Reorganize the wiki: sidebar, keyword index, document missing options
Add a sidebar and a generated A-Z keyword index; merge the two running pages;
rename Request-Actions, Conformational-Search and the VRC-TST page; move the
combinatorial and vdW options to Reaction search; document the options that
had no entry; drop rows for options removed from the code (Fireworks,
barrierless MESS blocks, rotdPy_inputs, vrc_tst_active_space); fix defaults.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
5534bb0
Reference: cite both KinBot papers
91737c7
Update setup requirements, backend table, file structure and index pages
3f49c12
Add the Stereochemistry page; document restart records, calculation names, MESS options and files
f1d6ad0
Document theory profiles, L0 options, fc_compile and scan settings; remove nn_pes, barrierless_saddle and NWChem
fbee3bc
document allow_l2_without_conf
6190247
document UQ frequency scaling parameters, fix keyword errors
- freq_uq: describe the log-uniform draw and the power-law application,
now that a factor and its reciprocal cancel exactly
- freq_uq_ref, freq_uq_max_exp: new keywords setting the reference
frequency and the cap on the low-frequency amplification
- imagfreq_uq: note that it is applied directly, without the
frequency-dependent scaling used for freq_uq
- uq: the on/off values were documented backwards, 0 is off
- erelfact_uq -> enrelfact_uq, the name the code actually accepts; the
documented spelling was rejected as an unrecognised option
- pstsymm_uq: was missing from the table
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
8e6d95c
document irc_maxcycle parameter for Gaussian IRC
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
a123b19
Update wiki: FairChem/UMA setup, ORCA docs, remove MESMER references
- Setting-Up: fix Python version to 3.10, add FairChem install/download
section with model table and sanity-check snippet, remove MESMER from
optional software list
- Master-Equation-Calculations: clarify only MESS is supported; remove
unsupported mesmer_command row
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
be2ed98
add FairChem/UMA and ORCA docs; fix Python version; add missing keywords
- Update qc parameter to list all 5 backends (gauss, nwchem, qchem, orca, fc)
- Add FairChem section: model download, task names, example input
- Add ORCA section with example input
- Add missing keywords: use_sella, sella_kwargs, sella_fmax, sella_steps,
calc_kwargs, imagfreq_threshold, guessmix, orcablocks, orcasimpleinput,
nn_model, fc_model_path, fc_task_name, fc_device
- Fix Python requirement 3.8 -> 3.10
- Add backend comparison table to setup page
6b91ad0
Updated Request Actions (markdown)
42bf9ac
Updated Quantum Chemistry (markdown)
83d7af6
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
ef7d8d3
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
0bf05b5
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
bcb3a24
Updated Quantum Chemistry (markdown)
bbabbba
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
aa0d579
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
b0488a6
Updated Request Actions (markdown)
1109fdc
Updated Input and Keywords (markdown)
db9d7ce
Updated Request Actions (markdown)
f5feda7
Updated Uncertainty Quantification (markdown)
2292b33
Updated Master Equation Calculations (markdown)
ebb292f
Updated Master Equation Calculations (markdown)
ba83755
Updated Computational Environment (markdown)
4338756
Updated Quantum Chemistry (markdown)
7289dda
Updated Variable reaction coordinate transition state theory (VRC‐TST) calculations (markdown)
626df25
Updated Conformational Search (markdown)
ff7c143
Updated Request Actions (markdown)
7ee6666
Updated Uncertainty Quantification (markdown)
d7bef1c