a840de4b in ???
#10  0x5601a844c5f8 in ???
#11  0x5601a8451995 in ???
#12  0x5601a845ad87 in ???
#13  0x5601a75f623d in ???
#14  0x5601a75ec09d in ???
#15  0x5601a75eb0fe in ???
#16  0x14b093f94b96 in ???
#17  0x5601a75eb159 in ???
#18  0xffffffffffffffff in ???
/home/software/dalton/build/dalton: línea 722: 19332 Instrucción ilegal     (`core' generado) $DALTON_EXE
Error in /home/software/dalton/build/dalton.x, exit code 132

SERIOUS ERROR:
DALTON finished with non-zero exit code: 132

File list in scratch directory:

total 24328
-rw-rw-r-- 1 fany fany     3065 oct 17 11:33 DALTON.CM
-rw-rw-r-- 1 fany fany    29603 oct 17 11:33 DALTON.OUT
-rw-rw-r-- 1 fany fany    17440 oct 17 11:33 LUINDF
-rw-rw-r-- 1 fany fany   676312 oct 17 11:33 AOPROPER
-rw-rw-r-- 1 fany fany 23987252 oct 17 11:33 AOTWOINT
-rw-rw-r-- 1 fany fany   118852 oct 17 11:33 AOONEINT
-rw-rw-r-- 1 fany fany     4121 oct 17 11:33 AMFI_MNF.INP
-rw-rw-r-- 1 fany fany     4541 oct 17 11:33 AMFI_SYMINFO.TXT
-rw-rw-r-- 1 fany fany     4577 oct 17 11:33 DALTON.BAS
-rw-rw-r-- 1 fany fany     6449 oct 17 11:33 LUSH.BAS
-rw-rw-r-- 1 fany fany      105 oct 17 11:33 midasifc.cartrot
-rw-rw-r-- 1 fany fany      332 oct 17 11:33 firstsym.wrl
-rw-rw-r-- 1 fany fany       82 oct 17 11:33 midasifc.cartorig
-rw-rw-r-- 1 fany fany     4957 oct 17 11:33 molden.inp
-rw-rw-r-- 1 fany fany        0 oct 17 11:33 molden_MOS.tmp
-rw-rw-r-- 1 fany fany        0 oct 17 11:33 DALTON.PROP
-rw-rw-r-- 1 fany fany        0 oct 17 11:33 DALTON.STAT
-rw-rw-r-- 1 fany fany        0 oct 17 11:33 midasifc.prop
-rw-rw-r-- 1 fany fany      111 oct 17 11:33 MOLECULE.INP
-rw-rw-r-- 1 fany fany      174 oct 17 11:33 DALTON.INP
24M     .
calculation_alpha_oxygen_aug-cc-pvqz.tar.gz has been copied to /home/fany/calculos/daltoncalc/oxigeno_O4_multiplicidad3
----------------------------------------------------------
WARNING for ERROR  (DALTON program stopped with exit code 132)
- THEREFORE scratch directory /tmp/DALTON_scratch_fany/calculation_alpha_oxygen_aug-cc-pvqz_19308 is not deleted
  by this script so you may restart the calculation, if possible
  ( /tmp/DALTON_scratch_fany/calculation_alpha_oxygen_aug-cc-pvqz_19308 may be deleted by your queueing system )
- REMEMBER to delete /tmp/DALTON_scratch_fany/calculation_alpha_oxygen_aug-cc-pvqz_19308 yourself !!!

Output from 'grep -n ERROR' :
687: SIRRDI, input ERROR. Number of active electrons is not consistent with spin multiplicity.
690:                        1 ERROR(s) occured in SIRIUS input processing.
692:                    Correct ERROR(s) and be welcome back
713:  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
717: Reason: *** ERROR *** SIRIUS input errors.

   mié oct 17 11:33:22 CEST 2018
   *****************************************
I suppose that I am not writing the input file correctly, but I have serious trouble for solving this. It would be very helpful if you could help me. I also attach the output file for calculations with spin multiplicity 1 and spin multiplicity 3.


Thank you in advance. Best regards,
Estefanía
Attachments
calculation_alpha_oxygen_aug-cc-pvqz.out
Spin multiplicity 3
(27.68 KiB) Downloaded 48 times
calculation_alpha_oxygen_aug-cc-pvqz.out
Spin multiplicity 1
(95.08 KiB) Downloaded 49 times
calculation_alpha_hydrogen_aug-cc-pvqz.out
MP2/aug-cc-pVQZ calculation
(74.17 KiB) Downloaded 47 times

xiongyan21
Posts: 164
Joined: 24 Sep 2014, 08:36
First name(s): yan
Last name(s): xiong
Affiliation: CENTRAL CHINA NORMAL UNIVERSITY
Country: China

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by xiongyan21 » 17 Oct 2018, 14:51

The first as well as the the third mp2 inputs can finish but the results might be wrong in terms of Prof. Ruud's analysis, while the DFT one, with the code modified according to Prof. Jessen's proposal on the forum, and the second mp2 one failed.
Perhaps you could resort to GAMESS to deal with the imaginary frequencies, but I am not sure whether your purpose could be realized using an ROHF reference, especially in the triplet case, because those meeting your requirements may not be implemented.

For the third one, I got quite different results using DALTON2016.2 and the warning of 648:@ INFO: All open shell orbitals are frozen in the MP2 calculation
Last edited by xiongyan21 on 19 Oct 2018, 11:48, edited 12 times in total.

hjaaj
Posts: 317
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by hjaaj » 17 Oct 2018, 16:37

For the hydrogen atom you can get the exact result with Hartree-Fock and you definitely do not want to run MP2 for the hydrogen atom.

The "*CONFIGURATION" input is for .MCSCF and is not used by .HF nor by .DFT.

Unrestricted DFT is not implemented in Dalton, restricted high-spin DFT is implemented. You need the ".SINGLY OCCUPIED" keyword in the SCF input to describe which orbitals should be singly occupied.

-- Hans Jørgen.

etorres
Posts: 7
Joined: 26 Sep 2018, 13:00
First name(s): Estefania
Last name(s): Torres Avila
Affiliation: University of Cadiz
Country: Spain

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by etorres » 23 Oct 2018, 18:03

xiongyan21 wrote:
17 Oct 2018, 14:51
The first as well as the the third mp2 inputs can finish but the results might be wrong in terms of Prof. Ruud's analysis, while the DFT one, with the code modified according to Prof. Jessen's proposal on the forum, and the second mp2 one failed.
Perhaps you could resort to GAMESS to deal with the imaginary frequencies, but I am not sure whether your purpose could be realized using an ROHF reference, especially in the triplet case, because those meeting your requirements may not be implemented.

For the third one, I got quite different results using DALTON2016.2 and the warning of 648:@ INFO: All open shell orbitals are frozen in the MP2 calculation
Hello Mr. Xiong. I also get the info message about open shell orbitals frozen, so I don't think this method is adequate for my purpose. I am commenting some issues about this below. About your different results, have you used the same file.mol ? We are running with the same Dalton version, so I think it should report identical results. If you could attach me your output file I could compare better.


For the hydrogen atom you can get the exact result with Hartree-Fock and you definitely do not want to run MP2 for the hydrogen atom.

The "*CONFIGURATION" input is for .MCSCF and is not used by .HF nor by .DFT.

Unrestricted DFT is not implemented in Dalton, restricted high-spin DFT is implemented. You need the ".SINGLY OCCUPIED" keyword in the SCF input to describe which orbitals should be singly occupied.

-- Hans Jørgen.
Thank you, Mr. Jørgen, I finally got to configure the system as I wanted. Nevertheless, I am not convinced by the reported results with MP2 and I think it is due to freezing open shell orbitals. I ran calculations about oxygen atom in singlet and triplet multiplicity, and energy value is higher for the triplet case. When I run with Hartree-Fock, energy results are as expected. (Attachment files: mp2_singlet, mp2_triplet, hf_singlet, hf_triplet)
Anyway, I finally decided to use DFT calculations for carbon and oxygen atoms. Although I got reasonable results, I also get the following warning message for triplet oxygen and triplet carbon:

Code: Select all

WARNING SIR_INTOPEN, old integral transformation not found as expected, ICASE = 2
 - ICASE = 1: MO integral file MOTWOINT does not exist
 - ICASE = 2: no MO integrals on MOTWOINT
 - ICASE = 3: transformation level on MOTWOINT not sufficient

 NSETUP: MO transformation level too low or no MO integral file found.
 NSETUP: generating MO 2-el. integral file. Transformation level:  4
What does this mean? Does it affect to the polarizabilities results? I found a topic in the forum in which this error was reported as a bug, but as that was three years ago I don't know if it was fixed (viewtopic.php?t=480). This message also appears in the HF calculations for triplet. (Attachment files: dft_singlet, dft_triplet, hf_singlet, hf_triplet)

Finally, I also wanted to ask if for HF open shell systems the program uses Pople-Nesbet equations? I have not found references to these equations in the manual.


Thank you very much in advance for all the support,
Best regards,
Estefania
Attachments
files.zip
(123.22 KiB) Downloaded 48 times

xiongyan21
Posts: 164
Joined: 24 Sep 2014, 08:36
First name(s): yan
Last name(s): xiong
Affiliation: CENTRAL CHINA NORMAL UNIVERSITY
Country: China

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by xiongyan21 » 24 Oct 2018, 05:46

Dear Prof. Estefania
The input used was from your calculation_alpha_hydrogen_aug-cc-pvqz.out attached here.

hjaaj
Posts: 317
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by hjaaj » 26 Oct 2018, 02:12

Dear Estefania,

The warning does not matter, the necessary integrals are generated as the last line of your quote says.

-- Hans Jørgen.

hjaaj
Posts: 317
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by hjaaj » 26 Oct 2018, 02:16

PS. In the newest master and the upcoming release Dalton2018, this inappropriate and confusing WARNING has been changed to an informational message.

hjaaj
Posts: 317
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: Error calculating polarizability for hydrogen α (i ω) exit code 139

Post by hjaaj » 26 Oct 2018, 02:19

PPS. No, the Pople-Nesbet-Berthier equations are for UHF. Dalton is doing ROHF.

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