Diffusion lammps 920641bbffbc

Merge pull request #399 from rbberger/docs_spelling_fixes
920641bbffbc
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Authored by sjplimp <sjplimp@sandia.gov> on Mar 7 2017, 17:47.

Description

Merge pull request #399 from rbberger/docs_spelling_fixes

Correct spelling errors in documentation

Details

Committed

GitHub <noreply@github.com>

Mar 7 2017, 17:47

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS08baaa9d8ede: Fix more typos in tools
rLAMMPSc2aabdec229c: Merge pull request #398 from stanmoore1/kokkos_changes

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Event Timeline

GitHub <noreply@github.com> committed rLAMMPS920641bbffbc: Merge pull request #399 from rbberger/docs_spelling_fixes (authored by sjplimp <sjplimp@sandia.gov>).Mar 7 2017, 17:47

Merged Changes

Commit	Author	Details	Committed
08baaa9d8ede	Richard Berger	Fix more typos in tools	Mar 7 2017
359af419a7ab	Richard Berger	Fix typo in python README	Mar 7 2017
21be86c42393	Richard Berger	Fix typos in txt2html	Mar 7 2017
d6800405a518	Richard Berger	Fix more typos in examples	Mar 7 2017
3a054d1a82b2	Richard Berger	Fix more typos in src files	Mar 7 2017
007f3c66a033	Richard Berger	Third batch of spelling fixes in manual	Mar 7 2017
32708860a9fa	Richard Berger	Add remaining false positives	Mar 7 2017
fc9eebb9367c	Richard Berger	Added spellcheck utility to documentation build	Mar 6 2017
dd76ac5010ae	Richard Berger	Fix typos in tools folder	Mar 6 2017
17486a9319f8	Richard Berger	Convert USER/lb/polymer files to UNIX line endings and remove trailing…	Mar 6 2017
778a79b8eef7	Richard Berger	Fix typos in examples folder	Mar 6 2017
7dd60f97377a	Richard Berger	Fix typos in src files	Mar 6 2017
084d831bce01	Richard Berger	Second batch of spelling fixes in manual	Mar 6 2017
e261bef7bba7	Richard Berger	Spelling fixes in source files	Mar 6 2017
fd78486086d9	Richard Berger	First batch of spelling fixes in manual	Mar 6 2017

Changes (393)

				Path
	M			bench/FERMI/README
	M			doc/.gitignore
	M			doc/Makefile
	M			doc/src/2001/input_commands.html
	M			doc/src/99/basics.html
	M			doc/src/99/crib.html
	M			doc/src/99/input_commands.html
	M			doc/src/Section_commands.txt
	M			doc/src/Section_errors.txt
	M			doc/src/Section_history.txt
	M			doc/src/Section_howto.txt
	M			doc/src/Section_modify.txt
	M			doc/src/Section_packages.txt
	M			doc/src/Section_perf.txt
	M			doc/src/Section_python.txt
	M			doc/src/Section_start.txt
	M			doc/src/Section_tools.txt
	M			doc/src/USER/atc/man_consistent_fe_initialization.html
	M			doc/src/accelerate_intel.txt
	M			doc/src/accelerate_kokkos.txt
	M			doc/src/angle_hybrid.txt
	M			doc/src/atom_modify.txt
	M			doc/src/atom_style.txt
	M			doc/src/balance.txt
	M			doc/src/body.txt
	M			doc/src/bond_hybrid.txt
	M			doc/src/change_box.txt
	M			doc/src/comm_style.txt
	M			doc/src/compute.txt
	M			doc/src/compute_angmom_chunk.txt
	M			doc/src/compute_centro_atom.txt
	M			doc/src/compute_chunk_atom.txt
	M			doc/src/compute_cna_atom.txt
	M			doc/src/compute_com.txt
	M			doc/src/compute_coord_atom.txt
	M			doc/src/compute_damage_atom.txt
	M			doc/src/compute_dilatation_atom.txt
	M			doc/src/compute_displace_atom.txt
	M			doc/src/compute_event_displace.txt
	M			doc/src/compute_global_atom.txt
	M			doc/src/compute_heat_flux.txt
	M			doc/src/compute_inertia_chunk.txt
	M			doc/src/compute_msd.txt
	M			doc/src/compute_msd_chunk.txt
	M			doc/src/compute_msd_nongauss.txt
	M			doc/src/compute_pair.txt
	M			doc/src/compute_pair_local.txt
	M			doc/src/compute_pe_atom.txt
	M			doc/src/compute_plasticity_atom.txt
	M			doc/src/compute_pressure.txt
	M			doc/src/compute_property_chunk.txt
	M			doc/src/compute_rdf.txt
	M			doc/src/compute_rigid_local.txt
	M			doc/src/compute_saed.txt
	M			doc/src/compute_smd_ulsph_num_neighs.txt
	M			doc/src/compute_stress_atom.txt
	M			doc/src/compute_temp_asphere.txt
	M			doc/src/compute_temp_body.txt
	M			doc/src/compute_temp_chunk.txt
	M			doc/src/compute_temp_profile.txt
	M			doc/src/compute_vacf.txt
	M			doc/src/create_atoms.txt
	M			doc/src/dihedral_hybrid.txt
	M			doc/src/dump.txt
	M			doc/src/dump_custom_vtk.txt
	M			doc/src/dump_image.txt
	M			doc/src/dump_modify.txt
	M			doc/src/fix_ave_chunk.txt
	M			doc/src/fix_ave_correlate.txt
	M			doc/src/fix_ave_time.txt
	M			doc/src/fix_balance.txt
	M			doc/src/fix_bond_break.txt
	M			doc/src/fix_bond_create.txt
	M			doc/src/fix_bond_swap.txt
	M			doc/src/fix_box_relax.txt
	M			doc/src/fix_cmap.txt
	M			doc/src/fix_colvars.txt
	M			doc/src/fix_controller.txt
	M			doc/src/fix_deform.txt
	M			doc/src/fix_deposit.txt
	M			doc/src/fix_eos_table.txt
	M			doc/src/fix_eos_table_rx.txt
	M			doc/src/fix_evaporate.txt
	M			doc/src/fix_gle.txt
	M			doc/src/fix_gravity.txt
	M			doc/src/fix_indent.txt
	M			doc/src/fix_langevin.txt
	M			doc/src/fix_langevin_eff.txt
	M			doc/src/fix_lb_fluid.txt
	M			doc/src/fix_modify.txt
	M			doc/src/fix_move.txt
	M			doc/src/fix_mscg.txt
	M			doc/src/fix_nph_asphere.txt
	M			doc/src/fix_nph_body.txt
	M			doc/src/fix_npt_asphere.txt
	M			doc/src/fix_npt_body.txt
	M			doc/src/fix_nve_asphere.txt
	M			doc/src/fix_nve_asphere_noforce.txt
	M			doc/src/fix_nve_body.txt
	M			doc/src/fix_nve_limit.txt
	M			doc/src/fix_nvt_asphere.txt
	M			doc/src/fix_nvt_body.txt
	M			doc/src/fix_nvt_sllod_eff.txt
	M			doc/src/fix_orient.txt
	M			doc/src/fix_phonon.txt
	M			doc/src/fix_pour.txt
	M			doc/src/fix_property_atom.txt
	M			doc/src/fix_qeq.txt
	M			doc/src/fix_qeq_comb.txt
	M			doc/src/fix_qeq_reax.txt
	M			doc/src/fix_reax_bonds.txt
	M			doc/src/fix_restrain.txt
	M			doc/src/fix_rigid.txt
	M			doc/src/fix_rx.txt
	M			doc/src/fix_saed_vtk.txt
	M			doc/src/fix_shake.txt
	M			doc/src/fix_smd_wall_surface.txt
	M			doc/src/fix_spring_self.txt
	M			doc/src/fix_srd.txt
	M			doc/src/fix_temp_berendsen.txt
	M			doc/src/fix_temp_csvr.txt
	M			doc/src/fix_temp_rescale.txt
	M			doc/src/fix_temp_rescale_eff.txt
	M			doc/src/fix_tfmc.txt
	M			doc/src/fix_thermal_conductivity.txt
	M			doc/src/fix_ttm.txt
	M			doc/src/fix_vector.txt
	M			doc/src/fix_viscosity.txt
	M			doc/src/fix_wall.txt
	M			doc/src/fix_wall_gran.txt
	M			doc/src/fix_wall_gran_region.txt
	M			doc/src/fix_wall_piston.txt
	M			doc/src/group.txt
	M			doc/src/if.txt
	M			doc/src/improper_hybrid.txt
	M			doc/src/improper_ring.txt
	M			doc/src/info.txt
	M			doc/src/jump.txt
	M			doc/src/kspace_modify.txt
	M			doc/src/kspace_style.txt
	M			doc/src/minimize.txt
	M			doc/src/molecule.txt
	M			doc/src/neb.txt
	M			doc/src/package.txt
	M			doc/src/pair_adp.txt
	M			doc/src/pair_agni.txt
	M			doc/src/pair_airebo.txt
	M			doc/src/pair_beck.txt
	M			doc/src/pair_body.txt
	M			doc/src/pair_bop.txt
	M			doc/src/pair_comb.txt
	M			doc/src/pair_coul.txt
	M			doc/src/pair_coul_diel.txt
	M			doc/src/pair_dpd.txt
	M			doc/src/pair_eam.txt
	M			doc/src/pair_edip.txt
	M			doc/src/pair_eff.txt
	M			doc/src/pair_eim.txt
	M			doc/src/pair_exp6_rx.txt
	M			doc/src/pair_gran.txt
	M			doc/src/pair_hbond_dreiding.txt
	M			doc/src/pair_hybrid.txt
	M			doc/src/pair_kim.txt
	M			doc/src/pair_line_lj.txt
	M			doc/src/pair_lj.txt
	M			doc/src/pair_lj_long.txt
	M			doc/src/pair_lj_smooth.txt
	M			doc/src/pair_lj_soft.txt
	M			doc/src/pair_lubricate.txt
	M			doc/src/pair_meam_spline.txt
	M			doc/src/pair_mgpt.txt
	M			doc/src/pair_mie.txt
	M			doc/src/pair_morse.txt
	M			doc/src/pair_peri.txt
	M			doc/src/pair_quip.txt
	M			doc/src/pair_resquared.txt
	M			doc/src/pair_smd_ulsph.txt
	M			doc/src/pair_smtbq.txt
	M			doc/src/pair_soft.txt
	M			doc/src/pair_sph_heatconduction.txt
	M			doc/src/pair_sph_idealgas.txt
	M			doc/src/pair_sph_lj.txt
	M			doc/src/pair_sph_taitwater.txt
	M			doc/src/pair_srp.txt
	M			doc/src/pair_table.txt
	M			doc/src/pair_tri_lj.txt
	M			doc/src/partition.txt
	M			doc/src/prd.txt
	M			doc/src/processors.txt
	M			doc/src/python.txt
	M			doc/src/read_data.txt
	M			doc/src/read_dump.txt
	M			doc/src/read_restart.txt
	M			doc/src/region.txt
	M			doc/src/replicate.txt
	M			doc/src/rerun.txt
	M			doc/src/restart.txt
	M			doc/src/run_style.txt
	M			doc/src/set.txt
	M			doc/src/suffix.txt
	M			doc/src/tad.txt
	M			doc/src/thermo.txt
	M			doc/src/thermo_style.txt
	M			doc/src/timer.txt
	M			doc/src/tutorial_drude.txt
	M			doc/src/tutorial_pylammps.txt
	M			doc/src/units.txt
	M			doc/src/variable.txt
	M			doc/src/write_dump.txt
	M			doc/utils/sphinx-config/conf.py
	A			doc/utils/sphinx-config/false_positives.txt
	M			doc/utils/txt2html/README.html
	M			doc/utils/txt2html/txt2html.cpp
	M			examples/KAPPA/README
	M			examples/README
	M			examples/USER/atc/README
	M			examples/USER/atc/fluids/in.bar1d_fluids
	M			examples/USER/atc/thermal/in.bar1d
	M			examples/USER/atc/thermal/in.bar1d_all_atoms
	M			examples/USER/atc/thermal/in.bar1d_combined
	M			examples/USER/atc/thermal/in.bar1d_flux
	M			examples/USER/atc/thermal/in.bar1d_frac_step
	M			examples/USER/atc/thermal/in.bar1d_hoover
	M			examples/USER/atc/thermal/in.bar1d_interpolate
	M			examples/USER/atc/thermal/in.bar1d_lumped
	M			examples/USER/lb/confined_colloid/in.confined_colloids
	M			examples/USER/lb/microrheology/in.microrheology_default_gamma
	M			examples/USER/lb/microrheology/in.microrheology_set_gamma
	M			examples/USER/lb/planewall/in.planewall_default_gamma
	M			examples/USER/lb/planewall/in.planewall_set_gamma
	M			examples/USER/lb/polymer/data.polymer
	M			examples/USER/lb/polymer/in.polymer_default_gamma
	M			examples/USER/lb/polymer/in.polymer_setgamma
	M			examples/USER/misc/srp/in.srp
	M			examples/USER/phonon/3-3D-FCC-Cu-EAM/README
	M			examples/USER/phonon/4-Graphene/README
	M			examples/USER/tally/README
	M			examples/VISCOSITY/README
	M			examples/accelerate/README
	M			lib/atc/LinearSolver.cpp
	M			python/README
	M			python/examples/demo.py
	M			python/examples/gui.py
	M			python/examples/mc.py
	M			python/examples/plot.py
	M			python/examples/simple.py
	M			python/examples/split.py
	M			python/examples/trivial.py
	M			python/examples/viz_atomeye.py
	M			python/examples/viz_gl.py
	M			python/examples/viz_pymol.py
	M			python/examples/viz_vmd.py
	M			python/examples/vizplotgui_atomeye.py
	M			python/examples/vizplotgui_gl.py
	M			python/examples/vizplotgui_pymol.py
	M			python/examples/vizplotgui_vmd.py
	M			src/ASPHERE/compute_erotate_asphere.h
	M			src/ASPHERE/compute_temp_asphere.h
	M			src/COLLOID/pair_lubricateU.cpp
	M			src/COLLOID/pair_lubricateU_poly.cpp
	M			src/COLLOID/pair_yukawa_colloid.h
	M			src/DEPEND/fastdep.c
	M			src/GPU/pair_born_gpu.h
	M			src/GPU/pair_zbl_gpu.h
	M			src/KIM/pair_kim.h
	M			src/KOKKOS/pair_reax_c_kokkos.cpp
	M			src/KSPACE/pair_buck_long_coul_long.h
	M			src/KSPACE/pppm_disp.h
	M			src/MANYBODY/pair_bop.h
	M			src/MISC/fix_ttm.h
	M			src/PYTHON/python.cpp
	M			src/PYTHON/python.h
	M			src/REAX/fix_reax_bonds.h
	M			src/REPLICA/neb.h
	M			src/REPLICA/prd.h
	M			src/REPLICA/tad.h
	M			src/REPLICA/temper.h
	M			src/RIGID/fix_rigid_small.cpp
	M			src/RIGID/fix_shake.h
	M			src/SHOCK/fix_append_atoms.h
	M			src/SNAP/pair_snap.cpp
	M			src/SRD/fix_srd.cpp
	M			src/SRD/fix_srd.h
	M			src/USER-AWPMD/atom_vec_wavepacket.h
	M			src/USER-DIFFRACTION/fix_saed_vtk.h
	M			src/USER-DPD/fix_eos_table_rx.h
	M			src/USER-DPD/pair_exp6_rx.cpp
	M			src/USER-LB/fix_lb_fluid.cpp
	M			src/USER-MANIFOLD/README
	M			src/USER-MANIFOLD/fix_manifoldforce.cpp
	M			src/USER-MANIFOLD/manifold.h
	M			src/USER-MISC/fix_grem.h
	M			src/USER-MISC/fix_imd.cpp
	M			src/USER-MISC/improper_ring.cpp
	M			src/USER-MISC/pair_edip.cpp
	M			src/USER-MISC/pair_edip.h
	M			src/USER-MISC/temper_grem.h
	M			src/USER-MOLFILE/molfile_interface.cpp
	M			src/USER-OMP/pair_buck_long_coul_long_omp.h
	M			src/USER-OMP/thr_data.cpp
	M			src/USER-QTB/fix_qbmsst.h
	M			src/USER-REAXC/README
	M			src/USER-REAXC/reaxc_nonbonded.cpp
	M			src/USER-SMD/pair_smd_triangulated_surface.cpp
	M			src/USER-SMTBQ/pair_smtbq.cpp
	M			src/USER-VTK/dump_custom_vtk.h
	M			src/angle.h
	M			src/atom.cpp
	M			src/atom.h
	M			src/atom_vec_hybrid.cpp
	M			src/atom_vec_tri.h
	M			src/balance.cpp
	M			src/balance.h
	M			src/bond.h
	M			src/citeme.h
	M			src/compute_angle.h
	M			src/compute_bond.h
	M			src/compute_chunk_atom.cpp
	M			src/compute_chunk_atom.h
	M			src/compute_cna_atom.h
	M			src/compute_contact_atom.h
	M			src/compute_coord_atom.h
	M			src/compute_dihedral.h
	M			src/compute_group_group.h
	M			src/compute_hexorder_atom.h
	M			src/compute_improper.h
	M			src/compute_orientorder_atom.h
	M			src/compute_pair.h
	M			src/compute_property_chunk.h
	M			src/compute_property_local.h
	M			src/create_atoms.cpp
	M			src/create_atoms.h
	M			src/dihedral.h
	M			src/domain.cpp
	M			src/dump_custom.h
	M			src/dump_local.h
	M			src/fix.h
	M			src/fix_addforce.h
	M			src/fix_ave_chunk.h
	M			src/fix_ave_histo_weight.cpp
	M			src/fix_ave_time.h
	M			src/fix_balance.cpp
	M			src/fix_deform.h
	M			src/fix_group.h
	M			src/fix_langevin.h
	M			src/fix_shear_history.cpp
	M			src/improper.h
	M			src/kspace.h
	M			src/library.cpp
	M			src/lmptype.h
	M			src/molecule.cpp
	M			src/molecule.h
	M			src/neighbor.cpp
	M			src/output.h
	M			src/pair_gauss.cpp
	M			src/procmap.cpp
	M			src/region_cylinder.h
	M			src/region_sphere.h
	M			src/rerun.cpp
	M			src/run.h
	M			src/thermo.cpp
	M			src/thermo.h
	M			src/variable.cpp
	M			src/variable.h
	M			tools/eff/cfg2lammps.py
	M			tools/i-pi/drivers/driver.f90
	M			tools/i-pi/ipi/engine/atoms.py
	M			tools/i-pi/ipi/engine/initializer.py
	M			tools/i-pi/ipi/engine/properties.py
	M			tools/i-pi/ipi/engine/simulation.py
	M			tools/i-pi/ipi/engine/thermostats.py
	M			tools/i-pi/ipi/interfaces/sockets.py
	M			tools/i-pi/ipi/utils/depend.py
	M			tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
	M			tools/moltemplate/src/bonds_by_type.py
	M			tools/moltemplate/src/chargepairs_by_type.py
	M			tools/moltemplate/src/dump2data.py
	M			tools/moltemplate/src/lttree.py
	M			tools/moltemplate/src/moltemplate.sh
	M			tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
	M			tools/moltemplate/src/moltemplate_force_fields/gaff.lt
	M			tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
	M			tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
	M			tools/moltemplate/src/nbody_by_type.py
	M			tools/moltemplate/src/ttree.py
	M			tools/moltemplate/src/ttree_lex.py
	M			tools/msi2lmp/frc_files/cvff_aug.frc
	M			tools/msi2lmp/frc_files/pcff.frc
	M			tools/msi2lmp/src/msi2lmp.h
	M			tools/phonon/dynmat.cpp
	M			tools/pymol_asphere/src/cartesian.cpp
	M			tools/pymol_asphere/src/cartesian.h
	M			tools/python/pizza/dump.py