Fix xtb opt with cartesian coordinates #247
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@@ Coverage Diff @@
## v1.3.5 #247 +/- ##
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Coverage 97.14% 97.15%
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Files 196 196
Lines 20172 20183 +11
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+ Hits 19597 19608 +11
Misses 575 575
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shoubhikraj
reviewed
Feb 7, 2023
| else: | ||
| list_of_ranges.append(f"{atom_range[0]}-{atom_range[-1]}") | ||
| atom_idxs = list( | ||
| sorted(int(i) + 1 for i in molecule.constraints.cartesian) |
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I am wondering if it would be useful to have autode log a warning if there is only one constrained atom in cartesian. (which does not really make sense). xTB seems to accept if one atom is mentioned in $constrain.
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I don't see anything bad happening if only one atom is constrained so not sure it should be a warning. Going to leave as is
(thanks for the review 👍🏼)
shoubhikraj
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Feb 7, 2023
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Feb 21, 2023
* Ignore doc paths for code CI (duartegroup#235) * Ignore doc paths for code CI * Update PR template * Add "ERROR" level to logging (duartegroup#231) * add ERROR level to logging * update docs for logging * update tests for logging * update changelog * Fix parsing Qchem v6 output (duartegroup#234) * Fix parsing Qchem v6 output * Fix units for values div mul (duartegroup#242) * Fix units for div mul * Update changelog * Update workflow (duartegroup#244) * Fix xtb opt with cartesian coordinates (duartegroup#247) * Fix xtb opt with cartesian coordinates * Update changelog [skip actions] * Remove hessian conversion on normal mode calculation (duartegroup#243) * Ensure no unit conversion in hessian * Use a copy for value and valuearray * Raise exception on value `to` with inplace * Add missed changelog updates * Template for v1.4.0 (duartegroup#203) * Make autodE compatible with Windows and change parallel process handling (duartegroup#202) * make autode compatible with windows: replace multiprocessing with joblib and loky * remove comment autode/utils.py * check total memory in utils * use loky for parallel processing * loky context is used for better handling of parallelisation * fixes for timeout wrapper in POSIX * use class instances instead of class attributes for Config * pass parent Config state into child processes * keep default timeout wrapper, also add new wrapper * separate parallelisation scheme for windows, restore default for linux/mac * fix test_config_in_worker_proc for posix * codecov on windows * add tests for config copy * change config implementation for updating in worker process * add context manager for temporary config, minor fix in experimental timeout for windows * add tests for context manager * use bash for installing xtb in CI runner * add tests for cleanup after timeout * exclude setup.py from codecov * make config picklable and easily readable * add test and minor fixes * move xtb install script to .github/scripts * use temporary_config for test_utils.py * update changelog and contributor list * resolve conflicts with v1.4.0 Co-authored-by: Tom Young <39765193+t-young31@users.noreply.github.com> * update docs (duartegroup#229) * update docs for windows installation and temporary_config * update docs for windows installation and temporary_config * minor edit Co-authored-by: Tom Young <39765193+t-young31@users.noreply.github.com> * Autouse tempoary_config (duartegroup#236) * minor fixes --------- Co-authored-by: Tom Young <39765193+t-young31@users.noreply.github.com>
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Resolves #245
Fixes cartesian coordinate constraints in XTB optimisations. I'm not convinced this ever worked correctly!
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