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rubenvdvijver alongd avcopan adewyer gitter-badger kacu9401 mbprend hwpang chrinide kfir4444 arshadzahangirchowdhury viktorzaverkin nora-khalil lpratalimaffeikinbot's Issues
Openbabel incompatible with Python 3.8.0
Hi everyone,
Just recently installed KinBot, and am trying to run the gvl_reactions example. I used the following to install pybel:
conda install -c openbabel openbabel
and am getting the following error message:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- openbabel -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.4,<3.5.0a0']
Your python: python[version='>=3.8.0']
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- feature:|@/linux-64::__glibc==2.17=0
- openbabel -> libgcc-ng -> __glibc[version='>=2.17']
Your installed version is: 2.17
(kinbot) [khalil.nor@c0235 gvl_reactions]$ y
bash: y: command not found
(kinbot) [khalil.nor@c0235 gvl_reactions]$ kinbot gvl.json
Warning: Pybel could not be imported.
Certain features or the whole code might not run properly.
Copyright 2018 National Technology & Engineering Solutions of Sandia,
LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS,
the U.S. Government retains certain rights in this software.
Pybel is required to use the smiles input format.
If pybel is unavailable, use the geometry as input.
Else install OpenBabel with python bindings.
Exiting...
I know that KinBot requires Python >=3.8, but what version of pybel should be installed that will be compatible with this version of python?
I am specifically trying to use PESViewer. Without pybel installed, I can still get a kinbot.log file when I run the gvl_reactions example, but would like to visualize the results with PESViewer.
Any help is greatly appreciated! Thank you!
AttributeError: 'StationaryPoint' object has no attribute 'maxbond'
Executing a code such as:
rxn_finder = ReactionFinder(well, params.par, qc)
rxn_finder.find_reactions()resulted in the following error:
File ".../KinBot/kinbot/reaction_finder.py", line 2284, in <genexpr>
if all(self.species.maxbond[instance[ii]][instance[ii + 1]] > 1 for ii in range(len(instance) - 2)):
AttributeError: 'StationaryPoint' object has no attribute 'maxbond'
Is it possible that a call such as self.species.calc_maxbond() is missing prior to L2284 of reaction_finder.py?
Installation and running kinbot
Hi,
I was trying to install kinbot locally sourcing from github. Due to python binding requirment or pybel for openbabel, which both did not work in my system. Therefore I installed kinbot and openbabel inside a conda environment.
I made a conda environment and installed kinbot (using pip) and openbabel (conda forge) with python=3.8
When typing kinbot after activating the environment gives as follows
To use KinBot, supply one argument being the input file!
which looks right.
Now i am trying to run a example case (propanol_homolytic_scissions), just by doing
kinbot propanol.json OR submitting the job via SLRUM it gives error as follows,
Traceback (most recent call last):
File "/users/test/.conda/envs/test/bin/kinbot", line 8, in
sys.exit(main())
File "/users/test/.conda/envs/test/lib/python3.8/site-packages/kinbot/kb.py", line 88, in main
qc.qc_opt(well0, well0.geom)
File "/users/test/.conda/envs/test/lib/python3.8/site-packages/kinbot/qc.py", line 529, in qc_opt
self.submit_qc(job)
File "/users/test/.conda/envs/test/lib/python3.8/site-packages/kinbot/qc.py", line 626, in submit_qc
process = subprocess.Popen(command, shell=False, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
File "/users/test/.conda/envs/test/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/users/test/.conda/envs/test/lib/python3.8/subprocess.py", line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'qsub'
qsub not found
but also produces some files, as below
601842261640800060001_well.pbs clean.sh kinbot.db kinbot.log log.out molpro propanol.json README
601842261640800060001_well.py geometry.xyz kinbotjob.sh localjob.sh me perm propanol.sh scratch
Note: I have a binary Gaussian 16 in my system which can be seperately invoked with g16 from anywhere.
Do I need to export Gaussian binary path or so?
Do you know what could be the problem? as in the kinbot wiki it is written kinbot is tested in g09.
Another context, if I install kinbolt and openbabel locally (not in conda environment) without pybel or python binding it says
If no pybel use python binding else use structure. I did not see any examples of kinbot with structure (does it mean xyz structure). Only saw with smiles?
OH + propene,Minor examples of recurring inconsistencies
Hello, I want to copy fig13 in the article with Kinbot, and the result is as follows. It can be seen that I seem to have no isomerization reaction, only bimolecular products lead to the end of the program, and there are two more paths (maybe the barrier_threshold is different), and the energy seems to be different (maybe the article did not add ZPE). Attached is my input file.
CH3CHOHCH2.txt
Update setup.py with new templates
It seems the setup.py file is out of sync with the templates in the tpl. We should try to find a way to automatically update this, or to use a small routine to read all the files in the tpl folder and add them to the KinBot build.
Conformer search using high level theory
Dear developers,
For some molecules with many hindered rotors, the conformer search at the L1 level seems not reliable so that the rotation will restart several times during HIR scan. maybe it is better to do the conformer search at a high level? OR providing an option for rotor scan at a different level.
Moreover, when I tried to use semiempirical method for pre-optimization of large molecules, I found there are some bugs. For example, variable "self.ssemi_empconf" is not defined in "optimize.py". and the number of variables is not equal to the return of the "self.species.semi_emp_confs.check_conformers" function. After fixing these problems, the semiempirical optimization still can not run correctly without further messages.
Regards
Installation issue
Hey,
I can see that for some reason the installation changed, but the instructions did not.
When trying to install the binary using conda I get the following:
$ conda install -c rdkit -c openbabel -c zadorlab kinbot python=3.8
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (python):
- kinbot -> matplotlib -> python[version='2.6.*|2.7.*|3.4.*|3.5.*|3.6.*|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|>=3.8|>=3.7|>=3.6|>=3.5|>=3.4,<3.5.0a0']
- kinbot -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']
- python=3.8
The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package readline conflicts for:
certifi -> python[version='>=3.9,<3.10.0a0'] -> readline[version='7.*|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.2,<9.0a0']
readline
kinbot -> python[version='>=2.7,<2.8.0a0'] -> readline[version='7.*|>=7.0,<8.0a0|>=8.0,<9.0a0']
python=3.8 -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.2,<9.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> readline[version='7.*|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.2,<9.0a0']
sqlite -> readline[version='>=8.0,<9.0a0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> readline[version='7.*|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.2,<9.0a0']
wheel -> python -> readline[version='7.*|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.2,<9.0a0']
Package sqlite conflicts for:
python=3.8 -> sqlite[version='>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.38.0,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.38.0,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0']
sqlite
setuptools -> python[version='>=3.8,<3.9.0a0'] -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.38.0,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0']
kinbot -> python[version='>=2.7,<2.8.0a0'] -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.31.1,<4.0a0|>=3.35.4,<4.0a0|>=3.40.0,<4.0a0|>=3.33.0,<4.0a0|>=3.30.1,<4.0a0|>=3.26.0,<4.0a0|>=3.24.0,<4.0a0']
wheel -> python -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.37.2,<4.0a0|>=3.38.0,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.38.0,<4.0a0|>=3.38.2,<4.0a0|>=3.38.3,<4.0a0|>=3.39.2,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0|>=3.37.2,<4.0a0']
Package _openmp_mutex conflicts for:
openssl -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5']
_openmp_mutex
zlib -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
libffi -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
readline -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
libuuid -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
xz -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
tk -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5']
libgcc-ng -> _openmp_mutex[version='>=4.5']
python=3.8 -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
ncurses -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
bzip2 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
sqlite -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
Package openssl conflicts for:
kinbot -> python[version='>=2.7,<2.8.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1k,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1e,<1.1.2a']
openssl
python=3.8 -> openssl[version='>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a']
pip -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.0.2l,<1.0.3a']
wheel -> python -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.0.2l,<1.0.3a']
certifi -> python[version='>=3.9,<3.10.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.0.2l,<1.0.3a']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.0.2l,<1.0.3a']
Package wheel conflicts for:
python=3.8 -> pip -> wheel
wheel
pip -> wheel
Package bzip2 conflicts for:
bzip2
certifi -> python[version='>=3.10,<3.11.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
kinbot -> openbabel -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
pip -> python[version='>=3.10,<3.11.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
wheel -> python -> bzip2[version='>=1.0.8,<2.0a0']
setuptools -> python[version='>=3.10,<3.11.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
Package ca-certificates conflicts for:
openssl -> ca-certificates
pip -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.8 -> openssl[version='>=1.1.1s,<1.1.2a'] -> ca-certificates
ca-certificates
certifi -> python -> ca-certificates
setuptools -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
wheel -> python -> ca-certificates
kinbot -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
Package ld_impl_linux-64 conflicts for:
ld_impl_linux-64
kinbot -> python[version='>=3.6,<3.7.0a0'] -> ld_impl_linux-64
wheel -> python -> ld_impl_linux-64[version='>=2.36.1']
pip -> python[version='>=3.8,<3.9.0a0'] -> ld_impl_linux-64[version='>=2.36.1']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> ld_impl_linux-64[version='>=2.36.1']
python=3.8 -> ld_impl_linux-64
certifi -> python[version='>=3.9,<3.10.0a0'] -> ld_impl_linux-64[version='>=2.36.1']
Package libgcc-ng conflicts for:
openssl -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
libgcc-ng
xz -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
bzip2 -> libgcc-ng[version='>=7.2.0|>=7.3.0']
tk -> zlib[version='>=1.2.12,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0']
kinbot -> matplotlib -> libgcc-ng[version='>=11.2.0|>=7.2.0|>=7.3.0|>=7.5.0']
sqlite -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
ncurses -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
readline -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
tk -> libgcc-ng[version='>=7.2.0|>=7.3.0|>=7.5.0']
libffi -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
wheel -> python -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
zlib -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
pip -> python[version='>=3.8,<3.9.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
python=3.8 -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0']
libuuid -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.2.0']
Package tzdata conflicts for:
setuptools -> python[version='>=3.10,<3.11.0a0'] -> tzdata
certifi -> python[version='>=3.9,<3.10.0a0'] -> tzdata
tzdata
wheel -> python -> tzdata
pip -> python[version='>=3.10,<3.11.0a0'] -> tzdata
Package tk conflicts for:
certifi -> python[version='>=3.9,<3.10.0a0'] -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
wheel -> python -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
python=3.8 -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0']
kinbot -> matplotlib -> tk[version='8.6.*|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.10,<8.7.0a0']
tk
setuptools -> python[version='>=3.8,<3.9.0a0'] -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
Package libuuid conflicts for:
certifi -> python[version='>=3.10,<3.11.0a0'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
wheel -> python -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
libuuid
pip -> python[version='>=3.10,<3.11.0a0'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
setuptools -> python[version='>=3.10,<3.11.0a0'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
Package _libgcc_mutex conflicts for:
libgomp -> _libgcc_mutex==0.1=main
tk -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1',build=main]
openssl -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1',build=main]
python=3.8 -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
ncurses -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
libgcc-ng -> _libgcc_mutex[version='*|0.1',build=main]
libffi -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
_libgcc_mutex
zlib -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
readline -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
libuuid -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
xz -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
bzip2 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build=main]
sqlite -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1',build=main]
Package libedit conflicts for:
python=3.8 -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']
sqlite -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']
Package xz conflicts for:
setuptools -> python[version='>=3.8,<3.9.0a0'] -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
xz
kinbot -> python[version='>=3.6,<3.7.0a0'] -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
python=3.8 -> xz[version='>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
wheel -> python -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
Package python conflicts for:
pip -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
pip -> wheel -> python
certifi -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
setuptools -> certifi[version='>=2016.9.26'] -> python
setuptools -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
wheel -> setuptools -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
wheel -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
Package setuptools conflicts for:
setuptools
wheel -> setuptools
python=3.8 -> pip -> setuptools
pip -> setuptools
kinbot -> matplotlib -> setuptools
Package libstdcxx-ng conflicts for:
sqlite -> ncurses[version='>=6.2,<7.0a0'] -> libstdcxx-ng[version='>=7.3.0']
libstdcxx-ng
wheel -> python -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
ncurses -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
pip -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
readline -> ncurses[version='>=6.2,<7.0a0'] -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
python=3.8 -> libffi[version='>=3.2.1,<3.3a0'] -> libstdcxx-ng[version='>=7.2.0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
kinbot -> matplotlib -> libstdcxx-ng[version='>=11.2.0|>=7.2.0|>=7.3.0|>=7.5.0']
python=3.8 -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0']
libffi -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']
Package ncurses conflicts for:
kinbot -> python[version='>=2.7,<2.8.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
sqlite -> ncurses[version='>=6.2,<7.0a0']
python=3.8 -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0']
wheel -> python -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
readline -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
python=3.8 -> ncurses[version='>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0']
sqlite -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='6.0.*|>=6.1,<7.0a0|>=6.3,<7.0a0']
ncurses
Package libffi conflicts for:
pip -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
wheel -> python -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
libffi
kinbot -> python[version='>=2.7,<2.8.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
python=3.8 -> libffi[version='>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0']
Package libgomp conflicts for:
libgcc-ng -> _openmp_mutex -> libgomp[version='>=7.5.0']
libgomp
Package zlib conflicts for:
tk -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
sqlite -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
pip -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
wheel -> python -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
setuptools -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
certifi -> python[version='>=3.9,<3.10.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
kinbot -> matplotlib -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0']
zlib
Package certifi conflicts for:
pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
setuptools -> certifi[version='>=2016.09|>=2016.9.26']
certifi
wheel -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:|@/linux-64::__glibc==2.35=0
- bzip2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libffi -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- libgcc-ng -> __glibc[version='>=2.17']
- libstdcxx-ng -> __glibc[version='>=2.17']
- libuuid -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- ncurses -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- openssl -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- python=3.8 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- readline -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- sqlite -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- tk -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- xz -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- zlib -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.35
allow setting memory by keyword
Preferably with different memory settings for the different types of jobs.
Reaction Mechanism
Hi,
I have several already calculated species from Gaussian. Is there a way to use them to derive the mechanism?
Thanks!
Visualization after a pes or Kinbot run?
Hello, after successfully finishing kinbot and pes tasks, I want to use pesviewer pesviewer.inp command to visualize potential energy surface, but to generate *.html file, I want to generate the following image how to do? thank you.
error with cycle in symmetry module
Traceback (most recent call last):
File "/home/jzador/.local/bin/kinbot", line 11, in <module>
load_entry_point('KinBot', 'console_scripts', 'kinbot')()
File "/home/jzador/KinBot/kinbot/kb.py", line 173, in main
rg.generate()
File "/home/jzador/KinBot/kinbot/reaction_generator.py", line 316, in generate
prod_opt.do_optimization()
File "/home/jzador/KinBot/kinbot/optimize.py", line 253, in do_optimization
symmetry.calculate_symmetry(self.species)
File "/home/jzador/KinBot/kinbot/symmetry.py", line 164, in calculate_symmetry
if species.atomid[cyc_nei[0]] == species.atomid[cyc_nei[1]]:
IndexError: list index out of range
Cycle is not detected for changing product
When a product is changed to something else, and that new product is cyclic (or has changed cycle), the cycle attribute is inherited from the original product and so KinBot does some unnecessary dihedral scans or other strange things.
"multiplicity" keyword appeared in route section of gaussian input file
While generating gaussian input file by kinbot, an unwanted keyword called "multiplicity" appeared in the route section causing error termination.
Invalid QChem input file format
Hi,
I'm using "qc": "qchem", but the generated QChem input file is formatted in a way that's not accepted by QChem. An ADDSEC argument is added under $rem with value $OPT and CONSTRAINT. The QChem calculation stops at Illegal rem input in read_rem error according to the output file.
Example Kinbot arguments
{
"title": "005",
"structure": [
"C", -2.577633181322523, -0.14899699736569763, -0.07009320293759329,
"C", -1.4710364844720145, 0.03988258853136189, -0.75032448258031,
"C", -0.1604917635492785, -0.5703266103263727, -0.3919795546490268,
"C", 0.8018278972888587, 0.5767209791158451, -0.14215601731303748,
"C", 2.178991157385679, 0.059339271574617665, 0.23352777583103357,
"H", -2.556372304909696, -0.7801537606225438, 0.8028529167299286,
"H", -3.4881061869665815, 0.32354520244998, -0.38688528578309284,
"H", -1.4917649457035762, 0.6733445897635278, -1.6267160667606906,
"H", 0.22447548582474966, -1.2334174456304299, -1.1935419248390915,
"H", -0.26597759790880043, -1.204604573308268, 0.511917577388464,
"H", 0.40977650064470755, 1.147928280817434, 0.7396010636033121,
"H", 0.8408829942731407, 1.2127708839806202, -1.027043850430413,
"H", 2.68398201445469, 0.8544480216185247, 0.821403187037373,
"H", 2.7918195957522594, -0.13837106750946224, -0.6468712969708699,
"H", 2.0796268192086607, -0.8121093630892011, 0.9106049588215894
],
"charge": 0,
"mult": 1,
"qc": "qchem",
"qc_command": "qchem",
"families": "intra_H_migration",
"queuing": "slurm",
"queue_template": "queue.tmp",
"scratch": "/global/scratch/users/ericyuan/KinBot"
}
Example QChem input file by KinBot
$comment
ASE generated input file
$end
$rem
METHOD B3LYP
BASIS STO-3G
JOBTYPE OPT
UNRESTRICTED TRUE
SCF_ALGORITHM DIIS_GDM
MAX_SCF_CYCLES 100
GEOM_OPT_MAX_CYCLES 500
SCF_CONVERGENCE 4
GEOM_OPT_TOL_GRADIENT 1500
GEOM_OPT_TOL_DISPLACEMENT 6000
GEOM_OPT_TOL_ENERGY 500
ADDSEC $OPT
CONSTRAINT
STRE 1 2 1.3382760256394144
STRE 1 6 1.0878758922264666
STRE 1 7 1.0860760178902613
STRE 2 3 1.5075948774964534
STRE 2 8 1.0918265854457123
STRE 3 4 1.5475057900669216
STRE 3 9 1.1018713063126104
STRE 3 10 1.098991334510338
STRE 4 5 1.536430012149745
STRE 4 11 1.0983972829511321
STRE 4 12 1.1000496422646011
STRE 5 13 1.096071787627103
STRE 5 14 1.0975509909543386
STRE 5 15 1.0972339650058218
BEND 2 1 6 121.71005680089769
ENDCONSTRAINT
$END
SYM_IGNORE TRUE
$end
$molecule
0 1
C -2.669788 -0.208572 -0.122289
C -1.528213 0.036435 -0.776323
C -0.172945 -0.504076 -0.396932
C 0.840984 0.607505 -0.034841
C 2.245720 0.059142 0.259493
H -2.699273 -0.849669 0.756119
H -3.617675 0.217208 -0.438173
H -1.546496 0.687539 -1.652574
H 0.240305 -1.087054 -1.235671
H -0.272641 -1.198574 0.448950
H 0.464268 1.161686 0.835472
H 0.893597 1.330531 -0.862230
H 2.948325 0.867855 0.491232
H 2.641531 -0.492269 -0.603003
H 2.232302 -0.627689 1.115066
$end
Example QChem output file
M. Scheurer, M. Schneider, P. E. Schneider, Tim K. Schramm, N. Sergueev,
S. M. Sharada, M. Sharma, Hengyuan Shen, W. Skomorowski, D. W. Small,
C. J. Stein, Alistair J. Sterling, Yingli Su, Yu-Chuan Su,
E. J. Sundstrom, J. Talbot, Zhen Tao, J. Thirman, Hung-Yi Tsai,
T. Tsuchimochi, N. M. Tubman, C. Utku, S. P. Veccham, O. Vydrov,
J. Wenzel, Jonathan Wong, J. Witte, A. Yamada, Chou-Hsun Yang, Kun Yao,
S. Yeganeh, S. R. Yost, A. Zech, F. Zeller, Igor Ying Zhang,
Xing Zhang, Yu Zhang, D. Zuev, A. Aspuru-Guzik, A. T. Bell,
N. A. Besley, K. B. Bravaya, B. R. Brooks, D. Casanova, Jeng-Da Chai,
Hsing-Ta Chen, S. Coriani, C. J. Cramer, A. E. DePrince, III,
R. A. DiStasio Jr., A. Dreuw, B. D. Dunietz, T. R. Furlani,
W. A. Goddard III, S. Grimme, S. Hammes-Schiffer, T. Head-Gordon,
W. J. Hehre, Chao-Ping Hsu, T.-C. Jagau, Yousung Jung, A. Klamt,
Jing Kong, D. S. Lambrecht, Xiangyuan Li, WanZhen Liang, N. J. Mayhall,
C. W. McCurdy, J. B. Neaton, T. Neudecker, C. Ochsenfeld,
J. A. Parkhill, R. Peverati, V. A. Rassolov, Haisheng Ren, Yihan Shao,
L. V. Slipchenko, R. P. Steele, J. E. Subotnik, A. J. W. Thom,
A. Tkatchenko, D. G. Truhlar, T. Van Voorhis, Fan Wang,
T. A. Wesolowski, K. B. Whaley, H. L. Woodcock III, P. M. Zimmerman,
S. Faraji, P. M. W. Gill, M. Head-Gordon, J. M. Herbert, A. I. Krylov
Contributors to earlier versions of Q-Chem not listed above:
R. D. Adamson, B. Austin, R. Baer, J. Baker, G. J. O. Beran,
K. Brandhorst, S. T. Brown, E. F. C. Byrd, Arup K. Chakraborty,
G. K. L. Chan, Chun-Min Chang, Yunqing Chen, C.-L. Cheng,
Siu Hung Chien, D. M. Chipman, D. L. Crittenden, H. Dachsel,
R. J. Doerksen, A. D. Dutoi, R. G. Edgar, J. Fosso-Tande,
L. Fusti-Molnar, D. Ghosh, A. Ghysels, A. Golubeva-Zadorozhnaya,
J. Gonthier, M. S. Gordon, S. R. Gwaltney, G. Hawkins, J. E. Herr,
A. Heyden, S. Hirata, E. G. Hohenstein, G. Kedziora, F. J. Keil,
C. Kelley, Jihan Kim, R. A. King, R. Z. Khaliullin, P. P. Korambath,
W. Kurlancheek, A. Laurent, A. M. Lee, M. S. Lee, S. V. Levchenko,
Ching Yeh Lin, D. Liotard, E. Livshits, R. C. Lochan, I. Lotan,
L. A. Martinez-Martinez, P. E. Maslen, N. Nair, D. P. O'Neill,
D. Neuhauser, E. Neuscamman, C. M. Oana, R. Olivares-Amaya, R. Olson,
T. M. Perrine, B. Peters, P. A. Pieniazek, A. Prociuk, Y. M. Rhee,
J. Ritchie, M. A. Rohrdanz, E. Rosta, N. J. Russ, H. F. Schaefer III,
M. W. Schmidt, N. E. Schultz, S. Sharma, N. Shenvi, C. D. Sherrill,
A. C. Simmonett, A. Sodt, T. Stein, D. Stuck, K. S. Thanthiriwatte,
V. Vanovschi, L. Vogt, Tao Wang, A. Warshel, M. A. Watson,
C. F. Williams, Q. Wu, X. Xu, Jun Yang, W. Zhang, Yan Zhao
Please cite Q-Chem as follows:
"Software for the frontiers of quantum chemistry:
An overview of developments in the Q-Chem 5 package"
J. Chem. Phys. 155, 084801 (2021)
https://doi.org/10.1063/5.0055522 (open access)
Q-Chem 6.1.0 for Intel X86 EM64T Linux
Parts of Q-Chem use Armadillo 9.900.5 (Nocturnal Misbehaviour).
http://arma.sourceforge.net/
Q-Chem begins on Wed Nov 8 14:01:03 2023
Host:
0
Scratch files written to /tmp/702262792321520790121_intra_H_migration_2_6.sv//
Jul923 |scratch|qcdevops|jenkins|workspace|build_RNUM -1
Processing $rem in /clusterfs/mp/software/qchem6.1/config/preferences:
Processing $rem in /global/home/users/ericyuan/.qchemrc:
Problem with processed rem input line:
ADDSEC $OPT
ADDSEC (rem variable) is not correct.
Please make sure the variable is legal and the spelling is correct.
Q-Chem fatal error occurred in module qparser/new_read_rem.C, line 429:
Illegal rem input in read_rem
Please submit a crash report at q-chem.com/reporter
Thanks.
random conf search produces too many cases for cycles
The limit is not well implemented when cycles are present.
FileNotFoundError: [Errno 2] No such file or directory
Hello, the following problems occurred when I used kinbot to simulate C6H6. I uploaded C6H6_1.jons text and kinbot.log file, how can I solve them, thank you
Product info scrambled on PES level
When a product is changing, something gets scrambled and the information doesn't get to the PES level, even though it is okay in the KinBot run. Causes to output A + A instead of A + B products.
Having trouble with setup
Hi, I was trying to run Kinbot but got some issues.
Environment:
Python 3.6
Queue: Slurm
What I have done:
- I have cloned
KinbotandASEunderzadorlaband installedpybel,rdkitand other necessary packages. I have added both~/kinbotand~/aseto my PYTHONPATH and~/kinbot/and~ase/binto my PATH. - I created an input file (
input.json, according to the documentation from your literature) for a calculation by g09, and that input file seemed to work. But the job soon terminated due to errors in Gaussian calculation. - I checked the Gaussian job log file, and the error was due to
force,optandfreqare in the arguments in the meantime. - I looked into the code, and I think in your ase code, you tried to remove
forcewhenfreqis added. So the case ideally should not happen. - Then, I thought that I might use a wrong ase version. I redo the setup and find that when I run
python setup.py install(or other lines you recommended), it will search forase 3.19.1frompypiand use as kinbot's default ase, which might be the problem.
Can you please provide any suggestions on this? Thanks.
Followup:
- I run the
python setup.py install --userinside~/aseas suggested by ASE. It seems to overwrite some of the settings by Kinbot, and it eventually works. Thanks
Two isomers share a same CHEMID
Hi,
I found two isomers share the same CHEMID as shown below. It makes Kinbot cannot generate the mess input.
I attached the PES log file, it is also weird because product "10000000000000000002_450970900380000000001" is not on the PES of well "461121220400020000002".
pes.log
propene Small example, cannot reproduce the result? Seek Assist
Hello, I want to run kinbot to get this result propene. At the end of the run, no path is generated. I looked at the output and I guessed that the path in the article should be 421261230750120000001_intra_H_migration_3_4. The program may consider 421261230750120000001_intra_H_migration_3_4_IRC_F_prod.com and 421261230750120000001_intra_H_migration_3_4_IRC_R_prod. com gets the same species, so without this path, how do I solve it? I uploaded the input file.
421261230750120000001_intra_H_migration_3_4_IRC_R_prod.log:
421261230750120000001_intra_H_migration_3_4_IRC_F_prod.log:
Some questions during using Kinbot
Hi,
There are some questions during my Kinbot using
- During reaction search, some fake TS possessing small negative frequency are always found, I think these cases can be filtered by limit the negative frequency higher than -100 or some value to avoid invalid IRC and conformer calculations, hence, I modified the reaction_generator.py as:
if status == 0 and freq[0] < -100. and freq[1] > 0.:
self.species.reac_ts_done[index] = 1
elif status == 0 and 0>freq[0] >= -100.:
logger.info('\tRxn search failed for {}, imaginary freq is lower than -100.'
.format(obj.instance_name))
self.species.reac_ts_done[index] = -999
and it works well for my system, but I am not sure whether other place also should be modified accordingly?
2. During Kinbot running, a error was occurred, is it caused by my modification?
30-Mar-23 10:40:35-ERROR:
Traceback (most recent call last):
File "/share/home/wd/anaconda3/envs/kinbot-new/bin/kinbot", line 8, in
sys.exit(main())
File "/share/home/wd/Kinbot_309/kinbot/kb.py", line 168, in main
rg.generate()
File "/share/home/wd/Kinbot_309/kinbot/reaction_generator.py", line 493, in generate
pr_opt.do_optimization()
File "/share/home/wd/Kinbot_309/kinbot/optimize.py", line 319, in do_optimization
self.species.kinbot_freqs, self.species.reduced_freqs = frequencies.get_frequencies(self.species,
File "/share/home/wd/Kinbot_309/kinbot/frequencies.py", line 35, in get_frequencies
hess /= np.sqrt(np.outer(masses, masses))
ValueError: operands could not be broadcast together with shapes (0,) (39,39)
3, Recently I try to use compound method in Guass, such as G4(SP) to calculate the L3 energy, I found codes in pes.py for Gauss SP energy reading, but it seems kinbot does not contain the code to generate input and submit files for Gauss L3 calculation. Besides, the code seems can not read the energy correctly from the log file. (for example, the single point keyword is "G4 Energy")
Can Gaussian be supported in the L3 sp energy calculation?
Some low-cost compound method such as cbs-qb3 in Gaussian is suitable for some large system, can these method be supported in L3 sp energy calculation?
About Kinbot, are there any questions in the document "Comprehensive Kinetics on the C7H7 Potential Energy Surface under Combustion Conditions"?
-
full_pes.html in SI is a potential energy surface integrating high energy and low energy. If so, is the path of high energy generation manually added to the original low energy potential energy surface?
-
trimmed_pes***.html, how is the reaction path obtained? By what means? All five entry point paths should be found at full_pes.html.
For example: trimmed_pes_cC5H5+C2H2.html file in the following figure. With C5H5+C2H2 as the entry point, why is this?
/bin/sh: g16: command not found
Hello everyone,
when I run the case in /examples/gvl_reactions, it returns error in "/bin/sh: g16: command not found", in our own computational environment, it provides a *.pbs template like following:
#! /bin/sh -x
#PBS -N uv_azo_trans_im_co2
#PBS -l nodes=1:ppn=52
#PBS -q batch
#PBS -j oe
Modify the Gaussian gjf file name here!
GJF="uv_azo_trans_im_co2.gjf"
####################
export GAUSS_SCRDIR=/tmp
export g09root=/opt/gaussian
. $g09root/g09/bsd/g09.profile
cd $PBS_O_WORKDIR
JOBNAME=basename "$GJF" .gjf
$g09root/g09/g09 < $GJF > "$JOBNAME.log"
I'm confused how to built the g09root in *.json?
Merge HS class with regular families
Will require adding some extra logic to the code, but we will get rid of significant code duplication.
Merge all submission code into one class
Right now, the submission of jobs to the queue or the the OS are done in several parts of the code, spread throughout the different classes. It would be good to merge all of this into one class to avoid duplication of code and to have more robust submission routines.
Problem with the PESViewer parameter energy_shift
Hello, I want to use the energy_shift parameter in PESViewer to adjust the entire potential energy surface energy, but every time tell me?
error.log:
Cannot recognize input line:
energy_shift -3.1
Repeated calculation of species during PES exploration
During the PES calculation, many species will appear in different wells, and repeatedly optimized several times, also, generated the L3 submit files several times, which needs to further selected manually. Is it possible to create a global database during PES calculation, and skip the species already calculated to reduce the cost.
Slurm example file request
I am new to slurm. Can you please provide the detailed example file for the Slurm batch process?
I got a little bit confused with the example provided in the overview. Thanks in advance.
invalid syntax match atom_pattern:
Hello, I installed the latest kinbot version, the following error appears, how to solve? Thank you!
Traceback (most recent call last):
File "/home/XXX/software/anaconda3/envs/kinbot_code/bin/kinbot", line 5, in
from kinbot.kb import main
File "/home/XXX/Kinbot/kinbot_code/Kinbot_code/Kinbot/kinbot/kb.py", line 10, in
from kinbot.reaction_finder import ReactionFinder
File "/home/XXX/Kinbot/kinbot_code/Kinbot_code/Kinbot/kinbot/reaction_finder.py", line 29, in
from kinbot.reactions.reac_R_Addition_MultipleBond import RAdditionMultipleBond
File "/home/XXX/Kinbot/kinbot_code/Kinbot_code/Kinbot/kinbot/reactions/reac_R_Addition_MultipleBond.py", line 44
match atom_pattern:
^
SyntaxError: invalid syntax
Having trouble using pesviewer?
When I use the command pesviewer pesviewer.inp to visualize the results, I get the following error. But the result is still normal output.
Traceback (most recent call last):
File "/home/xxx/software/anaconda3/envs/kinbot/bin/pesviewer", line 10, in
sys.exit(main())
File "/home/xxx/software/anaconda3/envs/kinbot/lib/python3.8/site-packages/pesviewer/pesviewer.py", line 1602, in main
create_interactive_graph(meps)
File "/home/xxx/software/anaconda3/envs/kinbot/lib/python3.8/site-packages/pesviewer/pesviewer.py", line 1411, in create_interactive_graph
norm_energy = (ts.energy - min_ts_energy) / ts_energy_range
ZeroDivisionError: float division by zero
Kinbot can not find the transition state of beta scission reactions for specific radical
I tried to search for the PES of DMF radical unimolecular decomposition using the Kinbot, but kinbot can not find the transition state for R_Addition_MultipleBond reactions (beta scission). For example, below is my radical.
Obviously, beta scission reactions can occur between bonds 2-3 or bond 2-1, but neither of these reactions was found by kinbot. It is not because the reaction barrier exceeds the cut-off value, but possibly due to the improperly generated initial structure.
I guess the beta scission of 2-1 bond corresponds to the R_Addition_MultipleBond_2_1_8 or R_Addition_MultipleBond_5_2_1? But both of these input files seem weird, and TS is not well located.
Other isomers in this PES also can not find the beta scission reactions. For example,
None of 3-2 , 3-4,and 3-11 bond breaks were found by kinbot. I have attached the kinbot.log files for the above two cases
kinbot_721842172121070000002.log
kinbot_721862261891070120002.log
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