running abacus with problem

[kenan12138]

Details

please check the screen print file in the abacus_cal.zip

some error happened in the progress.
env:
Ubuntu 22.04.4 LTS (Jammy Jellyfish)
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)
mpiicc for the Intel(R) MPI Library 2021.11 Build 20231005 for Linux* OS

Have you read FAQ on the online manual http://abacus.deepmodeling.com/en/latest/community/faq.html

• Yes, I have read the FAQ part on online manual.

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[QuantumMisaka]

@kenan12138 Thanks for your issue!
Your INPUT includes:

pseudo_dir              /mnt/SG15-Version1p0_Pseudopotential/SG15_ONCV_v1.0_upf

Please edit it to the directory format

pseudo_dir              /mnt/SG15-Version1p0_Pseudopotential

Also, the error message for wrong pseudopotential is confusing, in the warning.log:

In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_BETA.3> block.
 In SCAN_END, can't find: </PP_BETA.4> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_BETA.3> block.
 In SCAN_END, can't find: </PP_BETA.4> block.
 In SCAN_END, can't find: </PP_BETA.5> block.
 In SCAN_END, can't find: </PP_BETA.6> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_BETA.3> block.
 In SCAN_END, can't find: </PP_BETA.4> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_BETA.3> block.
 In SCAN_END, can't find: </PP_BETA.4> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_BETA.3> block.
 In SCAN_END, can't find: </PP_BETA.4> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 In SCAN_END, can't find: </PP_R> block.
 In SCAN_END, can't find: </PP_RAB> block.
 In SCAN_END, can't find: </PP_MESH> block.
 In SCAN_END, can't find: </PP_LOCAL> block.
 In SCAN_END, can't find: </PP_BETA.1> block.
 In SCAN_END, can't find: </PP_BETA.2> block.
 In SCAN_END, can't find: </PP_RHOATOM> block.
 AUTO_SET NBANDS to 82
 AUTO_SET NBANDS to 82

All the information indicates that there is something wrong with pseudopotential, but not specific.
@kirk0830 @mohanchen Any comments?

Also, Why you choose ecutwfc 60 and other INPUT setting for you calculation？ @kenan12138

[kirk0830]

seems at least the pseudopotential is not correctly read. I will try tomorrow

[kirk0830]

@kenan12138 @QuantumMisaka I can run the case smoothly with provided input. But there seems something wrong with the pseudopotential read-in procedure. The SCAN_END is quite an out-dated function, considering replace it with something new.

[kenan12138]

#5534 (comment)
I am a beginner in ABACUS. This INPUT file INPUT_PARAMETERS was set up by my supervisor:

suffix dipole_job2
pseudo_dir /mnt/SG15-Version1p0_Pseudopotential/SG15_ONCV_v1.0_upf
orbital_dir /mnt/SG15-Version1p0__StandardOrbitals-Version2p0_tdzp
#basis
basis_type lcao
#accuracy
ecutwfc 60
scf_nmax 100
scf_thr 1e-8
#Molecular_dynamics
calculation scf #md #scf
#md_type nve
#md_nstep 1
#md_dt 0.0024
#md_tfirst 0
#tddft
#esolver_type tddft
#output
out_dipole 1
out_stru 1
out_chg 1
out_bandgap 1
dft_functional hse
exx_separate_loop 0
exx_pca_threshold 0.0001
exx_c_threshold 0.0001
exx_dm_threshold 0.0001
exx_ccp_rmesh_times 1.0

My goal is to calculate the HOMO-LUMO gap of a molecule. However, when I calculated the gap using the PBE functional, the result differed significantly from the gaps obtained from Gaussian and ORCA. Therefore, I used this parameter set in the INPUT file to perform the calculation.

When using ABACUS 3.8.2, I encountered the error described above. I will now follow your suggestions and try running the calculation again. Thank you very much for your help!

[kenan12138]

@kenan12138 @QuantumMisaka I can run the case smoothly with provided input. But there seems something wrong with the pseudopotential read-in procedure. The SCAN_END is quite an out-dated function, considering replace it with something new.

Thank you for your reply. Could you please explain in more detail how to proceed with "considering replace it with something new"? What specific steps should be taken? I greatly appreciate your guidance.

[kirk0830]

@kenan12138 @QuantumMisaka I can run the case smoothly with provided input. But there seems something wrong with the pseudopotential read-in procedure. The SCAN_END is quite an out-dated function, considering replace it with something new.

Thank you for your reply. Could you please explain in more detail how to proceed with "considering replace it with something new"? What specific steps should be taken? I greatly appreciate your guidance.

@kenan12138 Hi, that is for ABACUS developers. I guess those warning may be printed merely by mistake, so there is something should be updated in ABACUS, but if you have some physical reference data, you can make comparison and check if your calculation with pseudopotential is reliable.

[kenan12138]

abacus_cal2478.zip
abacus_cal2478_siingle_C.zip
Hello, I used ABACUS 3.6.3 for my calculations and found that when calculating a single atom, the calculation can run to completion, although it does not converge. However, when calculating a complete molecule, it runs for a few steps (performing better than version 3.8.2) but still terminates. Could this be a memory issue?

[QuantumMisaka]

@kenan12138 For single atom calculation, you need some specific INPUT setting ,refer to #5009

[sunliang98]

@kenan12138 @QuantumMisaka I can run the case smoothly with provided input. But there seems something wrong with the pseudopotential read-in procedure. The SCAN_END is quite an out-dated function, considering replace it with something new.

Thank you for your reply. Could you please explain in more detail how to proceed with "considering replace it with something new"? What specific steps should be taken? I greatly appreciate your guidance.

@kenan12138 Hi, that is for ABACUS developers. I guess those warning may be printed merely by mistake, so there is something should be updated in ABACUS, but if you have some physical reference data, you can make comparison and check if your calculation with pseudopotential is reliable.

These warnings were triggered in error and do not affect the result. I will fix them.

[kenan12138]

@kenan12138 @QuantumMisaka I can run the case smoothly with provided input. But there seems something wrong with the pseudopotential read-in procedure. The SCAN_END is quite an out-dated function, considering replace it with something new.

Thank you for your reply. Could you please explain in more detail how to proceed with "considering replace it with something new"? What specific steps should be taken? I greatly appreciate your guidance.

@kenan12138 Hi, that is for ABACUS developers. I guess those warning may be printed merely by mistake, so there is something should be updated in ABACUS, but if you have some physical reference data, you can make comparison and check if your calculation with pseudopotential is reliable.

These warnings were triggered in error and do not affect the result. I will fix them.

The issue has been resolved. Previously, I used the command export OMP_NUM_THREADS=2 followed by mpirun -n 4 abacus, which caused an error. Now, I've used export OMP_NUM_THREADS=8 and mpirun -n 1 abacus, and it runs without any issues. Thanks everyone for your replies.