LICENSE.txt
MANIFEST.in
README.rst
setup.py
doc/Makefile
doc/backprop.png
doc/conf.py
doc/dg_backprop.rst
doc/dg_todo.rst
doc/index.rst
doc/rg_yaff.rst
doc/rg_yaff_analysis.rst
doc/rg_yaff_conversion.rst
doc/rg_yaff_pes.rst
doc/rg_yaff_sampling.rst
doc/rg_yaff_tune.rst
doc/tu_silica.rst
doc/ug_analysis.rst
doc/ug_atselect.rst
doc/ug_cite.rst
doc/ug_features.rst
doc/ug_forcefield.rst
doc/ug_install.rst
doc/ug_overview.rst
doc/ug_sampling.rst
doc/ug_system.rst
doc/ug_troubles.rst
doc/ug_tune.rst
doc/_build/html/_images/backprop.png
doc/_build/html/_static/comment-bright.png
doc/_build/html/_static/comment-close.png
doc/_build/html/_static/comment.png
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scripts/yaff-opttest
yaff/__init__.py
yaff/atselect.py
yaff/log.py
yaff/system.py
yaff/version.py
yaff.egg-info/PKG-INFO
yaff.egg-info/SOURCES.txt
yaff.egg-info/dependency_links.txt
yaff.egg-info/requires.txt
yaff.egg-info/top_level.txt
yaff/analysis/__init__.py
yaff/analysis/basic.py
yaff/analysis/blav.py
yaff/analysis/diffusion.py
yaff/analysis/hook.py
yaff/analysis/pca.py
yaff/analysis/rdf.py
yaff/analysis/spectrum.py
yaff/analysis/utils.py
yaff/analysis/test/__init__.py
yaff/analysis/test/common.py
yaff/analysis/test/test_basic.py
yaff/analysis/test/test_blav.py
yaff/analysis/test/test_diffusion.py
yaff/analysis/test/test_rdf.py
yaff/analysis/test/test_spectrum.py
yaff/conversion/__init__.py
yaff/conversion/common.py
yaff/conversion/cp2k.py
yaff/conversion/dlpoly.py
yaff/conversion/gaussian.py
yaff/conversion/xyz.py
yaff/conversion/test/__init__.py
yaff/conversion/test/test_cp2k.py
yaff/conversion/test/test_dlpoly.py
yaff/conversion/test/test_gaussian.py
yaff/conversion/test/test_xyz.py
yaff/data/opttest/DUBXXKHIPWMCDR-UHFFFAOYSA-N-pars-quickff.txt
yaff/data/opttest/DUBXXKHIPWMCDR-UHFFFAOYSA-N.chk
yaff/data/opttest/GZLNXARBGMAZKZ-KVFPUHGPSA-N-pars-quickff.txt
yaff/data/opttest/GZLNXARBGMAZKZ-KVFPUHGPSA-N.chk
yaff/data/opttest/JQWBTFGGAKGQPA-UHFFFAOYSA-N-pars-quickff.txt
yaff/data/opttest/JQWBTFGGAKGQPA-UHFFFAOYSA-N.chk
yaff/data/opttest/QRMPKOFEUHIBNM-ZKCHVHJHSA-N-pars-quickff.txt
yaff/data/opttest/QRMPKOFEUHIBNM-ZKCHVHJHSA-N.chk
yaff/data/opttest/WFZUBZAEFXETBF-UHFFFAOYSA-N-pars-quickff.txt
yaff/data/opttest/WFZUBZAEFXETBF-UHFFFAOYSA-N.chk
yaff/data/opttest/ZPJJOVNASWLIRQ-UHFFFAOYSA-N-pars-quickff.txt
yaff/data/opttest/ZPJJOVNASWLIRQ-UHFFFAOYSA-N.chk
yaff/data/opttest/alpha_quartz.chk
yaff/data/opttest/alpha_quartz_distorted.chk
yaff/data/opttest/cases.txt
yaff/data/opttest/merlonite_debug.pot
yaff/data/opttest/merlonite_fragment.chk
yaff/data/opttest/merlonite_fragment_overbonded.chk
yaff/data/opttest/water_dimer.chk
yaff/data/test/chloro_pos.xyz
yaff/data/test/chloro_vol.txt
yaff/data/test/cp2k-1.ener
yaff/data/test/dlpoly_HISTORY_an1
yaff/data/test/dlpoly_HISTORY_an2
yaff/data/test/dlpoly_HISTORY_sam
yaff/data/test/dlpoly_HISTORY_uo
yaff/data/test/gaussian_sioh4_md.log
yaff/data/test/gaussian_sioh4_md.xyz
yaff/data/test/guaianolide.xyz
yaff/data/test/guaianolide_framework_ordered.xyz
yaff/data/test/nobornane.xyz
yaff/data/test/parameters_alkane.txt
yaff/data/test/parameters_bks.txt
yaff/data/test/parameters_fake_d3bj.txt
yaff/data/test/parameters_fake_dampdisp1.txt
yaff/data/test/parameters_fake_exprep1.txt
yaff/data/test/parameters_fake_lj.txt
yaff/data/test/parameters_fake_mm3.txt
yaff/data/test/parameters_fake_qmdffrep.txt
yaff/data/test/parameters_fake_torsion1.txt
yaff/data/test/parameters_fake_torsion2.txt
yaff/data/test/parameters_formaldehyde_inversion.txt
yaff/data/test/parameters_glycine_fixq.txt
yaff/data/test/parameters_glycine_torsion.txt
yaff/data/test/parameters_nacl.txt
yaff/data/test/parameters_polyene.txt
yaff/data/test/parameters_water.txt
yaff/data/test/parameters_water_bendaharm.txt
yaff/data/test/parameters_water_bendcharm.txt
yaff/data/test/parameters_water_bondcross.txt
yaff/data/test/parameters_water_bondfues.txt
yaff/data/test/parameters_water_bondharm.txt
yaff/data/test/parameters_water_cross.txt
yaff/data/test/parameters_water_dampdisp1.txt
yaff/data/test/parameters_water_dampdisp2.txt
yaff/data/test/parameters_water_exprep1.txt
yaff/data/test/parameters_water_exprep2.txt
yaff/data/test/parameters_water_exprep3.txt
yaff/data/test/parameters_water_fixq.txt
yaff/data/test/parameters_water_fixq_dielectric.txt
yaff/data/test/parameters_water_lj.txt
yaff/data/test/parameters_water_mm3.txt
yaff/data/test/parameters_water_ubharm.txt
yaff/data/test/rhodium_complex_nobornane.xyz
yaff/data/test/water_hessian.chk
yaff/data/test/water_trajectory.xyz
yaff/examples/.gitignore
yaff/examples/000_overview/parameters.txt
yaff/examples/000_overview/simulation.py
yaff/examples/000_overview/system.chk
yaff/examples/001_tutorial_bks/all.sh
yaff/examples/001_tutorial_bks/bks.pot
yaff/examples/001_tutorial_bks/init/mksystem.py
yaff/examples/001_tutorial_bks/init/rvecs.txt
yaff/examples/001_tutorial_bks/init/struct.xyz
yaff/examples/001_tutorial_bks/nvt/analysis.py
yaff/examples/001_tutorial_bks/nvt/simulation.py
yaff/examples/001_tutorial_bks/opt/analysis.py
yaff/examples/001_tutorial_bks/opt/simulation.py
yaff/examples/002_external_trajectory/rdf.py
yaff/examples/002_external_trajectory/trajectory.xyz
yaff/examples/003_water_thermostat/md.py
yaff/examples/003_water_thermostat/parameters.txt
yaff/examples/003_water_thermostat/system.chk
yaff/examples/999_back_propagation/bp.py
yaff/pes/__init__.py
yaff/pes/cell.c
yaff/pes/cell.h
yaff/pes/cell.pxd
yaff/pes/constants.h
yaff/pes/dlist.c
yaff/pes/dlist.h
yaff/pes/dlist.pxd
yaff/pes/dlist.py
yaff/pes/ewald.c
yaff/pes/ewald.h
yaff/pes/ewald.pxd
yaff/pes/ext.pyx
yaff/pes/ff.py
yaff/pes/generator.py
yaff/pes/grid.c
yaff/pes/grid.h
yaff/pes/grid.pxd
yaff/pes/iclist.c
yaff/pes/iclist.h
yaff/pes/iclist.pxd
yaff/pes/iclist.py
yaff/pes/nlist.c
yaff/pes/nlist.h
yaff/pes/nlist.pxd
yaff/pes/nlist.py
yaff/pes/pair_pot.c
yaff/pes/pair_pot.h
yaff/pes/pair_pot.pxd
yaff/pes/parameters.py
yaff/pes/scaling.py
yaff/pes/slater.c
yaff/pes/slater.h
yaff/pes/slater.pxd
yaff/pes/truncation.c
yaff/pes/truncation.h
yaff/pes/truncation.pxd
yaff/pes/vlist.c
yaff/pes/vlist.h
yaff/pes/vlist.pxd
yaff/pes/vlist.py
yaff/pes/test/__init__.py
yaff/pes/test/common.py
yaff/pes/test/test_cell.py
yaff/pes/test/test_dlist.py
yaff/pes/test/test_ewald.py
yaff/pes/test/test_generator.py
yaff/pes/test/test_grid.py
yaff/pes/test/test_iclist.py
yaff/pes/test/test_md.py
yaff/pes/test/test_nlist.py
yaff/pes/test/test_pair_pot.py
yaff/pes/test/test_parameters.py
yaff/pes/test/test_pext.py
yaff/pes/test/test_scaling.py
yaff/pes/test/test_topology.py
yaff/pes/test/test_truncation.py
yaff/pes/test/test_vlist.py
yaff/sampling/__init__.py
yaff/sampling/dof.py
yaff/sampling/harmonic.py
yaff/sampling/io.py
yaff/sampling/iterative.py
yaff/sampling/npt.py
yaff/sampling/nvt.py
yaff/sampling/opt.py
yaff/sampling/trajectory.py
yaff/sampling/utils.py
yaff/sampling/verlet.py
yaff/sampling/test/__init__.py
yaff/sampling/test/common.py
yaff/sampling/test/test_dof.py
yaff/sampling/test/test_harmonic.py
yaff/sampling/test/test_npt.py
yaff/sampling/test/test_nvt.py
yaff/sampling/test/test_opt.py
yaff/sampling/test/test_utils.py
yaff/sampling/test/test_verlet.py
yaff/test/__init__.py
yaff/test/common.py
yaff/test/test_atselect.py
yaff/test/test_examples.py
yaff/test/test_system.py
yaff/tune/__init__.py
yaff/tune/cost.py
yaff/tune/transform.py
yaff/tune/test/__init__.py
yaff/tune/test/test_cost.py
yaff/tune/test/test_transform.py