[liggghts] branch master updated (093119e -> d0b88ee)
Anton Gladky
gladk at moszumanska.debian.org
Wed May 6 21:55:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository liggghts.
from 093119e Update patch.
adds 4d4603b Add some more files to exclude in d/copyright.
adds 39f1279 Imported Upstream version 3.1.0+repack1
adds 708fb84 Merge.
adds ea63dab Update patches.
adds a0b9219 Enable C++11 for build.
adds c74e08e Remove README.source.
adds 960f841 Update changelog.
new 6ac272b Use cme fix dpkg-control.
new d0b88ee Update changelog.
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
README | 15 +-
bench/Cu_u3.eam | 305 -
bench/GPU/README | 60 -
bench/GPU/in.eam.cpu | 24 -
bench/GPU/in.eam.cuda | 29 -
bench/GPU/in.eam.gpu | 31 -
bench/GPU/in.lj.cpu | 22 -
bench/GPU/in.lj.cuda | 27 -
bench/GPU/in.lj.gpu | 29 -
bench/GPU/in.rhodo.cpu | 30 -
bench/GPU/in.rhodo.cuda | 35 -
bench/GPU/in.rhodo.gpu | 37 -
bench/POTENTIALS/CH.airebo | 37592 ----
bench/POTENTIALS/CdTe.bop | 44 -
bench/POTENTIALS/Cu_u3.eam | 305 -
bench/POTENTIALS/Ni.adp | 43007 ----
bench/POTENTIALS/Ni.meam | 2 -
bench/POTENTIALS/README | 32 -
bench/POTENTIALS/Si.sw | 17 -
bench/POTENTIALS/Si.tersoff | 16 -
bench/POTENTIALS/ffield.comb | 98 -
bench/POTENTIALS/ffield.eim | 145 -
bench/POTENTIALS/ffield.reax | 274 -
bench/POTENTIALS/in.adp | 24 -
bench/POTENTIALS/in.airebo | 22 -
bench/POTENTIALS/in.bop | 31 -
bench/POTENTIALS/in.comb | 31 -
bench/POTENTIALS/in.dpd | 24 -
bench/POTENTIALS/in.eam | 23 -
bench/POTENTIALS/in.eff | 23 -
bench/POTENTIALS/in.eim | 25 -
bench/POTENTIALS/in.fene | 24 -
bench/POTENTIALS/in.gb | 41 -
bench/POTENTIALS/in.granular | 31 -
bench/POTENTIALS/in.lj | 22 -
bench/POTENTIALS/in.meam | 24 -
bench/POTENTIALS/in.peri | 86 -
bench/POTENTIALS/in.protein | 27 -
bench/POTENTIALS/in.reax | 22 -
bench/POTENTIALS/in.reaxc | 22 -
bench/POTENTIALS/in.rebo | 22 -
bench/POTENTIALS/in.spce | 39 -
bench/POTENTIALS/in.sw | 24 -
bench/POTENTIALS/in.tersoff | 24 -
bench/POTENTIALS/library.meam | 162 -
bench/POTENTIALS/log.26Jun12.adp.1 | 52 -
bench/POTENTIALS/log.26Jun12.adp.4 | 52 -
bench/POTENTIALS/log.26Jun12.airebo.1 | 63 -
bench/POTENTIALS/log.26Jun12.airebo.4 | 63 -
bench/POTENTIALS/log.26Jun12.bop.1 | 57 -
bench/POTENTIALS/log.26Jun12.bop.4 | 57 -
bench/POTENTIALS/log.26Jun12.comb.1 | 71 -
bench/POTENTIALS/log.26Jun12.comb.4 | 71 -
bench/POTENTIALS/log.26Jun12.dpd.1 | 52 -
bench/POTENTIALS/log.26Jun12.dpd.4 | 52 -
bench/POTENTIALS/log.26Jun12.eam.1 | 51 -
bench/POTENTIALS/log.26Jun12.eam.4 | 51 -
bench/POTENTIALS/log.26Jun12.eff.1 | 70 -
bench/POTENTIALS/log.26Jun12.eff.4 | 70 -
bench/POTENTIALS/log.26Jun12.eim.1 | 53 -
bench/POTENTIALS/log.26Jun12.eim.4 | 53 -
bench/POTENTIALS/log.26Jun12.fene.1 | 58 -
bench/POTENTIALS/log.26Jun12.fene.4 | 58 -
bench/POTENTIALS/log.26Jun12.gb.1 | 76 -
bench/POTENTIALS/log.26Jun12.gb.4 | 76 -
bench/POTENTIALS/log.26Jun12.granular.1 | 61 -
bench/POTENTIALS/log.26Jun12.granular.4 | 61 -
bench/POTENTIALS/log.26Jun12.lj.1 | 50 -
bench/POTENTIALS/log.26Jun12.lj.4 | 50 -
bench/POTENTIALS/log.26Jun12.meam.1 | 55 -
bench/POTENTIALS/log.26Jun12.meam.4 | 55 -
bench/POTENTIALS/log.26Jun12.peri.1 | 187 -
bench/POTENTIALS/log.26Jun12.peri.4 | 187 -
bench/POTENTIALS/log.26Jun12.protein.1 | 93 -
bench/POTENTIALS/log.26Jun12.protein.4 | 93 -
bench/POTENTIALS/log.26Jun12.reax.1 | 61 -
bench/POTENTIALS/log.26Jun12.reax.4 | 61 -
bench/POTENTIALS/log.26Jun12.reaxc.1 | 61 -
bench/POTENTIALS/log.26Jun12.reaxc.4 | 61 -
bench/POTENTIALS/log.26Jun12.rebo.1 | 63 -
bench/POTENTIALS/log.26Jun12.rebo.4 | 63 -
bench/POTENTIALS/log.26Jun12.spce.1 | 106 -
bench/POTENTIALS/log.26Jun12.spce.4 | 106 -
bench/POTENTIALS/log.26Jun12.sw.1 | 54 -
bench/POTENTIALS/log.26Jun12.sw.4 | 54 -
bench/POTENTIALS/log.26Jun12.tersoff.1 | 54 -
bench/POTENTIALS/log.26Jun12.tersoff.4 | 54 -
bench/POTENTIALS/reax_defs.h | 69 -
bench/README | 111 -
bench/data.chain | 95710 ---------
bench/data.chute | 64015 ------
bench/data.rhodo | 191072 ------------------
bench/in.chain | 25 -
bench/in.chain.scaled | 32 -
bench/in.chute | 33 -
bench/in.chute.scaled | 38 -
bench/in.eam | 32 -
bench/in.lj | 30 -
bench/in.rhodo | 27 -
bench/in.rhodo.scaled | 34 -
bench/log.30Jul13.chain.fixed.linux.1 | 59 -
bench/log.30Jul13.chain.fixed.linux.4 | 59 -
bench/log.30Jul13.chain.scaled.linux.4 | 75 -
bench/log.30Jul13.chute.fixed.linux.1 | 63 -
bench/log.30Jul13.chute.fixed.linux.4 | 63 -
bench/log.30Jul13.chute.scaled.linux.4 | 73 -
bench/log.30Jul13.eam.fixed.linux.1 | 67 -
bench/log.30Jul13.eam.fixed.linux.4 | 67 -
bench/log.30Jul13.eam.scaled.linux.4 | 67 -
bench/log.30Jul13.lj.fixed.linux.1 | 64 -
bench/log.30Jul13.lj.fixed.linux.4 | 64 -
bench/log.30Jul13.lj.scaled.linux.4 | 64 -
bench/log.30Jul13.rhodo.fixed.linux.1 | 99 -
bench/log.30Jul13.rhodo.fixed.linux.4 | 99 -
bench/log.30Jul13.rhodo.scaled.linux.4 | 120 -
cMake/FindEigen3.cmake | 80 -
debian/README.source | 2 -
debian/changelog | 16 +
debian/control | 92 +-
debian/copyright | 9 +-
debian/patches/01_add_cmake_files.patch | 20 +-
debian/patches/05_vtk6_support.patch | 12 +-
doc/Eqs/fix_sph_density_drift_corr_eq1.jpg | Bin 0 -> 5196 bytes
doc/Eqs/fix_sph_density_driftcorr_eq1.jpg | Bin 0 -> 5196 bytes
doc/Eqs/fix_sph_integrity_eq1.jpg | Bin 0 -> 3769 bytes
doc/Eqs/fix_sph_mixidx_eq1.jpg | Bin 0 -> 12779 bytes
doc/Eqs/fix_sph_mixidx_eq2.jpg | Bin 0 -> 3017 bytes
doc/Eqs/fix_sph_mixidx_eq3.jpg | Bin 0 -> 3118 bytes
doc/Eqs/fix_sph_mixidx_eq4.jpg | Bin 0 -> 3019 bytes
doc/Eqs/fix_sph_mixidx_eq5.jpg | Bin 0 -> 3014 bytes
doc/Eqs/fix_sph_mixidx_eq6.jpg | Bin 0 -> 3360 bytes
doc/Eqs/fix_sph_velgrad_eq1.jpg | Bin 0 -> 7428 bytes
doc/Eqs/model_C2_part_1.png | Bin 0 -> 3741 bytes
doc/Eqs/pair_gran_html_m225ba7de.png | Bin 15861 -> 16778 bytes
doc/Eqs/pair_sph_morris_tenscorr_eq1.jpg | Bin 17896 -> 17613 bytes
doc/Eqs/pair_sph_morris_tenscorr_eq2.jpg | Bin 13313 -> 2662 bytes
doc/Eqs/pair_sph_morris_tenscorr_eq3.jpg | Bin 11114 -> 6185 bytes
doc/Eqs/pair_sph_morris_tenscorr_eq4.jpg | Bin 8157 -> 13313 bytes
doc/Eqs/pair_sph_morris_tenscorr_eq5.jpg | Bin 5047 -> 11114 bytes
...rr_eq4.jpg => pair_sph_morris_tenscorr_eq6.jpg} | Bin
...rr_eq5.jpg => pair_sph_morris_tenscorr_eq7.jpg} | Bin
doc/Eqs/roughnessLength.png | Bin 0 -> 2090 bytes
doc/Manual.pdf | Bin 7935638 -> 7954859 bytes
doc/Section_commands.html | 2 +-
doc/Section_commands.txt | 1 +
doc/atom_style.txt | 21 +-
doc/dump_custom_vtk.html | 347 +
doc/dump_custom_vtk.txt | 335 +
doc/fix_check_timestep_gran.txt | 2 +-
doc/fix_mesh_surface.txt | 6 +-
doc/fix_wall_gran.html | 4 +-
doc/fix_wall_gran.txt | 4 +-
doc/gran_model_hertz.html | 2 +-
doc/gran_model_hertz.txt | 2 +-
doc/gran_model_hertz_stiffness.html | 2 +-
doc/gran_model_hertz_stiffness.txt | 2 +-
doc/gran_model_hooke.html | 2 +-
doc/gran_model_hooke.txt | 2 +-
doc/gran_model_hooke_stiffness.html | 2 +-
doc/gran_model_hooke_stiffness.txt | 2 +-
doc/gran_tangential_history.html | 5 +-
doc/gran_tangential_history.txt | 3 +-
.../heatTransferBed_paScal/Allrun_convective | 23 +
.../ParScale/heatTransferBed_paScal/README.md | 14 +
.../ParScale/heatTransferBed_paScal/cleanscript | 22 +
.../ParScale/heatTransferBed_paScal/genInput.m | 22 +
.../ParScale/heatTransferBed_paScal/in.liggghts | 107 +
.../heatTransferBed_paScal/pascal/0/heat.json | 807 +
.../heatTransferBed_paScal/pascal/0/radius.json | 807 +
.../heatTransferBed_paScal/pascal/in.pascal | 19 +
.../heatTransferBed_paScal/pascal/plotMe.m | 86 +
.../pascal/settings/coupling_liggghts.json | 7 +
.../pascal/settings/model_heatCapacity_solid.json | 8 +
.../pascal/settings/model_heatDensity_solid.json | 7 +
.../model_heatThermalConductivity_solid.json | 8 +
.../pascal/settings/model_heatTransferCoeff.json | 8 +
.../heatTransferBed_paScal}/post/.gitignore | 0
.../heatTransferBed_paScal/settings/parscale.json | 8 +
python/README | 100 -
python/examples/demo.py | 61 -
python/examples/gui.py | 112 -
python/examples/in.demo | 26 -
python/examples/in.gui | 24 -
python/examples/in.plot | 24 -
python/examples/in.simple | 23 -
python/examples/in.trivial | 22 -
python/examples/in.viz | 24 -
python/examples/pizza/dump.py | 1229 -
python/examples/pizza/gl.py | 1329 -
python/examples/pizza/gnu.py | 383 -
python/examples/pizza/pdbfile.py | 289 -
python/examples/pizza/vizinfo.py | 391 -
python/examples/pizza/vmd.py | 223 -
python/examples/plot.py | 75 -
python/examples/simple.py | 50 -
python/examples/trivial.py | 40 -
python/examples/viz_atomeye.py | 72 -
python/examples/viz_gl.py | 83 -
python/examples/viz_pymol.py | 82 -
python/examples/viz_vmd.py | 91 -
python/examples/vizplotgui_atomeye.py | 165 -
python/examples/vizplotgui_gl.py | 175 -
python/examples/vizplotgui_pymol.py | 174 -
python/examples/vizplotgui_vmd.py | 173 -
python/install.py | 67 -
python/lammps.py | 167 -
regress/benchmark.py | 235 -
regress/melt/in.melt | 20 -
regress/melt/log.melt.linux.4 | 60 -
regress/min/in.min | 26 -
regress/min/in.min.box | 31 -
regress/min/log.min.box.linux.4 | 335 -
regress/min/log.min.linux.4 | 97 -
regress/regression.sh | 14 -
src/ASPHERE/fix_nve_asphere.cpp | 20 +-
src/MAKE/Makefile.fedora | 2 +-
...akefile.ubuntuVTK6 => Makefile.fedora_vtk_fpic} | 32 +-
src/MAKE/Makefile.ubuntuVTK | 2 +-
src/MAKE/Makefile.ubuntuVTK6 | 2 +-
...{Makefile.ubuntuVTK => Makefile.ubuntuVTK_fpic} | 13 +-
src/Make.sh | 15 +-
src/Makefile | 2 +-
src/PASCAL/Install.sh | 72 +
src/PASCAL/fix_pascal_couple.cpp | 372 +
src/PASCAL/fix_pascal_couple.h | 83 +
src/RIGID/fix_rigid.cpp | 8 +-
src/RIGID/fix_rigid.h | 16 +-
src/abstract_mesh.h | 12 +-
src/associative_pointer_array.h | 13 +-
src/associative_pointer_array_I.h | 34 +-
src/atom.cpp | 10 +-
src/atom.h | 8 +-
src/atom_vec_sph.cpp | 10 +-
src/atom_vec_sph.h | 10 +-
src/atom_vec_sph_var.cpp | 10 +-
src/atom_vec_sph_var.h | 10 +-
src/atom_vec_sphere.cpp | 8 +-
src/atom_vec_sphere.h | 8 +-
src/atom_vec_sphere_w.cpp | 10 +-
src/bounding_box.cpp | 10 +-
src/bounding_box.h | 12 +-
src/cfd_datacoupling.cpp | 158 +-
src/cfd_datacoupling.h | 20 +-
src/cfd_datacoupling_file.cpp | 10 +-
src/cfd_datacoupling_file.h | 10 +-
src/cfd_datacoupling_mpi.cpp | 29 +-
src/cfd_datacoupling_mpi.h | 37 +-
src/cfd_datacoupling_simple.h | 48 +
src/cfd_regionmodel.h | 10 +-
src/cfd_regionmodel_none.cpp | 10 +-
src/cfd_regionmodel_none.h | 10 +-
src/cleanAllParScale.sh | 13 +
src/cohesion_model_sjkr.h | 10 +-
src/cohesion_model_sjkr2.h | 10 +-
src/comm.cpp | 11 +-
src/comm.h | 8 +-
src/comm_I.h | 10 +-
src/compute_angle_local.cpp | 2 +-
src/compute_bond_local.cpp | 2 +-
src/compute_contact_atom.cpp | 8 +-
src/compute_contact_atom.h | 8 +-
src/compute_dihedral_local.cpp | 2 +-
src/compute_erotate_sphere.cpp | 8 +-
src/compute_erotate_sphere.h | 8 +-
src/compute_erotate_sphere_atom.cpp | 8 +-
src/compute_erotate_sphere_atom.h | 8 +-
src/compute_improper_local.cpp | 2 +-
src/compute_nparticles_tracer_region.cpp | 10 +-
src/compute_nparticles_tracer_region.h | 10 +-
src/compute_pair_gran_local.cpp | 14 +-
src/compute_pair_gran_local.h | 10 +-
src/compute_pair_local.cpp | 2 +-
src/compute_pressure.cpp | 4 +-
src/compute_reduce.cpp | 4 +-
src/compute_stress_atom.cpp | 4 +-
src/compute_stress_atom.h | 4 +-
src/contact_interface.h | 10 +-
src/contact_model_constants.h | 12 +-
src/contact_models.cpp | 10 +-
src/contact_models.h | 10 +-
src/container.h | 10 +-
src/container_base.cpp | 29 +-
src/container_base.h | 18 +-
src/container_base_I.h | 10 +-
src/create_atoms.cpp | 31 +-
src/create_atoms.h | 4 +-
src/custom_value_tracker.cpp | 24 +-
src/custom_value_tracker.h | 14 +-
src/custom_value_tracker_I.h | 27 +-
src/debug_liggghts.h | 10 +-
src/delete_atoms.cpp | 5 +
src/delete_bonds.cpp | 4 +-
src/displace_atoms.cpp | 6 +-
src/domain.cpp | 8 +-
src/domain.h | 9 +-
src/domain_I.h | 25 +-
src/domain_wedge_dummy.h | 10 +-
src/dump_atom_vtk.cpp | 10 +-
src/dump_atom_vtk.h | 12 +-
src/dump_cfg.cpp | 3 +-
src/dump_custom.cpp | 20 +-
src/dump_custom.h | 8 +-
src/{dump_custom.cpp => dump_custom_vtk.cpp} | 1667 +-
src/{dump_custom.h => dump_custom_vtk.h} | 149 +-
src/dump_decomposition_vtk.cpp | 8 +-
src/dump_decomposition_vtk.h | 8 +-
src/dump_euler_vtk.cpp | 10 +-
src/dump_euler_vtk.h | 10 +-
src/dump_image.cpp | 4 +-
src/dump_mesh_stl.cpp | 10 +-
src/dump_mesh_stl.h | 10 +-
src/dump_mesh_vtk.cpp | 10 +-
src/dump_mesh_vtk.h | 10 +-
src/error.cpp | 8 +-
src/error.h | 8 +-
src/finish.cpp | 2 +-
src/fix.cpp | 8 +-
src/fix.h | 9 +-
src/fix_adapt.cpp | 20 +-
src/fix_adapt.h | 10 +-
src/fix_ave_correlate.cpp | 2 +-
src/fix_ave_euler.cpp | 10 +-
src/fix_ave_euler.h | 10 +-
src/fix_ave_histo.cpp | 2 +-
src/fix_ave_spatial.cpp | 8 +-
src/fix_ave_time.cpp | 6 +-
src/fix_cfd_coupling.cpp | 13 +-
src/fix_cfd_coupling.h | 10 +-
src/fix_cfd_coupling_convection.cpp | 20 +-
src/fix_cfd_coupling_convection.h | 10 +-
src/fix_cfd_coupling_force.cpp | 14 +-
src/fix_cfd_coupling_force.h | 10 +-
src/fix_cfd_coupling_force_implicit.cpp | 32 +-
src/fix_cfd_coupling_force_implicit.h | 12 +-
src/fix_check_timestep_gran.cpp | 21 +-
src/fix_check_timestep_gran.h | 12 +-
src/fix_check_timestep_sph.cpp | 12 +-
src/fix_check_timestep_sph.h | 10 +-
src/fix_contact_atom_counter_dummy.h | 4 +-
src/fix_contact_atom_counter_wall_dummy.h | 4 +-
src/fix_contact_history.cpp | 9 +-
src/fix_contact_history.h | 4 +-
src/fix_contact_history_mesh.cpp | 12 +-
src/fix_contact_history_mesh.h | 10 +-
src/fix_contact_history_mesh_I.h | 10 +-
src/fix_contact_property_atom_dummy.h | 10 +-
src/fix_contact_property_atom_wall_dummy.h | 10 +-
src/fix_deform.cpp | 4 +-
src/fix_deposit.cpp | 8 +-
src/fix_dummy.h | 7 +
src/fix_gravity.h | 4 +-
src/fix_heat_gran.cpp | 10 +-
src/fix_heat_gran.h | 10 +-
src/fix_heat_gran_conduction.cpp | 14 +-
src/fix_heat_gran_conduction.h | 10 +-
src/fix_insert.cpp | 54 +-
src/fix_insert.h | 15 +-
src/fix_insert_pack.cpp | 43 +-
src/fix_insert_pack.h | 12 +-
src/fix_insert_rate_region.cpp | 10 +-
src/fix_insert_rate_region.h | 10 +-
src/fix_insert_stream.cpp | 22 +-
src/fix_insert_stream.h | 21 +-
src/fix_lineforce.h | 3 +
src/fix_massflow_mesh.cpp | 222 +-
src/fix_massflow_mesh.h | 42 +-
src/fix_mesh.cpp | 15 +-
src/fix_mesh.h | 10 +-
src/fix_mesh_surface.cpp | 18 +-
src/fix_mesh_surface.h | 10 +-
src/fix_mesh_surface_stress.cpp | 94 +-
src/fix_mesh_surface_stress.h | 18 +-
src/fix_mesh_surface_stress_servo.cpp | 312 +-
src/fix_mesh_surface_stress_servo.h | 123 +-
src/fix_move.cpp | 4 +-
src/fix_move_mesh.cpp | 28 +-
src/fix_move_mesh.h | 12 +-
src/fix_neighlist_mesh.cpp | 22 +-
src/fix_neighlist_mesh.h | 13 +-
src/fix_nve_limit.cpp | 22 +-
src/fix_nve_sphere.cpp | 22 +-
src/fix_nve_sphere.h | 22 +-
src/fix_particledistribution_discrete.cpp | 47 +-
src/fix_particledistribution_discrete.h | 11 +-
src/fix_pour.cpp | 14 +-
src/fix_pour.h | 8 +-
src/fix_property_atom.cpp | 123 +-
src/fix_property_atom.h | 17 +-
src/fix_property_atom_tracer.cpp | 10 +-
src/fix_property_atom_tracer.h | 10 +-
src/fix_property_atom_tracer_stream.cpp | 10 +-
src/fix_property_atom_tracer_stream.h | 10 +-
src/fix_property_global.cpp | 10 +-
src/fix_property_global.h | 10 +-
src/fix_recenter.cpp | 2 +-
src/fix_region_variable.cpp | 10 +-
src/fix_region_variable.h | 10 +-
src/fix_rigid.cpp | 8 +-
src/fix_rigid.h | 16 +-
src/fix_scalar_transport_equation.cpp | 84 +-
src/fix_scalar_transport_equation.h | 42 +-
src/fix_sph.cpp | 10 +-
src/fix_sph.h | 10 +-
src/fix_sph_density_continuity.cpp | 15 +-
src/fix_sph_density_continuity.h | 10 +-
src/fix_sph_density_corr.cpp | 12 +-
src/fix_sph_density_corr.h | 10 +-
src/fix_sph_density_summation.cpp | 14 +-
src/fix_sph_density_summation.h | 10 +-
src/fix_sph_pressure.cpp | 10 +-
src/fix_sph_pressure.h | 10 +-
src/fix_template_multiplespheres.cpp | 56 +-
src/fix_template_multiplespheres.h | 15 +-
src/fix_template_sphere.cpp | 22 +-
src/fix_template_sphere.h | 13 +-
src/fix_tmd.cpp | 2 +-
src/fix_wall.cpp | 2 +-
src/fix_wall_gran.cpp | 28 +-
src/fix_wall_gran.h | 20 +-
src/fix_wall_gran_base.h | 10 +-
src/fix_wall_reflect.cpp | 2 +-
src/fix_wall_region_sph.cpp | 10 +-
src/fix_wall_region_sph.h | 10 +-
src/fix_wall_sph.cpp | 10 +-
src/fix_wall_sph.h | 10 +-
src/force.cpp | 8 +-
src/force.h | 8 +-
src/general_container.h | 17 +-
src/general_container_I.h | 45 +-
src/global_properties.cpp | 10 +-
src/global_properties.h | 11 +-
src/granular_pair_style.cpp | 10 +-
src/granular_pair_style.h | 10 +-
src/granular_styles.cpp | 10 +-
src/granular_wall.cpp | 10 +-
src/granular_wall.h | 10 +-
src/group.cpp | 8 +-
src/image.cpp | 2 +-
src/input.cpp | 12 +-
src/input.h | 8 +-
src/input_mesh_tet.cpp | 14 +-
src/input_mesh_tet.h | 10 +-
src/input_mesh_tri.cpp | 16 +-
src/input_mesh_tri.h | 10 +-
src/input_multisphere.cpp | 27 +-
src/input_multisphere.h | 16 +-
src/irregular.cpp | 2 +-
src/lammps.cpp | 8 +-
src/lattice.cpp | 4 +-
src/library.cpp | 20 +-
src/library_cfd_coupling.cpp | 10 +-
src/library_cfd_coupling.h | 10 +-
src/makeAllParScale.sh | 40 +
src/math_extra_liggghts.h | 10 +-
src/memory_ns.h | 4 +-
src/mesh_mover.cpp | 52 +-
src/mesh_mover.h | 19 +-
src/modified_andrew.cpp | 10 +-
src/modified_andrew.h | 10 +-
src/modify.cpp | 11 +-
src/modify.h | 9 +-
src/modify_liggghts.cpp | 25 +-
src/mpi_liggghts.h | 12 +-
src/multi_node_mesh.h | 10 +-
src/multi_node_mesh_I.h | 12 +-
src/multi_node_mesh_parallel.h | 10 +-
src/multi_node_mesh_parallel_I.h | 13 +-
src/multi_node_mesh_parallel_buffer_I.h | 11 +-
src/multi_vector_container.h | 10 +-
src/{fix_multisphere.h => multisphere_parallel.h} | 0
src/neigh_bond.cpp | 16 +-
src/neigh_derive.cpp | 6 +-
src/neigh_full.cpp | 2 +-
src/neigh_gran.cpp | 66 +-
src/neigh_half_nsq.cpp | 6 +-
src/neigh_respa.cpp | 32 +-
src/neighbor.cpp | 8 +-
src/neighbor.h | 10 +-
src/normal_model_hertz.h | 12 +-
src/normal_model_hertz_stiffness.h | 10 +-
src/normal_model_hooke.h | 10 +-
src/normal_model_hooke_hysteresis.h | 74 +-
src/normal_model_hooke_stiffness.h | 10 +-
src/os_specific.h | 10 +-
src/pair.cpp | 12 +-
src/pair_born_coul_wolf.cpp | 10 +-
src/pair_buck_coul_cut.cpp | 6 +-
src/pair_coul_dsf.cpp | 4 +-
src/pair_coul_wolf.cpp | 4 +-
src/pair_gran.cpp | 14 +-
src/pair_gran.h | 15 +-
src/pair_gran_base.h | 10 +-
src/pair_gran_proxy.cpp | 10 +-
src/pair_gran_proxy.h | 10 +-
src/pair_hybrid.cpp | 4 +-
src/pair_hybrid_overlay.cpp | 2 +-
src/pair_lj96_cut.cpp | 4 +-
src/pair_lj_cubic.cpp | 8 +-
src/pair_lj_cut.cpp | 4 +-
src/pair_lj_cut_coul_cut.cpp | 4 +-
src/pair_lj_cut_coul_debye.cpp | 6 +-
src/pair_lj_cut_coul_dsf.cpp | 6 +-
src/pair_lj_gromacs.cpp | 4 +-
src/pair_lj_gromacs_coul_gromacs.cpp | 10 +-
src/pair_lj_smooth.cpp | 6 +-
src/pair_mie_cut.cpp | 8 +-
src/pair_sph.cpp | 10 +-
src/pair_sph.h | 10 +-
src/pair_sph_artvisc_tenscorr.cpp | 10 +-
src/pair_sph_artvisc_tenscorr.h | 10 +-
src/pair_table.cpp | 4 +-
src/pair_zbl.cpp | 4 +-
src/particleToInsert.cpp | 40 +-
src/particleToInsert.h | 17 +-
src/primitive_wall.h | 10 +-
src/primitive_wall_definitions.h | 10 +-
src/probability_distribution.h | 12 +-
src/procmap.cpp | 8 +-
src/properties.cpp | 226 +
src/properties.h | 55 +
src/property_registry.cpp | 21 +-
src/property_registry.h | 14 +-
src/read_data.cpp | 14 +-
src/read_data.h | 8 +-
src/read_dump.cpp | 21 +-
src/read_restart.cpp | 6 +-
src/reader_native.cpp | 2 +-
src/reader_xyz.cpp | 2 +-
src/region.cpp | 10 +-
src/region.h | 8 +-
src/region_cone.cpp | 4 +-
src/region_mesh_tet.cpp | 10 +-
src/region_mesh_tet.h | 10 +-
src/region_mesh_tet_I.h | 10 +-
src/region_prism.cpp | 2 +-
src/region_wedge.cpp | 18 +-
src/region_wedge.h | 10 +-
src/rerun.cpp | 2 +-
src/rolling_model_cdt.h | 12 +-
src/rolling_model_epsd.h | 12 +-
src/rolling_model_epsd2.h | 12 +-
src/run.cpp | 2 +-
src/scalar_container.h | 52 +-
src/set.cpp | 12 +-
src/set.h | 8 +-
src/settings.h | 10 +-
src/sph_kernel_cubicspline.h | 10 +-
src/sph_kernel_cubicspline2D.h | 10 +-
src/sph_kernel_spiky.h | 10 +-
src/sph_kernel_spiky2D.h | 10 +-
src/sph_kernel_wendland.h | 10 +-
src/sph_kernel_wendland2D.h | 10 +-
src/sph_kernels.h | 10 +-
src/style_dump.h | 1 +
src/surface_mesh.h | 10 +-
src/surface_mesh_I.h | 12 +-
src/surface_model_default.h | 10 +-
src/tangential_model_history.h | 11 +-
src/tangential_model_no_history.h | 10 +-
src/thermo.cpp | 10 +-
src/thermo.h | 8 +-
src/tracking_mesh.h | 13 +-
src/tracking_mesh_I.h | 10 +-
src/tri_mesh.cpp | 10 +-
src/tri_mesh.h | 10 +-
src/tri_mesh_I.h | 10 +-
src/tri_mesh_planar.cpp | 10 +-
src/tri_mesh_planar.h | 10 +-
src/tri_mesh_planar_I.h | 10 +-
src/universe.cpp | 10 +-
src/utils.h | 10 +-
src/variable.cpp | 16 +-
src/vector_container.h | 10 +-
src/vector_liggghts.h | 69 +-
src/velocity.cpp | 10 +-
src/verlet.cpp | 8 +-
src/verlet_implicit.cpp | 4 +-
src/verlet_implicit.h | 4 +-
src/version_liggghts.h | 2 +-
src/version_liggghts.txt | 2 +-
src/volume_mesh.h | 10 +-
src/volume_mesh_I.h | 10 +-
src/write_dump.cpp | 2 +-
src/write_restart.cpp | 8 +-
src/write_restart.h | 8 +-
tools/Makefile | 41 -
tools/README | 46 -
tools/amber2lmp/README | 103 -
tools/amber2lmp/amber2lammps.py | 1009 -
tools/amber2lmp/dump2trj.py | 306 -
tools/amber2lmp/dump2trj99.py | 277 -
tools/binary2txt.cpp | 188 -
tools/ch2lmp/README | 130 -
tools/ch2lmp/charmm2lammps.pl | 1455 -
tools/ch2lmp/example/1ac7.data | 7207 -
tools/ch2lmp/example/1ac7.dump | 5931 -
tools/ch2lmp/example/1ac7.in | 31 -
tools/ch2lmp/example/1ac7.pdb | 529 -
tools/ch2lmp/example/1ac7.pdb1 | 5159 -
tools/ch2lmp/example/1ac7.pgn | 81 -
tools/ch2lmp/example/1ac7.psf | 1872 -
tools/ch2lmp/example/1ac7_ctrl.pdb | 1973 -
tools/ch2lmp/example/1ac7_ctrl.psf | 3630 -
tools/ch2lmp/example/1ac7_pared.pdb | 540 -
tools/ch2lmp/example/1ac7_trj.pdb | 1973 -
tools/ch2lmp/example/par_all27_na.prm | 1654 -
tools/ch2lmp/example/top_all27_na.rtf | 939 -
tools/ch2lmp/lammps2pdb.pl | 1137 -
tools/ch2lmp/main_manual | 12 -
tools/ch2lmp/other/crd2pdb.pl | 35 -
tools/ch2lmp/other/in_mkdcd | 10 -
tools/ch2lmp/other/in_mkpdb | 9 -
tools/ch2lmp/other/mkdcd.f | 322 -
tools/ch2lmp/other/mkdcd_f77.f | 352 -
tools/ch2lmp/other/mkpdb.f | 469 -
tools/ch2lmp/other/pdb_to_crd.f | 98 -
tools/chain.f | 321 -
tools/createatoms/Manual.pdf | Bin 553652 -> 0 bytes
tools/createatoms/README | 18 -
tools/createatoms/create.input | 197 -
tools/createatoms/createAtoms.f | 1210 -
tools/createatoms/createAtoms.h | 6 -
tools/data2xmovie.c | 366 -
tools/def.chain | 13 -
tools/def.chain.ab | 20 -
tools/def.micelle2d | 9 -
tools/eam_database/EAM.input | 9 -
tools/eam_database/EAM_code | 448 -
tools/eam_database/README | 22 -
tools/eam_database/create.f | 248 -
tools/eam_generate/Al_Zhou.c | 111 -
tools/eam_generate/Cu_Mishin1.c | 123 -
tools/eam_generate/Cu_Zhou.c | 111 -
tools/eam_generate/README | 8 -
tools/eam_generate/W_Zhou.c | 111 -
tools/eff/README | 48 -
tools/eff/VMD-input.py | 78 -
tools/eff/bohr2ang.py | 74 -
tools/eff/cfg2lammps.py | 377 -
tools/eff/h2.out | 65 -
tools/eff/h2.vmd | 215 -
tools/eff/h2.xyz | 13130 --
tools/eff/lmp2data.py | 144 -
tools/eff/lmp2radii.c | 2588 -
tools/eff/lmp2radii.py | 113 -
tools/eff/lmp2radii.pyx | 113 -
tools/eff/lmp2radii_col.py | 123 -
tools/eff/lmp2xyz.py | 113 -
tools/eff/radii.vmd | 240 -
tools/eff/restart2data-pEFF.cpp | 3520 -
tools/eff/setup.py | 12 -
tools/eff/structure_generators/Be-solid.pl | 131 -
tools/eff/structure_generators/Diamond.pl | 119 -
tools/eff/structure_generators/Li-hydride.pl | 93 -
.../eff/structure_generators/Li-solid-angstrom.pl | 92 -
tools/eff/structure_generators/Li-solid.pl | 92 -
.../structure_generators/Uniform-electron-gas.pl | 67 -
tools/eff/structure_generators/h2.pl | 67 -
tools/emacs/README.txt | 23 -
tools/emacs/lammps.el | 210 -
tools/ipp/README | 29 -
tools/ipp/fill_parameters_createAtoms.input | 15 -
tools/ipp/fill_parameters_lammps.input | 3 -
tools/ipp/ipp | 290 -
tools/ipp/template_createAtoms.input | 213 -
tools/ipp/template_lammps.input | 29 -
tools/kate/README.txt | 6 -
tools/kate/lammps.xml | 878 -
tools/lmp2arc/README | 136 -
tools/lmp2arc/src/Makefile | 18 -
tools/lmp2arc/src/ProcessPosFile01.c | 159 -
tools/lmp2arc/src/ProcessPosFile05.c | 157 -
tools/lmp2arc/src/ReadCarFile.c | 119 -
tools/lmp2arc/src/WriteArcFrame.c | 63 -
tools/lmp2arc/src/lmp2.h | 72 -
tools/lmp2arc/src/lmp2arc.c | 265 -
tools/lmp2arc/src/lmp2arc.doc | 94 -
tools/lmp2arc/src/unwrap_molecules.c | 105 -
tools/lmp2arc/test/correct/water8.arc | 398 -
tools/lmp2arc/test/correct/water8.arc.trueflags | 398 -
tools/lmp2arc/test/correct/water8.arc.unwrap | 398 -
tools/lmp2arc/test/water8.arc | 398 -
tools/lmp2arc/test/water8.arc.trueflags | 398 -
tools/lmp2arc/test/water8.car | 39 -
tools/lmp2arc/test/water8.pos | 303 -
tools/lmp2arc/test/water8_unwrap.arc | 398 -
tools/lmp2cfg/README.txt | 83 -
tools/lmp2cfg/examples/00001.cfg | 2939 -
tools/lmp2cfg/examples/00002.cfg | 2939 -
tools/lmp2cfg/examples/dump.atom | 8721 -
tools/lmp2cfg/examples/lmp2cfg_inp.txt | 26 -
tools/lmp2cfg/lmp2cfg.f | 164 -
tools/lmp2vmd/README.txt | 80 -
tools/matlab/README.pdf | Bin 44452 -> 0 bytes
tools/matlab/lmp2cfg.m | 254 -
tools/matlab/readEAM.m | 166 -
tools/matlab/readdump_all.m | 62 -
tools/matlab/readdump_one.m | 131 -
tools/matlab/readlog.m | 88 -
tools/matlab/readrdf.m | 142 -
tools/matlab/scandump.m | 57 -
tools/micelle2d.f | 233 -
tools/moltemplate/LICENSE.TXT | 28 -
tools/moltemplate/README.TXT | 61 -
tools/moltemplate/common/amber/README.TXT | 27 -
tools/moltemplate/common/amber/amberparm2lt.sh | 193 -
.../common/amber/amberparm_angle_to_lt.py | 50 -
.../common/amber/amberparm_bond_to_lt.py | 47 -
.../common/amber/amberparm_dihedral_to_lt.py | 157 -
.../common/amber/amberparm_improper_to_lt.py | 62 -
.../common/amber/amberparm_mass_to_lt.py | 19 -
.../common/amber/amberparm_pair_to_lt.py | 20 -
tools/moltemplate/common/gaff.lt | 11383 --
tools/moltemplate/common/graphene.lt | 106 -
.../common/images/graphene_unit_cell.jpg | Bin 13144 -> 0 bytes
.../common/images/ice_rect8_unitcell.png | Bin 21951 -> 0 bytes
.../common/images/spce_ball_and_stick.jpg | Bin 5644 -> 0 bytes
tools/moltemplate/common/spce.lt | 52 -
tools/moltemplate/common/spce_ice_rect8.lt | 57 -
tools/moltemplate/common/tip3p_1983.lt | 123 -
tools/moltemplate/common/tip3p_2004.lt | 97 -
tools/moltemplate/common/trappe1998.lt | 50 -
tools/moltemplate/common/watmw.lt | 54 -
.../CG_biomolecules/membrane+protein/README.TXT | 70 -
.../CG_biomolecules/membrane+protein/README_run.sh | 33 -
.../membrane+protein/README_setup.sh | 28 -
.../membrane+protein/README_visualize.txt | 87 -
.../images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg | Bin 85276 -> 0 bytes
.../images/membrane+protein_t=0ps_LR.jpg | Bin 71073 -> 0 bytes
.../images/membrane+protein_t=0ps_no_pbc_LR.jpg | Bin 51659 -> 0 bytes
.../images/membrane+protein_t=0ps_top_LR.jpg | Bin 67085 -> 0 bytes
.../images/membrane+protein_t=5000ps_LR.jpg | Bin 71011 -> 0 bytes
.../moltemplate_files/1beadProtSci2010.lt | 254 -
.../1beadProtSci2010_variations.lt | 225 -
.../moltemplate_files/CGLipidBr2005.lt | 198 -
.../calc_table/calc_CGLipidTableINTvsINT.py | 34 -
.../calc_table/version_charmm_cutoff/calc_table.py | 70 -
.../membrane+protein/moltemplate_files/system.lt | 207 -
.../moltemplate_files/table_int.dat | 1139 -
.../CG_biomolecules/membrane+protein/run.in.min | 35 -
.../CG_biomolecules/membrane+protein/run.in.npt | 60 -
.../CG_biomolecules/membrane+protein/run.in.nvt | 67 -
.../membrane_BranniganPRE2005/README.TXT | 33 -
.../membrane_BranniganPRE2005/README_run.sh | 33 -
.../membrane_BranniganPRE2005/README_setup.sh | 28 -
.../membrane_BranniganPRE2005/README_visualize.txt | 87 -
.../membrane_BranniganPRE2005/images/DLPC.jpg | Bin 4915 -> 0 bytes
.../images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg | Bin 58412 -> 0 bytes
.../DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg | Bin 36618 -> 0 bytes
.../images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg | Bin 62029 -> 0 bytes
.../membrane_BranniganPRE2005/images/DPPC.jpg | Bin 5834 -> 0 bytes
.../moltemplate_files/CGLipidBr2005Orig.lt | 191 -
.../moltemplate_files/calc_table/calc_table.py | 34 -
.../calc_table/version_charmm_cutoff/calc_table.py | 70 -
.../moltemplate_files/system.lt | 94 -
.../moltemplate_files/table_int.dat | 1139 -
.../membrane_BranniganPRE2005/run.in.min | 28 -
.../membrane_BranniganPRE2005/run.in.npt | 57 -
.../membrane_BranniganPRE2005/run.in.nvt | 53 -
.../1bead+chaperone/README.TXT | 33 -
.../frustrated+chaperonin/README.TXT | 32 -
.../frustrated+chaperonin/README_run.sh | 31 -
.../frustrated+chaperonin/README_setup.sh | 24 -
.../frustrated+chaperonin/README_visualize.txt | 87 -
.../psf_file_created_by_topotools/system.psf | 86 -
.../images/misfolded+chaperonin_t=0tau_LR.jpg | Bin 15784 -> 0 bytes
.../images/unfolded+chaperonin_t=508750tau_LR.jpg | Bin 17080 -> 0 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 -
.../moltemplate_files/1beadFrustrated_variants.lt | 85 -
.../moltemplate_files/chaperonin.lt | 41 -
.../generate_tables/calc_chaperone_table.py | 87 -
.../generate_tables/calc_dihedral_table.py | 67 -
.../moltemplate_files/system.lt | 45 -
.../moltemplate_files/table_chaperonin_h=0.475.dat | 1188 -
.../moltemplate_files/table_chaperonin_h=0.dat | 1187 -
.../table_dihedral_frustrated.dat | 735 -
.../frustrated+chaperonin/run.in.min | 25 -
.../frustrated+chaperonin/run.in.nvt | 48 -
.../frustrated+minichaperone/README.TXT | 38 -
.../frustrated+minichaperone/README_run.sh | 31 -
.../frustrated+minichaperone/README_setup.sh | 24 -
.../frustrated+minichaperone/README_visualize.txt | 87 -
.../psf_file_created_by_topotools/system.psf | 476 -
.../protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg | Bin 31162 -> 0 bytes
...tein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg | Bin 26258 -> 0 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 -
.../moltemplate_files/1beadFrustrated_variants.lt | 85 -
.../generate_tables/calc_chaperone_table.py | 87 -
.../generate_tables/calc_dihedral_table.py | 67 -
.../moltemplate_files/minichaperone.lt | 41 -
.../moltemplate_files/system.lt | 72 -
.../table_dihedral_frustrated.dat | 735 -
.../table_minichaperone_h=0.6.dat | 988 -
.../moltemplate_files/table_minichaperone_h=0.dat | 989 -
.../frustrated+minichaperone/run.in.min | 24 -
.../frustrated+minichaperone/run.in.nvt | 46 -
.../1bead+chaperone/frustrated/README.TXT | 29 -
.../1bead+chaperone/frustrated/README_run.sh | 21 -
.../1bead+chaperone/frustrated/README_setup.sh | 24 -
.../frustrated/README_visualize.txt | 87 -
.../psf_file_created_by_topotools/system.psf | 85 -
.../images/initial_conformation_t=0tau.jpg | Bin 23358 -> 0 bytes
.../images/misfolded_conformation_t=1250tau.jpg | Bin 23090 -> 0 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 -
.../moltemplate_files/1beadFrustrated_variants.lt | 85 -
.../generate_tables/calc_dihedral_table.py | 67 -
.../frustrated/moltemplate_files/system.lt | 20 -
.../table_dihedral_frustrated.dat | 735 -
.../1bead+chaperone/frustrated/run.in.min | 19 -
.../frustrated/run_short_sim.in.nvt | 50 -
.../unfrustrated+chaperonin/README.TXT | 32 -
.../unfrustrated+chaperonin/README_run.sh | 31 -
.../unfrustrated+chaperonin/README_setup.sh | 24 -
.../unfrustrated+chaperonin/README_visualize.txt | 87 -
.../psf_file_created_by_topotools/system.psf | 98 -
.../images/unfrustrated+chaperonin_t=0tau_LR.jpg | Bin 16267 -> 0 bytes
.../images/unfrustrated+chaperonin_t=105tau_LR.jpg | Bin 14944 -> 0 bytes
.../moltemplate_files/1beadUnfrustrated.lt | 255 -
.../1beadUnfrustrated_variants.lt | 45 -
.../moltemplate_files/chaperonin.lt | 41 -
.../generate_tables/calc_chaperone_table.py | 87 -
.../moltemplate_files/system.lt | 45 -
.../moltemplate_files/table_chaperonin_h=0.475.dat | 1188 -
.../moltemplate_files/table_chaperonin_h=0.dat | 1187 -
.../unfrustrated+chaperonin/run.in.min | 19 -
.../unfrustrated+chaperonin/run.in.nvt | 48 -
.../1bead+chaperone/unfrustrated/README.TXT | 27 -
.../1bead+chaperone/unfrustrated/README_run.sh | 31 -
.../1bead+chaperone/unfrustrated/README_setup.sh | 23 -
.../unfrustrated/README_visualize.txt | 87 -
.../psf_file_created_by_topotools/system.psf | 97 -
.../unfrustrated/images/unfrustrated_t=0tau_LR.jpg | Bin 7690 -> 0 bytes
.../images/unfrustrated_t=200tau_LR.jpg | Bin 7821 -> 0 bytes
.../moltemplate_files/1beadUnfrustrated.lt | 255 -
.../1beadUnfrustrated_variants.lt | 45 -
.../unfrustrated/moltemplate_files/system.lt | 11 -
.../1bead+chaperone/unfrustrated/run.in.min | 19 -
.../1bead+chaperone/unfrustrated/run.in.nvt | 46 -
.../1beadProtSci2010/README.TXT | 44 -
.../1beadProtSci2010/README_run.sh | 31 -
.../1beadProtSci2010/README_setup.sh | 23 -
.../1beadProtSci2010/README_visualize.txt | 87 -
.../1beadProtSci2010/images/4HelixBundle_t=0.jpg | Bin 38619 -> 0 bytes
.../1beadProtSci2010/images/4SheetBundle_t=0.jpg | Bin 49905 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 214 -
.../moltemplate_files/1beadProtSci2010.lt | 274 -
.../1beadProtSci2010/moltemplate_files/README.sh | 13 -
.../other_implementations/README.TXT | 13 -
.../charmm/1beadProtSci2010.lt | 411 -
.../class2/1beadProtSci2010.lt | 385 -
.../1beadProtSci2010/moltemplate_files/system.lt | 25 -
.../1beadProtSci2010/run.in.min | 19 -
.../1beadProtSci2010/run.in.nvt | 44 -
.../vesicle_Brannigan2005+Bellesia2010/README.TXT | 114 -
.../README_run.sh | 24 -
.../README_setup.sh | 50 -
.../README_visualize.txt | 87 -
.../images/vesicle_membrane+protein_L.jpg | Bin 284201 -> 0 bytes
.../moltemplate_files/1beadProtSci2010.lt | 233 -
.../1beadProtSci2010_variations.lt | 225 -
.../moltemplate_files/CGLipidBr2005.lt | 198 -
.../moltemplate_files/README.sh | 22 -
.../calc_table/calc_CGLipidTableINTvsINT.py | 34 -
.../calc_table/version_charmm_cutoff/calc_table.py | 70 -
.../moltemplate_files/system.lt | 192 -
.../moltemplate_files/table_int.dat | 1139 -
.../packmol_files/DLPC.xyz | 6 -
.../packmol_files/DPPC.xyz | 7 -
.../packmol_files/README.sh | 23 -
.../packmol_files/protein.xyz | 75 -
.../packmol_files/step1_proteins.inp | 49 -
.../packmol_files/step2_innerlayer.inp | 70 -
.../packmol_files/step3_outerlayer.inp | 70 -
.../vesicle_Brannigan2005+Bellesia2010/run.in.min | 53 -
.../vesicle_Brannigan2005+Bellesia2010/run.in.nvt | 70 -
.../CG_misc/2bead_heteropolymer/README.TXT | 17 -
.../CG_misc/2bead_heteropolymer/README_run.sh | 20 -
.../CG_misc/2bead_heteropolymer/README_setup.sh | 23 -
.../2bead_heteropolymer/README_visualize.txt | 86 -
.../images/2bead_heteropolymer_t=0.jpg | Bin 76183 -> 0 bytes
.../images/2bead_heteropolymer_t=1000ps.jpg | Bin 54472 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 1728 -
.../2bead_heteropolymer/moltemplate_files/2bead.lt | 128 -
.../moltemplate_files/2bead_forcefield.lt | 126 -
.../moltemplate_files/README.sh | 20 -
.../moltemplate_files/peptide.lt | 50 -
.../moltemplate_files/system.lt | 26 -
.../CG_misc/2bead_heteropolymer/run.in.nvt | 38 -
.../CG_misc/random_heteropolymer/README.TXT | 36 -
.../CG_misc/random_heteropolymer/README_run.sh | 14 -
.../CG_misc/random_heteropolymer/README_setup.sh | 23 -
.../random_heteropolymer/README_visualize.txt | 87 -
.../CG_misc/random_heteropolymer/images/2bead.jpg | Bin 2713 -> 0 bytes
.../CG_misc/random_heteropolymer/images/3bead.jpg | Bin 4410 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 277 -
.../images/random_heteropolymer_t=0ps.jpg | Bin 31115 -> 0 bytes
.../images/random_heteropolymer_t=1ns.jpg | Bin 29582 -> 0 bytes
.../moltemplate_files/monomers.lt | 115 -
.../moltemplate_files/polymer.lt | 82 -
.../moltemplate_files/system.lt | 33 -
.../CG_misc/random_heteropolymer/run.in.nvt | 29 -
.../examples/CG_misc/translocation/README.TXT | 23 -
.../examples/CG_misc/translocation/README_run.sh | 28 -
.../examples/CG_misc/translocation/README_setup.sh | 23 -
.../CG_misc/translocation/README_visualize.txt | 87 -
.../CG_misc/translocation/images/polymer_LR.jpg | Bin 5568 -> 0 bytes
.../CG_misc/translocation/images/solvent_LR.jpg | Bin 23407 -> 0 bytes
.../images/walls+solvent+polymer_t=0.jpg | Bin 105467 -> 0 bytes
.../CG_misc/translocation/images/walls_LR.jpg | Bin 13280 -> 0 bytes
.../translocation/moltemplate_files/monomer.lt | 111 -
.../translocation/moltemplate_files/polymer.lt | 35 -
.../translocation/moltemplate_files/solvent.lt | 23 -
.../moltemplate_files/solvent_single.lt | 22 -
.../translocation/moltemplate_files/system.lt | 55 -
.../translocation/moltemplate_files/wall_single.lt | 21 -
.../translocation/moltemplate_files/walls.lt | 23 -
.../examples/CG_misc/translocation/run.in.npt | 70 -
.../examples/CG_misc/translocation/run.in.nvt | 43 -
.../CG_solvent/cyclododecane+watMW/README.TXT | 28 -
.../CG_solvent/cyclododecane+watMW/README_run.sh | 31 -
.../CG_solvent/cyclododecane+watMW/README_setup.sh | 25 -
.../cyclododecane+watMW/README_visualize.txt | 87 -
.../images/cyclododecane+watMW_t=0ps_LR.jpg | Bin 51874 -> 0 bytes
.../images/cyclododecane+watMW_t=400ps_LR.jpg | Bin 39434 -> 0 bytes
.../images/cyclododecane+watMW_t=50ps_LR.jpg | Bin 39341 -> 0 bytes
.../cyclododecane+watMW/images/cyclopentane.jpg | Bin 12330 -> 0 bytes
.../images/cyclopentane_unrelaxed.jpg | Bin 12835 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 3669 -
.../cyclododecane+watMW/images/watMW.jpg | Bin 3141 -> 0 bytes
.../moltemplate_files/README.sh | 11 -
.../moltemplate_files/cyclododecane.lt | 55 -
.../moltemplate_files/system.lt | 62 -
.../moltemplate_files/trappe1998.lt | 50 -
.../version_more_comments/system.lt | 80 -
.../cyclododecane+watMW/moltemplate_files/watmw.lt | 54 -
.../CG_solvent/cyclododecane+watMW/run.in.npt | 58 -
.../CG_solvent/cyclododecane+watMW/run.in.nvt | 78 -
tools/moltemplate/examples/README.TXT | 24 -
.../waterTIP3P+isobutane/README.TXT | 42 -
.../waterTIP3P+isobutane/README_run.sh | 39 -
.../waterTIP3P+isobutane/README_setup.sh | 89 -
.../waterTIP3P+isobutane/README_visualize.txt | 87 -
.../waterTIP3P+isobutane/images/isobutane.jpg | Bin 24301 -> 0 bytes
.../images/water+isobutane_t=0_LR.jpg | Bin 104035 -> 0 bytes
.../images/water+isobutane_t=840ps_LR.jpg | Bin 73375 -> 0 bytes
.../waterTIP3P+isobutane/images/water.jpg | Bin 10076 -> 0 bytes
.../moltemplate_files/isobutane.lt | 51 -
.../moltemplate_files/system.lt | 31 -
.../waterTIP3P+isobutane/run.in.npt | 37 -
.../waterTIP3P+isobutane/run.in.nvt | 53 -
.../aluminum_crystal_strain/README.TXT | 54 -
.../aluminum_crystal_strain/README_setup.sh | 29 -
.../aluminum_crystal_strain/README_visualize.txt | 87 -
.../aluminum_crystal_strain/images/AlCell_LR.jpg | Bin 2364 -> 0 bytes
.../images/AlCrystal10x10x10_t=0steps_LR.jpg | Bin 30158 -> 0 bytes
.../images/AlCrystal10x10x10_t=20000steps_LR.jpg | Bin 29910 -> 0 bytes
.../moltemplate_files/README.sh | 22 -
.../moltemplate_files/al_cell.lt | 64 -
.../moltemplate_files/system.lt | 35 -
.../aluminum_crystal_strain/run.in | 76 -
.../cnad-cnt/README_FIRST.TXT | 83 -
.../cnad-cnt/README_step1_run_ltemplify.sh | 13 -
.../cnad-cnt/README_step2_run_moltemplate.sh | 18 -
.../cnad-cnt/README_step3_run_lammps.sh | 16 -
.../cnad-cnt/README_visualize.txt | 50 -
.../cnad-cnt/cnad-cnt.data | 1157 -
.../cnad-cnt/cnad-cnt.in | 49 -
.../cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg | Bin 29386 -> 0 bytes
.../cnad-cnt/images/cnad-cnt_orig.jpg | Bin 19144 -> 0 bytes
.../cnad-cnt/images/cnad.jpg | Bin 18403 -> 0 bytes
.../cnad-cnt/images/cnt.jpg | Bin 20633 -> 0 bytes
.../cnad-cnt_after_rotate_and_copy.psf | 598 -
.../cnad-cnt_orig.psf | 489 -
.../cnad-cnt/run.in.nvt | 46 -
.../cnad-cnt/system.lt | 29 -
.../all_atom_examples/ice_crystal/README_run.sh | 33 -
.../all_atom_examples/ice_crystal/README_setup.sh | 23 -
.../ice_crystal/README_visualize.txt | 87 -
.../images/ice_rect8_crystal_3x2x2_LR.jpg | Bin 25820 -> 0 bytes
.../ice_crystal/moltemplate_files/spce.lt | 52 -
.../moltemplate_files/spce_ice_rect8.lt | 57 -
.../ice_crystal/moltemplate_files/system.lt | 11 -
.../all_atom_examples/ice_crystal/run.in.npt | 38 -
.../all_atom_examples/ice_crystal/run.in.nvt | 61 -
.../all_atom_examples/nanotube+water/README.TXT | 51 -
.../all_atom_examples/nanotube+water/README_run.sh | 24 -
.../nanotube+water/README_setup.sh | 23 -
.../nanotube+water/README_visualize.txt | 77 -
.../psf_file_created_by_topotools/system.psf | 3195 -
.../nanotube+water/images/graphene_unit_cell.jpg | Bin 13144 -> 0 bytes
.../nanotube+walls+water_side_pbc_t=0ps_LR.jpg | Bin 30772 -> 0 bytes
.../nanotube+walls+water_side_pbc_t=108ps_LR.jpg | Bin 28367 -> 0 bytes
.../nanotube+walls+water_side_pbc_t=305ps_LR.jpg | Bin 27305 -> 0 bytes
.../nanotube+walls+water_top_nopbc_t=0_LR.jpg | Bin 33740 -> 0 bytes
.../images/nanotube+walls_side_nopbc_LR.jpg | Bin 18748 -> 0 bytes
.../nanotube+water/images/water_side_nopbc_LR.jpg | Bin 26968 -> 0 bytes
.../nanotube+water/moltemplate_files/README.sh | 27 -
.../nanotube+water/moltemplate_files/graphene.lt | 119 -
.../moltemplate_files/graphene_walls.lt | 54 -
.../nanotube+water/moltemplate_files/nanotube.lt | 24 -
.../nanotube+water/moltemplate_files/spce.lt | 52 -
.../nanotube+water/moltemplate_files/system.lt | 46 -
.../nanotube+water/moltemplate_files/water_box.lt | 20 -
.../all_atom_examples/nanotube+water/run.in.npt | 98 -
.../all_atom_examples/nanotube+water/run.in.nvt | 71 -
.../waterSPCE_from_PDBfile/README.TXT | 10 -
.../waterSPCE_from_PDBfile/README_run.sh | 31 -
.../waterSPCE_from_PDBfile/README_setup.sh | 32 -
.../waterSPCE_from_PDBfile/README_visualize.txt | 64 -
.../waterSPCE_from_PDBfile/moltemplate_files/.0 | 0
.../moltemplate_files/README.sh | 11 -
.../moltemplate_files/solvate.pdb | 782 -
.../moltemplate_files/spce.lt | 52 -
.../moltemplate_files/system.lt | 16 -
.../waterSPCE_from_PDBfile/run.in.npt | 52 -
.../waterSPCE_from_PDBfile/run.in.nvt | 67 -
.../waterSPCE+Na+Cl/README_run.sh | 33 -
.../waterSPCE+Na+Cl/README_setup.sh | 23 -
.../waterSPCE+Na+Cl/README_visualize.txt | 87 -
.../waterSPCE+Na+Cl/images/Cl.jpg | Bin 1577 -> 0 bytes
.../waterSPCE+Na+Cl/images/Na.jpg | Bin 1595 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 4257 -
.../waterSPCE+Na+Cl/images/wat.jpg | Bin 5644 -> 0 bytes
.../waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg | Bin 169027 -> 0 bytes
.../images/waterSPCE+Na+Cl_t=100ps.jpg | Bin 144377 -> 0 bytes
.../waterSPCE+Na+Cl/moltemplate_files/ions.lt | 60 -
.../waterSPCE+Na+Cl/moltemplate_files/spce.lt | 52 -
.../waterSPCE+Na+Cl/moltemplate_files/system.lt | 52 -
.../all_atom_examples/waterSPCE+Na+Cl/run.in.npt | 44 -
.../all_atom_examples/waterSPCE+Na+Cl/run.in.nvt | 61 -
.../examples/silly/pyramids_vs_gravity/README.TXT | 22 -
.../pyramids_vs_gravity/README_VMD_graphene.txt | 28 -
.../silly/pyramids_vs_gravity/README_setup.sh | 23 -
.../silly/pyramids_vs_gravity/README_visualize.txt | 76 -
.../images/pyramids_vs_gravity_t=04800steps_LR.jpg | Bin 88094 -> 0 bytes
.../images/pyramids_vs_gravity_t=12200steps_LR.jpg | Bin 91240 -> 0 bytes
.../images/pyramids_vs_gravity_t=33000steps_LR.jpg | Bin 98828 -> 0 bytes
.../moltemplate_files/README.sh | 15 -
.../moltemplate_files/graphene.lt | 61 -
.../moltemplate_files/graphene_wall.lt | 21 -
.../moltemplate_files/pyramids.lt | 283 -
.../moltemplate_files/system.lt | 80 -
.../examples/silly/pyramids_vs_gravity/run.in | 64 -
.../examples/silly/sierpinski/README.TXT | 45 -
.../examples/silly/sierpinski/README_setup.sh | 29 -
.../examples/silly/sierpinski/README_visualize.txt | 87 -
.../examples/silly/sierpinski/images/AlCell_LR.jpg | Bin 2364 -> 0 bytes
.../examples/silly/sierpinski/images/lvl1_LR.jpg | Bin 2623 -> 0 bytes
.../examples/silly/sierpinski/images/lvl2_LR.jpg | Bin 7722 -> 0 bytes
.../examples/silly/sierpinski/images/lvl3_LR.jpg | Bin 16455 -> 0 bytes
...serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg | Bin 82092 -> 0 bytes
.../serpinski_cube_lattice_8cells_t=7400_LR.jpg | Bin 21718 -> 0 bytes
.../silly/sierpinski/moltemplate_files/al_cell.lt | 64 -
.../elegant_inefficient_version/al_cell.lt | 64 -
.../sierpinski_cubes.lt | 34 -
.../elegant_inefficient_version/system.lt | 34 -
.../moltemplate_files/sierpinski_cubes.lt | 66 -
.../silly/sierpinski/moltemplate_files/system.lt | 36 -
tools/moltemplate/examples/silly/sierpinski/run.in | 38 -
tools/moltemplate/moltemplate_manual.pdf | Bin 697917 -> 0 bytes
tools/moltemplate/src/bonds_by_type.py | 379 -
tools/moltemplate/src/dump2data.py | 1263 -
tools/moltemplate/src/extract_lammps_data.py | 119 -
tools/moltemplate/src/ltemplify.py | 2236 -
tools/moltemplate/src/lttree.py | 745 -
tools/moltemplate/src/lttree_check.py | 2211 -
tools/moltemplate/src/lttree_postprocess.py | 335 -
tools/moltemplate/src/lttree_styles.py | 239 -
tools/moltemplate/src/moltemplate.sh | 1775 -
tools/moltemplate/src/nbody_Angles.py | 41 -
tools/moltemplate/src/nbody_Bonds.py | 31 -
tools/moltemplate/src/nbody_Dihedrals.py | 44 -
tools/moltemplate/src/nbody_Impropers.py | 49 -
.../nbody_Dihedrals_nosym.py | 32 -
.../nbody_ImpropersIJIKILnoswap.py | 33 -
.../nbody_ImpropersIJIKILswapJK.py | 49 -
.../nbody_ImpropersIJIKILswapJKL.py | 43 -
.../nbody_ImpropersJIJKJLnoswap.py | 32 -
.../nbody_ImpropersJIJKJLswapIK.py | 47 -
.../nbody_ImpropersJIJKJLswapIKL.py | 44 -
.../nbody_ImpropersJIJKJLswapJK.py | 48 -
tools/moltemplate/src/nbody_by_type.py | 639 -
tools/moltemplate/src/nbody_by_type_lib.py | 383 -
tools/moltemplate/src/nbody_by_type_lib_old.py | 312 -
.../moltemplate/src/nbody_fix_ttree_assignments.py | 149 -
tools/moltemplate/src/nbody_graph_search.py | 976 -
tools/moltemplate/src/nbody_reorder_atoms.py | 74 -
tools/moltemplate/src/ordereddict.py | 258 -
tools/moltemplate/src/pdbsort.py | 138 -
tools/moltemplate/src/postprocess_input_script.py | 146 -
tools/moltemplate/src/raw2data.py | 99 -
tools/moltemplate/src/remove_duplicate_atoms.py | 53 -
tools/moltemplate/src/remove_duplicates_nbody.py | 49 -
.../moltemplate/src/renumber_DATA_first_column.py | 69 -
tools/moltemplate/src/ttree.py | 4762 -
tools/moltemplate/src/ttree_lex.py | 2090 -
tools/moltemplate/src/ttree_matrix_stack.py | 618 -
tools/moltemplate/src/ttree_render.py | 115 -
tools/msi2lmp/README | 180 -
tools/msi2lmp/frc_files/README | 10 -
tools/msi2lmp/frc_files/cff91.frc | 4758 -
tools/msi2lmp/frc_files/clayff.frc | 154 -
tools/msi2lmp/frc_files/compass_published.frc | 1381 -
tools/msi2lmp/frc_files/cvff.frc | 4716 -
tools/msi2lmp/frc_files/cvff_aug.frc | 5180 -
tools/msi2lmp/frc_files/oplsaa.frc | 236 -
tools/msi2lmp/frc_files/pcff.frc | 5593 -
tools/msi2lmp/frc_files/pcff.rlb | 2 -
tools/msi2lmp/frc_files/pcff_templates.dat | 1927 -
tools/msi2lmp/src/CheckLists.c | 39 -
tools/msi2lmp/src/Forcefield.h | 35 -
tools/msi2lmp/src/GetParameters.c | 1309 -
tools/msi2lmp/src/InitializeItems.c | 140 -
tools/msi2lmp/src/MakeLists.c | 774 -
tools/msi2lmp/src/Makefile | 44 -
tools/msi2lmp/src/ReadCarFile.c | 329 -
tools/msi2lmp/src/ReadFrcFile.c | 120 -
tools/msi2lmp/src/ReadMdfFile.c | 415 -
tools/msi2lmp/src/SearchAndFill.c | 230 -
tools/msi2lmp/src/WriteDataFile.c | 390 -
tools/msi2lmp/src/msi2lmp.c | 416 -
tools/msi2lmp/src/msi2lmp.h | 222 -
tools/msi2lmp/test/PyAC_bulk-clayff.car | 1287 -
tools/msi2lmp/test/PyAC_bulk-clayff.mdf | 1308 -
tools/msi2lmp/test/benzene-class1.car | 19 -
tools/msi2lmp/test/benzene-class1.mdf | 40 -
tools/msi2lmp/test/benzene-class2a.car | 19 -
tools/msi2lmp/test/benzene-class2a.mdf | 40 -
tools/msi2lmp/test/benzene-class2b.car | 19 -
tools/msi2lmp/test/benzene-class2b.mdf | 40 -
tools/msi2lmp/test/crambin-class1.car | 649 -
tools/msi2lmp/test/crambin-class1.mdf | 840 -
tools/msi2lmp/test/data-compare.pl | 942 -
tools/msi2lmp/test/ethane-class1.car | 15 -
tools/msi2lmp/test/ethane-class1.mdf | 36 -
tools/msi2lmp/test/ethane-class2a.car | 15 -
tools/msi2lmp/test/ethane-class2a.mdf | 36 -
tools/msi2lmp/test/ethane-class2b.car | 15 -
tools/msi2lmp/test/ethane-class2b.mdf | 36 -
tools/msi2lmp/test/ethane-oplsaa.car | 15 -
tools/msi2lmp/test/ethane-oplsaa.mdf | 36 -
tools/msi2lmp/test/h2-h2o-class1.car | 13 -
tools/msi2lmp/test/h2-h2o-class1.mdf | 33 -
tools/msi2lmp/test/h2-h2o-class2b.car | 13 -
tools/msi2lmp/test/h2-h2o-class2b.mdf | 33 -
tools/msi2lmp/test/hap_crystal-class1.car | 95 -
tools/msi2lmp/test/hap_crystal-class1.mdf | 116 -
tools/msi2lmp/test/hap_crystal-class2b.car | 95 -
tools/msi2lmp/test/hap_crystal-class2b.mdf | 116 -
tools/msi2lmp/test/hydrogen-class1.car | 9 -
tools/msi2lmp/test/hydrogen-class1.mdf | 30 -
tools/msi2lmp/test/hydrogen-class2a.car | 9 -
tools/msi2lmp/test/hydrogen-class2a.mdf | 30 -
tools/msi2lmp/test/in.PyAC_bulk-clayff | 15 -
tools/msi2lmp/test/in.benzene-class1 | 15 -
tools/msi2lmp/test/in.benzene-class2a | 15 -
tools/msi2lmp/test/in.benzene-class2b | 15 -
tools/msi2lmp/test/in.crambin-class1 | 16 -
tools/msi2lmp/test/in.ethane-class1 | 14 -
tools/msi2lmp/test/in.ethane-class2a | 15 -
tools/msi2lmp/test/in.ethane-class2b | 15 -
tools/msi2lmp/test/in.ethane-oplsaa | 14 -
tools/msi2lmp/test/in.h2-h2o-class1 | 13 -
tools/msi2lmp/test/in.h2-h2o-class2b | 13 -
tools/msi2lmp/test/in.hap_crystal-class1 | 13 -
tools/msi2lmp/test/in.hap_crystal-class2b | 14 -
tools/msi2lmp/test/in.hydrogen-class1 | 12 -
tools/msi2lmp/test/in.hydrogen-class2a | 12 -
tools/msi2lmp/test/in.naphthalene-class1 | 15 -
tools/msi2lmp/test/in.naphthalene-class2a | 15 -
tools/msi2lmp/test/in.naphthalene-class2b | 15 -
tools/msi2lmp/test/in.nylon-class1 | 16 -
tools/msi2lmp/test/in.phen3_cff97-class1 | 16 -
tools/msi2lmp/test/in.water-class1 | 13 -
tools/msi2lmp/test/in.water-class2b | 13 -
tools/msi2lmp/test/naphthalene-class1.car | 25 -
tools/msi2lmp/test/naphthalene-class1.mdf | 46 -
tools/msi2lmp/test/naphthalene-class2a.car | 25 -
tools/msi2lmp/test/naphthalene-class2a.mdf | 46 -
tools/msi2lmp/test/naphthalene-class2b.car | 25 -
tools/msi2lmp/test/naphthalene-class2b.mdf | 46 -
tools/msi2lmp/test/nylon-class1.car | 124 -
tools/msi2lmp/test/nylon-class1.mdf | 142 -
tools/msi2lmp/test/phen3_cff97-class1.car | 29 -
tools/msi2lmp/test/phen3_cff97-class1.mdf | 57 -
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 1450 -
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2728 -
tools/msi2lmp/test/reference/benzene-class1.data | 135 -
tools/msi2lmp/test/reference/benzene-class1.data2 | 148 -
tools/msi2lmp/test/reference/benzene-class1.data3 | 135 -
tools/msi2lmp/test/reference/benzene-class2a.data | 179 -
tools/msi2lmp/test/reference/benzene-class2a.data2 | 192 -
tools/msi2lmp/test/reference/benzene-class2b.data | 179 -
tools/msi2lmp/test/reference/benzene-class2b.data2 | 192 -
tools/msi2lmp/test/reference/crambin-class1.data | 4727 -
tools/msi2lmp/test/reference/crambin-class1.data2 | 5370 -
tools/msi2lmp/test/reference/ethane-class1.data | 89 -
tools/msi2lmp/test/reference/ethane-class1.data2 | 97 -
tools/msi2lmp/test/reference/ethane-class2a.data | 141 -
tools/msi2lmp/test/reference/ethane-class2a.data2 | 150 -
tools/msi2lmp/test/reference/ethane-class2b.data | 141 -
tools/msi2lmp/test/reference/ethane-class2b.data2 | 150 -
tools/msi2lmp/test/reference/ethane-oplsaa.data | 89 -
tools/msi2lmp/test/reference/ethane-oplsaa.data2 | 97 -
tools/msi2lmp/test/reference/h2-h2o-class1.data | 55 -
tools/msi2lmp/test/reference/h2-h2o-class1.data2 | 59 -
tools/msi2lmp/test/reference/h2-h2o-class2b.data | 63 -
tools/msi2lmp/test/reference/h2-h2o-class2b.data2 | 67 -
.../msi2lmp/test/reference/hap_crystal-class1.data | 260 -
.../test/reference/hap_crystal-class1.data2 | 347 -
.../test/reference/hap_crystal-class2b.data | 328 -
.../test/reference/hap_crystal-class2b.data2 | 416 -
tools/msi2lmp/test/reference/hydrogen-class1.data | 36 -
tools/msi2lmp/test/reference/hydrogen-class1.data2 | 36 -
tools/msi2lmp/test/reference/hydrogen-class2a.data | 36 -
.../msi2lmp/test/reference/hydrogen-class2a.data2 | 36 -
.../msi2lmp/test/reference/naphthalene-class1.data | 185 -
.../test/reference/naphthalene-class1.data2 | 204 -
.../test/reference/naphthalene-class2a.data | 230 -
.../test/reference/naphthalene-class2a.data2 | 249 -
.../test/reference/naphthalene-class2b.data | 230 -
.../test/reference/naphthalene-class2b.data2 | 249 -
tools/msi2lmp/test/reference/nylon-class1.data | 898 -
tools/msi2lmp/test/reference/nylon-class1.data2 | 1016 -
.../msi2lmp/test/reference/phen3_cff97-class1.data | 258 -
.../test/reference/phen3_cff97-class1.data2 | 282 -
tools/msi2lmp/test/reference/water-class1.data | 49 -
tools/msi2lmp/test/reference/water-class1.data2 | 51 -
tools/msi2lmp/test/reference/water-class2b.data | 57 -
tools/msi2lmp/test/reference/water-class2b.data2 | 59 -
tools/msi2lmp/test/runtests.sh | 158 -
tools/msi2lmp/test/test.input | 27 -
tools/msi2lmp/test/water-class1.car | 10 -
tools/msi2lmp/test/water-class1.mdf | 31 -
tools/msi2lmp/test/water-class2b.car | 10 -
tools/msi2lmp/test/water-class2b.mdf | 31 -
tools/phonon/Makefile | 64 -
tools/phonon/README | 31 -
tools/phonon/dynmat.cpp | 602 -
tools/phonon/dynmat.h | 66 -
tools/phonon/green.cpp | 250 -
tools/phonon/green.h | 25 -
tools/phonon/interpolate.cpp | 310 -
tools/phonon/interpolate.h | 43 -
tools/phonon/main.cpp | 18 -
tools/phonon/memory.cpp | 51 -
tools/phonon/memory.h | 430 -
tools/phonon/phonon.cpp | 1266 -
tools/phonon/phonon.h | 59 -
tools/phonon/timer.cpp | 41 -
tools/phonon/timer.h | 24 -
tools/phonon/version.h | 1 -
tools/polybond/Manual.pdf | Bin 92552 -> 0 bytes
tools/polybond/README | 12 -
tools/polybond/lmpsdata.py | 1945 -
tools/pymol_asphere/README | 18 -
tools/pymol_asphere/doc/asphere_vis.1 | 241 -
tools/pymol_asphere/doc/asphere_vis.manpage | 228 -
tools/pymol_asphere/doc/asphere_vis.pdf | Bin 18920 -> 0 bytes
tools/pymol_asphere/examples/README | 16 -
tools/pymol_asphere/examples/colors.ellipse | 2 -
tools/pymol_asphere/src/Makefile | 200 -
tools/pymol_asphere/src/asphere_vis.cpp | 401 -
tools/pymol_asphere/src/cartesian.cpp | 1047 -
tools/pymol_asphere/src/cartesian.h | 493 -
tools/pymol_asphere/src/colors.cpp | 111 -
tools/pymol_asphere/src/colors.h | 59 -
tools/pymol_asphere/src/commandline.cpp | 504 -
tools/pymol_asphere/src/commandline.h | 214 -
tools/pymol_asphere/src/error.cpp | 280 -
tools/pymol_asphere/src/error.h | 218 -
tools/pymol_asphere/src/glsurface.cpp | 595 -
tools/pymol_asphere/src/glsurface.h | 195 -
tools/pymol_asphere/src/m_constants.h | 67 -
tools/pymol_asphere/src/make_manpages.sh | 24 -
tools/pymol_asphere/src/misc.cpp | 428 -
tools/pymol_asphere/src/misc.h | 165 -
tools/pymol_asphere/src/miscm.cpp | 212 -
tools/pymol_asphere/src/miscm.h | 89 -
tools/pymol_asphere/src/spherical.cpp | 147 -
tools/pymol_asphere/src/spherical.h | 113 -
tools/python/README | 113 -
tools/python/dump2cfg.py | 32 -
tools/python/dump2pdb.py | 37 -
tools/python/dump2xyz.py | 32 -
tools/python/dumpsort.py | 26 -
tools/python/log2txt.py | 32 -
tools/python/logplot.py | 28 -
tools/python/neb_combine.py | 88 -
tools/python/neb_final.py | 71 -
tools/python/pizza/cfg.py | 187 -
tools/python/pizza/dump.py | 1231 -
tools/python/pizza/gnu.py | 383 -
tools/python/pizza/log.py | 338 -
tools/python/pizza/pdbfile.py | 289 -
tools/python/pizza/xyz.py | 121 -
tools/reax/Cutoff.dic | 14 -
tools/reax/README.txt | 22 -
tools/reax/bondConnectCheck.f90 | 232 -
tools/reax/bonds.reax | 784 -
tools/reax/mol_fra.c | 801 -
tools/reax/reaxc_bond.pl | 152 -
tools/restart2data.cpp | 4227 -
tools/vim/README.txt | 54 -
tools/vim/lammps.vim | 63 -
tools/vim/mysyntax.vim | 4 -
tools/vim/vimrc | 2 -
tools/xmgrace/README | 16 -
tools/xmgrace/lammpsplot.cpp | 830 -
tools/xmgrace/lammpsplot.pdf | Bin 71715 -> 0 bytes
tools/xmgrace/logplotawk.oneliner | 7 -
tools/xmgrace/logplotgrep.oneliner | 6 -
tools/xmgrace/plotthermodata.awk | 18 -
tools/xmovie/Makefile | 63 -
tools/xmovie/README | 51 -
tools/xmovie/Xdefaults | 51 -
tools/xmovie/control.c | 1340 -
tools/xmovie/dummy.c | 63 -
tools/xmovie/dummy.dat | 8004 -
tools/xmovie/hpsort.c | 43 -
tools/xmovie/read.c | 1239 -
tools/xmovie/resource.h | 244 -
tools/xmovie/scene.c | 673 -
tools/xmovie/toascii.c | 425 -
tools/xmovie/tobinary.c | 525 -
tools/xmovie/version.c | 15 -
tools/xmovie/xmovie.c | 282 -
tools/xmovie/xmovie.h | 161 -
1328 files changed, 8580 insertions(+), 701644 deletions(-)
delete mode 100755 bench/Cu_u3.eam
delete mode 100755 bench/GPU/README
delete mode 100755 bench/GPU/in.eam.cpu
delete mode 100755 bench/GPU/in.eam.cuda
delete mode 100755 bench/GPU/in.eam.gpu
delete mode 100755 bench/GPU/in.lj.cpu
delete mode 100755 bench/GPU/in.lj.cuda
delete mode 100755 bench/GPU/in.lj.gpu
delete mode 100755 bench/GPU/in.rhodo.cpu
delete mode 100755 bench/GPU/in.rhodo.cuda
delete mode 100755 bench/GPU/in.rhodo.gpu
delete mode 100755 bench/POTENTIALS/CH.airebo
delete mode 100755 bench/POTENTIALS/CdTe.bop
delete mode 100755 bench/POTENTIALS/Cu_u3.eam
delete mode 100755 bench/POTENTIALS/Ni.adp
delete mode 100755 bench/POTENTIALS/Ni.meam
delete mode 100755 bench/POTENTIALS/README
delete mode 100755 bench/POTENTIALS/Si.sw
delete mode 100755 bench/POTENTIALS/Si.tersoff
delete mode 100755 bench/POTENTIALS/ffield.comb
delete mode 100755 bench/POTENTIALS/ffield.eim
delete mode 100755 bench/POTENTIALS/ffield.reax
delete mode 100755 bench/POTENTIALS/in.adp
delete mode 100755 bench/POTENTIALS/in.airebo
delete mode 100755 bench/POTENTIALS/in.bop
delete mode 100755 bench/POTENTIALS/in.comb
delete mode 100755 bench/POTENTIALS/in.dpd
delete mode 100755 bench/POTENTIALS/in.eam
delete mode 100755 bench/POTENTIALS/in.eff
delete mode 100755 bench/POTENTIALS/in.eim
delete mode 100755 bench/POTENTIALS/in.fene
delete mode 100755 bench/POTENTIALS/in.gb
delete mode 100755 bench/POTENTIALS/in.granular
delete mode 100755 bench/POTENTIALS/in.lj
delete mode 100755 bench/POTENTIALS/in.meam
delete mode 100755 bench/POTENTIALS/in.peri
delete mode 100755 bench/POTENTIALS/in.protein
delete mode 100755 bench/POTENTIALS/in.reax
delete mode 100755 bench/POTENTIALS/in.reaxc
delete mode 100755 bench/POTENTIALS/in.rebo
delete mode 100755 bench/POTENTIALS/in.spce
delete mode 100755 bench/POTENTIALS/in.sw
delete mode 100755 bench/POTENTIALS/in.tersoff
delete mode 100755 bench/POTENTIALS/library.meam
delete mode 100755 bench/POTENTIALS/log.26Jun12.adp.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.adp.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.airebo.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.airebo.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.bop.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.bop.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.comb.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.comb.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.dpd.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.dpd.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.eam.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.eam.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.eff.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.eff.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.eim.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.eim.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.fene.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.fene.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.gb.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.gb.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.granular.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.granular.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.lj.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.lj.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.meam.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.meam.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.peri.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.peri.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.protein.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.protein.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.reax.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.reax.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.reaxc.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.reaxc.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.rebo.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.rebo.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.spce.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.spce.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.sw.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.sw.4
delete mode 100755 bench/POTENTIALS/log.26Jun12.tersoff.1
delete mode 100755 bench/POTENTIALS/log.26Jun12.tersoff.4
delete mode 100755 bench/POTENTIALS/reax_defs.h
delete mode 100755 bench/README
delete mode 100755 bench/data.chain
delete mode 100755 bench/data.chute
delete mode 100755 bench/data.rhodo
delete mode 100755 bench/in.chain
delete mode 100755 bench/in.chain.scaled
delete mode 100755 bench/in.chute
delete mode 100755 bench/in.chute.scaled
delete mode 100755 bench/in.eam
delete mode 100755 bench/in.lj
delete mode 100755 bench/in.rhodo
delete mode 100755 bench/in.rhodo.scaled
delete mode 100755 bench/log.30Jul13.chain.fixed.linux.1
delete mode 100755 bench/log.30Jul13.chain.fixed.linux.4
delete mode 100755 bench/log.30Jul13.chain.scaled.linux.4
delete mode 100755 bench/log.30Jul13.chute.fixed.linux.1
delete mode 100755 bench/log.30Jul13.chute.fixed.linux.4
delete mode 100755 bench/log.30Jul13.chute.scaled.linux.4
delete mode 100755 bench/log.30Jul13.eam.fixed.linux.1
delete mode 100755 bench/log.30Jul13.eam.fixed.linux.4
delete mode 100755 bench/log.30Jul13.eam.scaled.linux.4
delete mode 100755 bench/log.30Jul13.lj.fixed.linux.1
delete mode 100755 bench/log.30Jul13.lj.fixed.linux.4
delete mode 100755 bench/log.30Jul13.lj.scaled.linux.4
delete mode 100755 bench/log.30Jul13.rhodo.fixed.linux.1
delete mode 100755 bench/log.30Jul13.rhodo.fixed.linux.4
delete mode 100755 bench/log.30Jul13.rhodo.scaled.linux.4
delete mode 100755 cMake/FindEigen3.cmake
delete mode 100644 debian/README.source
create mode 100755 doc/Eqs/fix_sph_density_drift_corr_eq1.jpg
create mode 100755 doc/Eqs/fix_sph_density_driftcorr_eq1.jpg
create mode 100755 doc/Eqs/fix_sph_integrity_eq1.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq1.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq2.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq3.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq4.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq5.jpg
create mode 100755 doc/Eqs/fix_sph_mixidx_eq6.jpg
create mode 100755 doc/Eqs/fix_sph_velgrad_eq1.jpg
create mode 100644 doc/Eqs/model_C2_part_1.png
copy doc/Eqs/{pair_sph_morris_tenscorr_eq4.jpg => pair_sph_morris_tenscorr_eq6.jpg} (100%)
copy doc/Eqs/{pair_sph_morris_tenscorr_eq5.jpg => pair_sph_morris_tenscorr_eq7.jpg} (100%)
create mode 100644 doc/Eqs/roughnessLength.png
create mode 100644 doc/dump_custom_vtk.html
create mode 100644 doc/dump_custom_vtk.txt
create mode 100755 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/Allrun_convective
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/README.md
create mode 100755 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/cleanscript
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/genInput.m
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/in.liggghts
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/0/heat.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/0/radius.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/in.pascal
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/plotMe.m
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/settings/coupling_liggghts.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/settings/model_heatCapacity_solid.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/settings/model_heatDensity_solid.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/settings/model_heatThermalConductivity_solid.json
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/pascal/settings/model_heatTransferCoeff.json
copy examples/LIGGGHTS/Tutorials_public/{chute_wear => ParScale/heatTransferBed_paScal}/post/.gitignore (100%)
create mode 100644 examples/LIGGGHTS/Tutorials_public/ParScale/heatTransferBed_paScal/settings/parscale.json
delete mode 100755 python/README
delete mode 100755 python/examples/demo.py
delete mode 100755 python/examples/gui.py
delete mode 100755 python/examples/in.demo
delete mode 100755 python/examples/in.gui
delete mode 100755 python/examples/in.plot
delete mode 100755 python/examples/in.simple
delete mode 100755 python/examples/in.trivial
delete mode 100755 python/examples/in.viz
delete mode 100755 python/examples/pizza/dump.py
delete mode 100755 python/examples/pizza/gl.py
delete mode 100755 python/examples/pizza/gnu.py
delete mode 100755 python/examples/pizza/pdbfile.py
delete mode 100755 python/examples/pizza/vizinfo.py
delete mode 100755 python/examples/pizza/vmd.py
delete mode 100755 python/examples/plot.py
delete mode 100755 python/examples/simple.py
delete mode 100755 python/examples/trivial.py
delete mode 100755 python/examples/viz_atomeye.py
delete mode 100755 python/examples/viz_gl.py
delete mode 100755 python/examples/viz_pymol.py
delete mode 100755 python/examples/viz_vmd.py
delete mode 100755 python/examples/vizplotgui_atomeye.py
delete mode 100755 python/examples/vizplotgui_gl.py
delete mode 100755 python/examples/vizplotgui_pymol.py
delete mode 100755 python/examples/vizplotgui_vmd.py
delete mode 100755 python/install.py
delete mode 100755 python/lammps.py
delete mode 100755 regress/benchmark.py
delete mode 100755 regress/melt/in.melt
delete mode 100755 regress/melt/log.melt.linux.4
delete mode 100755 regress/min/in.min
delete mode 100755 regress/min/in.min.box
delete mode 100755 regress/min/log.min.box.linux.4
delete mode 100755 regress/min/log.min.linux.4
delete mode 100755 regress/regression.sh
copy src/MAKE/{Makefile.ubuntuVTK6 => Makefile.fedora_vtk_fpic} (83%)
copy src/MAKE/{Makefile.ubuntuVTK => Makefile.ubuntuVTK_fpic} (87%)
create mode 100644 src/PASCAL/Install.sh
create mode 100644 src/PASCAL/fix_pascal_couple.cpp
create mode 100644 src/PASCAL/fix_pascal_couple.h
create mode 100644 src/cfd_datacoupling_simple.h
create mode 100755 src/cleanAllParScale.sh
copy src/{dump_custom.cpp => dump_custom_vtk.cpp} (57%)
copy src/{dump_custom.h => dump_custom_vtk.h} (60%)
create mode 100755 src/makeAllParScale.sh
copy src/{fix_multisphere.h => multisphere_parallel.h} (100%)
create mode 100644 src/properties.cpp
create mode 100644 src/properties.h
delete mode 100755 tools/Makefile
delete mode 100755 tools/README
delete mode 100755 tools/amber2lmp/README
delete mode 100755 tools/amber2lmp/amber2lammps.py
delete mode 100755 tools/amber2lmp/dump2trj.py
delete mode 100755 tools/amber2lmp/dump2trj99.py
delete mode 100755 tools/binary2txt.cpp
delete mode 100755 tools/ch2lmp/README
delete mode 100755 tools/ch2lmp/charmm2lammps.pl
delete mode 100755 tools/ch2lmp/example/1ac7.data
delete mode 100755 tools/ch2lmp/example/1ac7.dump
delete mode 100755 tools/ch2lmp/example/1ac7.in
delete mode 100755 tools/ch2lmp/example/1ac7.pdb
delete mode 100755 tools/ch2lmp/example/1ac7.pdb1
delete mode 100755 tools/ch2lmp/example/1ac7.pgn
delete mode 100755 tools/ch2lmp/example/1ac7.psf
delete mode 100755 tools/ch2lmp/example/1ac7_ctrl.pdb
delete mode 100755 tools/ch2lmp/example/1ac7_ctrl.psf
delete mode 100755 tools/ch2lmp/example/1ac7_pared.pdb
delete mode 100755 tools/ch2lmp/example/1ac7_trj.pdb
delete mode 100755 tools/ch2lmp/example/par_all27_na.prm
delete mode 100755 tools/ch2lmp/example/top_all27_na.rtf
delete mode 100755 tools/ch2lmp/lammps2pdb.pl
delete mode 100755 tools/ch2lmp/main_manual
delete mode 100755 tools/ch2lmp/other/crd2pdb.pl
delete mode 100755 tools/ch2lmp/other/in_mkdcd
delete mode 100755 tools/ch2lmp/other/in_mkpdb
delete mode 100755 tools/ch2lmp/other/mkdcd.f
delete mode 100755 tools/ch2lmp/other/mkdcd_f77.f
delete mode 100755 tools/ch2lmp/other/mkpdb.f
delete mode 100755 tools/ch2lmp/other/pdb_to_crd.f
delete mode 100755 tools/chain.f
delete mode 100755 tools/createatoms/Manual.pdf
delete mode 100755 tools/createatoms/README
delete mode 100755 tools/createatoms/create.input
delete mode 100755 tools/createatoms/createAtoms.f
delete mode 100755 tools/createatoms/createAtoms.h
delete mode 100755 tools/data2xmovie.c
delete mode 100755 tools/def.chain
delete mode 100755 tools/def.chain.ab
delete mode 100755 tools/def.micelle2d
delete mode 100755 tools/eam_database/EAM.input
delete mode 100755 tools/eam_database/EAM_code
delete mode 100755 tools/eam_database/README
delete mode 100755 tools/eam_database/create.f
delete mode 100755 tools/eam_generate/Al_Zhou.c
delete mode 100755 tools/eam_generate/Cu_Mishin1.c
delete mode 100755 tools/eam_generate/Cu_Zhou.c
delete mode 100755 tools/eam_generate/README
delete mode 100755 tools/eam_generate/W_Zhou.c
delete mode 100755 tools/eff/README
delete mode 100755 tools/eff/VMD-input.py
delete mode 100755 tools/eff/bohr2ang.py
delete mode 100755 tools/eff/cfg2lammps.py
delete mode 100755 tools/eff/h2.out
delete mode 100755 tools/eff/h2.vmd
delete mode 100755 tools/eff/h2.xyz
delete mode 100755 tools/eff/lmp2data.py
delete mode 100755 tools/eff/lmp2radii.c
delete mode 100755 tools/eff/lmp2radii.py
delete mode 100755 tools/eff/lmp2radii.pyx
delete mode 100755 tools/eff/lmp2radii_col.py
delete mode 100755 tools/eff/lmp2xyz.py
delete mode 100755 tools/eff/radii.vmd
delete mode 100755 tools/eff/restart2data-pEFF.cpp
delete mode 100755 tools/eff/setup.py
delete mode 100755 tools/eff/structure_generators/Be-solid.pl
delete mode 100755 tools/eff/structure_generators/Diamond.pl
delete mode 100755 tools/eff/structure_generators/Li-hydride.pl
delete mode 100755 tools/eff/structure_generators/Li-solid-angstrom.pl
delete mode 100755 tools/eff/structure_generators/Li-solid.pl
delete mode 100755 tools/eff/structure_generators/Uniform-electron-gas.pl
delete mode 100755 tools/eff/structure_generators/h2.pl
delete mode 100755 tools/emacs/README.txt
delete mode 100755 tools/emacs/lammps.el
delete mode 100755 tools/ipp/README
delete mode 100755 tools/ipp/fill_parameters_createAtoms.input
delete mode 100755 tools/ipp/fill_parameters_lammps.input
delete mode 100755 tools/ipp/ipp
delete mode 100755 tools/ipp/template_createAtoms.input
delete mode 100755 tools/ipp/template_lammps.input
delete mode 100755 tools/kate/README.txt
delete mode 100755 tools/kate/lammps.xml
delete mode 100755 tools/lmp2arc/README
delete mode 100755 tools/lmp2arc/src/Makefile
delete mode 100755 tools/lmp2arc/src/ProcessPosFile01.c
delete mode 100755 tools/lmp2arc/src/ProcessPosFile05.c
delete mode 100755 tools/lmp2arc/src/ReadCarFile.c
delete mode 100755 tools/lmp2arc/src/WriteArcFrame.c
delete mode 100755 tools/lmp2arc/src/lmp2.h
delete mode 100755 tools/lmp2arc/src/lmp2arc.c
delete mode 100755 tools/lmp2arc/src/lmp2arc.doc
delete mode 100755 tools/lmp2arc/src/unwrap_molecules.c
delete mode 100755 tools/lmp2arc/test/correct/water8.arc
delete mode 100755 tools/lmp2arc/test/correct/water8.arc.trueflags
delete mode 100755 tools/lmp2arc/test/correct/water8.arc.unwrap
delete mode 100755 tools/lmp2arc/test/water8.arc
delete mode 100755 tools/lmp2arc/test/water8.arc.trueflags
delete mode 100755 tools/lmp2arc/test/water8.car
delete mode 100755 tools/lmp2arc/test/water8.pos
delete mode 100755 tools/lmp2arc/test/water8_unwrap.arc
delete mode 100755 tools/lmp2cfg/README.txt
delete mode 100755 tools/lmp2cfg/examples/00001.cfg
delete mode 100755 tools/lmp2cfg/examples/00002.cfg
delete mode 100755 tools/lmp2cfg/examples/dump.atom
delete mode 100755 tools/lmp2cfg/examples/lmp2cfg_inp.txt
delete mode 100755 tools/lmp2cfg/lmp2cfg.f
delete mode 100755 tools/lmp2vmd/README.txt
delete mode 100755 tools/matlab/README.pdf
delete mode 100755 tools/matlab/lmp2cfg.m
delete mode 100755 tools/matlab/readEAM.m
delete mode 100755 tools/matlab/readdump_all.m
delete mode 100755 tools/matlab/readdump_one.m
delete mode 100755 tools/matlab/readlog.m
delete mode 100755 tools/matlab/readrdf.m
delete mode 100755 tools/matlab/scandump.m
delete mode 100755 tools/micelle2d.f
delete mode 100755 tools/moltemplate/LICENSE.TXT
delete mode 100755 tools/moltemplate/README.TXT
delete mode 100755 tools/moltemplate/common/amber/README.TXT
delete mode 100755 tools/moltemplate/common/amber/amberparm2lt.sh
delete mode 100755 tools/moltemplate/common/amber/amberparm_angle_to_lt.py
delete mode 100755 tools/moltemplate/common/amber/amberparm_bond_to_lt.py
delete mode 100755 tools/moltemplate/common/amber/amberparm_dihedral_to_lt.py
delete mode 100755 tools/moltemplate/common/amber/amberparm_improper_to_lt.py
delete mode 100755 tools/moltemplate/common/amber/amberparm_mass_to_lt.py
delete mode 100755 tools/moltemplate/common/amber/amberparm_pair_to_lt.py
delete mode 100755 tools/moltemplate/common/gaff.lt
delete mode 100755 tools/moltemplate/common/graphene.lt
delete mode 100755 tools/moltemplate/common/images/graphene_unit_cell.jpg
delete mode 100755 tools/moltemplate/common/images/ice_rect8_unitcell.png
delete mode 100755 tools/moltemplate/common/images/spce_ball_and_stick.jpg
delete mode 100755 tools/moltemplate/common/spce.lt
delete mode 100755 tools/moltemplate/common/spce_ice_rect8.lt
delete mode 100755 tools/moltemplate/common/tip3p_1983.lt
delete mode 100755 tools/moltemplate/common/tip3p_2004.lt
delete mode 100755 tools/moltemplate/common/trappe1998.lt
delete mode 100755 tools/moltemplate/common/watmw.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
delete mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/run.in.npt
delete mode 100755 tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
delete mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
delete mode 100755 tools/moltemplate/examples/README.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/graphene_unit_cell.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
delete mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/README.TXT
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/README_setup.sh
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/README_visualize.txt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt
delete mode 100755 tools/moltemplate/examples/silly/sierpinski/run.in
delete mode 100755 tools/moltemplate/moltemplate_manual.pdf
delete mode 100755 tools/moltemplate/src/bonds_by_type.py
delete mode 100755 tools/moltemplate/src/dump2data.py
delete mode 100755 tools/moltemplate/src/extract_lammps_data.py
delete mode 100755 tools/moltemplate/src/ltemplify.py
delete mode 100755 tools/moltemplate/src/lttree.py
delete mode 100755 tools/moltemplate/src/lttree_check.py
delete mode 100755 tools/moltemplate/src/lttree_postprocess.py
delete mode 100755 tools/moltemplate/src/lttree_styles.py
delete mode 100755 tools/moltemplate/src/moltemplate.sh
delete mode 100755 tools/moltemplate/src/nbody_Angles.py
delete mode 100755 tools/moltemplate/src/nbody_Bonds.py
delete mode 100755 tools/moltemplate/src/nbody_Dihedrals.py
delete mode 100755 tools/moltemplate/src/nbody_Impropers.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILnoswap.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLnoswap.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIK.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIKL.py
delete mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py
delete mode 100755 tools/moltemplate/src/nbody_by_type.py
delete mode 100755 tools/moltemplate/src/nbody_by_type_lib.py
delete mode 100755 tools/moltemplate/src/nbody_by_type_lib_old.py
delete mode 100755 tools/moltemplate/src/nbody_fix_ttree_assignments.py
delete mode 100755 tools/moltemplate/src/nbody_graph_search.py
delete mode 100755 tools/moltemplate/src/nbody_reorder_atoms.py
delete mode 100755 tools/moltemplate/src/ordereddict.py
delete mode 100755 tools/moltemplate/src/pdbsort.py
delete mode 100755 tools/moltemplate/src/postprocess_input_script.py
delete mode 100755 tools/moltemplate/src/raw2data.py
delete mode 100755 tools/moltemplate/src/remove_duplicate_atoms.py
delete mode 100755 tools/moltemplate/src/remove_duplicates_nbody.py
delete mode 100755 tools/moltemplate/src/renumber_DATA_first_column.py
delete mode 100755 tools/moltemplate/src/ttree.py
delete mode 100755 tools/moltemplate/src/ttree_lex.py
delete mode 100755 tools/moltemplate/src/ttree_matrix_stack.py
delete mode 100755 tools/moltemplate/src/ttree_render.py
delete mode 100755 tools/msi2lmp/README
delete mode 100755 tools/msi2lmp/frc_files/README
delete mode 100755 tools/msi2lmp/frc_files/cff91.frc
delete mode 100755 tools/msi2lmp/frc_files/clayff.frc
delete mode 100755 tools/msi2lmp/frc_files/compass_published.frc
delete mode 100755 tools/msi2lmp/frc_files/cvff.frc
delete mode 100755 tools/msi2lmp/frc_files/cvff_aug.frc
delete mode 100755 tools/msi2lmp/frc_files/oplsaa.frc
delete mode 100755 tools/msi2lmp/frc_files/pcff.frc
delete mode 100755 tools/msi2lmp/frc_files/pcff.rlb
delete mode 100755 tools/msi2lmp/frc_files/pcff_templates.dat
delete mode 100755 tools/msi2lmp/src/CheckLists.c
delete mode 100755 tools/msi2lmp/src/Forcefield.h
delete mode 100755 tools/msi2lmp/src/GetParameters.c
delete mode 100755 tools/msi2lmp/src/InitializeItems.c
delete mode 100755 tools/msi2lmp/src/MakeLists.c
delete mode 100755 tools/msi2lmp/src/Makefile
delete mode 100755 tools/msi2lmp/src/ReadCarFile.c
delete mode 100755 tools/msi2lmp/src/ReadFrcFile.c
delete mode 100755 tools/msi2lmp/src/ReadMdfFile.c
delete mode 100755 tools/msi2lmp/src/SearchAndFill.c
delete mode 100755 tools/msi2lmp/src/WriteDataFile.c
delete mode 100755 tools/msi2lmp/src/msi2lmp.c
delete mode 100755 tools/msi2lmp/src/msi2lmp.h
delete mode 100755 tools/msi2lmp/test/PyAC_bulk-clayff.car
delete mode 100755 tools/msi2lmp/test/PyAC_bulk-clayff.mdf
delete mode 100755 tools/msi2lmp/test/benzene-class1.car
delete mode 100755 tools/msi2lmp/test/benzene-class1.mdf
delete mode 100755 tools/msi2lmp/test/benzene-class2a.car
delete mode 100755 tools/msi2lmp/test/benzene-class2a.mdf
delete mode 100755 tools/msi2lmp/test/benzene-class2b.car
delete mode 100755 tools/msi2lmp/test/benzene-class2b.mdf
delete mode 100755 tools/msi2lmp/test/crambin-class1.car
delete mode 100755 tools/msi2lmp/test/crambin-class1.mdf
delete mode 100755 tools/msi2lmp/test/data-compare.pl
delete mode 100755 tools/msi2lmp/test/ethane-class1.car
delete mode 100755 tools/msi2lmp/test/ethane-class1.mdf
delete mode 100755 tools/msi2lmp/test/ethane-class2a.car
delete mode 100755 tools/msi2lmp/test/ethane-class2a.mdf
delete mode 100755 tools/msi2lmp/test/ethane-class2b.car
delete mode 100755 tools/msi2lmp/test/ethane-class2b.mdf
delete mode 100755 tools/msi2lmp/test/ethane-oplsaa.car
delete mode 100755 tools/msi2lmp/test/ethane-oplsaa.mdf
delete mode 100755 tools/msi2lmp/test/h2-h2o-class1.car
delete mode 100755 tools/msi2lmp/test/h2-h2o-class1.mdf
delete mode 100755 tools/msi2lmp/test/h2-h2o-class2b.car
delete mode 100755 tools/msi2lmp/test/h2-h2o-class2b.mdf
delete mode 100755 tools/msi2lmp/test/hap_crystal-class1.car
delete mode 100755 tools/msi2lmp/test/hap_crystal-class1.mdf
delete mode 100755 tools/msi2lmp/test/hap_crystal-class2b.car
delete mode 100755 tools/msi2lmp/test/hap_crystal-class2b.mdf
delete mode 100755 tools/msi2lmp/test/hydrogen-class1.car
delete mode 100755 tools/msi2lmp/test/hydrogen-class1.mdf
delete mode 100755 tools/msi2lmp/test/hydrogen-class2a.car
delete mode 100755 tools/msi2lmp/test/hydrogen-class2a.mdf
delete mode 100755 tools/msi2lmp/test/in.PyAC_bulk-clayff
delete mode 100755 tools/msi2lmp/test/in.benzene-class1
delete mode 100755 tools/msi2lmp/test/in.benzene-class2a
delete mode 100755 tools/msi2lmp/test/in.benzene-class2b
delete mode 100755 tools/msi2lmp/test/in.crambin-class1
delete mode 100755 tools/msi2lmp/test/in.ethane-class1
delete mode 100755 tools/msi2lmp/test/in.ethane-class2a
delete mode 100755 tools/msi2lmp/test/in.ethane-class2b
delete mode 100755 tools/msi2lmp/test/in.ethane-oplsaa
delete mode 100755 tools/msi2lmp/test/in.h2-h2o-class1
delete mode 100755 tools/msi2lmp/test/in.h2-h2o-class2b
delete mode 100755 tools/msi2lmp/test/in.hap_crystal-class1
delete mode 100755 tools/msi2lmp/test/in.hap_crystal-class2b
delete mode 100755 tools/msi2lmp/test/in.hydrogen-class1
delete mode 100755 tools/msi2lmp/test/in.hydrogen-class2a
delete mode 100755 tools/msi2lmp/test/in.naphthalene-class1
delete mode 100755 tools/msi2lmp/test/in.naphthalene-class2a
delete mode 100755 tools/msi2lmp/test/in.naphthalene-class2b
delete mode 100755 tools/msi2lmp/test/in.nylon-class1
delete mode 100755 tools/msi2lmp/test/in.phen3_cff97-class1
delete mode 100755 tools/msi2lmp/test/in.water-class1
delete mode 100755 tools/msi2lmp/test/in.water-class2b
delete mode 100755 tools/msi2lmp/test/naphthalene-class1.car
delete mode 100755 tools/msi2lmp/test/naphthalene-class1.mdf
delete mode 100755 tools/msi2lmp/test/naphthalene-class2a.car
delete mode 100755 tools/msi2lmp/test/naphthalene-class2a.mdf
delete mode 100755 tools/msi2lmp/test/naphthalene-class2b.car
delete mode 100755 tools/msi2lmp/test/naphthalene-class2b.mdf
delete mode 100755 tools/msi2lmp/test/nylon-class1.car
delete mode 100755 tools/msi2lmp/test/nylon-class1.mdf
delete mode 100755 tools/msi2lmp/test/phen3_cff97-class1.car
delete mode 100755 tools/msi2lmp/test/phen3_cff97-class1.mdf
delete mode 100755 tools/msi2lmp/test/reference/PyAC_bulk-clayff.data
delete mode 100755 tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2
delete mode 100755 tools/msi2lmp/test/reference/benzene-class1.data
delete mode 100755 tools/msi2lmp/test/reference/benzene-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/benzene-class1.data3
delete mode 100755 tools/msi2lmp/test/reference/benzene-class2a.data
delete mode 100755 tools/msi2lmp/test/reference/benzene-class2a.data2
delete mode 100755 tools/msi2lmp/test/reference/benzene-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/benzene-class2b.data2
delete mode 100755 tools/msi2lmp/test/reference/crambin-class1.data
delete mode 100755 tools/msi2lmp/test/reference/crambin-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/ethane-class1.data
delete mode 100755 tools/msi2lmp/test/reference/ethane-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/ethane-class2a.data
delete mode 100755 tools/msi2lmp/test/reference/ethane-class2a.data2
delete mode 100755 tools/msi2lmp/test/reference/ethane-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/ethane-class2b.data2
delete mode 100755 tools/msi2lmp/test/reference/ethane-oplsaa.data
delete mode 100755 tools/msi2lmp/test/reference/ethane-oplsaa.data2
delete mode 100755 tools/msi2lmp/test/reference/h2-h2o-class1.data
delete mode 100755 tools/msi2lmp/test/reference/h2-h2o-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/h2-h2o-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/h2-h2o-class2b.data2
delete mode 100755 tools/msi2lmp/test/reference/hap_crystal-class1.data
delete mode 100755 tools/msi2lmp/test/reference/hap_crystal-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/hap_crystal-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/hap_crystal-class2b.data2
delete mode 100755 tools/msi2lmp/test/reference/hydrogen-class1.data
delete mode 100755 tools/msi2lmp/test/reference/hydrogen-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/hydrogen-class2a.data
delete mode 100755 tools/msi2lmp/test/reference/hydrogen-class2a.data2
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class1.data
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class2a.data
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class2a.data2
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/naphthalene-class2b.data2
delete mode 100755 tools/msi2lmp/test/reference/nylon-class1.data
delete mode 100755 tools/msi2lmp/test/reference/nylon-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/phen3_cff97-class1.data
delete mode 100755 tools/msi2lmp/test/reference/phen3_cff97-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/water-class1.data
delete mode 100755 tools/msi2lmp/test/reference/water-class1.data2
delete mode 100755 tools/msi2lmp/test/reference/water-class2b.data
delete mode 100755 tools/msi2lmp/test/reference/water-class2b.data2
delete mode 100755 tools/msi2lmp/test/runtests.sh
delete mode 100755 tools/msi2lmp/test/test.input
delete mode 100755 tools/msi2lmp/test/water-class1.car
delete mode 100755 tools/msi2lmp/test/water-class1.mdf
delete mode 100755 tools/msi2lmp/test/water-class2b.car
delete mode 100755 tools/msi2lmp/test/water-class2b.mdf
delete mode 100755 tools/phonon/Makefile
delete mode 100755 tools/phonon/README
delete mode 100755 tools/phonon/dynmat.cpp
delete mode 100755 tools/phonon/dynmat.h
delete mode 100755 tools/phonon/green.cpp
delete mode 100755 tools/phonon/green.h
delete mode 100755 tools/phonon/interpolate.cpp
delete mode 100755 tools/phonon/interpolate.h
delete mode 100755 tools/phonon/main.cpp
delete mode 100755 tools/phonon/memory.cpp
delete mode 100755 tools/phonon/memory.h
delete mode 100755 tools/phonon/phonon.cpp
delete mode 100755 tools/phonon/phonon.h
delete mode 100755 tools/phonon/timer.cpp
delete mode 100755 tools/phonon/timer.h
delete mode 100755 tools/phonon/version.h
delete mode 100755 tools/polybond/Manual.pdf
delete mode 100755 tools/polybond/README
delete mode 100755 tools/polybond/lmpsdata.py
delete mode 100755 tools/pymol_asphere/README
delete mode 100755 tools/pymol_asphere/doc/asphere_vis.1
delete mode 100755 tools/pymol_asphere/doc/asphere_vis.manpage
delete mode 100755 tools/pymol_asphere/doc/asphere_vis.pdf
delete mode 100755 tools/pymol_asphere/examples/README
delete mode 100755 tools/pymol_asphere/examples/colors.ellipse
delete mode 100755 tools/pymol_asphere/src/Makefile
delete mode 100755 tools/pymol_asphere/src/asphere_vis.cpp
delete mode 100755 tools/pymol_asphere/src/cartesian.cpp
delete mode 100755 tools/pymol_asphere/src/cartesian.h
delete mode 100755 tools/pymol_asphere/src/colors.cpp
delete mode 100755 tools/pymol_asphere/src/colors.h
delete mode 100755 tools/pymol_asphere/src/commandline.cpp
delete mode 100755 tools/pymol_asphere/src/commandline.h
delete mode 100755 tools/pymol_asphere/src/error.cpp
delete mode 100755 tools/pymol_asphere/src/error.h
delete mode 100755 tools/pymol_asphere/src/glsurface.cpp
delete mode 100755 tools/pymol_asphere/src/glsurface.h
delete mode 100755 tools/pymol_asphere/src/m_constants.h
delete mode 100755 tools/pymol_asphere/src/make_manpages.sh
delete mode 100755 tools/pymol_asphere/src/misc.cpp
delete mode 100755 tools/pymol_asphere/src/misc.h
delete mode 100755 tools/pymol_asphere/src/miscm.cpp
delete mode 100755 tools/pymol_asphere/src/miscm.h
delete mode 100755 tools/pymol_asphere/src/spherical.cpp
delete mode 100755 tools/pymol_asphere/src/spherical.h
delete mode 100755 tools/python/README
delete mode 100755 tools/python/dump2cfg.py
delete mode 100755 tools/python/dump2pdb.py
delete mode 100755 tools/python/dump2xyz.py
delete mode 100755 tools/python/dumpsort.py
delete mode 100755 tools/python/log2txt.py
delete mode 100755 tools/python/logplot.py
delete mode 100755 tools/python/neb_combine.py
delete mode 100755 tools/python/neb_final.py
delete mode 100755 tools/python/pizza/cfg.py
delete mode 100755 tools/python/pizza/dump.py
delete mode 100755 tools/python/pizza/gnu.py
delete mode 100755 tools/python/pizza/log.py
delete mode 100755 tools/python/pizza/pdbfile.py
delete mode 100755 tools/python/pizza/xyz.py
delete mode 100755 tools/reax/Cutoff.dic
delete mode 100755 tools/reax/README.txt
delete mode 100755 tools/reax/bondConnectCheck.f90
delete mode 100755 tools/reax/bonds.reax
delete mode 100755 tools/reax/mol_fra.c
delete mode 100755 tools/reax/reaxc_bond.pl
delete mode 100755 tools/restart2data.cpp
delete mode 100755 tools/vim/README.txt
delete mode 100755 tools/vim/lammps.vim
delete mode 100755 tools/vim/mysyntax.vim
delete mode 100755 tools/vim/vimrc
delete mode 100755 tools/xmgrace/README
delete mode 100755 tools/xmgrace/lammpsplot.cpp
delete mode 100755 tools/xmgrace/lammpsplot.pdf
delete mode 100755 tools/xmgrace/logplotawk.oneliner
delete mode 100755 tools/xmgrace/logplotgrep.oneliner
delete mode 100755 tools/xmgrace/plotthermodata.awk
delete mode 100755 tools/xmovie/Makefile
delete mode 100755 tools/xmovie/README
delete mode 100755 tools/xmovie/Xdefaults
delete mode 100755 tools/xmovie/control.c
delete mode 100755 tools/xmovie/dummy.c
delete mode 100755 tools/xmovie/dummy.dat
delete mode 100755 tools/xmovie/hpsort.c
delete mode 100755 tools/xmovie/read.c
delete mode 100755 tools/xmovie/resource.h
delete mode 100755 tools/xmovie/scene.c
delete mode 100755 tools/xmovie/toascii.c
delete mode 100755 tools/xmovie/tobinary.c
delete mode 100755 tools/xmovie/version.c
delete mode 100755 tools/xmovie/xmovie.c
delete mode 100755 tools/xmovie/xmovie.h
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/liggghts.git
More information about the debian-science-commits
mailing list