gjf-flux

Name: gjf-flux
Author: jinzhezenggroup

113stars23forks

How to install gjf-flux?

jinzhezenggroup/computational-chemistry-agent-skills/gjf-flux

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

Installs into the current project.

Summary

Assemble and extract Gaussian .gjf input file sections (directives, route, title, molecule blocks, appendices) and build single- or multi-step Link1 jobs from modular component files. USE WHEN needed for generating, refactoring, templating, or scripting Gaussian job files.

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SKILL.md

1	# gjf-flux (Gaussian Job File Assembly & Extraction)
2
3	`gjf-flux` is a command-line workflow for modular Gaussian `.gjf` files:
4
5	- Extract a specific section from an existing `.gjf` (including Link1 multi-step jobs).
6	- Assemble directives/route/molecule/appendix blocks into a complete `.gjf`, or merge multiple tasks into a Link1 job.
7
8	## When to use
9
10	Use this skill when you need to:
11
12	- Reuse parts of Gaussian inputs across many calculations (e.g., route lines, molecule blocks, basis/constraints appendices).
13	- Programmatically build `.gjf` jobs from smaller files (fragments, templates, parameterized directives).
14	- Inspect/compare `.gjf` files by extracting specific sections.
15
16	## Assumptions / Parsing model (important)
17
18	`gjf-flux` assumes a standard Gaussian input layout:
19
20	- Link1 steps are separated by a blank line, then `--Link1--`, then a newline.
21	- Within each Link1 step, blocks are separated by blank lines.
22	- The route section begins at the first line starting with `#` and continues through subsequent lines.
23	- A molecule block is detected when the first line of a block looks like paired integers
24	(e.g., `0 1` or `0 1 0 1 0 1`), representing charge/multiplicity pairs.
25
26	If a `.gjf` deviates from these conventions, extraction may fail or misclassify blocks.
27
28	## Inputs you should request from the user
29
30	When helping a user, clarify:
31
32	1. Target action: extract vs assemble.
33	1. File paths:
34	- Existing `.gjf` to read, or component files to assemble.
35	1. For Link1 jobs:
36	- Which step to extract (`job_index`, 0-based), or how many steps to assemble.
37	1. Molecule content:
38	- Total charge/multiplicity, fragment charge/multiplicity (if using fragments), coordinate format.
39	1. Appendices:
40	- Whether there are basis sets, ECPs, ModRedundant constraints, etc.
41
42	## Core commands (cheat sheet)
43
44	### 1) Extract a section from a `.gjf`
45
46	```bash
47	uvx gjf-flux extract <section_name> <FILE.gjf> [--job_index N]
48	```
49
50	Where `<section_name>` is one of:
51
52	- `directives`
53	- `route`
54	- `title`
55	- `molecule` or `molecule-<idx>`
56	- `appendix` or `appendix-<idx>`
57
58	Notes:
59
60	- `<idx>` is 0-based.
61	- `--job_index` selects the Link1 step (0-based, default `0`).
62
63	Examples:
64
65	```bash
66	# Extract the route line from the first Link1 step
67	uvx gjf-flux extract route input.gjf
68
69	# Extract the second molecule block from step 0
70	uvx gjf-flux extract molecule-1 input.gjf
71
72	# Extract the first appendix block from Link1 step 2
73	uvx gjf-flux extract appendix-0 input.gjf --job_index 2
74	```
75
76	### 2) Assemble directives (Link0 commands)
77
78	```bash
79	uvx gjf-flux assemble directives --chk FILE --mem SIZE --nprocshared N
80	```
81
82	This command accepts key/value pairs in the form `--key value`.
83
84	Examples:
85
86	```bash
87	uvx gjf-flux assemble directives --chk job.chk --mem 16GB --nprocshared 16
88	```
89
90	Tip: redirect to a file for later composition:
91
92	```bash
93	uvx gjf-flux assemble directives --chk job.chk --mem 16GB --nprocshared 16 > directives.txt
94	```
95
96	### 3) Assemble the route section (`#` line)
97
98	```bash
99	uvx gjf-flux assemble route [-l p\|n\|t\|""] <keywords...>
100	```
101
102	Examples:
103
104	```bash
105	#p Opt B3LYP/6-31G(d)
106	uvx gjf-flux assemble route -l p Opt B3LYP/6-31G(d)
107
108	# Use quotes for keywords with parentheses
109	uvx gjf-flux assemble route -l p "Opt(MaxCycle=100)" "Freq"
110	```
111
112	Tip:
113
114	```bash
115	uvx gjf-flux assemble route -l p "Opt(MaxCycle=100)" "Freq" > route.txt
116	```
117
118	### 4) Merge molecule fragments into one molecule block
119
120	```bash
121	uvx gjf-flux assemble molecules <frag1.txt> <frag2.txt> ... [--as-fragment] [--charge INT] [--multi INT]
122	```
123
124	Each fragment file must follow this format:
125
126	- Line 1: `charge multiplicity` (e.g., `0 1`)
127	- Following lines: atomic coordinates (Gaussian-style)
128
129	Modes:
130
131	- Default: merges into a single molecule block.
132	- `--as-fragment`: assigns `Fragment=1,2,...` tags and expands the charge/multiplicity header.
133
134	Examples:
135
136	```bash
137	# Merge two fragments into a single molecule block
138	uvx gjf-flux assemble molecules fragA.txt fragB.txt > molecule.txt
139
140	# Merge as fragments, overriding total charge/multiplicity
141	uvx gjf-flux assemble molecules fragA.txt fragB.txt --as-fragment --charge 0 --multi 1 > molecule.txt
142	```
143
144	### 5) Assemble appendices
145
146	```bash
147	uvx gjf-flux assemble appendices <app1.txt> <app2.txt> ...
148	```
149
150	Examples:
151
152	```bash
153	uvx gjf-flux assemble appendices basis.txt modredundant.txt > appendix.txt
154	```
155
156	### 6) Assemble a complete single-step `.gjf`
157
158	```bash
159	uvx gjf-flux assemble job \
160	--directives directives.txt \
161	--route route.txt \

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gjf-flux

113stars23forks

View on GitHub

How to install gjf-flux?

jinzhezenggroup/computational-chemistry-agent-skills/gjf-flux

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

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# gjf-flux (Gaussian Job File Assembly & Extraction)
2
3	`gjf-flux` is a command-line workflow for modular Gaussian `.gjf` files:
4
5	- Extract a specific section from an existing `.gjf` (including Link1 multi-step jobs).
6	- Assemble directives/route/molecule/appendix blocks into a complete `.gjf`, or merge multiple tasks into a Link1 job.
7
8	## When to use
9
10	Use this skill when you need to:
11
12	- Reuse parts of Gaussian inputs across many calculations (e.g., route lines, molecule blocks, basis/constraints appendices).
13	- Programmatically build `.gjf` jobs from smaller files (fragments, templates, parameterized directives).
14	- Inspect/compare `.gjf` files by extracting specific sections.
15
16	## Assumptions / Parsing model (important)
17
18	`gjf-flux` assumes a standard Gaussian input layout:
19
20	- Link1 steps are separated by a blank line, then `--Link1--`, then a newline.
21	- Within each Link1 step, blocks are separated by blank lines.
22	- The route section begins at the first line starting with `#` and continues through subsequent lines.
23	- A molecule block is detected when the first line of a block looks like paired integers
24	(e.g., `0 1` or `0 1 0 1 0 1`), representing charge/multiplicity pairs.
25
26	If a `.gjf` deviates from these conventions, extraction may fail or misclassify blocks.
27
28	## Inputs you should request from the user
29
30	When helping a user, clarify:
31
32	1. Target action: extract vs assemble.
33	1. File paths:
34	- Existing `.gjf` to read, or component files to assemble.
35	1. For Link1 jobs:
36	- Which step to extract (`job_index`, 0-based), or how many steps to assemble.
37	1. Molecule content:
38	- Total charge/multiplicity, fragment charge/multiplicity (if using fragments), coordinate format.
39	1. Appendices:
40	- Whether there are basis sets, ECPs, ModRedundant constraints, etc.
41
42	## Core commands (cheat sheet)
43
44	### 1) Extract a section from a `.gjf`
45
46	```bash
47	uvx gjf-flux extract <section_name> <FILE.gjf> [--job_index N]
48	```
49
50	Where `<section_name>` is one of:
51
52	- `directives`
53	- `route`
54	- `title`
55	- `molecule` or `molecule-<idx>`
56	- `appendix` or `appendix-<idx>`
57
58	Notes:
59
60	- `<idx>` is 0-based.
61	- `--job_index` selects the Link1 step (0-based, default `0`).
62
63	Examples:
64
65	```bash
66	# Extract the route line from the first Link1 step
67	uvx gjf-flux extract route input.gjf
68
69	# Extract the second molecule block from step 0
70	uvx gjf-flux extract molecule-1 input.gjf
71
72	# Extract the first appendix block from Link1 step 2
73	uvx gjf-flux extract appendix-0 input.gjf --job_index 2
74	```
75
76	### 2) Assemble directives (Link0 commands)
77
78	```bash
79	uvx gjf-flux assemble directives --chk FILE --mem SIZE --nprocshared N
80	```
81
82	This command accepts key/value pairs in the form `--key value`.
83
84	Examples:
85
86	```bash
87	uvx gjf-flux assemble directives --chk job.chk --mem 16GB --nprocshared 16
88	```
89
90	Tip: redirect to a file for later composition:
91
92	```bash
93	uvx gjf-flux assemble directives --chk job.chk --mem 16GB --nprocshared 16 > directives.txt
94	```
95
96	### 3) Assemble the route section (`#` line)
97
98	```bash
99	uvx gjf-flux assemble route [-l p\|n\|t\|""] <keywords...>
100	```
101
102	Examples:
103
104	```bash
105	#p Opt B3LYP/6-31G(d)
106	uvx gjf-flux assemble route -l p Opt B3LYP/6-31G(d)
107
108	# Use quotes for keywords with parentheses
109	uvx gjf-flux assemble route -l p "Opt(MaxCycle=100)" "Freq"
110	```
111
112	Tip:
113
114	```bash
115	uvx gjf-flux assemble route -l p "Opt(MaxCycle=100)" "Freq" > route.txt
116	```
117
118	### 4) Merge molecule fragments into one molecule block
119
120	```bash
121	uvx gjf-flux assemble molecules <frag1.txt> <frag2.txt> ... [--as-fragment] [--charge INT] [--multi INT]
122	```
123
124	Each fragment file must follow this format:
125
126	- Line 1: `charge multiplicity` (e.g., `0 1`)
127	- Following lines: atomic coordinates (Gaussian-style)
128
129	Modes:
130
131	- Default: merges into a single molecule block.
132	- `--as-fragment`: assigns `Fragment=1,2,...` tags and expands the charge/multiplicity header.
133
134	Examples:
135
136	```bash
137	# Merge two fragments into a single molecule block
138	uvx gjf-flux assemble molecules fragA.txt fragB.txt > molecule.txt
139
140	# Merge as fragments, overriding total charge/multiplicity
141	uvx gjf-flux assemble molecules fragA.txt fragB.txt --as-fragment --charge 0 --multi 1 > molecule.txt
142	```
143
144	### 5) Assemble appendices
145
146	```bash
147	uvx gjf-flux assemble appendices <app1.txt> <app2.txt> ...
148	```
149
150	Examples:
151
152	```bash
153	uvx gjf-flux assemble appendices basis.txt modredundant.txt > appendix.txt
154	```
155
156	### 6) Assemble a complete single-step `.gjf`
157
158	```bash
159	uvx gjf-flux assemble job \
160	--directives directives.txt \
161	--route route.txt \

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