Phase 0 – Inventory and triage (2026-09-30)

Result: in format 2.0 flowcharts, only a node’s parameters are settings. Paul’s view holds for every current plug-in. Every other attribute is either a constant or run-time state set in the step’s __init__, or a cache that the GUI derives from the parameters. The exceptions are three kinds of legacy file, written before a plug-in moved its settings into parameters; only one of them needs handling in the converter.

Method

• Parsed every flowchart on this Mac (1,332 files; the 38 other *.flow files are JavaScript type files in seamm_webui/frontend/node_modules) and listed each attribute outside _uuid, _title, extension, parameters and x/y/w/h, keeping only non-empty values (not None, 0, "", [], {}, or citation_level 2).

• For each attribute found, traced it to the plug-in’s code: where it is set, and whether any headless code reads it before setting it.

• Counted jobs and flowcharts in each machine’s datastore (read-only queries).

Extra attributes in current plug-ins: all junk

Step	Attributes	Where they come from
Table (table_step)	calls	Counter set to 0 in __init__, incremented in run (table.py:37, :326). A non-zero value restored from a file would shift the frequency test; none was found.
Loop (loop_step)	table, table_handle	None in __init__, set in run from the table variable (loop.py:83-84, :320-321). Always None in files.
Energy, Optimization, BandStructure, DOS, ChooseParameters (dftbplus_step); FHI-aims sub-steps	results, mapping_to_primitive, mapping_from_primitive	None in __init__ (dftbplus_step/base.py:96-99, fhi_aims_step/substep.py:44-48), set while running. Always None in files.
Reaction Path	optimizer	None in __init__, set while running (reaction_path.py:182, :1574). Always None in files.
Diffusivity, Thermal Conductivity	tensor_labels, colors, citation_level 1, the analysis arrays	Plotting constants and a citation level set in __init__; the arrays are empty in every file.
Every node	_tables	A GUI cache: TkNode.setup_results sets node.tables from the table entries of the results parameter (tk_node.py:1164-1179), and Node.existing_tables() gathers them so later steps can offer the tables in their dropdowns. Derivable from the parameters; phase 2 must recompute it when a flowchart is loaded.
Gaussian Energy, Optimization, Wavefunction Stability, Thermodynamics; Thermochemistry	_method (non-null in 349 nodes)	A GUI cache: set by reset_dialog from the method parameter (gaussian_step/tk_energy.py:226-242) and read only by the Tk results tab to filter the results list (tk_node.py:1055, :1194). The headless code uses get_method(P). Recomputed whenever the dialog opens. Nothing in the current thermochemistry_step reads it (one node, from an older version).
Every node	_title	Always the class’s default title (12 pairs such as FromSMILESStep → “from SMILES”, NVT → “NVT dynamics”). No plug-in or GUI code lets a user rename a step. Derivable; not needed in 3.0.

The comment in Node.to_dict() that keeps _method “because forcefield_step/forcefield.py does not use parameters yet” is stale: forcefield_step uses ForcefieldParameters (forcefield.py:40).

Legacy files: settings stored as attributes

Where	What	Handling
lammps_step Minimization, versions 2023.6.17 to 2024.7.21.1 (11 nodes in job directories on this Mac)	convergence, etol, ftol (a Pint quantity), maxiters, maxevals and their *_method / *_variable companions. These were the real settings until commit 5ee392d (2025-03-16) moved them into MinimizationParameters. 9 nodes hold the old defaults; 2 use ``convergence: crude``. All *_method values are “is” (a literal value).	Map in the converter (one small legacy table): convergence, etol, ftol → the parameters of the same name; maxiters → nsteps and maxevals → nevaluations (to confirm against 5ee392d in phase 3). Loading these files today silently runs them with the current defaults.
table_step before commit acfb417 (2021-12-21): ~/SEAMM/flowcharts/tutorial3.flow only (3 Table nodes, parameters null)	_method (“read”, “save”, “print current row”), name, filename, index_column, …	Replace the file with Tutorial 3 from Zenodo (record 10108673, 2023) rather than mapping.
seamm_dashboard/data/projects/MyProject/Job_000001/flowchart.flow	A test fixture from before plug-in versions and Parameters: LAMMPS settings as attributes, _visited, _description, and a lammps_flowchart key.	Leave it or delete it; the old Dashboard is superseded by the webui.

Other findings

• Malformed edges. Three SEAMM_DEV jobs (3885, 3886, 3976) contain five edges with edge_type null (3) or "next" (2) instead of "execution" – flowcharts built by scripts that called add_edge without an edge type, the exact pitfall the builder removes. The converter treats any edge with subtype next as an execution edge.

• Edge subtypes across all files: next 16,837, loop 695, exit 433. A loop at the end of a flowchart has no exit edge.

• Subflowcharts are stored under the key subflowchart by all 20 plug-ins that have one (DFTB+, LAMMPS, MOPAC, ORCA, Gaussian, Psi4, VASP, FHI-aims, TorchANI, Dimer Builder, Reaction Path, Structure, Subflowchart, Diffusivity, Thermal Conductivity, Thermochemistry, Thermomechanical, Energy Scan, Conformer Search, …), except lammps_flowchart in the Dashboard fixture.

• Parameter values are plain JSON (str 194,538; list 5,226; float 5,006; dict 4,691; int 3,429). No Pint, datetime or other encoded object appears inside a parameter; the only Pint value found is the legacy Minimization ftol attribute.

• YAML round trip. PyYAML 6.0.3’s safe_dump quotes yes, no, on, null, ~ and 0.10, and safe_load gets back exactly the same strings; ORCA:DFT@B3LYP/bse:def2-SVPD, $SMILES and 2026.6.28 pass unquoted. So the converter, which starts from typed JSON, needs no snapshot of parameter kinds. Coercing by kind (D3) is still needed for hand-written specs.

Inventory

Jobs and flowcharts in each datastore (jobs rows / flowcharts rows / distinct flowcharts used by jobs / first job), 2026-09-30:

Machine and datastore	Jobs	Flowcharts	Used by jobs	First job
This Mac, ~/SEAMM_DEV	2,076	981	950	2022-02-24
This Mac, ~/SEAMM	322	282	168	2023-11-07
This Mac, ~/SEAMM/SV	109	127	79	2022-02-25
ChemAI, seamm user (/D3/psaxe/SEAMM/Jobs)	2,477	321	252	2022-09-16
ChemAI, psaxe	0	0	0
MolSSI10 (/mnt/hdd2/psaxe/SEAMM/Jobs)	347	237	164	2023-06-29
TinkerCliffs/ARC (/projects/seamm/SEAMM/Jobs)	53,081	56	56	2025-05-28
paul.local	0	0	0

Loose flowcharts outside job directories: this Mac 115 (~/SEAMM/flowcharts 27, Testing/ 27, package tests and docs); a few dozen on each of ChemAI (~/ARC, ~/GM, ~/flowcharts, Science_Flowcharts), TinkerCliffs (~/GM, ~/flowcharts) and MolSSI10 (~/Work, tests).

Every job directory holds its own flowchart.flow, so TinkerCliffs has about 53,000 copies of 56 flowcharts. The migration converts by content: hash each file’s text, convert each distinct flowchart once, and reuse the result.

Consequences for the design

• D4 simplifies. No settings hooks are needed: a node’s settings are its parameters, full stop. A 3.0 step is its step name, parameters, sub-steps (for subflowchart steps) and optional layout. title is dropped.

• Phase 2 must rebuild the GUI caches on load: node.tables from the results parameter (a headless helper beside TkNode.setup_results) and each step’s method when its dialog opens (already the case). Test with the Exercise-Tk-dialogs pattern on a flowchart with tables.

• D10’s frozen converter is generic apart from one legacy table (lammps_step Minimization before 2025.3.16). No snapshot of plug-in parameter kinds is needed.

• Migration by content hash, with a cache, because of the job arrays.

• Remove the stale _method exception and comment from Node.to_dict() when the 2.0 writer is removed (phase 3).