reacnetgenerator

Name: reacnetgenerator
Author: jinzhezenggroup

113stars23forks

How to install reacnetgenerator?

jinzhezenggroup/computational-chemistry-agent-skills/reacnetgenerator

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill reacnetgenerator

Installs into the current project.

Summary

Run ReacNetGenerator on reactive MD trajectories to generate reaction networks and reports. Use when the user wants to analyze LAMMPS dump/xyz/bond trajectories with ReacNetGenerator. Handles LAMMPS dump quirks like x/y/z vs xs/ys/zs by converting to x/y/z (orthorhombic + triclin

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SKILL.md

1	# ReacNetGenerator
2
3	## 10-second quickstart
4
5	- Run a standard LAMMPS dump workflow:
6	- `uvx --refresh --from reacnet-md-tools rng-pipeline ...`
7	- Analyze existing outputs (no rerun):
8	- `uvx --refresh --from reacnet-md-tools rng-query ...`
9
10	If you need full official flags (e.g. `--cell`, `--nopbc`, `--use-ase`, `--miso`, HMM matrices), use native:
11
12	- `uvx --refresh --from reacnetgenerator reacnetgenerator ...`
13
14	## What this skill is for
15
16	Use this skill for reactive MD post-processing when the user wants to:
17
18	- run ReacNetGenerator on `bond`, `dump`, `xyz`, or `extxyz` trajectories
19	- handle common LAMMPS trajectory issues before running analysis
20	- choose between a high-level wrapper (`reacnet-md-tools`) and the native `reacnetgenerator` CLI
21	- inspect generated `.reactionabcd` / `.species` outputs after a run
22
23	## References (read only when needed)
24
25	Read only what is relevant:
26
27	- If the user asks about official flags or default values: [references/cli.md](references/cli.md)
28	- If the user asks about PBC/cell/`--nopbc` or input-type choice: [references/pbc-and-inputs.md](references/pbc-and-inputs.md)
29	- If the user wants copy-paste commands: [references/examples.md](references/examples.md)
30
31	## Tool-selection rule
32
33	Choose the narrowest tool that solves the user’s request:
34
35	1. Use `rng-pipeline` by default for standard LAMMPS dump workflows.
36	1. Use native `reacnetgenerator` when the user needs official low-level flags not exposed by the wrapper.
37	1. Use `rng-query` when the user already has `.reactionabcd` / `.species` outputs and wants analysis rather than rerunning.
38	1. Use `rng-webapp` only when the user explicitly wants an interactive local browser UI.
39
40	## Ask only for the missing inputs
41
42	Usually you only need:
43
44	- trajectory path(s)
45	- input type: `bond \| dump \| xyz \| extxyz` if not obvious
46	- atom names for `-a/--atomname` unless they can be inferred from a LAMMPS data file
47	- whether the run should be treated as periodic, only if cell information is missing or ambiguous
48
49	Do not ask unnecessary questions when the trajectory already contains enough information.
50
51	## Default execution policy
52
53	### Preferred default: wrapper CLIs (`reacnet-md-tools`)
54
55	Use `reacnet-md-tools` for routine runs because it is safer and more agent-friendly:
56
57	- handles standard LAMMPS dump workflows
58	- can infer atom names from nearby `.data` files
59	- writes outputs into a predictable `out/<basename>/` directory
60	- reduces manual CLI assembly errors
61
62	When running the wrapper from an agent, prefer `uvx` so the latest published version is resolved automatically:
63
64	```bash
65	uvx --refresh --from reacnet-md-tools rng-pipeline --help
66	uvx --refresh --from reacnet-md-tools rng-query --help
67	```
68
69	### Fallback: native `reacnetgenerator`
70
71	Use native `reacnetgenerator` when the user explicitly needs official flags such as:
72
73	- `--miso`
74	- `--use-ase`
75	- `--ase-cutoff-mult`
76	- `--ase-pair-cutoffs`
77	- `--nopbc`
78	- `--cell`
79	- `-n/--nproc`
80	- `-s/--selectatoms`
81	- `--matrixa`
82	- `--matrixb`
83	- `--urls`
84
85	If using native CLI, follow the official flag semantics in [references/cli.md](references/cli.md).
86
87	## Decision rules
88
89	### Input type
90
91	- If the file clearly looks like a LAMMPS dump (`ITEM:` blocks), treat it as `dump`.
92	- If the input is a bond trajectory such as `bonds.reaxc`, treat it as `bond` / `lammpsbondfile`.
93	- If the input is `.xyz`, treat it as `xyz` unless it is explicitly `extxyz`.
94
95	### PBC / cell
96
97	Read [references/pbc-and-inputs.md](references/pbc-and-inputs.md) when choosing `--cell` or `--nopbc`.
98
99	Short version:
100
101	- For LAMMPS dump/lammpstrj with valid `BOX BOUNDS`, do not ask for `--cell`.
102	- For XYZ without cell info, ask whether the system should be treated as periodic.
103	- Use `--nopbc` only when the run is truly non-periodic, already unwrapped/reconstructed, or lacks meaningful periodic cell semantics.
104
105	### HMM
106
107	- For a quick first pass, use `--nohmm` unless the user e

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reacnetgenerator

113stars23forks

View on GitHub

How to install reacnetgenerator?

jinzhezenggroup/computational-chemistry-agent-skills/reacnetgenerator

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill reacnetgenerator

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# ReacNetGenerator
2
3	## 10-second quickstart
4
5	- Run a standard LAMMPS dump workflow:
6	- `uvx --refresh --from reacnet-md-tools rng-pipeline ...`
7	- Analyze existing outputs (no rerun):
8	- `uvx --refresh --from reacnet-md-tools rng-query ...`
9
10	If you need full official flags (e.g. `--cell`, `--nopbc`, `--use-ase`, `--miso`, HMM matrices), use native:
11
12	- `uvx --refresh --from reacnetgenerator reacnetgenerator ...`
13
14	## What this skill is for
15
16	Use this skill for reactive MD post-processing when the user wants to:
17
18	- run ReacNetGenerator on `bond`, `dump`, `xyz`, or `extxyz` trajectories
19	- handle common LAMMPS trajectory issues before running analysis
20	- choose between a high-level wrapper (`reacnet-md-tools`) and the native `reacnetgenerator` CLI
21	- inspect generated `.reactionabcd` / `.species` outputs after a run
22
23	## References (read only when needed)
24
25	Read only what is relevant:
26
27	- If the user asks about official flags or default values: [references/cli.md](references/cli.md)
28	- If the user asks about PBC/cell/`--nopbc` or input-type choice: [references/pbc-and-inputs.md](references/pbc-and-inputs.md)
29	- If the user wants copy-paste commands: [references/examples.md](references/examples.md)
30
31	## Tool-selection rule
32
33	Choose the narrowest tool that solves the user’s request:
34
35	1. Use `rng-pipeline` by default for standard LAMMPS dump workflows.
36	1. Use native `reacnetgenerator` when the user needs official low-level flags not exposed by the wrapper.
37	1. Use `rng-query` when the user already has `.reactionabcd` / `.species` outputs and wants analysis rather than rerunning.
38	1. Use `rng-webapp` only when the user explicitly wants an interactive local browser UI.
39
40	## Ask only for the missing inputs
41
42	Usually you only need:
43
44	- trajectory path(s)
45	- input type: `bond \| dump \| xyz \| extxyz` if not obvious
46	- atom names for `-a/--atomname` unless they can be inferred from a LAMMPS data file
47	- whether the run should be treated as periodic, only if cell information is missing or ambiguous
48
49	Do not ask unnecessary questions when the trajectory already contains enough information.
50
51	## Default execution policy
52
53	### Preferred default: wrapper CLIs (`reacnet-md-tools`)
54
55	Use `reacnet-md-tools` for routine runs because it is safer and more agent-friendly:
56
57	- handles standard LAMMPS dump workflows
58	- can infer atom names from nearby `.data` files
59	- writes outputs into a predictable `out/<basename>/` directory
60	- reduces manual CLI assembly errors
61
62	When running the wrapper from an agent, prefer `uvx` so the latest published version is resolved automatically:
63
64	```bash
65	uvx --refresh --from reacnet-md-tools rng-pipeline --help
66	uvx --refresh --from reacnet-md-tools rng-query --help
67	```
68
69	### Fallback: native `reacnetgenerator`
70
71	Use native `reacnetgenerator` when the user explicitly needs official flags such as:
72
73	- `--miso`
74	- `--use-ase`
75	- `--ase-cutoff-mult`
76	- `--ase-pair-cutoffs`
77	- `--nopbc`
78	- `--cell`
79	- `-n/--nproc`
80	- `-s/--selectatoms`
81	- `--matrixa`
82	- `--matrixb`
83	- `--urls`
84
85	If using native CLI, follow the official flag semantics in [references/cli.md](references/cli.md).
86
87	## Decision rules
88
89	### Input type
90
91	- If the file clearly looks like a LAMMPS dump (`ITEM:` blocks), treat it as `dump`.
92	- If the input is a bond trajectory such as `bonds.reaxc`, treat it as `bond` / `lammpsbondfile`.
93	- If the input is `.xyz`, treat it as `xyz` unless it is explicitly `extxyz`.
94
95	### PBC / cell
96
97	Read [references/pbc-and-inputs.md](references/pbc-and-inputs.md) when choosing `--cell` or `--nopbc`.
98
99	Short version:
100
101	- For LAMMPS dump/lammpstrj with valid `BOX BOUNDS`, do not ask for `--cell`.
102	- For XYZ without cell info, ask whether the system should be treated as periodic.
103	- Use `--nopbc` only when the run is truly non-periodic, already unwrapped/reconstructed, or lacks meaningful periodic cell semantics.
104
105	### HMM
106
107	- For a quick first pass, use `--nohmm` unless the user e

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Type