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    • Simulating a polyanion–counterion–solvent electric double-layer capactor using the Gaussian core model with smeared electrostatics
  • API Reference
    • algorithm
      • accelerated
        • numba_dot
        • numba_histogram
        • numba_histogram_bin_edges
        • numba_inner
        • numba_inner_parallel
      • correlation
        • correlation_fft
        • correlation_shift
        • msd_fft
        • msd_shift
      • molecule
        • center_of_mass
        • radius_of_gyration
      • topology
        • convert_cell_representation
        • create_atoms
        • get_cell_representation
        • reduce_box_vectors
        • unwrap
        • unwrap_edge
        • wrap
      • unit
        • get_lj_scale_factors
        • get_scale_factors
        • is_unitless
        • strip_unit
      • utility
        • depth_first_search
        • find_connected_nodes
        • get_closest_factors
        • is_lower_triangular
        • rebin
        • replicate
    • analysis
      • base
        • DynamicAnalysisBase
        • Hash
        • NumbaAnalysisBase
        • ParallelAnalysisBase
        • SerialAnalysisBase
      • electrostatics
        • calculate_relative_permittivity
        • DipoleMoment
      • polymer
        • calculate_relaxation_time
        • correlation_fft
        • correlation_shift
        • EndToEndVector
        • Gyradius
        • SingleChainStructureFactor
      • profile
        • calculate_potential_profile
        • calculate_surface_charge_density
        • DensityProfile
      • reader
        • LAMMPSDumpTrajectoryReader
      • structure
        • calculate_coordination_numbers
        • calculate_structure_factor
        • cosine_column_sum
        • cosine_column_sum_inplace
        • delta_fourier_transform_sum
        • generate_spherical_wavevectors
        • numba_cosine_sum
        • numba_cross_pythagorean_trigonometric_identity
        • numba_delta_fourier_transform
        • numba_pythagorean_trigonometric_identity
        • numba_sine_sum
        • psf_trigonometric
        • radial_fourier_transform
        • radial_histogram
        • sine_column_sum
        • sine_column_sum_inplace
        • ssf_trigonometric
        • zeroth_order_hankel_transform
        • IntermediateScatteringFunction
        • RadialDistributionFunction
        • StructureFactor
      • thermodynamics
        • ConstantVolumeHeatCapacity
      • transport
        • calculate_conductivity
        • calculate_electrophoretic_mobilities
        • calculate_transference_numbers
        • calculate_transport_coefficients
        • msd_fft
        • msd_shift
        • Onsager
    • fit
      • distribution
        • weibull
      • exponential
        • biexp
        • exp
        • exp1
        • exp2
        • stretched_exp
      • fourier
        • fourier
        • fourier1
        • fourier2
        • fourier3
        • fourier4
        • fourier5
        • fourier6
        • fourier7
        • fourier8
      • gaussian
        • gauss
        • gauss1
        • gauss2
        • gauss3
        • gauss4
        • gauss5
        • gauss6
        • gauss7
        • gauss8
      • polynomial
        • poly
        • poly1
        • poly2
        • poly3
        • poly4
        • poly5
        • poly6
        • poly7
        • poly8
        • poly9
      • power
        • power
        • power1
        • power2
    • lammps
      • topology
        • create_atoms
        • write_data
    • openmm
      • bond
        • fene
      • file
        • NetCDFFile
      • pair
        • coul_gauss
        • dpd
        • gauss
        • lj_coul
        • ljts
        • solvation
        • wca
        • yukawa
      • reporter
        • NetCDFReporter
      • system
        • add_electric_field
        • add_image_charges
        • add_slab_correction
        • estimate_pressure_tensor
        • register_particles
      • topology
        • create_atoms
        • get_subset
      • unit
        • get_lj_scale_factors
        • get_scale_factors
      • utility
        • optimize_pme
    • plot
      • axis
        • set_up_tabular_legend
      • color
        • adjust_lightness
      • rcparam
        • update
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mdcraft¶

MDCraft¶

mdcraft.algorithm

Algorithms

mdcraft.analysis

Simulation state data and trajectory analysis

mdcraft.fit

Curve fitting models

mdcraft.lammps

LAMMPS tools

mdcraft.openmm

OpenMM tools

mdcraft.plot

Plotting settings and tools

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Simulating a polyanion–counterion–solvent electric double-layer capactor using the Gaussian core model with smeared electrostatics
Copyright © 2023–2024 Benjamin Ye, Pierre Walker
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