Index A | B | C | E | F | G | H | I | L | M | N | O | P | R | S | T | U | Y A ActiveOUP (class in gamdpy) add_potential_functions() (in module gamdpy) Angles (class in gamdpy) apply_cubic_spline_cutoff() (in module gamdpy) apply_gromacs_cutoff() (in module gamdpy) apply_shifted_force_cutoff() (in module gamdpy) apply_shifted_potential_cutoff() (in module gamdpy) atomic_scale() (gamdpy.Configuration method) autotune() (gamdpy.Simulation method) B Bonds (class in gamdpy) Brownian (class in gamdpy) C calc_dynamics() (in module gamdpy.tools) calculate_molecular_center_of_masses() (in module gamdpy.tools) calculate_molecular_dipoles() (in module gamdpy.tools) calculate_molecular_velocities() (in module gamdpy.tools) CalculatorHydrodynamicCorrelations (class in gamdpy) CalculatorHydrodynamicProfile (class in gamdpy) CalculatorRadialDistribution (class in gamdpy) CalculatorStructureFactor (class in gamdpy) CalculatorWidomInsertion (class in gamdpy) columns() (gamdpy.ScalarSaver method) compress() (gamdpy.Simulation method) Configuration (class in gamdpy) configuration_from_rumd3() (in module gamdpy) configuration_to_lammps() (in module gamdpy) configuration_to_rumd3() (in module gamdpy) conversion_factors() (in module gamdpy) copy_to_device() (gamdpy.Configuration method) (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) copy_to_host() (gamdpy.Configuration method) (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) cos_angle_function() (in module gamdpy) E exponential_repulsion() (in module gamdpy) extract() (gamdpy.ScalarSaver method) extract_as_dict() (gamdpy.ScalarSaver method) F from_h5() (gamdpy.Configuration class method) G gaussian_core_model() (in module gamdpy) generate_q_vectors() (gamdpy.CalculatorStructureFactor method) get_apply_PBC() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_default_compute_flags() (in module gamdpy) get_default_compute_plan() (in module gamdpy) get_default_sim() (in module gamdpy) get_dist_moved_exceeds_limit_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_dist_sq_dr_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_dist_sq_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_h5() (gamdpy.tools.TrajectoryIO method) get_lengths() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_loop_x_addition() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_loop_x_shift_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_name() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_potential_energy() (gamdpy.Configuration method) get_times() (gamdpy.ScalarSaver method) get_volume() (gamdpy.Configuration method) (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_volume_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) GradientDescent (class in gamdpy) H harmonic_angle_function() (in module gamdpy) harmonic_bond_function() (in module gamdpy) harmonic_repulsion() (in module gamdpy) hertzian() (in module gamdpy) I info() (gamdpy.ScalarSaver method) L LeesEdwards (class in gamdpy) LJ_12_6() (in module gamdpy) LJ_12_6_sigma_epsilon() (in module gamdpy) load_h5() (gamdpy.tools.TrajectoryIO method) load_rumd3() (gamdpy.tools.TrajectoryIO method) M make_fixed_interactions() (in module gamdpy) make_function_constant() (in module gamdpy) make_function_ramp() (in module gamdpy) make_function_sin() (in module gamdpy) make_IPL_n() (in module gamdpy) make_lattice() (gamdpy.Configuration method) make_LJ_m_n() (in module gamdpy) make_planar_calculator() (in module gamdpy) make_positions() (gamdpy.Configuration method) make_potential_function_from_sympy() (in module gamdpy) merge_exclusions() (gamdpy.PairPotential method) MomentumReset (class in gamdpy) N NPT_Atomic (class in gamdpy) NPT_Langevin (class in gamdpy) NVE (class in gamdpy) NVT (class in gamdpy) NVT_Langevin (class in gamdpy) O Orthorhombic (class in gamdpy) P PairPotential (class in gamdpy) Planar (class in gamdpy) plot_molecule() (in module gamdpy) print_h5_attributes() (in module gamdpy.tools) print_h5_structure() (in module gamdpy.tools) R randomize_velocities() (gamdpy.Configuration method) read() (gamdpy.CalculatorRadialDistribution method) (gamdpy.CalculatorStructureFactor method) (gamdpy.CalculatorWidomInsertion method) Relaxtemp (class in gamdpy) RestartSaver (class in gamdpy) run() (gamdpy.Simulation method) run_timeblocks() (gamdpy.Simulation method) S SAAP() (in module gamdpy) save() (gamdpy.Configuration method) save_average() (gamdpy.CalculatorRadialDistribution method) (gamdpy.CalculatorStructureFactor method) save_h5() (gamdpy.tools.TrajectoryIO method) save_internal_state() (gamdpy.ActiveOUP method) (gamdpy.Brownian method) (gamdpy.GradientDescent method) (gamdpy.NPT_Atomic method) (gamdpy.NPT_Langevin method) (gamdpy.NVE method) (gamdpy.NVT method) (gamdpy.NVT_Langevin method) (gamdpy.SLLOD method) ScalarSaver (class in gamdpy) scale() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) select_gpu() (in module gamdpy) set_kinetic_temperature() (gamdpy.Configuration method) setup_planar_interactions() (in module gamdpy) Simulation (class in gamdpy) SLLOD (class in gamdpy) status() (gamdpy.Simulation method) StressSaver (class in gamdpy) summary() (gamdpy.Simulation method) T Tether (class in gamdpy) thermodynamics_NpT() (in module gamdpy.tools) thermodynamics_NVT() (in module gamdpy.tools) TrajectoryIO (class in gamdpy.tools) TrajectorySaver (class in gamdpy) U universal_zbl_potential() (in module gamdpy) update() (gamdpy.CalculatorRadialDistribution method) (gamdpy.CalculatorStructureFactor method) (gamdpy.CalculatorWidomInsertion method) Y yukawa() (in module gamdpy)