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Dear Colleague,

I was impressed by description of your GaussSum program and tried to install it on my PC with Windows 10. I used all-in-one bundle of Python/Numpy/Matplotlib/GaussSum (the easier method) GaussSum-3.0.2-amd64.msi.

After the installation I tried to start the program by double clicking the respective shortcut, but the program did not start and a message window appeared on the screen, see attachment.

I checked the message and found out that the folders mentioned in the message are absent.

I tried to install the program using the second possibility presented on your site, but the result was exactly the same.

Please, help

Dear all,

I would like to report what I think it is a small error in the routine of GaussSum. In the vibfreq.py file, when the exponential term is calculated, the following is written correctly?

"exponential = -6.626068e-34 * 299792458 * frequency / (1.3806503e-23 * temperature)"

I think that this light velocity value is in units of cm/sec. If so, the correct value should be 299792458e2. Therefore:

"exponential = -6.626068e-34 * 299792458e2 * frequency / (1.3806503e-23 * temperature)"

This small modification allows a better description of the Raman intensities at low-frequency, at least in my calculations.

Does this make sense?

Best,

José Gadelha, PhD
Department of Materials Science
UFMA, Imperatriz

Dear Gausssum developers:
Thanks for developing this software. I'm facing some troubles to execute it on linux. This is what I got when I tried to run it.
Traceback (most recent call last):
File "/home/seru/opt/GaussSum-3.0.2/GaussSum.py", line 23, in
import gausssum.gausssumgui
File "/home/seru/opt/GaussSum-3.0.2/gausssum/gausssumgui.py", line 27, in
from gausssum.preferencesbox import PreferencesPopupBox
File "/home/seru/opt/GaussSum-3.0.2/gausssum/preferencesbox.py", line 21, in
class PreferencesPopupBox(simpledialog.Dialog):
NameError: name 'simpledialog' is not defined

I could fix this adding import tkinter.simpledialog as simpledialog in gaussumgui.py y preferencesbox.py.

Then the next error: from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
ImportError: cannot import name 'NavigationToolbar2TkAgg' from 'matplotlib.backends.backend_tkagg' (/home/seru/.local/lib/python3.10/site-packages/matplotlib/backends/backend_tkagg.py)

These can be fixed by deleting Agg in NavigationToolbar2Tk on plot.py... then I could see the window.. I can open the log file, but when I try to see the pot there's no new window with the plot.

I think that is a problem with the python version... Do you have information about how to fix this?

Thanks in advance,

I am attempting to GaussSum 3.0 to process UV and CD spectra from G16 output. The software has been set up on a system running Centos 7 with python 3.8.1 and the latest, at the time of writing this email, versions of numpy, matplotlib, and cclib. The GaussSum program launches normally.

When I attempt to examine electronic transitions (either UV for CD) I get the following error message.

From what I can tell, the units are not being parsed correctly? I don’t know where this error is arising from. If I use the MSI version of the software for Windows, everything works fine. However, I need the scriptable to option function as I will need to process many structures at a time.

Can you please assist?

I believe there is something wrong with the changes mentioned in issue #18
In electrontrans.py the argument for convertor should be "wavenumber" instead of "wavenumbers".
Also line 43 in plot.py shoul use NavigationToolbar2Tk instead of NavigationToolbar2TkAgg

Dear all,

I'm having a problem running gausssum 3.0 with the gamess-us (GAMESS VERSION = 30 SEP 2018 (R3)) output file. Basically, I would like to plot Raman and IR spectrum, but loading an output file from gamess-us the following error appears "cclib has problems parsing". The attached file is an example. I figured out that when I delete two spaces before the frequency numbers everythings goes well. For example:

This
"
1 2 3 4 5
FREQUENCY: 0.09 0.00 0.00 0.00 0.05
"
becoming this
"
1 2 3 4 5
FREQUENCY: 0.09 0.00 0.00 0.00 0.05
"

However, I would like to know if someone can help me with a better solution.

Best,

Jose Gadelha
h2o.raman.zip

I faced with cclib problem parsing my orca output files.

I found problems with plotting the DOS for the calculation with different electronic temperatures. I got this message

Does any idea how to solve these problems?

I tried to analyse tddft results from ORCA5 calculations using GaussSum3.0. But I receive message as below,

Could anyone help me with this issue?

thanks

When I used the output file of Gamess with Mult=2 and SCF=ROHF i get error
So for structures like C19B , I cant get the DOS analysis

Where I tried with gaussum 2 and 3 in windows
the problem is the same

Dear All,
I am using Gausssum to plot dos/pdos of my cluster.
I have actually installed the most updated version of Gausssum (3.0.2) and accordingly cclib should be the most updated version.
But what I get is the error message "cclib has problems parsing output file".
It is a bit unexpected since DOS/PDOS of very similar calculations were successfully calculated and plotted.
Here the flavour of my calculation. Can anybody give me any hint to fix the error?
(Mind that the calculation ends normally).

g09 << EOF
%mem=64GB
%nproc=24
%chk=allFAsmallB3LYPdosSARC.chk
#b3lyp/Gen Pseudo=Read iop(3/33=1,3/36=-1) pop=full

Many thanks for your kind help.
Regards,

How can I make the software generate shell EDDM Scripts rather than bat ones? I want to avoid having to manually turn them into .sh files. Thank you in advance!

I want to automate extraction of DOS because of the sheer volume of .log files, but am unable to do so. I need a way to direct GaussSum to calculate DOS automatically, where I specify the file path, upper and lower bounds, anf FWHM.

Any help is appreciated.

Thanks

Hi,

I have noticed that GaussSum 3.0 which I was using does not parse the log file from Gaussian03 (TD-SCF calculations) correctly - it looks OK but in the GaussSum output the first transition is missing (but it is present in Gaussian log). I have updated GaussSum to newest version 3.0.2 and it does not open mentioned file at all (it reported error parsing log file). So I have installed the version 3.0.1 and it works properly (opens the file and there are no missing transitions). I hope that this information will be helpful.

Kind regards,

Bolesław Barszcz

Hello,

I believe I have found a bug in the IR/Raman output code regarding the x values written to the file vs the x values that were calculated in the peak broadening function. It appears to me that the values calculated after the function and used in the plot provided by GaussSum do not match the ones output to the text file. The relevant lines of code are listed below:

Calculation of x values in utils.py:

x values written to file:

x values used in plot (same values from Spectrum class in utils.py):

It appears to me that the formula used to calculate the x values is different in the two cases. I speculate that the reason the x values are being calculated a second time is so that an integer step would be used when the width is divisible by numpoints. However, I do not believe this is valid as the new x values don't correspond to the calculated y values.

When comparing a plot of the data from one of my output files to the one displayed by GaussSum, the peaks are shifted slightly. With the parameters start=0, end=4000, and numpoints=500, the shift is as much as 8 units for the peaks that occur at lower frequencies. The effect is much less visually noticable when setting numpoints higher, but is still present. It is much easier to see the effect when spectrum.xvalues is printed to the terminal and compared to the output data.

I believe a fix for this would be to not recalculate the x values. If an integer step is desired when the width is divisible by numpoints, then the function in utils.py should be modified slightly. I would be happy to submit a pull request if you would like.

Dear GaussSum developers,

I have calculated ECD sprectra and I have been searching the dimension of the y-axis of the spectra, which is signed with epsilon. In the generated CDspectrum.txt Abs is mentioned without any dimension. Epsilon would be the molar absorption coefficient calculated from this Abs value or maybe ellipitcity?

Thank you in advance!

Regards,

I installed GaussSum on my laptop with Debian 10, but I am having problems to make any type of graph from Gaussian 16 output file. I only get error messages (as seen in the photos below). Any help will be very welcome.

It is my kind request to you to please help in providing the updated GaussSum version compatible with ORCA 5 as soon as possible so that the research work will be simplified to a greater extent all because of your software. Thanks so much.

I have some big molecules and I want to parse the output from freq=raman calculations but only the first 500 vibrations are processed by Gausssum. Is there a way around this aside from editing the log file?

Reported by: *anonymous

When I run $ python3 GaussSum.py the full output is :
Traceback (most recent call last):
File "GaussSum.py", line 23, in
import gausssum.gausssumgui
File "/Users/ronaldbirke/Downloads/GaussSum-3.0.2/gausssum/gausssumgui.py", line 29, in
from gausssum.popanalysis import Popanalysis
File "/Users/ronaldbirke/Downloads/GaussSum-3.0.2/gausssum/popanalysis.py", line 20, in
from .plot import DisplayPlot
File "/Users/ronaldbirke/Downloads/GaussSum-3.0.2/gausssum/plot.py", line 22, in
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
ImportError: cannot import name 'NavigationToolbar2TkAgg' from 'matplotlib.backends.backend_tkagg' (/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/backends/backend_tkagg.py)

Problem is that GaussSum.py can't find tkinter. How can this be solved?

I am attempting to visualize electronic transitions using a Gaussian log file however I have the following error:

Traceback (most recent call last): File "D:\Tools\GaussSum\gausssum\src\gausssum\gausssumgui.py", line 415, in runscript File "D:\Tools\GaussSum\gausssum\src\gausssum\electrontrans.py", line 274, in ET AttributeError: 'ccData_optdone_bool' object has no attribute 'filename'

This error happens with almost every one of my log files, however a few have successfully produced the spectrum and I do not know why. I am running GaussSum 3.0.2 on Windows.

Thanks in advance

Dear developper,

First, thank you for this amazing package!
Soon, I will not be able to use Gaussview anymore, therefore I need another good package to convolute my spectra.

However, I noticed differences between the convolution from GaussSum and GaussView for the IR ones.

I struggled to find the right equation on the web, and finally found it here:

https://www.researchgate.net/publication/279441865_Infrared_Intensity_and_Lorentz_Epsilon_Curve_from_%27Gaussian%27_FREQ_Output?channel=doi&linkId=5592755508ae47a34910f493&showFulltext=true

Therefore, I adapted the lorentzian equation from the 'utils.py' file from

return float(height)*a/( (peak-x)**2 + a )

to

return float(2/math.pi) * (100/math.log(10)) * float(height) * (width / ((4*(peak-x)**2) + width**2))

and I now have 100% agreement with GaussView!

If you could update this line so that the community gets the right convolution, it would be amazing!

Thank you.

Hello!
I am testing Gaussum 3.0 on Ubuntu 14.04.
I try to load the attached example39.dat (CH4 Raman spectra) file created by the current Gamess-US (17 May 2013).
While loading it, the program crashes immeadiatly with the following output on the terminal:

python3 GaussSum.py 
Traceback (most recent call last):
  File "GaussSum.py", line 17, in <module>
    import gausssum.gausssumgui
  File "/home/mhahn1/Downloads/GaussSum-3.0/gausssum/gausssumgui.py", line 29, in <module>
    from gausssum.popanalysis import Popanalysis
  File "/home/mhahn1/Downloads/GaussSum-3.0/gausssum/popanalysis.py", line 21, in <module>
    from .plot import DisplayPlot
  File "/home/mhahn1/Downloads/GaussSum-3.0/gausssum/plot.py", line 20, in <module>
    import matplotlib
ImportError: No module named 'matplotlib'
mhahn1@ws7860:~/Downloads/GaussSum-3.0$ python3 GaussSum.py 
Log file type not identified.
Exception in Tkinter callback
Traceback (most recent call last):
  File "/usr/lib/python3.4/tkinter/__init__.py", line 1490, in __call__
    return self.func(*args)
  File "/home/mhahn1/Downloads/GaussSum-3.0/gausssum/gausssumgui.py", line 487, in fileopen
    self.logfile = ccopen(self.inputfilename)
  File "/home/mhahn1/Downloads/GaussSum-3.0/gausssum/cclib/parser/ccopen.py", line 102, in ccopen
    return filetype(source, *args, **kargs)
TypeError: 'NoneType' object is not callable
```~~


In case you need any further information  just let me know.
Thank you very much in advance.
Best regards Benjamin

Reported by: *anonymous

Dear All,

I am writing to ask about an error of GaussSum.
I ran a DOS calculation, using the output file of GAMESS (the method is DFTB), however, only an error message "cclib has problems parsing qm.out" was displayed.

Could you tell me whether the log files of DFTB (GAMESS) are available.

Sincerely,

Jun Oshiki

I have a problem!
When I'm try to run the gausssum in debian I have this messages:

[ fuganti@turing ~/softwares/gausssum/GaussSum-3.0.2/GaussSum-3.0.2 ]

python3.7 ./GaussSum.py
Traceback (most recent call last):
File "./GaussSum.py", line 23, in
import gausssum.gausssumgui
File "/home/fuganti/softwares/gausssum/GaussSum-3.0.2/GaussSum-3.0.2/gausssum/gausssumgui.py", line 29, in
from gausssum.popanalysis import Popanalysis
File "/home/fuganti/softwares/gausssum/GaussSum-3.0.2/GaussSum-3.0.2/gausssum/popanalysis.py", line 20, in
from .plot import DisplayPlot
File "/home/fuganti/softwares/gausssum/GaussSum-3.0.2/GaussSum-3.0.2/gausssum/plot.py", line 22, in
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
ImportError: cannot import name 'NavigationToolbar2TkAgg' from 'matplotlib.backends.backend_tkagg' (/usr/lib/python3/dist-packages/matplotlib/backends/backend_tkagg.py)
[ fuganti@turing ~/softwares/gausssum/GaussSum-3.0.2/GaussSum-3.0.2 ]

I try the old versions of the python and the same message appear. This happened after upgrade the debian for the 8.0 and up.
Any solution?