Index A | B | C | E | F | G | H | L | M | N | O | P | R | S | T | U A add_potential_functions() (in module gamdpy) Angles (class in 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) Configuration (class in gamdpy) configuration_from_rumd3() (in module gamdpy) configuration_to_lammps() (in module gamdpy) configuration_to_rumd3() (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) E extract_scalars() (in module gamdpy) F from_h5() (gamdpy.Configuration class method) G 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_volume() (gamdpy.Configuration method) (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) get_volume_function() (gamdpy.LeesEdwards method) (gamdpy.Orthorhombic method) GradientDescent (class in gamdpy) Gravity (class in gamdpy) H harmonic_bond_function() (in module gamdpy) harmonic_repulsion() (in module gamdpy) hertzian() (in module gamdpy) 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) 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) 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) 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) TrajectoryIO (class in gamdpy.tools) TrajectorySaver (class in gamdpy) U update() (gamdpy.CalculatorRadialDistribution method) (gamdpy.CalculatorStructureFactor method) (gamdpy.CalculatorWidomInsertion method)