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exact ts search #73

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7 tasks done
Tracked by #5
joshkamm opened this issue May 7, 2024 · 0 comments · May be fixed by #85
Open
7 tasks done
Tracked by #5

exact ts search #73

joshkamm opened this issue May 7, 2024 · 0 comments · May be fixed by #85
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joshkamm commented May 7, 2024 •
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  • turn on exact ts search in pyGSM
  • output a separate file that contains just the transition state xyz
  • aggregate all of the transition states into a single multi-xyz file (in stk_se_de_gsm_single_node_parallel)?
  • check suzuki example output on athena from submitting as slurm script
  • fix issue with opt_i.xyz files
  • remind myself how visualization handles some strings failing and do the same thing when searching for optimized ts's
  • sort transition_states.xyz by energy
@joshkamm joshkamm mentioned this issue May 7, 2024
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@joshkamm joshkamm self-assigned this May 7, 2024
joshkamm added a commit that referenced this issue Jun 19, 2024
@joshkamm
#73 uncomment ts search following de_gsm
a43c3c5
@joshkamm joshkamm linked a pull request Jul 17, 2024 that will close this issue
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joshkamm added a commit that referenced this issue Jul 18, 2024
@joshkamm
#73 wip aggregating all transition states into single xyz file
a4199c3
joshkamm added a commit that referenced this issue Jul 19, 2024
@joshkamm
#73 aggregate all transition states into a single xyz file
b6cd7de
joshkamm added a commit that referenced this issue Aug 13, 2024
@joshkamm
#73 move aggregate_transition_states to own function
3aadebf 
also globbed files instead enumerating in case some strings fail
joshkamm added a commit that referenced this issue Aug 14, 2024
@joshkamm
#73 sort transition_states.xyz by energy
0e3f327
joshkamm added a commit that referenced this issue Aug 22, 2024
@joshkamm
#73 add pixi tasks for running examples
e7df226
joshkamm added a commit that referenced this issue Sep 4, 2024
@joshkamm
#73 update example output
f64e709 
also updated gitignore and pixi tasks
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joshkamm/issue73 ZimmermanGroup/py-conformational-sampling
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