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duartegroup / autodE

automated reaction profile generation
https://duartegroup.github.io/autodE/
MIT License
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Failed to create a complete set of delocalised internal coordinates #313

Open eneas77 opened 6 months ago

eneas77 commented 6 months ago

Hi,

Running a TS search of a LDA deprotonation of a carbonyl compound, the following error appears halting the TS calculation:

"RuntimeError: Failed to create a complete set of delocalised internal coordinates. 125 < 3 N_atoms - 6. Likely due to missing primitives"

This happens after conformer calculation, at the TS stage, in both versions 1.4.1 & 1.3.5.

Any help will be appreciated.

Thanks.

E77

eneas77 commented 5 months ago

Hi,

v1.4.2 still fails in this. Any hints about what is going on?

Thanks

shoubhikraj commented 5 months ago

@eneas77 Does this happen during the adaptive path search, or during the TS optimisation? (If the adaptive path worked correctly, there should be a <hash>_hl_ad_<num>.xyz, or <hash>_ll_ad_<num>.xyz file in the transition_states folder (or a subfolder inside. The <hash> is alphanumeric and the <num> is a series of numbers.)

eneas77 commented 5 months ago

@shoubhikraj The following is a snapshot of the TS folder files:

f1B65f_BRs.txt f1B65f_ll_ad_20-35_3-20_hess_nwchem.nw f1B65f_ll_ad_20-35_3-20_hess_nwchem.out f1B65f_ll_ad_20-35_3-20_path.pdf f1B65f_ll_ad_20-35_3-20_path.xyz f1B65f_reactant.xyz /initial_path TS_f1B65f_ll_ad_20-35_3-20_hess_nwchem.nw TS_f1B65f_ll_ad_20-35_3-20_hess_nwchem.out TS_f1B65f_ll_ad_20-35_3-20_opt_10_hess_nwchem.nw TS_f1B65f_ll_ad_20-35_3-20_opt_10_hess_nwchem.out TS_f1B65f_ll_ad_20-35_3-20_opt_20_hess_nwchem.nw TS_f1B65f_ll_ad_20-35_3-20_opt_20_hess_nwchem.out TS_f1B65f_ll_ad_20-35_3-20_opt_30_hess_nwchem.nw TS_f1B65f_ll_ad_20-35_3-20_opt_30_hess_nwchem.out TS_f1B65f_ll_ad_20-35_3-20_optts_nwchem0_opt_trj.xyz TS_f1B65f_ll_ad_20-35_3-20_optts_nwchem_opt_trj.xyz

My guess is it happens during the TS opt.

Thanks