fix(skills): align runtime and input validation guidance

ACK: keep the training command as dp because DP-GEN appends backend flags; accept NumPy directories or HDF5 init data; qualify descriptor spelling by installed backend; remove the assets layout assumption; and add an explicit post-iteration monitoring stage.

NAK: the older findings about list numbering, TensorFlow-only wording, empty systems syntax, missing confirmation, absent resources, remote_root and batch casing requirements, link containment, and weak machine-field assertions are already resolved in the current tree, so no duplicate changes are needed.

Author: SchrodingersCattt

skills/dpgen-run/SKILL.md

@@ -36,5 +36,5 @@ Use this skill for the iterative train, explore, label, and retrain workflow.
 
 - Never merge the JSON files or invent paths, queues, modules, or commands.
 - Preserve descriptor, backend, thresholds, schedules, ensemble, and `type_map` choices.
-- Spell `se_atten_v2` exactly; `fp_style: "none"` is invalid for current `dpgen run`.
+- Check `se_atten_v2` against the installed backend; `fp_style: "none"` is invalid.
 - Stop and ask when required scientific or execution inputs are undiscoverable.

skills/dpgen-run/references/validation-and-run.md

@@ -19,13 +19,15 @@ DP-GEN can fill it from `init_data_sys`. Verify `deepmd_version` and the
 installed stack before using version-specific descriptors or features.
 
 `train_backend` accepts `tensorflow` and `pytorch`, but compatibility still
-depends on the installed DeePMD-kit and descriptor. Verify the combination;
-spell `se_atten_v2` exactly. Ordinary LAMMPS exploration uses the default
+depends on the installed DeePMD-kit and descriptor. Verify descriptor spelling
+against that backend; current releases register `se_atten_v2`.
+Ordinary LAMMPS exploration uses the default
 `model_devi_engine`; set an alternative only when verified. Current `dpgen run`
 does not accept `fp_style: "none"`.
 
-Each `init_data_sys` directory must contain `type_map.raw`, `type.raw`, and
-`set.000/`; every `type_map.raw` must match `param.json.type_map` exactly.
+Each `init_data_sys` entry may be a DeepMD NumPy system directory or an HDF5
+file. Each NumPy directory must contain at least `type.raw` and `set.000/`.
+When `type_map.raw` is present, it must match `param.json.type_map` exactly.
 
 ## 2. `machine.json` essentials
 
@@ -38,8 +40,8 @@ for generic local, scheduler, and SSH shapes.
 
 The launcher shell and dispatched tasks are different environments. Scheduler
 jobs must activate their own runtime through `source_list`; outer activation is
-not inherited reliably. The training command must select the same backend as
-`train_backend` (for DeePMD-kit 3.x PyTorch this may be `dp --pt`). Validate
+not inherited reliably. Keep the training command as `dp`; DP-GEN appends
+backend flags such as `--pt` or `--jax` from `train_backend`. Validate
 commands, context types, batch aliases, roots, and resources against installed
 DPDispatcher rather than normalizing by assumption.
 

skills/dpgen-run/references/workflow.md

@@ -17,6 +17,12 @@ contexts, and resources, and `dpgen run param.json machine.json` as the launcher
 Preparation needs Python and DP-GEN. Execution also needs DeePMD-kit, the
 exploration engine, the selected FP software, and any scheduler runtime.
 
+## Monitoring stage
+
+After each iteration, record RMSE, model-deviation, and FP outcomes by system
+and condition. Use [monitoring guidance](monitoring.md) before changing settings
+or restarting a stalled iteration.
+
 ## Preparation policy
 
 Inspect existing configuration files, training inputs, dataset metadata, and
@@ -38,12 +44,12 @@ project/
 |-- machine.json
 |-- init_data/
 |   `-- raw_xxx/          # DeepMD NumPy system(s)
-|-- assets/               # structures and runtime support files
+|-- inputs/               # optional structures and backend inputs
 `-- iter.*/               # created by DP-GEN
 ```
 
 Keep repeated experiments in separate, clearly named directories derived from a
-reviewed base configuration. Backend-specific files belong under `assets/` or
+reviewed base configuration. Backend-specific files belong under `inputs/` or
 the path explicitly required by the selected backend.
 
 ## Reporting contract