phonopy

Name: phonopy
Author: jinzhezenggroup

113stars23forks

How to install phonopy?

jinzhezenggroup/computational-chemistry-agent-skills/phonopy

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

Installs into the current project.

Summary

General phonon-workflow skill built around phonopy, independent of force backend. USE WHEN you need to prepare finite-displacement phonon calculations, build force constants, and analyze phonon properties (band structure, DOS, thermal quantities) while obtaining forces from diffe

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SKILL.md

1	# Phonopy (Backend-Agnostic)
2
3	Use this skill as a general phonon orchestration layer.
4
5	It treats force calculation as a pluggable backend step and focuses on `phonopy` data flow.
6
7	## Scope
8
9	This skill should:
10
11	- generate displacement supercells from a user-provided structure
12	- define and validate force-collection requirements
13	- build force constants from collected forces
14	- run phonon analysis (band, DOS, thermal properties)
15	- summarize assumptions and remaining decisions
16
17	This skill should not:
18
19	- assume a single force engine
20	- fabricate force data
21	- submit cluster jobs directly
22
23	If execution/submission is required, hand off run steps to submission skills (for example `dpdisp-submit`) and backend-specific input skills.
24
25	## Hard requirement
26
27	Phonon workflows require both:
28
29	- a valid initial structure (unit cell / primitive context)
30	- force data on displaced supercells (or precomputed force constants)
31
32	If either is missing, stop and ask for it.
33
34	## Backend abstraction
35
36	Force provider may be one of:
37
38	- DFT backend (for example VASP or QE)
39	- ML force field backend (for example DeePMD/LAMMPS)
40
41	The role split should be:
42
43	1. `phonopy` skill: displacement generation, dataset/force-constant assembly, phonon analysis
44	1. backend skill: compute forces for each displaced supercell
45
46	## Expected workflow
47
48	1. Read and validate initial structure.
49	1. Confirm phonon objective (`band`, `dos`, `thermal`, combinations).
50	1. Choose supercell and displacement settings.
51	1. Generate displaced supercells (`phonopy -d` style).
52	1. Route displaced structures to selected backend for force evaluation.
53	1. Collect forces and build `FORCE_SETS` or force constants.
54	1. Run requested phonon analysis and export outputs.
55	1. Report assumptions, convergence caveats, and next steps.
56
57	For concrete command patterns, see `references/commands-and-workflow.md`.
58
59	## Parameters to collect
60
61	### Must provide
62
63	- initial structure file (placeholder examples like `structure.ext` mean real files such
64	as `POSCAR`, `.cif`, or other backend-compatible structure formats)
65	- backend choice for force evaluation
66	- supercell setting (matrix or size)
67	- displacement amplitude (`--amplitude` policy)
68	- target phonon outputs (`band`, `dos`, `thermal`)
69
70	### Usually should be explicit
71
72	- primitive matrix choice
73	- symmetry tolerance settings
74	- q-point mesh for DOS/thermal calculations
75	- band path definition source (if band requested)
76
77	### Task-specific
78
79	For `band`:
80
81	- high-symmetry path definition
82	- number of points per segment
83
84	For `dos`/`thermal`:
85
86	- mesh density
87	- temperature range/step for thermal properties
88
89	## Required behavior
90
91	1. Validate structure periodicity and cell.
92	1. Make backend boundary explicit before running force steps.
93	1. Keep traceable mapping between each displacement and force file.
94	1. Check force dataset completeness before force-constant build.
95	1. Report non-analytic corrections / long-range settings status when relevant.
96	1. Flag unresolved scientific choices instead of guessing silently.
97
98	## Defaulting policy
99
100	Allowed only for low-risk defaults with explicit labels.
101
102	Reasonable defaults:
103
104	- finite-displacement workflow as baseline
105	- moderate displacement amplitude for first pass
106	- standard mesh/band resolution for exploratory analysis
107
108	Do not silently invent:
109
110	- backend force results
111	- production-level convergence settings
112	- band path conventions when crystal standard is unclear
113
114	## Expected output
115
116	Provide:
117
118	1. generated displacement task layout
119	1. force-data assembly status (`FORCE_SETS`/force constants)
120	1. requested phonon outputs (band/DOS/thermal files)
121	1. explicit assumptions and unresolved decisions
122	1. handoff guidance if backend execution/submission is pending
123
124	## Common failure points
125
126	- missing or inconsistent force files for displacements
127	- supercell too small for stable phonon results
128	- inconsistent units/conventions across backend outputs
129	- imaginary modes caused by insufficient convergence or setup choices
130	- unclear band path convention for non-standard cells

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phonopy

113stars23forks

View on GitHub

How to install phonopy?

jinzhezenggroup/computational-chemistry-agent-skills/phonopy

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

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Phonopy (Backend-Agnostic)
2
3	Use this skill as a general phonon orchestration layer.
4
5	It treats force calculation as a pluggable backend step and focuses on `phonopy` data flow.
6
7	## Scope
8
9	This skill should:
10
11	- generate displacement supercells from a user-provided structure
12	- define and validate force-collection requirements
13	- build force constants from collected forces
14	- run phonon analysis (band, DOS, thermal properties)
15	- summarize assumptions and remaining decisions
16
17	This skill should not:
18
19	- assume a single force engine
20	- fabricate force data
21	- submit cluster jobs directly
22
23	If execution/submission is required, hand off run steps to submission skills (for example `dpdisp-submit`) and backend-specific input skills.
24
25	## Hard requirement
26
27	Phonon workflows require both:
28
29	- a valid initial structure (unit cell / primitive context)
30	- force data on displaced supercells (or precomputed force constants)
31
32	If either is missing, stop and ask for it.
33
34	## Backend abstraction
35
36	Force provider may be one of:
37
38	- DFT backend (for example VASP or QE)
39	- ML force field backend (for example DeePMD/LAMMPS)
40
41	The role split should be:
42
43	1. `phonopy` skill: displacement generation, dataset/force-constant assembly, phonon analysis
44	1. backend skill: compute forces for each displaced supercell
45
46	## Expected workflow
47
48	1. Read and validate initial structure.
49	1. Confirm phonon objective (`band`, `dos`, `thermal`, combinations).
50	1. Choose supercell and displacement settings.
51	1. Generate displaced supercells (`phonopy -d` style).
52	1. Route displaced structures to selected backend for force evaluation.
53	1. Collect forces and build `FORCE_SETS` or force constants.
54	1. Run requested phonon analysis and export outputs.
55	1. Report assumptions, convergence caveats, and next steps.
56
57	For concrete command patterns, see `references/commands-and-workflow.md`.
58
59	## Parameters to collect
60
61	### Must provide
62
63	- initial structure file (placeholder examples like `structure.ext` mean real files such
64	as `POSCAR`, `.cif`, or other backend-compatible structure formats)
65	- backend choice for force evaluation
66	- supercell setting (matrix or size)
67	- displacement amplitude (`--amplitude` policy)
68	- target phonon outputs (`band`, `dos`, `thermal`)
69
70	### Usually should be explicit
71
72	- primitive matrix choice
73	- symmetry tolerance settings
74	- q-point mesh for DOS/thermal calculations
75	- band path definition source (if band requested)
76
77	### Task-specific
78
79	For `band`:
80
81	- high-symmetry path definition
82	- number of points per segment
83
84	For `dos`/`thermal`:
85
86	- mesh density
87	- temperature range/step for thermal properties
88
89	## Required behavior
90
91	1. Validate structure periodicity and cell.
92	1. Make backend boundary explicit before running force steps.
93	1. Keep traceable mapping between each displacement and force file.
94	1. Check force dataset completeness before force-constant build.
95	1. Report non-analytic corrections / long-range settings status when relevant.
96	1. Flag unresolved scientific choices instead of guessing silently.
97
98	## Defaulting policy
99
100	Allowed only for low-risk defaults with explicit labels.
101
102	Reasonable defaults:
103
104	- finite-displacement workflow as baseline
105	- moderate displacement amplitude for first pass
106	- standard mesh/band resolution for exploratory analysis
107
108	Do not silently invent:
109
110	- backend force results
111	- production-level convergence settings
112	- band path conventions when crystal standard is unclear
113
114	## Expected output
115
116	Provide:
117
118	1. generated displacement task layout
119	1. force-data assembly status (`FORCE_SETS`/force constants)
120	1. requested phonon outputs (band/DOS/thermal files)
121	1. explicit assumptions and unresolved decisions
122	1. handoff guidance if backend execution/submission is pending
123
124	## Common failure points
125
126	- missing or inconsistent force files for displacements
127	- supercell too small for stable phonon results
128	- inconsistent units/conventions across backend outputs
129	- imaginary modes caused by insufficient convergence or setup choices
130	- unclear band path convention for non-standard cells

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