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docs/_static/api/box_example.py
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docs/_static/engine-examples/leapfrog.py
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docs/_static/examples/extending-example/engine/vvintegratorc.py
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docs/_static/examples/extending-example/potential/ljpotentialc.py
docs/_static/examples/extending-example/potential/ljpotentialfp.py
docs/_static/examples/extending-example/potential/setup.py
docs/_static/examples/extending-example/potentialfb/ljpotentialc.py
docs/_static/examples/extending-example/potentialfb/ljpotentialf.py
docs/_static/examples/extending-example/potentialfb/md_forward_backward_ext.py
docs/_static/examples/extending-example/potentialfb/setup.py
docs/_static/examples/gromacs-hydrate/orderp.py
docs/_static/examples/permeability/flat_potential.py
docs/_static/examples/pso-example/ackley.py
docs/_static/examples/pso-example/pso_run.py
docs/_static/examples/pso-example/psoengine.py
docs/_static/examples/pyvisa-analysis/orderp.py
docs/_static/examples/retis2d-hysteresis/order-x.py
docs/_static/examples/retis2d-hysteresis/order-xy.py
docs/_static/examples/retis2d-hysteresis/potential.py
docs/_static/examples/retis2d-wca/orderp.py
docs/_static/exercises/retis.py
docs/_static/exercises/retis_movie.py
docs/_static/orderparameter-examples/orderparameter1.py
docs/_static/orderparameter-examples/orderparameter2.py
docs/ext/pyretis_collapse_block.py
docs/ext/pyretis_highlight.py
docs/ext/pyretis_input_example.py
docs/ext/pyretis_keyword.py
docs/ext/pyretis_translator.py
docs/ext/pyretisstyle.py
examples/extending/integrator-langevin/test_random.py
examples/extending/integrator-langevin/vvintegratorf.py
examples/extending/integrator-vv/c/md_nve.py
examples/extending/integrator-vv/c/setup.py
examples/extending/integrator-vv/c/test_vvintegrator.py
examples/extending/integrator-vv/c/vvintegratorc.py
examples/extending/integrator-vv/fortran/md_nve.py
examples/extending/integrator-vv/fortran/test_vvintegrator.py
examples/extending/integrator-vv/fortran/vvintegratorf.py
examples/extending/lennard-jones/plot_results.py
examples/extending/lennard-jones/time_lj_numba.py
examples/extending/lennard-jones/time_lj_numpy.py
examples/extending/lennard-jones/time_lj_python.py
examples/extending/lennard-jones/c/ljpotentialc.py
examples/extending/lennard-jones/c/md_nve.py
examples/extending/lennard-jones/c/setup.py
examples/extending/lennard-jones/c/test_ljforces.py
examples/extending/lennard-jones/c/time_ljforces.py
examples/extending/lennard-jones/fortran/ljpotentialf.py
examples/extending/lennard-jones/fortran/md_nve.py
examples/extending/lennard-jones/fortran/test_ljforces.py
examples/extending/lennard-jones/fortran/time_ljforces.py
examples/extending/lennard-jones/fortran-pointer/ljpotentialfp.py
examples/extending/lennard-jones/fortran-pointer/md_nve.py
examples/extending/lennard-jones/fortran-pointer/test_ljforces.py
examples/extending/lennard-jones/fortran-pointer/time_ljforces.py
examples/extending/lennard-jones/omp-potential/ljpotentialfp.py
examples/extending/lennard-jones/omp-potential/plot_results.py
examples/extending/lennard-jones/omp-potential/test_ljforces.py
examples/extending/lennard-jones/omp-potential/time_ljforces.py
examples/extending/order-parameter/orderparameter1.py
examples/molecular_dynamics/md_movie_2d/md_movie_2d.py
examples/molecular_dynamics/md_nve/md_nve.py
examples/molecular_dynamics/md_nve/md_nve_plain.py
examples/molecular_dynamics/md_nve/forward_backward/md_forward_backward.py
examples/molecular_dynamics/md_nve/forward_backward/external/md_forward_backward_ext.py
examples/molecular_dynamics/md_nve/forward_backward/external/cpython3/ljpotentialc.py
examples/molecular_dynamics/md_nve/forward_backward/external/cpython3/setup.py
examples/molecular_dynamics/md_nve/forward_backward/external/fortran/ljpotentialf.py
examples/molecular_dynamics/md_nve/from_settings/plot_bokeh.py
examples/molecular_dynamics/md_nve/from_settings/plot_thermo.py
examples/molecular_dynamics/md_nve/real_units/compare.py
examples/molecular_dynamics/md_wca/md_movie_2d_wca.py
examples/molecular_dynamics/new_integrator/doublependulum.py
examples/molecular_dynamics/new_integrator/myintegrator.py
examples/molecular_dynamics/new_integrator/run_pendulum.py
examples/other/particle_swarm/ackley.py
examples/other/particle_swarm/pso_run.py
examples/other/particle_swarm/psoengine.py
examples/path_sampling/1D-double-well-retis-movie/retis.py
examples/path_sampling/1D-double-well-retis-movie/retis_intro.py
examples/path_sampling/1D-double-well-retis-movie/retis_movie.py
examples/path_sampling/1D-double-well-retis-movie/retis_movie_log.py
examples/path_sampling/2D-hysteresis/order.py
examples/path_sampling/2D-hysteresis/potential.py
examples/path_sampling/2D-hysteresis/interactive/interactive-x.py
examples/path_sampling/2D-hysteresis/interactive/interactive-xy.py
examples/path_sampling/2D-hysteresis/interactive/interactive-y.py
examples/path_sampling/2D-hysteresis/retis-x/plot_potential.py
examples/path_sampling/2D-hysteresis/retis-x/plot_traj.py
examples/path_sampling/2D-hysteresis/retis-xy/orderp.py
examples/path_sampling/2D-hysteresis/retis-xy/plot_traj.py
examples/path_sampling/2D-hysteresis/retis-y/plot_traj.py
examples/path_sampling/2D-wca/high-barrier/generate_initial.py
examples/path_sampling/2D-wca/high-barrier/c-for-python3/setup.py
examples/path_sampling/2D-wca/high-barrier/c-for-python3/test_orderparameter.py
examples/path_sampling/2D-wca/high-barrier/c-for-python3/test_wcaforces.py
examples/path_sampling/2D-wca/high-barrier/c-for-python3/wcafunctions.py
examples/path_sampling/2D-wca/low-barrier/generate_initial.py
examples/path_sampling/2D-wca/low-barrier/orderp.py
examples/path_sampling/2D-wca/low-barrier/c-for-python3/orderp.py
examples/path_sampling/2D-wca/low-barrier/c-for-python3/setup.py
examples/path_sampling/2D-wca/low-barrier/c-for-python3/test_wcaforces.py
examples/path_sampling/2D-wca/low-barrier/c-for-python3/wcafunctions.py
examples/path_sampling/gromacs-hydrate/orderp.py
examples/path_sampling/gromacs-hydrate/test_order.py
examples/test/test-cp2k/test-cp2k/test_cp2k.py
examples/test/test-cp2k/test-cp2k/test_cp2k_step.py
examples/test/test-cp2k/test-integrate/compare_cp2k_energies.py
examples/test/test-cp2k/test-integrate/compare_energies.py
examples/test/test-cp2k/test-integrate/make_inp.py
examples/test/test-cp2k/test-retis-load/compare.py
examples/test/test-gromacs/gmx/compare.py
examples/test/test-gromacs/gmx/copy_last_path.py
examples/test/test-gromacs/gmx/copy_restart_files.py
examples/test/test-gromacs/gmx/gromacs.py
examples/test/test-gromacs/gmx/make_mdp.py
examples/test/test-gromacs/gmx/merge_files.py
examples/test/test-gromacs/gmx/orderp.py
examples/test/test-gromacs/test-gromacs/test_gromacs.py
examples/test/test-gromacs/test-integrate/compare_energies.py
examples/test/test-gromacs/test-load/test-load-sparse/load-traj/orderp.py
examples/test/test-gromacs/test-repptis/compare.py
examples/test/test-gromacs/test-retis/compare.py
examples/test/test-internal/compare-internal-with-lammps/run_md_comparison.py
examples/test/test-internal/md-restart/compare.py
examples/test/test-internal/mdflux-restart/compare.py
examples/test/test-internal/partial-path/compare.py
examples/test/test-internal/partial-path/flat-potential.py
examples/test/test-internal/retis/compare.py
examples/test/test-internal/retis-ss-wt-wf/compare.py
examples/test/test-internal/tis-multiple/compare.py
examples/test/test-internal/tis-restart/compare.py
examples/test/test-lammps/lammps_testing/plotting.py
examples/test/test-lammps/test-dump-phasepoint/test_lammps.py
examples/test/test-lammps/test-integrate/plotting.py
examples/test/test-lammps/test-integrate/test_lammps.py
examples/test/test-lammps/test-modify-velocities/test_lammps.py
examples/test/test-lammps/test-propagate/plotting.py
examples/test/test-lammps/test-propagate/test_lammps.py
examples/test/test-pyvisa/lib/compare_hdf5.py
examples/test/test-pyvisa/lib/compare_order.py
examples/umbrella_sampling/umbrella_sampling_mc.py
examples/umbrella_sampling/umbrella_sampling_mc_movie.py
examples/umbrella_sampling/fancy_movie/umbrella_sampling_mc_fancy_movie.py
pyretis/__init__.py
pyretis/info.py
pyretis/version.py
pyretis.egg-info/PKG-INFO
pyretis.egg-info/SOURCES.txt
pyretis.egg-info/dependency_links.txt
pyretis.egg-info/entry_points.txt
pyretis.egg-info/requires.txt
pyretis.egg-info/top_level.txt
pyretis/analysis/__init__.py
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pyretis/analysis/energy_analysis.py
pyretis/analysis/flux_analysis.py
pyretis/analysis/histogram.py
pyretis/analysis/order_analysis.py
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pyretis/bin/pyretisanalyse.py
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pyretis/core/__init__.py
pyretis/core/box.py
pyretis/core/common.py
pyretis/core/montecarlo.py
pyretis/core/particlefunctions.py
pyretis/core/particles.py
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pyretis/core/system.py
pyretis/core/tis.py
pyretis/core/units.py
pyretis/engines/__init__.py
pyretis/engines/cp2k.py
pyretis/engines/engine.py
pyretis/engines/external.py
pyretis/engines/gromacs.py
pyretis/engines/gromacs2.py
pyretis/engines/internal.py
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pyretis/engines/openmm.py
pyretis/forcefield/__init__.py
pyretis/forcefield/factory.py
pyretis/forcefield/forcefield.py
pyretis/forcefield/potential.py
pyretis/forcefield/potentials/__init__.py
pyretis/forcefield/potentials/potentials.py
pyretis/forcefield/potentials/pairpotentials/__init__.py
pyretis/forcefield/potentials/pairpotentials/lennardjones.py
pyretis/forcefield/potentials/pairpotentials/pairpotential.py
pyretis/forcefield/potentials/pairpotentials/wca.py
pyretis/initiation/__init__.py
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pyretis/inout/__init__.py
pyretis/inout/archive.py
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pyretis/inout/fileio.py
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pyretis/inout/formats/snapshot.py
pyretis/inout/formats/txt_table.py
pyretis/inout/formats/xyz.py
pyretis/inout/plotting/__init__.py
pyretis/inout/plotting/mpl_plotting.py
pyretis/inout/plotting/plotting.py
pyretis/inout/plotting/txt_plotting.py
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pyretis/inout/report/report_md.py
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pyretis/orderparameter/__init__.py
pyretis/orderparameter/orderangle.py
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pyretis/pyvisa/__init__.py
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pyretis/pyvisa/orderparam_density.py
pyretis/pyvisa/plotting.py
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pyretis/pyvisa/statistical_methods.py
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pyretis/setup/__init__.py
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pyretis/setup/createforcefield.py
pyretis/setup/createsimulation.py
pyretis/setup/createsystem.py
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pyretis/simulation/mc_simulation.py
pyretis/simulation/md_simulation.py
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test/engines/__init__.py
test/engines/aprogram.py
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test/engines/mockgmx.py
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test/engines/mockmdrun.py
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