sobEDA计算的输出结果中没有出现“Final results”的信息

〇66 · 发表于 Post on 2024-8-21 09:03:01

各位老师您好
我在学习“使用sobEDA和sobEDAw方法做非常准确、快速、方便、普适的能量分解分析”（http://bbs.keinsci.com/thread-39446-1-1.html）这个帖子后，
我想对大概一百多个原子组成的分子分成三个片段，进行能量分解的计算。

输入文件已上传，如下：

fragment.txt (31 Bytes, 下载次数 Times of downloads: 1)

sobEDA.sh (14.48 KB, 下载次数 Times of downloads: 1)

system.xyz (6.7 KB, 下载次数 Times of downloads: 0)

template.gjf (87 Bytes, 下载次数 Times of downloads: 4)

但是最后得到的输出文件result.txt里只有三个片段里各部分片段的能量，
而没有类似于例子中的“ Final results”这些结果，也没有Total interaction energy，E_rep，E_orb等能量的结果，如下：

result.txt (1.68 KB, 下载次数 Times of downloads: 6)

（例子H2O...NH3中输出文件result.txt里比我多出的部分：

*************************
***** Final results *****
*************************

Total interaction energy:    -7.18 kcal/mol

Physical components of interaction energy derived by sobEDA:
Electrostatic (E_els): -12.15 kcal/mol
Exchange (E_x):    -6.40 kcal/mol
Pauli repulsion (E_rep):    20.28 kcal/mol
Exchange-repulsion (E_xrep = E_x + E_rep):    13.88 kcal/mol
Orbital (E_orb):    -5.38 kcal/mol
DFT correlation (E_DFTc):    -2.70 kcal/mol
Dispersion correction (E_dc):    -0.83 kcal/mol
Coulomb correlation (E_c = E_DFTc + E_dc):    -3.53 kcal/mol）

想麻烦请教一下老师，我的输入文件中哪里有问题需要改正，哪些细节被我忽略掉了，感谢各位老师的解答！

其他：考虑到分子较大（需要计算100-170个原子左右），所以我选用的基组仅限于最低可接受级别，泛函基组的选用是b3lyp/6-31G*（就这个级别的一个分子都要跑三四个小时）。

dzdhp · 发表于 Post on 2024-8-21 09:16:43

你这是还没算完中途报错了，看sob老师文中第四节解决办法

sobereva · 发表于 Post on 2024-8-21 09:18:47

从result.txt看，任务根本都没算完
普通双路服务器上，跑这种大小的体系的sobEDA能量分解轻轻松松。算不动说明应该换机子，并且确保任务是并行计算的

〇66 · 发表于 Post on 2024-8-21 09:40:57

sobereva 发表于 2024-8-21 09:18
从result.txt看，任务根本都没算完
普通双路服务器上，跑这种大小的体系的sobEDA能量分解轻轻松松。算不动 ...

谢谢sob老师解答，我是在集群上跑的，有没有多任务并行的办法呢

〇66 · 发表于 Post on 2024-8-21 09:45:32

dzdhp 发表于 2024-8-21 09:16
你这是还没算完中途报错了，看sob老师文中第四节解决办法

好的，那我再等等看，谢谢

〇66 · 发表于 Post on 2024-8-21 15:13:23

sobereva 发表于 2024-8-21 09:18
从result.txt看，任务根本都没算完
普通双路服务器上，跑这种大小的体系的sobEDA能量分解轻轻松松。算不动 ...

老师我重新跑了一下，还是没有得到想要的结果，这是result.txt的信息，可以帮忙再看看吗？

Number of fragments: 3

Charge and spin multiplicity of fragment 1: 0 2
Indices of atoms in fragment 1: 1-31
Generating Gaussian input file of fragment 1 via Multiwfn (fragment1.gjf)
Running: g16 < fragment1.gjf &> fragment1.out
Finished successfully!
Running: formchk fragment1.chk fragment1.fch
Energy components of fragment 1:
E_tot = -747.827754314 Hartree
E_T = 740.570278 Hartree
E_els = -1379.343554314 Hartree
E_x = -103.535681 Hartree
E_c = -5.518797 Hartree
E_disp = 0 Hartree

Charge and spin multiplicity of fragment 2: 0 3
Indices of atoms in fragment 2: 32-83
Generating Gaussian input file of fragment 2 via Multiwfn (fragment2.gjf)
Running: g16 < fragment2.gjf &> fragment2.out
Finished successfully!
Running: formchk fragment2.chk fragment2.fch
Energy components of fragment 2:
E_tot = -1339.60448830 Hartree
E_T = 1326.754296 Hartree
E_els = -2472.26438330 Hartree
E_x = -184.321921 Hartree
E_c = -9.772480 Hartree
E_disp = 0 Hartree

Charge and spin multiplicity of fragment 3: 0 2
Indices of atoms in fragment 3: 84-114
Generating Gaussian input file of fragment 3 via Multiwfn (fragment3.gjf)
Running: g16 < fragment3.gjf &> fragment3.out
Finished successfully!
Running: formchk fragment3.chk fragment3.fch
Energy components of fragment 3:
E_tot = -747.827753684 Hartree
E_T = 740.570265 Hartree
E_els = -1379.343542684 Hartree
E_x = -103.535678 Hartree
E_c = -5.518798 Hartree
E_disp = 0 Hartree

Note: Calculation of whole system will be conducted in unrestricted way

Generating fch file of promolecular state via Multiwfn (promol.fch)
Running: unfchk promol.fch promol.chk
Generating Gaussian input file of promolecular state via Multiwfn (promol.gjf)
Running: g16 < promol.gjf &> promol.out
Finished successfully!
Energy components of promolecular state:
E_tot = -2836.27970720 Hartree
E_T = 2807.894839 Hartree
E_els = -5231.45036120 Hartree
E_x = -391.837642 Hartree
E_c = -20.886543 Hartree
E_disp = 0 Hartree

Generating Gaussian input file of final state (final.gjf)
Running: g16 < final.gjf &> final.out

〇66 · 发表于 Post on 2024-8-21 17:25:02

sobereva 发表于 2024-8-21 09:18
从result.txt看，任务根本都没算完
普通双路服务器上，跑这种大小的体系的sobEDA能量分解轻轻松松。算不动 ...

不好意思老师，现在终于是跑好了，但是我是从今早9点跑到了下午4点，...区区一百个原子用最入门的基组跑了7个小时也太久了吧。再麻烦问一下老师，我是在超算平台上进行计算的，有没有什么快一点的方法，或者让他们并行？

最终结果：
Number of fragments: 3

Charge and spin multiplicity of fragment 1: 0 2
Indices of atoms in fragment 1: 1-31
Generating Gaussian input file of fragment 1 via Multiwfn (fragment1.gjf)
Running: g16 < fragment1.gjf &> fragment1.out
Finished successfully!
Running: formchk fragment1.chk fragment1.fch
Energy components of fragment 1:
E_tot = -747.827754314 Hartree
E_T = 740.570278 Hartree
E_els = -1379.343554314 Hartree
E_x = -103.535681 Hartree
E_c = -5.518797 Hartree
E_disp = 0 Hartree

Charge and spin multiplicity of fragment 2: 0 3
Indices of atoms in fragment 2: 32-83
Generating Gaussian input file of fragment 2 via Multiwfn (fragment2.gjf)
Running: g16 < fragment2.gjf &> fragment2.out
Finished successfully!
Running: formchk fragment2.chk fragment2.fch
Energy components of fragment 2:
E_tot = -1339.60448830 Hartree
E_T = 1326.754296 Hartree
E_els = -2472.26438330 Hartree
E_x = -184.321921 Hartree
E_c = -9.772480 Hartree
E_disp = 0 Hartree

Charge and spin multiplicity of fragment 3: 0 2
Indices of atoms in fragment 3: 84-114
Generating Gaussian input file of fragment 3 via Multiwfn (fragment3.gjf)
Running: g16 < fragment3.gjf &> fragment3.out
Finished successfully!
Running: formchk fragment3.chk fragment3.fch
Energy components of fragment 3:
E_tot = -747.827753684 Hartree
E_T = 740.570265 Hartree
E_els = -1379.343542684 Hartree
E_x = -103.535678 Hartree
E_c = -5.518798 Hartree
E_disp = 0 Hartree

Note: Calculation of whole system will be conducted in unrestricted way

Generating fch file of promolecular state via Multiwfn (promol.fch)
Running: unfchk promol.fch promol.chk
Generating Gaussian input file of promolecular state via Multiwfn (promol.gjf)
Running: g16 < promol.gjf &> promol.out
Finished successfully!
Energy components of promolecular state:
E_tot = -2836.27970720 Hartree
E_T = 2807.894839 Hartree
E_els = -5231.45036120 Hartree
E_x = -391.837642 Hartree
E_c = -20.886543 Hartree
E_disp = 0 Hartree

Generating Gaussian input file of final state (final.gjf)
Running: g16 < final.gjf &> final.out
Finished successfully!
Energy components of final state:
E_tot = -2835.42288879 Hartree
E_T = 2808.960417 Hartree
E_els = -5231.85341379 Hartree
E_x = -391.608941 Hartree
E_c = -20.920951 Hartree
E_disp = 0 Hartree
Frozen state energy: -2834.23003777676 Hartree

*************************
***** Final results *****
*************************

Total interaction energy: -102.22 kcal/mol

Physical components of interaction energy derived by sobEDA:
Electrostatic (E_els): -313.05 kcal/mol
Exchange (E_x): -278.84 kcal/mol
Pauli repulsion (E_rep): 1286.19 kcal/mol
Exchange-repulsion (E_xrep = E_x + E_rep): 1007.35 kcal/mol
Orbital (E_orb): -748.53 kcal/mol
DFT correlation (E_DFTc): -47.98 kcal/mol
Dispersion correction (E_dc): 0.00 kcal/mol
Coulomb correlation (E_c = E_DFTc + E_dc): -47.98 kcal/mol

Please do not forget to cite original paper of Multiwfn program and sobEDA method in your work!

sobereva · 发表于 Post on 2024-8-22 00:53:46

〇66 发表于 2024-8-21 17:25
不好意思老师，现在终于是跑好了，但是我是从今早9点跑到了下午4点，...区区一百个原子用最入门的基组跑 ...

先弄清楚是否并行了

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