Tests: We need update some reference data of integrated tests

[WHUweiqingzhou]

Describe the Testing Issue

After #4493, warnings are not allowed anymore in CI tests. However, #4493 only changed threshold to make CI pass, instead of changing refs themselves. At that time, there were 64 warnings/fatal errors.

The List:

Warning: NG]    61 test cases out of 1227 failed.
1: 101_PW_15_lowz
1: 101_PW_15_paw
1: 101_PW_blps_pseudopots
1: 101_PW_upf201_uspp_NaCl
1: 101_PW_Coulomb
1: 102_PW_BPCG
1: 103_PW_CF_CS_S1_smallg
1: 103_PW_CF_CS_S2_smallg
1: 104_PW_NC_magnetic
1: 105_PW_FD_smearing
1: 105_PW_GA_smearing
1: 107_PW_outWfcR
1: 108_PW_RE
1: 108_PW_RE_MB
1: 109_PW_CR_fix_a
1: 109_PW_CR_fix_ab
1: 109_PW_CR_fix_abc
1: 109_PW_CR_fix_ac
1: 109_PW_CR_fix_b
1: 109_PW_CR_fix_bc
1: 109_PW_CR_fix_c
1: 109_PW_CR_moveatoms
1: 110_PW_SY_symmetry_LiRh
1: 111_PW_elec_add
1: 111_PW_elec_minus
1: 111_PW_S2_elec_add
1: 111_PW_S2_elec_minus
1: 115_PW_sol_H2
1: 116_PW_scan_Si2_nspin2
1: 120_PW_KP_MD_NPT
1: 120_PW_KP_MD_NVT
1: 133_PW_DJ_PK
1: 150_PW_15_CR_VDW3
1: 170_PW_MD_1O
1: 170_PW_MD_2O
1: 180_PW_SDFT_10S_M
1: 180_PW_SDFT_10S_P
1: 181_PW_SDFT_5D10S
1: 182_PW_SDFT_ALL
1: 183_PW_MD_SDFT_10S
1: 183_PW_MD_SDFT_5D10S
1: 183_PW_MD_SDFT_ALL
1: 184_PW_BNDPAR_SDFT_10S
1: 184_PW_BNDPAR_SDFT_5D10S
1: 184_PW_KPAR_SDFT_ALL
1: 185_PW_SDFT_10D10S_METHD2
1: 185_PW_SDFT_10S_METHD2
1: 186_PW_SDOS_10D10S
1: 186_PW_SNLKG_10D10S
1: 250_NO_KP_CR_VDW3ABC
1: 281_NO_KP_HSE
1: 286_NO_KP_CR_HSE
1: 384_NO_GO_S1_HSE_loop0_PU
1: 601_NO_TDDFT_H2_restart
1: 601_NO_TDDFT_CO
1: 601_NO_TDDFT_CO_occ
1: 803_PW_LT_bcc
1: 806_PW_LT_st
1: 802_PW_LT_fcc
1: 807_PW_LT_bct
1: 810_PW_LT_fco

For GPU tests:

102_PW_CG_GPU
102_PW_DA_davidson_GPU
102_PW_BPCG_GPU

We now need each relevant developer to claim their respective test cases and confirm whether the current functionality is normal. After confirmation, the threshold needs to be lowered to the following levels:

threshold 0.0000001
force_threshold 0.0001 
stress_threshold 0.001
fatal_threshold 1

Additional Context

No response

Task list for Issue attackers (only for developers)

• [ ] Understand the testing issue described by the developer.
• [ ] Review the specific test case, expected and actual results, and any error messages.
• [ ] Identify the root cause of the test failure or issue.
• [ ] If a possible solution is suggested, evaluate its feasibility and effectiveness.
• [ ] Implement a fix for the test failure or issue, or create a new test case if needed.
• [ ] Verify that the fix resolves the testing issue and the test case passes.
• [ ] Review and update any relevant documentation, such as test plans or user guides.
• [ ] Ensure the testing issue is resolved and close the ticket.
• [ ] Share any lessons learned or best practices with the team to prevent similar issues in the future.