oqp.SimulationManager

SimulationManager — Unified Python interface for multi-scale simulations in OpenQP.

Supports four modes:
    qp        : Pure QM single-point (OpenQP)
    qmmm      : QM/MM (OpenQP + OpenMM via QMMM_MD)
    namd      : Non-adiabatic MD (PyRAI2MD + OpenQP)
    namd_qmmm : NAMD with QM/MM potential (PyRAI2MD + OpenQP + OpenMM)

Minimal usage
-------------
    manager = SimulationManager.from_template(
        "template_namd.json",
        folder="Nac_run",
        title="test1-1",
        xyz="test1-1.xyz",
    )
    manager.show_config()
    manager.run()

Attributes

ELEMENT_TO_Z
BUILTIN_TEMPLATES

Classes

OpenQPEngine
PyRAI2MDEngine
SimulationManager

Module Contents

ELEMENT_TO_Z

BUILTIN_TEMPLATES

class OpenQPEngine(config=None)

Runner = None

config

project

workdir

input_dict

back_door_data

results = None

setup_input(folder, openqp_content, title)

setup_input_with_xyz(folder, openqp_content, xyz_content, title)

prepare()

run()

run_qmmm()

class PyRAI2MDEngine(mode, config=None)

mode

config

prepare()

setup_files(folder, input_content, openqp_content, xyz_content, title)

Write the three NAMD files into folder:
    title           — PyRAI2MD control file
    title.openqp    — OpenQP electronic structure input
    title.xyz       — molecular coordinates

run(folder, title)

class SimulationManager(mode=None, folder='.', title='test1-1', xyz=None, pdb=None, qm_atoms=None, sections=None, namd=None, template=None, openqp_content=None, xyz_content=None, input_content=None, configs=None)

Unified interface for QM, QM/MM, NAMD, and NAMD-QM/MM simulations.

For NAMD modes, three files are generated in the working folder:
    title           — PyRAI2MD control (&CONTROL, &MOLECULE, &openqp, &MD)
    title.openqp    — OpenQP input ([input], [scf], [tdhf], [properties], ...)
    title.xyz       — molecular coordinates

:param mode: One of 'qp', 'qmmm', 'namd', 'namd_qmmm'.
:type mode: str
:param folder: Working directory.
:type folder: str
:param title: Project name (used for all filenames).
:type title: str
:param xyz: XYZ coordinates.
:type xyz: str or path
:param pdb: PDB file for QM/MM modes.
:type pdb: str or path, optional
:param qm_atoms: QM atom selection for QM/MM (e.g. '0-2').
:type qm_atoms: str, optional
:param sections: OpenQP section overrides.
:type sections: dict, optional
:param namd: PyRAI2MD section overrides (control, molecule, openqp, md).
:type namd: dict, optional
:param template: JSON template path or built-in name.
:type template: str, optional
:param openqp_content: Pre-built inputs (bypass auto-generation).
:type openqp_content: str, optional
:param xyz_content: Pre-built inputs (bypass auto-generation).
:type xyz_content: str, optional
:param input_content: Pre-built inputs (bypass auto-generation).
:type input_content: str, optional
:param configs: Engine-level config overrides.
:type configs: dict, optional

VALID_MODES

mode

folder = '.'

title = 'test1-1'

configs

openqp = None

pyrai2md = None

static check_dependencies()

Print the installation status of all required packages.

.. rubric:: Example

SimulationManager.check_dependencies()
# OpenQP      (QM engine)    ✓ installed (0.3.1)
# OpenMM      (MM engine)    ✓ installed (8.1.1)
# PyRAI2MD    (NAMD driver)  ✗ not installed

save_template(filepath, description=None)

Save current settings as a reusable JSON template.

classmethod from_template(template, **overrides)

Create a SimulationManager from a template with per-job overrides.

static list_templates(directory=None)

List built-in and user templates.

static create_template(filepath, mode, description=None, sections=None, namd=None)

Create a template JSON file from scratch.

show_config(name=None)

Inspect generated inputs.

name=None      → print all to console
name='openqp'  → return OpenQP input string
name='namd'    → return PyRAI2MD control string
name='xyz'     → return XYZ string
name='pdb'     → return PDB string
name='sections'→ return OpenQP sections dict
name='namd_sections' → return NAMD sections dict

set_config(section, key, value)

Modify OpenQP sections and regenerate .inp/.openqp.

.. rubric:: Example

manager.set_config("input", "basis", "cc-pvdz")
manager.set_config("tdhf", "nstate", 8)
manager.set_config("qmmm", "temperature", 350.0)

set_namd_config(section, key, value)

Modify PyRAI2MD control sections and regenerate control file.

:param section: One of 'control', 'molecule', 'openqp', 'md'.
:type section: str
:param key: Parameter name (e.g. 'step', 'temp', 'nstate').
:type key: str
:param value: New value.
:type value: any
:param Example: manager.set_namd_config("md", "step", 200)
                manager.set_namd_config("md", "temp", 350)
                manager.set_namd_config("molecule", "ci", 8)
                manager.set_namd_config("openqp", "threads", 80)

set_xyz(xyz)

set_pdb(pdb)

prepare()

run()

Rewrite files from current config, then execute.