Computational-chemistry-agent-skills dft-qe

Generate Quantum ESPRESSO DFT input tasks from a user-provided structure plus user-specified DFT settings. Use when the user wants to prepare QE calculations such as SCF, NSCF, relax, vc-relax, MD, bands, DOS, or phonons starting from a structure file or coordinates together with pseudopotentials, functional choice, cutoffs, k-point settings, smearing, spin/charge, and convergence parameters. This skill prepares the QE task only; use a separate submission skill such as dpdisp-submit to submit the generated task.

install

source · Clone the upstream repo

git clone https://github.com/jinzhezenggroup/computational-chemistry-agent-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/quantum-chemistry/dft-qe" ~/.claude/skills/jinzhezenggroup-computational-chemistry-agent-skills-dft-qe && rm -rf "$T"

manifest: quantum-chemistry/dft-qe/SKILL.md

source content

DFT with Quantum ESPRESSO

Use this skill to build a QE DFT task from a user-provided structure and DFT settings.

Scope

This skill should:

require a user-provided structure
read or normalize the structure input
identify the target calculation type
collect the minimum required DFT settings
generate the QE input file
organize the task directory in a way that can be handed off to a submission skill
state assumptions and unresolved choices

This skill should not:

submit jobs
manage schedulers
handle remote execution
invent critical scientific parameters

If the user wants the task submitted, hand off to another skill such as

dpdisp-submit

after the QE task is generated.

Hard requirement

The user must provide a structure.

Do not generate a QE task without a user-provided structure source. If the structure is missing, stop and ask for it.

Structure input convention

Use this bundled example-plus-layout pattern as the reference:

generated QE input example:
```
assets/pw-water-0.in
```
user-provided structure staging pattern:
```
openclaw_input/
```
containing files such as
```
structure.xyz
```
and
```
CELL
```

Treat this as the canonical pattern for what the user is expected to provide and what this skill is expected to generate.

The structure format does not need to be fixed to xyz. If the user provides another reasonable atomistic structure format, convert or normalize it as needed. When format conversion is needed, use the

dpdata-cli

skill.

For periodic systems, ensure cell information is preserved. If a plain xyz file is used, cell data must be provided separately, for example through a

CELL

file.

For a concrete file-oriented workflow, see

references/commands-and-workflow.md

Expected workflow

Start from a user-provided structure.
Normalize the structure into the task layout if needed.
Determine the target QE calculation type.
Collect only the missing critical DFT parameters.
Generate the QE input file.
Place the generated task in a runnable task directory.
If submission is requested, pass that directory to
```
dpdisp-submit
```
.

DFT parameters to collect

Must provide

Do not generate a formal QE task unless these are known or explicitly confirmed:

```
calculation
```
```
input_dft
```
```
ecutwfc
```
```
pseudo_dir
```
pseudopotential file for each element

Usually should be explicit

These should normally be confirmed rather than guessed:

```
vdw_corr
```
when dispersion may matter
```
ecutrho
```
when relevant to the pseudopotential family or workflow
```
K_POINTS
```
setting, for example
```
gamma
```
or an automatic mesh
occupation / smearing settings for metallic or ambiguous systems
```
conv_thr
```
```
electron_maxstep
```

Task-specific additions

Also collect task-dependent parameters when relevant.

For

relax

vc-relax

```
forc_conv_thr
```
```
etot_conv_thr
```
```
cell_dofree
```
for
```
vc-relax
```

For

md

```
nstep
```
```
dt
```
```
ion_temperature
```
```
tempw
```
```
ion_dynamics
```

For spin-polarized or magnetic systems:

```
nspin
```
```
starting_magnetization
```
charge or spin-related settings if requested

For advanced workflows if explicitly requested:

Hubbard U settings
hybrid-functional settings
electric field settings such as
```
edir
```
,
```
emaxpos
```
, or related controls

Do not ask for everything at once; ask only for the missing essentials.

Required behavior

Inspect the provided structure if accessible.
Determine elements, cell information, and coordinate representation.
If format normalization is needed, convert the structure using
```
dpdata-cli
```
.
Confirm the QE task type.
Gather only the missing critical DFT settings.
Generate the QE input yourself.
Explain assumptions clearly.
Flag unresolved scientific choices instead of hiding them.
Prepare the task directory so another skill can submit it.

Template pattern

Use the QE example input included in this repository:

assets/pw-water-0.in

as the reference pattern for how a QE task is organized and how the

pw.x

input is laid out.

In this workflow:

the user provides the structure in
```
openclaw_input
```
-style form
this skill generates the QE input task, analogous to files like
```
assets/pw-water-0.in
```
a separate submission skill handles the job script and submission stage

Do not hard-code the example chemistry. Reuse only the workflow pattern.

Defaulting policy

Allowed only for low-risk, clearly labeled assumptions.

Reasonable provisional defaults:

```
calculation='scf'
```
for a plain single-point request
standard electronic convergence threshold when the user does not care
basic verbosity settings

Do not silently invent:

structure data
pseudopotential filenames
production cutoffs
production k-point meshes
magnetic state for open-shell systems
Hubbard / vdW / hybrid settings
metallic smearing behavior when the system character is unclear

Expected output

Provide:

the full QE input file
a short summary of the chosen settings
explicit assumptions
any decisions the user should still confirm
the generated task directory or file set for the next skill
if submission is requested, explicitly say the next step is
```
dpdisp-submit
```

Minimal

pw.x

structure

&CONTROL
  calculation = 'scf'
  prefix = 'system'
  outdir = './'
/
&SYSTEM
  ibrav = 0
  nat = ...
  ntyp = ...
  ecutwfc = ...
  ecutrho = ...
/
&ELECTRONS
  conv_thr = 1.0d-8
/
ATOMIC_SPECIES
...
CELL_PARAMETERS angstrom
...
ATOMIC_POSITIONS angstrom
...
K_POINTS automatic
kx ky kz 0 0 0

Handoff rule

When the user asks to submit the generated QE task, do not implement submission logic here. Instead:

finish generating the QE task directory and input file
tell the user the task is ready for submission
hand off to
```
dpdisp-submit
```

Common failure points

missing user-provided structure
missing cell for periodic systems
incomplete pseudopotential mapping
```
nat
```
/
```
ntyp
```
inconsistent with the structure
missing or poor cutoffs
missing or inappropriate smearing
omitted spin settings for magnetic cases
requesting post-processing or phonons without prerequisite context