From d6800405a518d957e438ee959852b2bf38c9997e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 7 Mar 2017 00:57:23 -0500 Subject: [PATCH] Fix more typos in examples --- bench/FERMI/README | 2 +- examples/README | 2 +- examples/USER/atc/README | 4 ++-- examples/USER/atc/fluids/in.bar1d_fluids | 2 +- examples/USER/atc/thermal/in.bar1d | 2 +- examples/USER/atc/thermal/in.bar1d_all_atoms | 2 +- examples/USER/atc/thermal/in.bar1d_combined | 2 +- examples/USER/atc/thermal/in.bar1d_flux | 2 +- examples/USER/atc/thermal/in.bar1d_frac_step | 2 +- examples/USER/atc/thermal/in.bar1d_hoover | 2 +- examples/USER/atc/thermal/in.bar1d_interpolate | 2 +- examples/USER/atc/thermal/in.bar1d_lumped | 2 +- examples/USER/misc/srp/in.srp | 2 +- examples/USER/phonon/3-3D-FCC-Cu-EAM/README | 2 +- examples/USER/phonon/4-Graphene/README | 2 +- examples/USER/tally/README | 2 +- examples/VISCOSITY/README | 2 +- examples/accelerate/README | 2 +- python/examples/demo.py | 2 +- python/examples/gui.py | 2 +- python/examples/mc.py | 2 +- python/examples/plot.py | 2 +- python/examples/simple.py | 2 +- python/examples/split.py | 2 +- python/examples/trivial.py | 2 +- python/examples/viz_atomeye.py | 2 +- python/examples/viz_gl.py | 2 +- python/examples/viz_pymol.py | 2 +- python/examples/viz_vmd.py | 2 +- python/examples/vizplotgui_atomeye.py | 2 +- python/examples/vizplotgui_gl.py | 2 +- python/examples/vizplotgui_pymol.py | 2 +- python/examples/vizplotgui_vmd.py | 2 +- 33 files changed, 34 insertions(+), 34 deletions(-) diff --git a/bench/FERMI/README b/bench/FERMI/README index f8772483d1..db3f527bdc 100644 --- a/bench/FERMI/README +++ b/bench/FERMI/README @@ -14,7 +14,7 @@ lmp_linux_mixed lmp_linux_double The precision (single, mixed, double) refers to the GPU and USER-CUDA -pacakge precision. See the README files in the lib/gpu and lib/cuda +package precision. See the README files in the lib/gpu and lib/cuda directories for instructions on how to build the packages with different precisions. The GPU and USER-CUDA sub-sections of the doc/Section_accelerate.html file also describes this process. diff --git a/examples/README b/examples/README index 87f14779ac..5880bb78d7 100644 --- a/examples/README +++ b/examples/README @@ -93,7 +93,7 @@ peri: Peridynamic model of cylinder impacted by indenter pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script -qeq: use of QEQ pacakge for charge equilibration +qeq: use of QEQ package for charge equilibration reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void diff --git a/examples/USER/atc/README b/examples/USER/atc/README index f3a852dfe3..aa874f3300 100644 --- a/examples/USER/atc/README +++ b/examples/USER/atc/README @@ -65,7 +65,7 @@ elastic: in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field @@ -146,7 +146,7 @@ elastic: in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field diff --git a/examples/USER/atc/fluids/in.bar1d_fluids b/examples/USER/atc/fluids/in.bar1d_fluids index 63ef0e2744..af152bfbab 100644 --- a/examples/USER/atc/fluids/in.bar1d_fluids +++ b/examples/USER/atc/fluids/in.bar1d_fluids @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d b/examples/USER/atc/thermal/in.bar1d index e8b61c412a..5591f7177d 100644 --- a/examples/USER/atc/thermal/in.bar1d +++ b/examples/USER/atc/thermal/in.bar1d @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# temperature is initially 20 everywhere and the left boundary BC is fixed at 40. # The result should show heat diffusing through the FEM to the MD and back out # to the FEM on the right. Insufficient time is captured to reach the linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_all_atoms b/examples/USER/atc/thermal/in.bar1d_all_atoms index 6b855f37b1..2c8851137f 100644 --- a/examples/USER/atc/thermal/in.bar1d_all_atoms +++ b/examples/USER/atc/thermal/in.bar1d_all_atoms @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_combined b/examples/USER/atc/thermal/in.bar1d_combined index 1f960dbab7..767544d2d4 100644 --- a/examples/USER/atc/thermal/in.bar1d_combined +++ b/examples/USER/atc/thermal/in.bar1d_combined @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing the boundaries should be observed, diff --git a/examples/USER/atc/thermal/in.bar1d_flux b/examples/USER/atc/thermal/in.bar1d_flux index 0103f00b5b..eae32ec5b2 100644 --- a/examples/USER/atc/thermal/in.bar1d_flux +++ b/examples/USER/atc/thermal/in.bar1d_flux @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/USER/atc/thermal/in.bar1d_frac_step index ca722e79aa..eddec44b52 100644 --- a/examples/USER/atc/thermal/in.bar1d_frac_step +++ b/examples/USER/atc/thermal/in.bar1d_frac_step @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_hoover b/examples/USER/atc/thermal/in.bar1d_hoover index 50e8f02166..2f0518d0d2 100644 --- a/examples/USER/atc/thermal/in.bar1d_hoover +++ b/examples/USER/atc/thermal/in.bar1d_hoover @@ -1,6 +1,6 @@ # AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_interpolate b/examples/USER/atc/thermal/in.bar1d_interpolate index e7db0d3856..0333bf117d 100644 --- a/examples/USER/atc/thermal/in.bar1d_interpolate +++ b/examples/USER/atc/thermal/in.bar1d_interpolate @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_lumped b/examples/USER/atc/thermal/in.bar1d_lumped index eb305a6252..153f7b632d 100644 --- a/examples/USER/atc/thermal/in.bar1d_lumped +++ b/examples/USER/atc/thermal/in.bar1d_lumped @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/misc/srp/in.srp b/examples/USER/misc/srp/in.srp index 234026e9cb..018d916292 100644 --- a/examples/USER/misc/srp/in.srp +++ b/examples/USER/misc/srp/in.srp @@ -24,7 +24,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 -# auto normalization of thermo quantites is turned off by pair srp +# auto normalization of thermo quantities is turned off by pair srp # just divide by natoms variable natoms equal count(all) variable nPotEng equal c_thermo_pe/v_natoms diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README index 57e7be5394..235c66e256 100644 --- a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README +++ b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README @@ -1,5 +1,5 @@ This directory illustrates the usage of fix-phonon to calculate the dynamical -matrix as well as phonon dispersion curve for FCC Cu based on EAM potentail. +matrix as well as phonon dispersion curve for FCC Cu based on EAM potential. The files under this directory: diff --git a/examples/USER/phonon/4-Graphene/README b/examples/USER/phonon/4-Graphene/README index 1e16f0af69..3791bc679c 100644 --- a/examples/USER/phonon/4-Graphene/README +++ b/examples/USER/phonon/4-Graphene/README @@ -1,5 +1,5 @@ This directory illustrates the usage of fix-phonon to calculate the dynamical -matrix as well as phonon dispersion curve for Graphene based on a Tersoff potentail. +matrix as well as phonon dispersion curve for Graphene based on a Tersoff potential. The files under this directory: diff --git a/examples/USER/tally/README b/examples/USER/tally/README index 4c2e40e76e..fcc58e6e0d 100644 --- a/examples/USER/tally/README +++ b/examples/USER/tally/README @@ -3,4 +3,4 @@ Examples and tests for USER-TALLY compute styles. The examples in this directory show where and how compute tally styles are equivalent to other facilities in LAMMPS and thus they can also be used to validate their correct function. Various columns should have -equivalent or idential output as indicated in the input. +equivalent or identical output as indicated in the input. diff --git a/examples/VISCOSITY/README b/examples/VISCOSITY/README index 98ca9fbe3d..38bee0c58d 100644 --- a/examples/VISCOSITY/README +++ b/examples/VISCOSITY/README @@ -24,7 +24,7 @@ times; the G-K and Einstein systems need to run longer to generate good statisti The scripts were all run on a single processor. They all run in a minute or so and produce the accompanying log files and profile files -(for velocity or momemtum flux). +(for velocity or momentum flux). See the Movies page of the LAMMPS web site (http://lammps.sandia.gov/movies.html), for animations of the NEMD diff --git a/examples/accelerate/README b/examples/accelerate/README index 2a494a1680..1fab296a53 100644 --- a/examples/accelerate/README +++ b/examples/accelerate/README @@ -130,7 +130,7 @@ lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj # 2 MPI, 4 thread/MPI Note that when running with just 1 thread/MPI, "-pk kokkos neigh half" -was speficied to use half neighbor lists which are faster when running +was specified to use half neighbor lists which are faster when running on just 1 thread. ** KOKKOS package for CUDA diff --git a/python/examples/demo.py b/python/examples/demo.py index 958ebcd04b..5d2b62fee3 100755 --- a/python/examples/demo.py +++ b/python/examples/demo.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # demo.py # Purpose: illustrate use of many library interface commands diff --git a/python/examples/gui.py b/python/examples/gui.py index 3fc1d7e36c..ac96448b43 100755 --- a/python/examples/gui.py +++ b/python/examples/gui.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # gui.py # Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI diff --git a/python/examples/mc.py b/python/examples/mc.py index 9e7317218b..fb2bfabab9 100755 --- a/python/examples/mc.py +++ b/python/examples/mc.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # mc.py # Purpose: mimic operation of example/MC/in.mc via Python diff --git a/python/examples/plot.py b/python/examples/plot.py index efb9ecaa68..c67509f650 100755 --- a/python/examples/plot.py +++ b/python/examples/plot.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # plot.py # Purpose: plot Temp of running LAMMPS simulation via GnuPlot in Pizza.py diff --git a/python/examples/simple.py b/python/examples/simple.py index 6336c89de3..da07a69997 100755 --- a/python/examples/simple.py +++ b/python/examples/simple.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # simple.py # Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python diff --git a/python/examples/split.py b/python/examples/split.py index 719877d826..77e605092e 100755 --- a/python/examples/split.py +++ b/python/examples/split.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # split.py # Purpose: similar to simple.py, but first the world communicator diff --git a/python/examples/trivial.py b/python/examples/trivial.py index 0e3d6b91af..e52f1745e0 100755 --- a/python/examples/trivial.py +++ b/python/examples/trivial.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # trivial.py # Purpose: run a LAMMPS input script via Python diff --git a/python/examples/viz_atomeye.py b/python/examples/viz_atomeye.py index 3803b2e79c..d9cf4dcef2 100755 --- a/python/examples/viz_atomeye.py +++ b/python/examples/viz_atomeye.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_atomeye.py # Purpose: viz running LAMMPS simulation via AtomEye diff --git a/python/examples/viz_gl.py b/python/examples/viz_gl.py index 476509ad43..5878b68502 100755 --- a/python/examples/viz_gl.py +++ b/python/examples/viz_gl.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_gl.py # Purpose: viz running LAMMPS simulation via GL tool in Pizza.py diff --git a/python/examples/viz_pymol.py b/python/examples/viz_pymol.py index 02178a0fb0..0950b3668b 100755 --- a/python/examples/viz_pymol.py +++ b/python/examples/viz_pymol.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_pymol.py # Purpose: viz running LAMMPS simulation via PyMol diff --git a/python/examples/viz_vmd.py b/python/examples/viz_vmd.py index 807a8c9d55..f592857566 100755 --- a/python/examples/viz_vmd.py +++ b/python/examples/viz_vmd.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_vmd.py # Purpose: viz running LAMMPS simulation via VMD diff --git a/python/examples/vizplotgui_atomeye.py b/python/examples/vizplotgui_atomeye.py index 71730974df..02f119b726 100755 --- a/python/examples/vizplotgui_atomeye.py +++ b/python/examples/vizplotgui_atomeye.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_atomeye.py # Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI diff --git a/python/examples/vizplotgui_gl.py b/python/examples/vizplotgui_gl.py index 937670e511..c4847667fd 100755 --- a/python/examples/vizplotgui_gl.py +++ b/python/examples/vizplotgui_gl.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_gl.py # Purpose: viz running LAMMPS simulation via GL tool with plot and GUI diff --git a/python/examples/vizplotgui_pymol.py b/python/examples/vizplotgui_pymol.py index c7a8a00c6d..11be498741 100755 --- a/python/examples/vizplotgui_pymol.py +++ b/python/examples/vizplotgui_pymol.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_pymol.py # Purpose: viz running LAMMPS simulation via PyMol with plot and GUI diff --git a/python/examples/vizplotgui_vmd.py b/python/examples/vizplotgui_vmd.py index 9eab0865e2..0003ebc929 100755 --- a/python/examples/vizplotgui_vmd.py +++ b/python/examples/vizplotgui_vmd.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_vmd.py # Purpose: viz running LAMMPS simulation via VMD with plot and GUI