packmol-generate-mixture

Name: packmol-generate-mixture
Author: jinzhezenggroup

113stars23forks

How to install packmol-generate-mixture?

jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill packmol-generate-mixture

Installs into the current project.

Summary

A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined

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SKILL.md

1	# packmol-generate-mixture
2
3	Use Packmol to generate an initial packed configuration for a molecular mixture.
4
5	## Agent responsibilities (do these in order)
6
7	1. Collect inputs (ask if missing; do not guess):
8
9	- component structure files (XYZ), one per species (e.g. `species1.xyz`, `species2.xyz`)
10	- molecule counts for each species (e.g. `species1: 100`, `species2: 650`)
11	- either target density (g/cm^3) or a fixed cubic box length (Å)
12	- Packmol `tolerance` (Å)
13	- output location: output directory + output filename prefix (system name)
14
15	1. Validate inputs:
16
17	- confirm XYZ files exist and are readable
18	- confirm the first line (atom count) matches the number of coordinate lines
19	- if density-based box estimation is requested: confirm each molecule’s elemental composition can be inferred from the XYZ symbols
20
21	1. Decide box size:
22
23	- If user provides `box_length_A`: use it.
24	- Else compute `box_length_A` from density (see formula below).
25
26	1. Create a working folder at the requested output location:
27
28	- copy the component XYZ files into it (or reference them with absolute paths)
29
30	1. Write Packmol input `${system_name}.inp`:
31
32	- one `structure ... end structure` block per component
33	- all components share the same `inside box 0 0 0 L L L`
34
35	1. Run Packmol locally:
36
37	- Prefer: `uvx packmol -i ${system_name}.inp`
38	- If you need to force the source package: `uvx --from packmol packmol -i ${system_name}.inp`
39
40	1. Report results:
41
42	- exact output paths (inp, xyz, log)
43	- final box length (Å) and the parameters used (counts, density or fixed L, tolerance)
44	- basic sanity checks (total molecules, total atoms)
45
46	1. (Optional) Post-process for LAMMPS
47
48	If the user plans to run LAMMPS (especially ReaxFF), they often need a LAMMPS data file with correct box bounds.
49
50	- If you convert XYZ -> LAMMPS data with dpdata, dpdata may write default box bounds (e.g., 0..100 Å).
51	- Fix the bounds to match the Packmol cubic box length using `lammps-md-tools` from PyPI:
52
53	```bash
54	uvx --from lammps-md-tools lammps-fix-box \
55	--in input.data \
56	--out output.boxfix.data \
57	--L 60.690 \
58	--wrap
59	```
60
61	This rewrites `xlo/xhi`, `ylo/yhi`, `zlo/zhi` to `0..L`, zeroes tilt factors, and optionally wraps atoms into the box.
62
63	## What to ask the user (plain language)
64
65	If the user didn’t specify them, ask at minimum:
66
67	- Packing counts: how many molecules of each species? (e.g., `species1=100, species2=650`)
68	- Box definition: do you want to estimate a cubic box from a target density (g/cm^3), or do you want to provide a fixed cubic box length L (Å)?
69	- Tolerance: what Packmol `tolerance` (Å) should be used? (common starting point: 2.0 Å)
70	- Output location: which directory should receive the results, and what system name / filename prefix should be used?
71
72	If the user says “use defaults”, propose defaults:
73
74	- `tolerance = 2.0 Å`
75	- output dir: a `packed/` subfolder under the folder containing the input XYZ
76	- (density) do not assume; ask for it, but you may suggest a starting value the user can confirm.
77
78	## Input schema (recommended)
79
80	Example (replace with your own species/files):
81
82	```yaml
83	system_name: mixture_pack
84	output_dir: /path/to/output/packed
85	# Choose ONE of the following:
86	density_g_cm3: 0.25
87	# box_length_A: 60.69
88
89	tolerance_A: 2.0
90	components:
91	- name: species1
92	structure_file: /path/to/species1.xyz
93	number: 100
94	- name: species2
95	structure_file: /path/to/species2.xyz
96	number: 650
97	```
98
99	## Density → cubic box length (Å)
100
101	When `density_g_cm3` is provided and `box_length_A` is not, estimate L from total mass:
102
103	- infer each molecule’s elemental composition from its XYZ symbols
104	- use standard atomic masses (g/mol)
105	- compute total molar mass of the whole configuration (g/mol)
106	- convert to mass per configuration: `m_cfg = M_total / N_A` (g)
107	- compute volume in cm^3: `V_cm3 = m_cfg / density_g_cm3`
108	- convert to Å^3: `V_A3 = V_cm3 * 1e24`
109	- cubic length: `L_A = V_A3 ** (1/3)`
110
111	This is an initial packing estimate (geometry construction), not an equilibrated density.
112
113	## Output contract

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packmol-generate-mixture

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View on GitHub

How to install packmol-generate-mixture?

jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill packmol-generate-mixture

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# packmol-generate-mixture
2
3	Use Packmol to generate an initial packed configuration for a molecular mixture.
4
5	## Agent responsibilities (do these in order)
6
7	1. Collect inputs (ask if missing; do not guess):
8
9	- component structure files (XYZ), one per species (e.g. `species1.xyz`, `species2.xyz`)
10	- molecule counts for each species (e.g. `species1: 100`, `species2: 650`)
11	- either target density (g/cm^3) or a fixed cubic box length (Å)
12	- Packmol `tolerance` (Å)
13	- output location: output directory + output filename prefix (system name)
14
15	1. Validate inputs:
16
17	- confirm XYZ files exist and are readable
18	- confirm the first line (atom count) matches the number of coordinate lines
19	- if density-based box estimation is requested: confirm each molecule’s elemental composition can be inferred from the XYZ symbols
20
21	1. Decide box size:
22
23	- If user provides `box_length_A`: use it.
24	- Else compute `box_length_A` from density (see formula below).
25
26	1. Create a working folder at the requested output location:
27
28	- copy the component XYZ files into it (or reference them with absolute paths)
29
30	1. Write Packmol input `${system_name}.inp`:
31
32	- one `structure ... end structure` block per component
33	- all components share the same `inside box 0 0 0 L L L`
34
35	1. Run Packmol locally:
36
37	- Prefer: `uvx packmol -i ${system_name}.inp`
38	- If you need to force the source package: `uvx --from packmol packmol -i ${system_name}.inp`
39
40	1. Report results:
41
42	- exact output paths (inp, xyz, log)
43	- final box length (Å) and the parameters used (counts, density or fixed L, tolerance)
44	- basic sanity checks (total molecules, total atoms)
45
46	1. (Optional) Post-process for LAMMPS
47
48	If the user plans to run LAMMPS (especially ReaxFF), they often need a LAMMPS data file with correct box bounds.
49
50	- If you convert XYZ -> LAMMPS data with dpdata, dpdata may write default box bounds (e.g., 0..100 Å).
51	- Fix the bounds to match the Packmol cubic box length using `lammps-md-tools` from PyPI:
52
53	```bash
54	uvx --from lammps-md-tools lammps-fix-box \
55	--in input.data \
56	--out output.boxfix.data \
57	--L 60.690 \
58	--wrap
59	```
60
61	This rewrites `xlo/xhi`, `ylo/yhi`, `zlo/zhi` to `0..L`, zeroes tilt factors, and optionally wraps atoms into the box.
62
63	## What to ask the user (plain language)
64
65	If the user didn’t specify them, ask at minimum:
66
67	- Packing counts: how many molecules of each species? (e.g., `species1=100, species2=650`)
68	- Box definition: do you want to estimate a cubic box from a target density (g/cm^3), or do you want to provide a fixed cubic box length L (Å)?
69	- Tolerance: what Packmol `tolerance` (Å) should be used? (common starting point: 2.0 Å)
70	- Output location: which directory should receive the results, and what system name / filename prefix should be used?
71
72	If the user says “use defaults”, propose defaults:
73
74	- `tolerance = 2.0 Å`
75	- output dir: a `packed/` subfolder under the folder containing the input XYZ
76	- (density) do not assume; ask for it, but you may suggest a starting value the user can confirm.
77
78	## Input schema (recommended)
79
80	Example (replace with your own species/files):
81
82	```yaml
83	system_name: mixture_pack
84	output_dir: /path/to/output/packed
85	# Choose ONE of the following:
86	density_g_cm3: 0.25
87	# box_length_A: 60.69
88
89	tolerance_A: 2.0
90	components:
91	- name: species1
92	structure_file: /path/to/species1.xyz
93	number: 100
94	- name: species2
95	structure_file: /path/to/species2.xyz
96	number: 650
97	```
98
99	## Density → cubic box length (Å)
100
101	When `density_g_cm3` is provided and `box_length_A` is not, estimate L from total mass:
102
103	- infer each molecule’s elemental composition from its XYZ symbols
104	- use standard atomic masses (g/mol)
105	- compute total molar mass of the whole configuration (g/mol)
106	- convert to mass per configuration: `m_cfg = M_total / N_A` (g)
107	- compute volume in cm^3: `V_cm3 = m_cfg / density_g_cm3`
108	- convert to Å^3: `V_A3 = V_cm3 * 1e24`
109	- cubic length: `L_A = V_A3 ** (1/3)`
110
111	This is an initial packing estimate (geometry construction), not an equilibrated density.
112
113	## Output contract

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