yangwangmadrid/ezreson

An efficient toolkit for chemical resonance analysis based on quantum chemistry calculations. It implements the quantitative theory of resonance by expansion of the wave function from a DFT/HF calculation in terms of those of the Lewis structures.

ezreson's Issues

Unwanted covalent bonds in Lewis structures

Hi.

I wanted to apply WFRT to H2N-Ph-Ph-NH2. Everything is fine except that its ordering is not as definite as that of a monocyclic molecule. The ordering I set is Atoms = 14 4 3 2 1 6 5 7 8 10 12 11 9 13, but four resonance structures that interest me given by EzReson have ridiculous covalent bonds 4-9, 2-12, 4-8 and 6-12. They are

   89    0.0904382232      26   56   49   77   86   24   92  105     14: 13: 3-2 6-5 1-7 8-10 12-11 4-9
   90    0.0904381388      14   56   49   77   43   89   92  105     14: 13: 4-3 6-5 1-7 8-10 2-12 11-9
   91    0.0904027302      26   56   49   20   82   89   92  105     14: 13: 3-2 6-5 1-7 4-8 10-12 11-9
   92    0.0904024906      26   18   49   77   60   89   92  105     14: 13: 3-2 4-5 1-7 8-10 6-12 11-9

What does this mean?

Error reading fchk file

HI,
I'm trying to use EzReson and reached the step that generate and exam LMOs.
My error:

Traceback (most recent call last):
  File "/home/shaoqz/bin/EzReson//ezreson.py", line 503, in <module>
    runJob_LMO( p.basename )
  File "/home/shaoqz/bin/EzReson//ezreson.py", line 314, in runJob_LMO
    FchkInfo = readFchk( basename + '.fchk' )
  File "/home/shaoqz/bin/EzReson/readFchk.py", line 506, in readFchk
    NBas, NBasIndp, atIx, aoIx, E_tot, E_SCF, E, C, QMull
UnboundLocalError: local variable 'QMull' referenced before assignment

So I looked into the readFchk.py and found QMull search for a re pattern
^\s*Mulliken\s+Charges\s+[A-Z]\s+[A-Z]+=\s+\d+.*
But I do not even have the word Mulliken in my .fchk file. My fchk file was generated by formchk of gaussian09 and my structure was a doublet.
Do you have any suggestions on my case? Thank you!
Also is .gjf necessary for EzReson? The README says it should be together with .33 .fchk and .out but no in the WeChat paper.

---

My usage was:
TS-P.in:

File = TS-P-opt
Job = LMO 

In the command line:
ezreson TS-P.in > TS-P.out

And three file (.33 .fchk .out) was under the same dir generated by gaussian:

...
# uwb97xd/def2tzvp pop=nboread

Title

2 2
...
$NBO
  NOBOND
  AONAO=W
  archive file=TS-P-opt
$END

计算共轭分子三重态，报错

汪老师：

您好。听闻EzReson可以处理开壳层波函数了，我就拿了个共轭分子三重态试一试，结果报错如下。

(base) freeman@freeman-ThinkPad-S5-S540:~/g09/MyMol/erotate$ ezreson E1t_nbo_lmo.in # 算局域轨道
Traceback (most recent call last):
  File "/home/freeman/EzReson_v3.0_release/ezreson.py", line 1475, in <module>
    runJob_LMO( p.basename )
  File "/home/freeman/EzReson_v3.0_release/ezreson.py", line 842, in runJob_LMO
    CAONAO = readNBOMat( basename + '.33', naoInfo.NBas, naoInfo.NNAO  )
  File "/home/freeman/EzReson_v3.0_release/readNBOMat.py", line 224, in readNBOMat
    if spin <= 1: # spin-restricted
UnboundLocalError: local variable 'spin' referenced before assignment

请问是怎么回事呢？