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ZHAOXIAO - 2022-07-19

Hi Felix,

I am having troubles with python3 to use this fancy tool. And it really feels painful to retrieve everything on my ubuntu 22.04 back to python2 compatible.
So, will you release a python3 version of ChemTraYzer recently?
Thanks.

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- Felix Schmalz - 2022-07-21
  
  Hi,
  we are refactoring ChemTraYzer at the moment, making it compatible with python3 and more MD codes. We plan to release a first version this year.
  Best, Felix
  
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tim rnav - 2022-08-01

Hi Felix,
When I try to run CTY with -start flag (1e04), it is taking very long time to begin. Is there anyway to accelerate this time such that it will start running from the specified timestep immediately?
Thanks.

Last edit: tim rnav 2022-08-01

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- Felix Schmalz - 2022-08-10
  
  Hi Tim,
  CTY scans through the LAMMPS/ReaxFF bond order file until the start time comes up, that can take some time. You can try deleting the part in the file from time steps 0 - 1e4 manually, and omit the start flag.
  Best, Felix
  
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chengyx - 2022-08-03

Hello, I use this script to analysis the reactions in Al/C/H/O system. I have add Var 13:3, and Cor 13:6 in processing.py. I met a mistake after python analyzing.py 2500K.reac.reac -main reac -dp 0.1 -gen id , pointing out that OverflowError: long int too large to convert to float. So how can I solve this problem? Thanks.

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- Felix Schmalz - 2022-08-10
  
  Hi chengyx,
  
  I'm guessing you are simulating a aluminum slab, which is not recommended, because the current version of CTY is developed for gas phase reactions only. How this creates the error, I can only guess:
  In this step, CTY computes and sums up the reactant concentrations for a specific reaction to calculate a rate constant (see more at https://doi.org/10.1021/acs.jctc.7b00524 Eq.3). According to a test on stackoverflow, this error comes up after numbers get larger than 170 factorial.
  So, there are either large numbers of reactants (tmpB) per reaction or large time intervals between the reactions (dt). In any case, CTY can't reliably handle solids.
  
  Best, Felix
  
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  - chengyx - 2022-09-30
    
    Hi, Felix,
    I used CTY to simulate the reaction of Al spherical particle (D=3 nm, 700 atoms) and ethanol. As you said, it's too complex to analyze. Thereby, I downscaled the simulation system, turned the diameter of Al to 1 nm and it worked. CTY helps me to figure out the reaction mechanisms. Thank you for your reply.
    
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ZHAOXIAO - 2022-08-06

Hi Felix,
The attatched file is my output from reaxff run. When I use CTY to analyzer it, my command is like,

python2 processing.py H2O2+Ag/reaxff_out.bonds -i 1:1 -i 2:8 -i 3:47 -norec 5

I already added ".Val" and ".Cor" for silver in processing.py. And I got the following error,

Processing files ...
H2O2+Ag/reaxff_out.bonds reading all steps, staring at timestep 0,
using 10000 bytes memory, a static cutoff of 0.5, considering 5
steps for recrossing and reading each 1th step of connectivity.
Identifying 1: 1, 2: 8, 3: 47
/home/xiao/Softwares/anaconda3/envs/py2/lib/python2.7/site-packages/openbabel/init.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel"
warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')
Traceback (most recent call last):
File "/home/xiao/Softwares/ChemTraYzer_2.1/processing.py", line 1210, in <module>
proc = Processing(Reader=reader, Identify=identify[f], Start=worktime[f], Storage=storage[f], Static=static[f])
File "/home/xiao/Softwares/ChemTraYzer_2.1/processing.py", line 211, in init
self.reaction, self.atom, self.molecule, self.bond[not self.switch] = self.initSystem()
File "/home/xiao/Softwares/ChemTraYzer_2.1/processing.py", line 443, in initSystem
mol[1] = self.canonical(mol[0],atoms)
File "/home/xiao/Softwares/ChemTraYzer_2.1/processing.py", line 791, in canonical
bond.SetBO(1)
AttributeError: 'OBBond' object has no attribute 'SetBO'</module>

I searched online but got no clue on how to solve this problem. Could you give a try on my out file in your computer? Thanks in advance!

reaxff_out.bonds

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- Felix Schmalz - 2022-08-26
  
  Dear Zhao Xiao,
  
  please use openbabel version 2. The warnings and errors come from version 3.x of openbabel, in which they changed some names, e.g. setBO to setBondOrder:
  https://openbabel.org/dev-api/deprecated.shtml
  Or you change the source code of CTY, then this might help:
  https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html
  
  Best, Felix
  
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afsaneh khajeh - 2022-08-20

Hi Dear Developers,

I am trying to use your helpful code for processing and analyzing my bond-order results form lammps.
I could run the "processing.py" for my "Eqbonds.reaxc" file and the "reac" file was generated, However in the next step during running "analyzing.py" I get the following warning several times:

Open Babel Warning in OpenBabel::OBSmilesParser::InsertTetrahedralRef
Warning: Overwriting previously set reference id.

I could run both steps for the examples you provided, and there was no problem there.

I was wondering if any package is missing or it comes from somewhere else?

Thanks in advance!

Last edit: afsaneh khajeh 2022-08-22

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- Felix Schmalz - 2022-08-26
  
  Dear Afsaneh,
  
  apparently this is an openbabel issue when reading/converting SMILES, and I don't know if they have fixed it:
  https://sourceforge.net/p/openbabel/bugs/625/
  It could mean that some SMILES of more complex molecules than in our example are not calculated correctly. The analyzing part computes rate constants for reactions, which is not affected by incorrect SMILES. But to be sure, check your CTY results to see if you find the molecules you expected. If two different species got the same SMILES because of that issue, those will be treated as the same.
  
  Hope that helps,
  Best, Felix
  
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Jie Xiao - 2022-08-31

Hello,

I have two questions.

First, I get an error when I use the command 'python processing.py example/bonds.tatb -i 1:6 -i 2:1 -i 3:8 -norec 5', and the error is as follows: attempt to read from example/bonds.tatb failed. Please check whether file is broken or does not exist. File will be ignored ... I have checked the file 'bonds.tatb', and I feel nothing wrong with it. I've also tried other bonds files that I've calculated myself, and I get this error message too.

Second, is it possible to use CTY to directly analyze the xyz file already calculated by LAMMPS to obtain the reaction list?

Looking forward to the reply!

Best regards,
Xiao

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- ZHAOXIAO - 2022-09-02
  
  Hi,
  
  Your first question may be related to the dir name of example file. Check it carefully (examples not example). Or you can try it with your own file. If it still happens, modify everything on you linux computer to be the same version mentioned on the website.
  As for your second question, I dont think it can be done without pre-processing. You can also ask the developers.
  
  Good luck!
  
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  - Jie Xiao - 2022-09-06
    
    Hello，
    
    Thank you very much for your reply!
    
    The previous problems have been solved. Now I have a new problem and would like to ask you for some advice. The file with the .reac extension obtained from the processing.py file has information about reaction species. For example, there are species with ":" symbols such as "O=O:C[C]", and species with "C=C1OO1", what do they mean?
    
    Thanks again for your reply!
    
    Best regards,
    Xiao
    
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    - Felix Schmalz - 2022-09-12
      
      Hello Xiao,
      
      ChemTraYzer relies on connectivity changes in the trajectory. So, it's not enough to just input XYZ. However, we are working on a new version which will include a basic bond guessing algorithm for exactly this case.
      The colon ":" is our choice of separating SMILES from one another, because this character doesn't appear in the SMILES generated by openbabel. So, "O=O:C[C]" are two species, and "C=C1OO1" is one (e.g. see https://molview.org/?q=C=C1OO1).
      
      Hope that helps,
      Kind regards,
      Felix
      
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Zhang Biao - 2022-09-28

Hi Felix,
When I use CTY to analyzer it, my command is like,
python2 analyzing.py bonds5-1200.reaxc.reac -main bonds5-1200 -p CCCCCCCC/C=C/CCC[CH]CC[O]:C=O,CCCCCCCCC=CCCCC=C
error:
Traceback (most recent call last):
File "analyzing.py", line 1030, in <module>
if plot: anly.drawProfile(Plot=plot, Timestep=timestep)
File "analyzing.py", line 484, in drawProfile
ax.append(plt.subplot2grid((nsub,msub),(i%nsub,i//nsub),colspan=1,rowspan=1))
File "/home/zxs/.local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 1237, in subplot2grid
colspan=colspan)
File "/home/zxs/.local/lib/python2.7/site-packages/matplotlib/gridspec.py", line 63, in new_subplotspec
subplotspec = self[loc1:loc1+rowspan, loc2:loc2+colspan]
File "/home/zxs/.local/lib/python2.7/site-packages/matplotlib/gridspec.py", line 161, in getitem
[_normalize(k1, nrows), _normalize(k2, ncols)], (nrows, ncols))
File "/home/zxs/.local/lib/python2.7/site-packages/matplotlib/gridspec.py", line 153, in _normalize
raise IndexError("invalid index")
IndexError: invalid index
Please give me some suggestions！Thanks!
Best regards,
Biao</module>

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Jingyi Yu - 2023-02-21

Hi Felix,
I have noticed that the event counts of few reactions in the "reac.reac.tab" file shows "-1". So what does the negative value mean? Is there a problem with my input file?

reac.reac.tab

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- Felix Schmalz - 2023-02-28
  
  Hi Jingyi Yu,
  it just means that the reverse reaction occured. Reverse in regard to what is printed in the third and fourth line.
  Best, Felix
  
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gaohang - 2023-02-23

Hello
I have some trouble about processpy.
... list of species indices generated
... list of reaction indices generated
Traceback (most recent call last):
File "analyzing.py", line 1012, in <module>
anly.depictMolecules(Resize=resize)
File "analyzing.py", line 644, in depictMolecules
call(['mkdir',folder])
File "C:\Python27\lib\subprocess.py", line 172, in call
return Popen(popenargs, *kwargs).wait()
File "C:\Python27\lib\subprocess.py", line 394, in init
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 644, in _execute_child
startupinfo)
WindowsError: [Error 2]
please help me!
Bestwish</module>

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- Felix Schmalz - 2023-02-28
  
  Hi Gaohang,
  The error seems to come up while creating a folder. What name did you choose for your files (the "-main" option)? The folder will contain this name and some characters are not allowed (e.g. "<>\ / |"). If that seems correct, write permissions might be the problem here.
  Best, Felix
  
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  - gaohang - 2023-02-28
    
    Hi Felix,
    Thank you for your help. I deleted the call command in the code. Although there are some problems with the running interface, the result looks good. Now I have another problem. I run the process module to process my file, but it has an error. The error code is as follows: Processing files
    bonds.reaxff reading all steps, staring at timestep 0, using 10000
    bytes memory, a static cutoff of 0.5, considering 100 steps for
    recrossing and reading each 1th step of connectivity.
    Identifying 1: 8, 2: 14, 3: 9, 4: 1
    Traceback (most recent call last):
    File "processing.py", line 1215, in <module>
    timestep, tmp = proc.processStep(Recrossing=recrossing, Steps=recsteps, Skip=skip, Close=True)
    File "processing.py", line 279, in processStep
    self.timestep, self.bond[self.switch] = self.extractBonds(Step=self.step, Bond=self.bond[self.switch], Static=self.static)
    File "processing.py", line 570, in extractBonds
    self.atom[ID].q = Q
    KeyError: 226
    I am considering whether chemtrayzer cannot handle the increase of particle number in the system, because I adopted the deposition command in lammps. The number of particles in the system in step 0 is 225, and the number of particles in the system in step 50 is 227. I don't know if my guess is correct. I hope you can help me.
    Best, Gaohang</module>
    
    Last edit: gaohang 2023-02-28
    
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xy_wang - 2023-03-13

Hello Felix Scgmalz,
Thank you for providing such useful software.
I have encountered the following problems while using it. I am using ChemTraYzer_2.0 version. My research system includes elemental fluorine. In the data file, #1 is carbon, #2 is oxygen, #3 is fluorine, and #4 is hydrogen. The error is reported as follows.
ERROR:
some elements are not supported by the internal valence list.
Please extend the list of supported elements by adding to
Processing.Val
I'm not quite sure how to add the elements, can you provide some guidance?
Best wish to you

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- Wassja A. Kopp - 2023-03-21
  
  Thank you for contacting us and sharing your interesting application.
  If your version corresponds to 2.0 from the sourceforge download site, the issue should be in the “processing.py” file.
  Therein, lines 154 and 155 contain dictionaries that assign to element numbers the corresponding valencies. In the version from sourceforge, these do contain values for element number 9 (flourine):
  self.Val = {1: 1, 2: 0, 6: 4, 7: 5, 8: 2, 9: 1, 10: 0, 16: 6, 17: 1, 18: 0}
  self.Cor = {1: 1, 2: 0, 6: 4, 7: 3, 8: 2, 9: 1, 10: 0, 16: 6, 17: 1, 18: 0}
  Is this also the same for your version?
  
  Initialization of a “Processing” object can take an “Identify” dictionary. This may contain your assignment of enumeration to element numbers. What do you give as “Identify” dictionary? According to your information, I guess it should look like (1:6, 2: 8, 3: 9, 4:1)
  
  Do you use LAMMPS? Which force field and parametrization do you employ?
  
  Best Regards
  Wassja A. Kopp
  On behalf of the ChemTraYzer Team
  
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  - xy_wang - 2023-03-22
    
    Thank you for your reply.
    With your help, the problem we encountered has been solved. Thank you for providing such an interesting package!
    
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xy_wang - 2023-03-13

Dear Felix,
Thank you for providing us with such useful software!
The "add element" problem we encountered before has been solved.
I have three questions for you.
1) I don't quite understand the statement "python processing.py bonds.tatb -n 0 -i 1:6 -i 2:1 -i 3:8 -norec 100"
-n I don't quite understand, the readme file explains "ALL timesteps which have been written to 'bonds.tatb"
Does this timestep refer to the timestep recorded in the bond.tatb file or the timestep set by the in.reax file,(0.1fs)
Here are the first few lines of my bond.tatb file.
"# Timestep 7

Number of particles 1670

Max number of bonds per atom 4 with coarse bond order cutoff 0.300

Particle connection table and bond orders

id type nb id_1... .id_nb mol bo_1... .bo_nb abo .bo_nb abo nlp q"

2)"-norec xx"I can't understand how to set this parameter? Will setting the parameter have an effect on the calculation results?
3) The first line of the "reac.rate" file: "R<id>;S<id>'s;Formula's;SMILES;k;klo;kup;N"
Does k represent the rate constant? And what does klo;kup;N stand for?
Best wish to you</id></id>

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Chemical Trajectory Analyzer Wiki

A software package for processing and analyzing chemical trajectories

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Number of particles 1670

Max number of bonds per atom 4 with coarse bond order cutoff 0.300

Particle connection table and bond orders

id type nb id_1... .id_nb mol bo_1... .bo_nb abo .bo_nb abo nlp q"