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标题: 计算含有Pr的原子簇ORCA报错signal 6 (Aborted). [打印本页]
作者
Author: DoorBell    时间: 2019-4-22 18:13
标题: 计算含有Pr的原子簇ORCA报错signal 6 (Aborted).
各位老师好！
在ORCA计算含有重元素Pr的原子簇时总是崩溃退出，已经调整了输入文件的基组和收敛标准但没什么用。。。
ORCA4.1.1和4.1.2都有这个问题，对应用的都是OpenMPI3.1.3

输入文件：
  1. ! HF

  3. ! NODIIS SlowConv

  5. %scf
  6.     maxIter 1000
  7.     MaxIntMem 81920
  8.     MaxDisk 1024000
  9. end

  11. %basis
  12.     basis "def2-TZVP"
  13. end

  15. %maxCore 5120

  17. %pal
  18.     nProcs 16
  19. end

  21. %output
  22.     XYZFile true
  23. end

  25. * xyz -1 5
  26. Pr                -0.95184600   -0.00034200    0.00000000    newGTO "SARC-DKH-TZVP" end
  27. ...
  28. *
复制代码
输出文件：
  1. ...
  2. ------------------------------
  3. INITIAL GUESS: MODEL POTENTIAL
  4. ------------------------------
  5. Loading Hartree-Fock densities                     ... done
  6.   calling /work/chem/Software/ORCA_411/orca HF-1-5-PrB8_atom59.inp > HF-1-5-PrB8_atom59.out in order to generate an atomic fitting density for atom 0 (Pr with ECP) on-the-fly...
  7.     atom 0 (Pr), assumed electronic state with S=4: 1s2 2s2 2p6 3s2 3p6 4s2 3d10 4p6 5s2 4d10 5p6 6s2 4f3           ... [file orca_scf/scfguess.cpp, line 4720, Process 0]:
  8. Error encountered when trying to calculate the atomic fitting density!

  10. ORCA finished by error termination in SCF
  11. Calling Command: mpirun -np 16  /work/chem/Software/ORCA_411/orca_scf_mpi HF-1-5-PrB8.gbw b HF-1-5-PrB8
  12. [file orca_tools/qcmsg.cpp, line 458]:
  13.   .... aborting the run
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报错信息：
  1. [file orca_scf/scfguess.cpp, line 4720, Process 0]:
  2. Error encountered when trying to calculate the atomic fitting density!
  3. [r13n40:58358] *** Process received signal ***
  4. [r13n40:58358] Signal: Aborted (6)
  5. [r13n40:58358] Signal code:  (-6)
  6. [r13n40:58358] [ 0] /lib64/libc.so.6(+0x36280)[0x2b7e0a9e2280]
  7. [r13n40:58358] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b7e0a9e2207]
  8. [r13n40:58358] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b7e0a9e38f8]
  9. [r13n40:58358] [ 3] /work/chem/Software/ORCA_411/orca_scf_mpi[0x7954d2]
  10. [r13n40:58358] [ 4] /work/chem/Software/ORCA_411/orca_scf_mpi[0x50f23c]
  11. [r13n40:58358] [ 5] /work/chem/Software/ORCA_411/orca_scf_mpi[0x462a60]
  12. [r13n40:58358] [ 6] /work/chem/Software/ORCA_411/orca_scf_mpi[0x46e65a]
  13. [r13n40:58358] [ 7] /work/chem/Software/ORCA_411/orca_scf_mpi[0x47570c]
  14. [r13n40:58358] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b7e0a9ce3d5]
  15. [r13n40:58358] [ 9] /work/chem/Software/ORCA_411/orca_scf_mpi[0x461e11]
  16. [r13n40:58358] *** End of error message ***
  17. --------------------------------------------------------------------------
  18. Primary job  terminated normally, but 1 process returned
  19. a non-zero exit code. Per user-direction, the job has been aborted.
  20. --------------------------------------------------------------------------
  21. --------------------------------------------------------------------------
  22. mpirun noticed that process rank 0 with PID 0 on node r13n40 exited on signal 6 (Aborted).
  23. --------------------------------------------------------------------------
  24. [file orca_tools/qcmsg.cpp, line 458]:
  25.   .... aborting the run
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还请各位老师能不吝赐教！非常感谢！


作者
Author: sobereva    时间: 2019-4-22 18:17
换个初猜方式再试

PS：你不会真想用HF算吧
作者
Author: DoorBell    时间: 2019-4-22 19:11
sobereva 发表于 2019-4-22 18:17
换个初猜方式再试

PS：你不会真想用HF算吧

非常感谢sob老师！

在%scf加入Guess HCore之后可以计算了，不过就是初猜超级烂，迭代一次能量能下降几十个Eh。
另外HF就是先做一次粗略的计算拿产生的.gbw做初猜用的。
作者
Author: chrinide    时间: 2019-4-22 19:54
你输入文件有问题，用 def2-TZVP计算的时候 Pr元素是默认带 def2-ECP 的赝势计算，随后你将 Pr元素换用全电子 SARC-DKH-TZVP 基组，你让ORCA懵逼了，到底是做赝势ECP计算，还是全电子DKH标量相对论计算，知道不，所以ORCA挂逼了!!!!!!!

解决方法一：直接def2-TZVP的赝势计算，算含Pr的肯定没问题，别再瞎改用全电子基组

解决方法二：改用全电子标量相对论计算，加关键词DKH或者ZORA，用相关的全电子基组
作者
Author: DoorBell    时间: 2019-4-22 20:52
chrinide 发表于 2019-4-22 19:54
你输入文件有问题，用 def2-TZVP计算的时候 Pr元素是默认带 def2-ECP 的赝势计算，随后你将 Pr元素换用全电 ...

呃，不过SARC-DKH-TZVP是我因为崩溃而加上的
不加SARC-DKH-TZVP的错误报告：
  1. ------------------------------
  2. INITIAL GUESS: MODEL POTENTIAL
  3. ------------------------------
  4. Loading Hartree-Fock densities                     ... done
  5.   calling /work/chem/Software/ORCA_411/orca HF-1-5-PrB8_atom59.inp > HF-1-5-PrB8_atom59.out in order to generate an atomic fitting density for atom 0 (Pr with ECP) on-the-fly...
  6.     atom 0 (Pr), assumed electronic state with S=4: 1s2 2s2 2p6 3s2 3p6 4s2 3d10 4p6 5s2 4d10 5p6 6s2 4f3           ... [file orca_scf/scfguess.cpp, line 4720, Process 0]:
  7. Error encountered when trying to calculate the atomic fitting density!

  9. ORCA finished by error termination in SCF
  10. Calling Command: mpirun -np 16  /work/chem/Software/ORCA_411/orca_scf_mpi HF-1-5-PrB8.gbw b HF-1-5-PrB8
  11. [file orca_tools/qcmsg.cpp, line 458]:
  12.   .... aborting the run
复制代码
  1. [file orca_scf/scfguess.cpp, line 4720, Process 0]:
  2. Error encountered when trying to calculate the atomic fitting density!
  3. [r13n41:339870] *** Process received signal ***
  4. [r13n41:339870] Signal: Aborted (6)
  5. [r13n41:339870] Signal code:  (-6)
  6. [r13n41:339870] [ 0] /lib64/libc.so.6(+0x36280)[0x2b1d0b237280]
  7. [r13n41:339870] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b1d0b237207]
  8. [r13n41:339870] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b1d0b2388f8]
  9. [r13n41:339870] [ 3] /work/chem/Software/ORCA_411/orca_scf_mpi[0x7954d2]
  10. [r13n41:339870] [ 4] /work/chem/Software/ORCA_411/orca_scf_mpi[0x50f23c]
  11. [r13n41:339870] [ 5] /work/chem/Software/ORCA_411/orca_scf_mpi[0x462a60]
  12. [r13n41:339870] [ 6] /work/chem/Software/ORCA_411/orca_scf_mpi[0x46e65a]
  13. [r13n41:339870] [ 7] /work/chem/Software/ORCA_411/orca_scf_mpi[0x47570c]
  14. [r13n41:339870] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b1d0b2233d5]
  15. [r13n41:339870] [ 9] /work/chem/Software/ORCA_411/orca_scf_mpi[0x461e11]
  16. [r13n41:339870] *** End of error message ***
  17. --------------------------------------------------------------------------
  18. Primary job  terminated normally, but 1 process returned
  19. a non-zero exit code. Per user-direction, the job has been aborted.
  20. --------------------------------------------------------------------------
  21. --------------------------------------------------------------------------
  22. mpirun noticed that process rank 0 with PID 0 on node r13n41 exited on signal 6 (Aborted).
  23. --------------------------------------------------------------------------
  24. [file orca_tools/qcmsg.cpp, line 458]:
  25.   .... aborting the run
复制代码
作者
Author: chrinide    时间: 2019-4-22 21:00
DoorBell 发表于 2019-4-22 20:52
呃，不过SARC-DKH-TZVP是我因为崩溃而加上的
不加SARC-DKH-TZVP的错误报告：

你发输入文件给我瞧瞧吧
作者
Author: DoorBell    时间: 2019-4-23 11:24
chrinide 发表于 2019-4-22 21:00
你发输入文件给我瞧瞧吧

就是最上面那个文件直接删掉SARC-DKH-TZVP那一句
作者
Author: chrinide    时间: 2019-4-23 14:51
DoorBell 发表于 2019-4-23 11:24
就是最上面那个文件直接删掉SARC-DKH-TZVP那一句

坐标给的不全吧
作者
Author: DoorBell    时间: 2019-11-11 14:18
最近这个问题又出现了，经过仔细的观察，问题产生的原因是$orcadir/orca $jobName_atomXX.inp > $jobName_atomXX.out这一步没有成功运行，具体原因不详，但更改运行ORCA的命令（例如加入&或者用nohup等）有一定几率避免这个问题



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