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1.0.2

Getting started

  • 1. Installation
    • 1.1. Dependencies
    • 1.2. Install in docker
    • 1.3. Common issues
      • 1.3.1. Numpy errors while importing the Fortran force kernels
      • 1.3.2. Error building pfft-python due to missing curl/wget
  • 2. Usage overview for HylleraasMD
    • 2.1. Running parallel simulations
    • 2.2. Running tests
  • 3. Configuration file
    • 3.1. Configuration file keywords
      • 3.1.1. Metadata keywords
      • 3.1.2. Particle keywords
      • 3.1.3. Simulation keywords
      • 3.1.4. Field keywords
      • 3.1.5. Bond keywords
      • 3.1.6. Electrostatic keywords
  • 4. Topology and structure file
    • 4.1. Required datasets
    • 4.2. Optional datasets
  • 5. Command line arguments
    • 5.1. Required arguments
    • 5.2. Optional arguments
  • 6. Constants and Units

Examples

  • 1. Examples
    • 1.1. Ideal gas
    • 1.2. Ideal chains
    • 1.3. Stiff rods
    • 1.4. Helixes
    • 1.5. Phase separation
    • 1.6. Diblock copolymers
    • 1.7. Lipid bilayer self-assembly
    • 1.8. Peptide in lipid bilayer
    • 1.9. SDS

Theory

  • 1. Theory
    • 1.1. External potential
    • 1.2. Force interpolation
    • 1.3. Reciprocal space calculations
    • 1.4. Filter
    • 1.5. Hamiltonian form
  • 2. Intramolecular bonds
    • 2.1. Two-particle bonds
    • 2.2. Three-particle bonds
    • 2.3. Four-particle bonds
  • 3. Electrostatic interactions
    • 3.1. Specifying electrostatics

Developer documentation

  • 1. Interaction energy functionals
    • 1.1. \(\chi\)–interaction and \(\kappa\)–incompressibility
    • 1.2. Only \(\kappa\)–incompressibility
    • 1.3. Only \(\phi^2\)
    • 1.4. Implementing new interaction energy forms
  • 2. Filtering
    • 2.1. Implementing new filters
  • 3. Benchmarks
    • 3.1. Bonded forces
    • 3.2. Particle–field forces
  • 4. API reference
    • 4.1. Integrator
      • integrate_position()
      • integrate_velocity()
    • 4.2. Thermostat
      • _random_chi_squared()
      • _random_gaussian()
      • csvr_thermostat()
    • 4.3. Hamiltonian
      • Hamiltonian
        • Hamiltonian.__init__()
        • Hamiltonian._setup()
      • SquaredPhi
        • SquaredPhi.__init__()
        • SquaredPhi.setup()
      • DefaultNoChi
        • DefaultNoChi.__init__()
        • DefaultNoChi.setup()
      • DefaultWithChi
        • DefaultWithChi.__init__()
        • DefaultWithChi.setup()
    • 4.4. Force
      • Angle
        • Angle.atom_3
      • Bond
        • Bond.atom_1
        • Bond.atom_2
        • Bond.equilibrium
        • Bond.strength
      • Chi
        • Chi.atom_1
        • Chi.atom_2
        • Chi.interaction_energy
      • Dielectric_type
        • Dielectric_type.atom_1
        • Dielectric_type.dielectric_value
      • Dihedral
        • Dihedral.atom_1
        • Dihedral.atom_2
        • Dihedral.atom_3
        • Dihedral.atom_4
        • Dihedral.coeffs
        • Dihedral.dih_type
      • compute_angle_forces__plain()
      • compute_bond_forces__plain()
      • compute_dihedral_forces__plain()
      • dipole_forces_redistribution()
      • find_all_paths()
      • prepare_bonds()
      • prepare_bonds_old()
      • prepare_index_based_bonds()
      • propensity_potential_coeffs()
    • 4.5. Logger
      • Logger
        • Logger.setup()
      • MPIFilterRoot
        • MPIFilterRoot.filter()
      • MPIFilterAll
        • MPIFilterAll.filter()
    • 4.6. Input parser
      • Config
        • Config.a
        • Config.angle_bonds
        • Config.barostat
        • Config.barostat_type
        • Config.bonds
        • Config.box_size
        • Config.cancel_com_momentum
        • Config.chi
        • Config.conv_crit
        • Config.convergence_type
        • Config.coulomb_constant
        • Config.coulombtype
        • Config.dielectric_const
        • Config.dielectric_type
        • Config.dihedrals
        • Config.domain_decomposition
        • Config.dtype
        • Config.file_name
        • Config.gas_constant
        • Config.hamiltonian
        • Config.initial_energy
        • Config.integrator
        • Config.kappa
        • Config.m
        • Config.mass
        • Config.max_molecule_size
        • Config.mesh_size
        • Config.n_b
        • Config.n_flush
        • Config.n_particles
        • Config.n_print
        • Config.n_steps
        • Config.name
        • Config.pol_mixing
        • Config.pressure
        • Config.respa_inner
        • Config.rho0
        • Config.self_energy
        • Config.sigma
        • Config.start_temperature
        • Config.tags
        • Config.target_pressure
        • Config.target_temperature
        • Config.tau
        • Config.tau_p
        • Config.thermostat_coupling_groups
        • Config.thermostat_work
        • Config.time_step
        • Config.type_charges
      • check_NPT_conditions()
      • check_angles()
      • check_bonds()
      • check_box_size()
      • check_cancel_com_momentum()
      • check_charges()
      • check_charges_types_list()
      • check_chi()
      • check_config()
      • check_dielectric()
      • check_dihedrals()
      • check_domain_decomposition()
      • check_hamiltonian()
      • check_integrator()
      • check_m()
      • check_mass()
      • check_max_molecule_size()
      • check_n_b()
      • check_n_flush()
      • check_n_particles()
      • check_n_print()
      • check_name()
      • check_start_and_target_temperature()
      • check_tau()
      • check_thermostat_coupling_groups()
      • parse_config_toml()
      • read_config_toml()
      • sort_dielectric_by_type_id()
    • 4.7. Field
      • compute_field_and_kinetic_energy()
      • compute_field_energy_q_GPE()
      • compute_field_force()
      • compute_self_energy_q()
      • domain_decomposition()
      • initialize_pm()
      • update_field()
      • update_field_force_q()
      • update_field_force_q_GPE()
    • 4.8. File input/output
      • OutDataset
        • OutDataset.close_file()
        • OutDataset.flush()
        • OutDataset.is_open()
      • distribute_input()
      • setup_time_dependent_element()
      • store_data()
      • store_static()

Links

  • PyPI
  • Source code
  • Issue tracker
  • Citation
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© Copyright 2021, Morten Ledum, Xinmeng Li, Samiran Sen, Manuel Carrer, Sigbjørn Løland Bore.

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