pymatgen-structure

Name: pymatgen-structure
Author: jinzhezenggroup

113stars23forks

How to install pymatgen-structure?

jinzhezenggroup/computational-chemistry-agent-skills/pymatgen-structure

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

Installs into the current project.

Summary

Structure manipulation and crystal analysis workflows based on pymatgen. USE WHEN you need to read/write common atomistic formats (CIF, POSCAR, XYZ), build supercells, perform site substitution/doping, inspect symmetry (space group), or compute local structure descriptors for mat

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SKILL.md

1	# pymatgen Structure Operations
2
3	Use this skill to perform structure preprocessing and analysis with `pymatgen`.
4
5	## Scope
6
7	This skill should:
8
9	- require at least one user-provided structure file
10	- parse and normalize common structure formats
11	- perform requested geometry edits (for example supercell, substitution)
12	- run basic crystal analysis (for example symmetry, composition)
13	- write explicit output files and summarize key changes
14
15	This skill should not:
16
17	- submit HPC jobs
18	- run expensive DFT/MD production calculations
19	- invent missing scientific intent (for example random doping strategy) without confirmation
20
21	If the user asks for DFT submission, hand off to a submission skill such as `dpdisp-submit` after preprocessing is done.
22
23	## Hard requirement
24
25	The user must provide an input structure source (file path or explicit coordinates + lattice).
26
27	If structure input is missing, stop and ask for it.
28
29	## Supported input/output formats
30
31	Typical input formats:
32
33	- `cif`
34	- `POSCAR` / `CONTCAR`
35	- `xyz` (for non-periodic or when cell is provided separately)
36	- other formats supported by `pymatgen` IO backends
37
38	Typical output formats:
39
40	- `cif`
41	- `POSCAR`
42	- `xyz`
43	- optional JSON summaries
44
45	## Expected workflow
46
47	1. Read user-provided structure.
48	1. Validate periodicity and cell information.
49	1. Confirm requested operation (convert, supercell, substitution, analysis).
50	1. Collect only missing critical parameters.
51	1. Execute operation via `pymatgen`.
52	1. Write output structure(s) and a short result summary.
53	1. If requested, prepare handoff-ready files for downstream skills.
54
55	For concrete command patterns, see `references/commands-and-workflow.md`.
56
57	## Operations this skill should handle
58
59	### A) Format conversion
60
61	- convert between `cif` / `POSCAR` / `xyz`
62	- preserve lattice and species ordering when possible
63
64	### B) Supercell construction
65
66	- apply scaling matrix, for example `[[2,0,0],[0,2,0],[0,0,1]]`
67	- report final atom count and new lattice vectors
68
69	### C) Substitution / doping-like edits
70
71	- deterministic site substitution by species or by explicit site index
72	- report stoichiometry before/after
73	- ask user before applying random substitutions
74
75	### D) Symmetry and composition analysis
76
77	- reduced formula
78	- lattice parameters
79	- space group symbol/number
80	- optional primitive/conventional standardization when explicitly requested
81
82	### E) Local environment quick checks
83
84	- nearest-neighbor distances or coordination-style summaries
85	- report method/threshold assumptions
86
87	## Parameters to collect
88
89	### Must provide
90
91	- input structure path
92	- target operation type
93	- output path (or output naming rule)
94
95	### Operation-specific
96
97	For format conversion:
98
99	- output format
100
101	For supercell:
102
103	- scaling matrix or `(na, nb, nc)`
104
105	For substitution:
106
107	- source species/site selection
108	- target species
109	- substitution fraction or exact indices
110
111	For symmetry analysis:
112
113	- symmetry tolerance (if non-default behavior is desired)
114
115	## Required behavior
116
117	1. Check file existence/readability before processing.
118	1. Detect and report missing lattice info for periodic workflows.
119	1. Do not silently drop atoms or reorder species without notice.
120	1. Explicitly show assumptions (for example tolerance values).
121	1. Return exact output file paths.
122
123	## Defaulting policy
124
125	Allowed only for low-risk defaults, clearly labeled.
126
127	Reasonable defaults:
128
129	- symmetry tolerance defaults from `pymatgen` when user does not specify
130	- output basename derived from input name + operation suffix
131
132	Do not silently invent:
133
134	- lattice for periodic systems
135	- substitution ratio for doping tasks
136	- magnetic/electronic settings (outside this skill's scope)
137
138	## Expected output
139
140	Provide:
141
142	1. output file path(s)
143	1. concise summary of changes (atom count, composition, lattice deltas)
144	1. analysis result highlights (for example space group)
145	1. explicit assumptions and unresolved choices
146	1. next-step suggestion when user wants downstream DFT/MD submission
147
148	## Common failure points
149
150	- unreadable input file or ambiguous format
151	- xyz input lacking periodic cell when periodic workflow is requested
152	- invalid scaling matrix or impossible substitution request
153	- too aggressive tolerances causing unstable symmetry classification

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pymatgen-structure

113stars23forks

View on GitHub

How to install pymatgen-structure?

jinzhezenggroup/computational-chemistry-agent-skills/pymatgen-structure

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

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# pymatgen Structure Operations
2
3	Use this skill to perform structure preprocessing and analysis with `pymatgen`.
4
5	## Scope
6
7	This skill should:
8
9	- require at least one user-provided structure file
10	- parse and normalize common structure formats
11	- perform requested geometry edits (for example supercell, substitution)
12	- run basic crystal analysis (for example symmetry, composition)
13	- write explicit output files and summarize key changes
14
15	This skill should not:
16
17	- submit HPC jobs
18	- run expensive DFT/MD production calculations
19	- invent missing scientific intent (for example random doping strategy) without confirmation
20
21	If the user asks for DFT submission, hand off to a submission skill such as `dpdisp-submit` after preprocessing is done.
22
23	## Hard requirement
24
25	The user must provide an input structure source (file path or explicit coordinates + lattice).
26
27	If structure input is missing, stop and ask for it.
28
29	## Supported input/output formats
30
31	Typical input formats:
32
33	- `cif`
34	- `POSCAR` / `CONTCAR`
35	- `xyz` (for non-periodic or when cell is provided separately)
36	- other formats supported by `pymatgen` IO backends
37
38	Typical output formats:
39
40	- `cif`
41	- `POSCAR`
42	- `xyz`
43	- optional JSON summaries
44
45	## Expected workflow
46
47	1. Read user-provided structure.
48	1. Validate periodicity and cell information.
49	1. Confirm requested operation (convert, supercell, substitution, analysis).
50	1. Collect only missing critical parameters.
51	1. Execute operation via `pymatgen`.
52	1. Write output structure(s) and a short result summary.
53	1. If requested, prepare handoff-ready files for downstream skills.
54
55	For concrete command patterns, see `references/commands-and-workflow.md`.
56
57	## Operations this skill should handle
58
59	### A) Format conversion
60
61	- convert between `cif` / `POSCAR` / `xyz`
62	- preserve lattice and species ordering when possible
63
64	### B) Supercell construction
65
66	- apply scaling matrix, for example `[[2,0,0],[0,2,0],[0,0,1]]`
67	- report final atom count and new lattice vectors
68
69	### C) Substitution / doping-like edits
70
71	- deterministic site substitution by species or by explicit site index
72	- report stoichiometry before/after
73	- ask user before applying random substitutions
74
75	### D) Symmetry and composition analysis
76
77	- reduced formula
78	- lattice parameters
79	- space group symbol/number
80	- optional primitive/conventional standardization when explicitly requested
81
82	### E) Local environment quick checks
83
84	- nearest-neighbor distances or coordination-style summaries
85	- report method/threshold assumptions
86
87	## Parameters to collect
88
89	### Must provide
90
91	- input structure path
92	- target operation type
93	- output path (or output naming rule)
94
95	### Operation-specific
96
97	For format conversion:
98
99	- output format
100
101	For supercell:
102
103	- scaling matrix or `(na, nb, nc)`
104
105	For substitution:
106
107	- source species/site selection
108	- target species
109	- substitution fraction or exact indices
110
111	For symmetry analysis:
112
113	- symmetry tolerance (if non-default behavior is desired)
114
115	## Required behavior
116
117	1. Check file existence/readability before processing.
118	1. Detect and report missing lattice info for periodic workflows.
119	1. Do not silently drop atoms or reorder species without notice.
120	1. Explicitly show assumptions (for example tolerance values).
121	1. Return exact output file paths.
122
123	## Defaulting policy
124
125	Allowed only for low-risk defaults, clearly labeled.
126
127	Reasonable defaults:
128
129	- symmetry tolerance defaults from `pymatgen` when user does not specify
130	- output basename derived from input name + operation suffix
131
132	Do not silently invent:
133
134	- lattice for periodic systems
135	- substitution ratio for doping tasks
136	- magnetic/electronic settings (outside this skill's scope)
137
138	## Expected output
139
140	Provide:
141
142	1. output file path(s)
143	1. concise summary of changes (atom count, composition, lattice deltas)
144	1. analysis result highlights (for example space group)
145	1. explicit assumptions and unresolved choices
146	1. next-step suggestion when user wants downstream DFT/MD submission
147
148	## Common failure points
149
150	- unreadable input file or ambiguous format
151	- xyz input lacking periodic cell when periodic workflow is requested
152	- invalid scaling matrix or impossible substitution request
153	- too aggressive tolerances causing unstable symmetry classification

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