diff --git a/doc/src/2001/input_commands.html b/doc/src/2001/input_commands.html index e37d01a0d4..f80185a9f3 100644 --- a/doc/src/2001/input_commands.html +++ b/doc/src/2001/input_commands.html @@ -689,7 +689,7 @@ coeffs: types remainder no other parameters required -used with "create temp" commmand to initialize velocities of atoms +used with "create temp" command to initialize velocities of atoms by default, the "create temp" command initializes the velocities of all atoms, this command limits the initialization to a group of atoms this command is only in force for the next "create temp" command, any @@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files when the minimizer is invoked this command means create a restart file at the end of the minimization with the filename filename.timestep.min a restart file stores atom and force-field information in binary form -allows program to restart from where it left off (see "read restart" commmand) +allows program to restart from where it left off (see "read restart" command) Default = 0 diff --git a/doc/src/99/input_commands.html b/doc/src/99/input_commands.html index 1de02b1686..41b9cb4f7a 100644 --- a/doc/src/99/input_commands.html +++ b/doc/src/99/input_commands.html @@ -477,7 +477,7 @@ coeffs: types remainder no other parameters required -used with "create temp" commmand to initialize velocities of atoms +used with "create temp" command to initialize velocities of atoms by default, the "create temp" command initializes the velocities of all atoms, this command limits the initialization to a group of atoms this command is only in force for the next "create temp" command, any @@ -1343,7 +1343,7 @@ value of 0 means never create one program will toggle between 2 filenames as the run progresses so always have at least one good file even if the program dies in mid-write restart file stores atom positions and velocities in binary form -allows program to restart from where it left off (see "read restart" commmand) +allows program to restart from where it left off (see "read restart" command) Default = 0 diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index c36c961de3..5cb7b3b7d6 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -361,7 +361,7 @@ Settings: "timer"_timer.html, "timestep"_timestep.html -Operations within timestepping (fixes) and diagnositics (computes): +Operations within timestepping (fixes) and diagnostics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 950ae77d19..c66a276bfa 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -992,7 +992,7 @@ file. :dd LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 factor that partitions the computation between real space and k-space -for Disptersion interactions. :dd +for Dispersion interactions. :dd {Cannot create an atom map unless atoms have IDs} :dt @@ -2005,7 +2005,7 @@ Self-explanatory. :dd {Cannot use fix reax/bonds without pair_style reax} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt @@ -2131,7 +2131,7 @@ Self-explanatory. :dd {Cannot use newton pair with born/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use newton pair with buck/coul/cut/gpu pair style} :dt @@ -2291,7 +2291,7 @@ Self-explanatory. :dd {Cannot use newton pair with zbl/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use non-zero forces in an energy minimization} :dt @@ -2641,11 +2641,11 @@ uses a pairwise neighbor list. :dd {Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd +Radius cannot be bigger than 1/2 of a non-axis periodic dimension. :dd {Compute chunk/atom bin/sphere radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of any periodic dimention. :dd +Radius cannot be bigger than 1/2 of any periodic dimension. :dd {Compute chunk/atom compute array is accessed out-of-range} :dt @@ -2706,15 +2706,15 @@ It will only store IDs if its compress option is enabled. :dd {Compute chunk/atom stores no coord1 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord2 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord3 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom variable is not atom-style variable} :dt @@ -2735,11 +2735,11 @@ is used to find clusters. :dd {Compute cna/atom cutoff is longer than pairwise cutoff} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute cna/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute com/chunk does not use chunk/atom compute} :dt @@ -2747,7 +2747,7 @@ The style of the specified compute is not chunk/atom. :dd {Compute contact/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute contact/atom requires atom style sphere} :dt @@ -2760,7 +2760,7 @@ since those atoms are not in the neighbor list. :dd {Compute coord/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute damage/atom requires peridynamic potential} :dt @@ -2835,7 +2835,7 @@ Cannot compute order parameter beyond cutoff. :dd {Compute hexorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute improper/local used when impropers are not allowed} :dt @@ -2881,11 +2881,11 @@ Cannot compute order parameter beyond cutoff. :dd {Compute orientorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute pair must use group all} :dt -Pair styles accumlate energy on all atoms. :dd +Pair styles accumulate energy on all atoms. :dd {Compute pe must use group all} :dt @@ -2935,7 +2935,7 @@ The style of the specified compute is not chunk/atom. :dd {Compute property/local cannot use these inputs together} :dt Only inputs that generate the same number of datums can be used -togther. E.g. bond and angle quantities cannot be mixed. :dd +together. E.g. bond and angle quantities cannot be mixed. :dd {Compute property/local does not (yet) work with atom_style template} :dt @@ -3638,7 +3638,7 @@ Self-explanatory. :dd {Cutoffs missing in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Cutoffs missing in pair_style lj/long/coul/long} :dt @@ -4617,11 +4617,11 @@ An index for the array is out of bounds. :dd {Fix ave/time compute does not calculate a scalar} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate a vector} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate an array} :dt @@ -6171,7 +6171,7 @@ map command will force an atom map to be created. :dd {Initial temperatures not all set in fix ttm} :dt -Self-explantory. :dd +Self-explanatory. :dd {Input line quote not followed by whitespace} :dt @@ -6199,7 +6199,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd {Insufficient Jacobi rotations for triangle} :dt -The calculation of the intertia tensor of the triangle failed. This +The calculation of the inertia tensor of the triangle failed. This should not happen if it is a reasonably shaped triangle. :dd {Insufficient memory on accelerator} :dt @@ -6463,15 +6463,15 @@ Self-explanatory. :dd {Invalid attribute in dump custom command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump local command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump modify command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid basis setting in create_atoms command} :dt @@ -6737,7 +6737,7 @@ or cause multiple files to be written. :dd Filenames used with the dump xyz style cannot be binary or cause files to be written by each processor. :dd -{Invalid dump_modify threshhold operator} :dt +{Invalid dump_modify threshold operator} :dt Operator keyword used for threshold specification in not recognized. :dd @@ -6751,7 +6751,7 @@ The fix is not recognized. :dd {Invalid fix ave/time off column} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid fix box/relax command for a 2d simulation} :dt @@ -7313,7 +7313,7 @@ Self-explanatory. Check the input script or data file. :dd {LJ6 off not supported in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Label wasn't found in input script} :dt @@ -7526,7 +7526,7 @@ Self-explanatory. :dd {Molecule template ID for create_atoms does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Molecule template ID for fix deposit does not exist} :dt @@ -7792,7 +7792,7 @@ Self-explanatory. :dd {Must use variable energy with fix addforce} :dt -Must define an energy vartiable when applyting a dynamic +Must define an energy variable when applying a dynamic force during minimization. :dd {Must use variable energy with fix efield} :dt @@ -8042,7 +8042,7 @@ Self-explanatory. :dd {Non digit character between brackets in variable} :dt -Self-explantory. :dd +Self-explanatory. :dd {Non integer # of swaps in temper command} :dt @@ -8663,7 +8663,7 @@ not be invoked by bond_style quartic. :dd {Pair style does not support compute group/group} :dt The pair_style does not have a single() function, so it cannot be -invokded by the compute group/group command. :dd +invoked by the compute group/group command. :dd {Pair style does not support compute pair/local} :dt @@ -8948,11 +8948,11 @@ Self-explanatory. :dd {Pair yukawa/colloid requires atom style sphere} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid requires atoms with same type have same radius} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid/gpu requires atom style sphere} :dt @@ -10025,7 +10025,7 @@ make sense in between runs. :dd {Threshhold for an atom property that isn't allocated} :dt -A dump threshhold has been requested on a quantity that is +A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. :dd {Timestep must be >= 0} :dt @@ -10087,7 +10087,7 @@ to a large size. :dd {Too many atom triplets for pair bop} :dt The number of three atom groups for angle determinations exceeds the -expected number. Check your atomic structrure to ensure that it is +expected number. Check your atomic structure to ensure that it is realistic. :dd {Too many atoms for dump dcd} :dt @@ -10155,7 +10155,7 @@ to a large size. :dd {Too many timesteps} :dt -The cummulative timesteps must fit in a 64-bit integer. :dd +The cumulative timesteps must fit in a 64-bit integer. :dd {Too many timesteps for NEB} :dt @@ -10796,7 +10796,7 @@ Self-explanatory. :dd {Variable name for fix deform does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Variable name for fix efield does not exist} :dt @@ -11083,7 +11083,7 @@ for a dihedral) and adding a small amount of stretch. :dd {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt -Self-explantory. :dd +Self-explanatory. :dd {Calling write_dump before a full system init.} :dt @@ -11537,7 +11537,7 @@ neigh_modify exclude command. :dd If a thermo_style command is used after a thermo_modify command, the settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify commmand acts on +default values. This is because the thermo_modify command acts on the currently defined thermo style, and a thermo_style command creates a new style. :dd @@ -11886,7 +11886,7 @@ Self-explanatory. :dd {Using largest cutoff for buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Using largest cutoff for lj/long/coul/long} :dt diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index b69d69614a..010462ce7e 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -618,7 +618,7 @@ any of the parameters above, though it becomes a different model in that mode of usage. The SPC/E (extended) water model is the same, except -the partial charge assignemnts change: +the partial charge assignments change: O charge = -0.8476 H charge = 0.4238 :all(b),p @@ -982,10 +982,10 @@ used with non-orthogonal basis vectors to define a lattice that will tile a triclinic simulation box via the "create_atoms"_create_atoms.html command. -A second use is to run Parinello-Rahman dyanamics via the "fix +A second use is to run Parinello-Rahman dynamics via the "fix npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure -tensor. The analalog for an "energy minimization"_minimize.html is +tensor. The analog for an "energy minimization"_minimize.html is the "fix box/relax"_fix_box_relax.html command. A third use is to shear a bulk solid to study the response of the @@ -1392,7 +1392,7 @@ custom"_dump.html command. There is also a "dump local"_dump.html format where the user specifies what local values to output. A pre-defined index keyword can be -specified to enumuerate the local values. Two additional kinds of +specified to enumerate the local values. Two additional kinds of keywords can also be specified (c_ID, f_ID), where a "compute"_compute.html or "fix"_fix.html or "variable"_variable.html provides the values to be output. In each case, the compute or fix @@ -1640,14 +1640,14 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. -DPD thermostatting alters pairwise interactions in a manner analagous +DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix langevin"_fix_langevin.html. Any of the thermostatting fixes can use temperature computes that remove bias which has two effects. First, the current calculated temperature, which is compared to the requested target temperature, is -caluclated with the velocity bias removed. Second, the thermostat +calculated with the velocity bias removed. Second, the thermostat adjusts only the thermal temperature component of the particle's velocities, which are the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the @@ -2013,7 +2013,7 @@ a simple Lennard-Jones fluid model. Also, see "this section"_Section_howto.html#howto_21 of the manual for an analogous discussion for viscosity. -The thermal conducitivity tensor kappa is a measure of the propensity +The thermal conductivity tensor kappa is a measure of the propensity of a material to transmit heat energy in a diffusive manner as given by Fourier's law @@ -2099,7 +2099,7 @@ and grad(Vstream) is the spatial gradient of the velocity of the fluid moving in another direction, normal to the area through which the momentum flows. Viscosity thus has units of pressure-time. -The first method is to perform a non-equlibrium MD (NEMD) simulation +The first method is to perform a non-equilibrium MD (NEMD) simulation by shearing the simulation box via the "fix deform"_fix_deform.html command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to thermostat the fluid via the SLLOD equations of motion. @@ -2125,7 +2125,7 @@ the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is swapped between atoms in two different layers of the simulation box in a different dimension. This induces a velocity gradient which can be monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cummulative momentum transfer that it performs. +The fix tallies the cumulative momentum transfer that it performs. See the "fix viscosity"_fix_viscosity.html command for details. The fourth method is based on the Green-Kubo (GK) formula which @@ -2353,7 +2353,7 @@ largest cluster or fastest diffusing molecule. :l Example calculations with chunks :h5 -Here are eaxmples using chunk commands to calculate various +Here are examples using chunk commands to calculate various properties: (1) Average velocity in each of 1000 2d spatial bins: @@ -2424,7 +2424,7 @@ which both have their up- and downsides. The first approach is to set desired real-space an kspace accuracies via the {kspace_modify force/disp/real} and {kspace_modify force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependend on the chosen unit +specified in force units and are thus dependent on the chosen unit settings. For real units, 0.0001 and 0.002 seem to provide reasonable accurate and efficient computations for the real-space and kspace accuracies. 0.002 and 0.05 work well for most systems using lj @@ -2478,7 +2478,7 @@ arithmetic mixing rule substantially increases the computational cost. The computational overhead can be reduced using the {kspace_modify mix/disp geom} and {kspace_modify splittol} commands. The first command simply enforces geometric mixing of the dispersion -coeffiecients in kspace computations. This introduces some error in +coefficients in kspace computations. This introduces some error in the computations but will also significantly speed-up the simulations. The second keyword sets the accuracy with which the dispersion coefficients are approximated using a matrix factorization @@ -2497,7 +2497,7 @@ to specify this command explicitly. 6.25 Polarizable models :link(howto_25),h4 In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environements. Polarizable +materials respond to their electrostatic environments. Polarizable systems can be simulated in LAMMPS using three methods: the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html @@ -2738,7 +2738,7 @@ the core/shell particles, but only assign a center-of-mass velocity to the pairs. This can be done by using the {bias} keyword of the "velocity create"_velocity.html command and assigning the "compute temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html commmand, e.g. +"velocity"_velocity.html command, e.g. velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt index 228c7199fd..2e2d5d77f3 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -159,17 +159,17 @@ pack_comm_vel: add velocity info to communication buffer (required) pack_comm_hybrid: store extra info unique to this atom style (optional) unpack_comm: retrieve an atom's info from the buffer (required) unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retreive extra info unique to this atom style (optional) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) pack_reverse: store an atom's info in a buffer communicating partial forces (required) pack_reverse_hybrid: store extra info unique to this atom style (optional) unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retreive extra info unique to this atom style (optional) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) pack_border_vel: add velocity info to buffer (required) pack_border_hybrid: store extra info unique to this atom style (optional) unpack_border: retrieve an atom's info from the buffer (required) unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retreive extra info unique to this atom style (optional) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) pack_exchange: store all an atom's info to migrate to another processor (required) unpack_exchange: retrieve an atom's info from the buffer (required) size_restart: number of restart quantities associated with proc's atoms (required) @@ -517,7 +517,7 @@ class. See region.h for details. inside: determine whether a point is in the region surface_interior: determine if a point is within a cutoff distance inside of surc surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-depedent variable :tb(s=:) +shape_update : change region shape if set by time-dependent variable :tb(s=:) :line @@ -601,16 +601,16 @@ Adding keywords for the "thermo_style custom"_thermo_style.html command "here"_Section_modify.html#mod_13 on this page. Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaulate() method. Search for +editing one section of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding a new group function can be done by editing one section of the -Variable::evaulate() method. Search for the word "customize" to find +Variable::evaluate() method. Search for the word "customize" to find the appropriate location. You may need to add a new method to the Group class as well (see the group.cpp file). Accessing a new atom-based vector can be done by editing one section -of the Variable::evaulate() method. Search for the word "customize" +of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding new "compute styles"_compute.html (whose calculated values can @@ -740,7 +740,7 @@ entry to add to the USER-MISC/README file in that dir, along with the contribute several individual features. :l If you want your contribution to be added as a user-contribution and -it is several related featues, it is probably best to make it a user +it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index b9b96d66ad..00b1fb1067 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -462,7 +462,7 @@ options you are optimizing for: CPU acceleration via OpenMP, GPU acceleration, or Intel Xeon Phi. (You can build multiple times to create LAMMPS executables for different hardware.) It also requires a C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is -used, and an appopriate KOKKOS_ARCH setting should be made in your +used, and an appropriate KOKKOS_ARCH setting should be made in your Makefile.machine for your GPU hardware and NVIDIA software. The simplest way to do this is to use Makefile.kokkos_cuda or @@ -1848,7 +1848,7 @@ See this doc page to get started: The persons who created the USER-SMTBQ package are Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at -these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact them directly if you have any questions. Examples: examples/USER/smtbq diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index bd4dfcf538..e1d5f0f867 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -662,7 +662,7 @@ or integers (int **) is returned. You need to specify the appropriate data type via the type argument. For extract_compute() and extract_fix(), the global, per-atom, or -local data calulated by the compute or fix can be accessed. What is +local data calculated by the compute or fix can be accessed. What is returned depends on whether the compute or fix calculates a scalar or vector or array. For a scalar, a single double value is returned. If the compute or fix calculates a vector or array, a pointer to the diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 2146830753..9f6c113449 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -362,7 +362,7 @@ installed on your platform. If MPI is installed on your system in the usual place (under /usr/local), you also may not need to specify these 3 variables, assuming /usr/local is in your path. On some large parallel machines which use "modules" for their compile/link -environements, you may simply need to include the correct module in +environments, you may simply need to include the correct module in your build environment, before building LAMMPS. Or the parallel machine may have a vendor-provided MPI which the compiler has no trouble finding. @@ -430,7 +430,7 @@ use the KISS library described above. You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, so the compiler and linker can find the needed FFT header and library files. Note that on some large parallel machines which use "modules" -for their compile/link environements, you may simply need to include +for their compile/link environments, you may simply need to include the correct module in your build environment. Or the parallel machine may have a vendor-provided FFT library which the compiler has no trouble finding. @@ -450,7 +450,7 @@ you must also manually specify the correct library, namely -lsfftw or The FFT_INC variable also allows for a -DFFT_SINGLE setting that will use single-precision FFTs with PPPM, which can speed-up long-range -calulations, particularly in parallel or on GPUs. Fourier transform +calculations, particularly in parallel or on GPUs. Fourier transform and related PPPM operations are somewhat insensitive to floating point truncation errors and thus do not always need to be performed in double precision. Using the -DFFT_SINGLE setting trades off a little @@ -1008,7 +1008,7 @@ Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or rename if desired. Likewise it creates an executable named src/lmp_auto, which you can rename using the -o switch if desired. -The most recently executed Make.py commmand is saved in +The most recently executed Make.py command is saved in src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke the last command, or you can save a sequence of one or more Make.py commands to a file and invoke the file of commands using "-r". You @@ -1064,7 +1064,7 @@ src/MAKE/Makefile.foo and perform the build in the directory Obj_shared_foo. This is so that each file can be compiled with the -fPIC flag which is required for inclusion in a shared library. The build will create the file liblammps_foo.so which another application -can link to dyamically. It will also create a soft link liblammps.so, +can link to dynamically. It will also create a soft link liblammps.so, which will point to the most recently built shared library. This is the file the Python wrapper loads by default. diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index f469390ced..83fb7a6bce 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -471,7 +471,7 @@ These tools were written by Aidan Thompson at Sandia. restart2data tool :h4,link(restart) NOTE: This tool is now obsolete and is not included in the current -LAMMPS distribution. This is becaues there is now a +LAMMPS distribution. This is because there is now a "write_data"_write_data.html command, which can create a data file from within an input script. Running LAMMPS with the "-r" "command-line switch"_Section_start.html#start_7 as follows: diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index 088e6db113..cbb5e2e435 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -428,7 +428,7 @@ to the card. This allows for overlap of MPI communication of forces with computation on the coprocessor when the "newton"_newton.html setting is "on". The default is dependent on the style being used, however, better performance may be achieved by setting this option -explictly. +explicitly. When using offload with CPU Hyper-Threading disabled, it may help performance to use fewer MPI tasks and OpenMP threads than available diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index 3d31344c24..26e35e23d1 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -234,7 +234,7 @@ provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is given in "Section 5.3"_Section_accelerate.html#acc_3. -KOKKOS_ARCH=KNC enables compiler switches needed when compling for an +KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an Intel Phi processor. KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism @@ -272,7 +272,7 @@ coprocessor support you need to insure there are one or more MPI tasks per coprocessor, and choose the number of coprocessor threads to use per MPI task (via the "-k" command-line switch discussed below). The product of MPI tasks * coprocessor threads/task should not exceed the -maximum number of threads the coproprocessor is designed to run, +maximum number of threads the coprocessor is designed to run, otherwise performance will suffer. This value is 240 for current generation Xeon Phi(TM) chips, which is 60 physical cores * 4 threads/core. Note that with the KOKKOS package you do not need to @@ -333,7 +333,7 @@ device=CUDA are the same. You must still use the "-k on" "command-line switch"_Section_start.html#start_7 to enable the KOKKOS package, and -specify its additional arguments for hardware options appopriate to +specify its additional arguments for hardware options appropriate to your system, as documented above. Use the "suffix kk"_suffix.html command, or you can explicitly add a diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 9ba817a663..6a8588e08a 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -115,7 +115,7 @@ particle. For the {ellipsoid} style, the particles are ellipsoids and each stores a flag which indicates whether it is a finite-size ellipsoid or a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diamters of the ellipsoid and a quaternion 4-vector +vector with the 3 diameters of the ellipsoid and a quaternion 4-vector with its orientation. For the {dipole} style, a point dipole is defined for each point @@ -195,7 +195,7 @@ the {bstyle} argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its orientation @@ -280,7 +280,7 @@ The {dpd} style is part of the USER-DPD package for dissipative particle dynamics (DPD). The {meso} style is part of the USER-SPH package for smoothed particle -hydrodyanmics (SPH). See "this PDF +hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for the diff --git a/doc/src/balance.txt b/doc/src/balance.txt index b9d36452a6..9951e44a91 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -12,7 +12,7 @@ balance command :h3 balance thresh style args ... keyword args ... :pre -thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l +thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l one style/arg pair can be used (or multiple for {x},{y},{z}) :l style = {x} or {y} or {z} or {shift} or {rcb} :l {x} args = {uniform} or Px-1 numbers between 0 and 1 @@ -30,7 +30,7 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l {shift} args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting. With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically inducces a different number of atoms assigned to each processor. Details on the various weighting options and examples for how they can be used are "given below"_#weighted_balance. diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index c6556e0fc9..c9c4d7a3b6 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -289,7 +289,7 @@ the create_box command is encountered in the input script. The {remap} keyword remaps atom coordinates from the last saved box size/shape to the current box state. For example, if you stretch the box in the x dimension or tilt it in the xy plane via the {x} and {xy} -keywords, then the {remap} commmand will dilate or tilt the atoms to +keywords, then the {remap} command will dilate or tilt the atoms to conform to the new box size/shape, as if the atoms moved with the box as it deformed. diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 8ecfd81af1..eed190aeb2 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -235,7 +235,7 @@ section of "this page"_Section_commands.html#cmd_5. "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"ti"_compute_ti.html - thermodyanmic integration free energy values +"ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 0a48ccb5be..4e4b03d167 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -18,8 +18,8 @@ lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l zero or more keyword/value pairs may be appended :l keyword = {axes} :l {axes} value = {no} or {yes} - {no} = do not calulate 3 symmetry axes - {yes} = calulate 3 symmetry axes :pre + {no} = do not calculate 3 symmetry axes + {yes} = calculate 3 symmetry axes :pre :ule [Examples:] @@ -108,7 +108,7 @@ symmetry axis, followed by the second, and third symmetry axes in columns 5-7 and 8-10. The centrosymmetry values are unitless values >= 0.0. Their magnitude -depends on the lattice style due to the number of contibuting neighbor +depends on the lattice style due to the number of contributing neighbor pairs in the summation in the formula above. And it depends on the local defects surrounding the central atom, as described above. For the {axes yes} case, the vector components are also unitless, since diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index e6083ad615..b1550875a4 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -459,7 +459,7 @@ The original chunk IDs (before renumbering) can be accessed by the which outputs the original IDs as one of the columns in its global output array. For example, using the "compute cluster/atom" command discussed above, the original 5 unique chunk IDs might be atom IDs -(27,4982,58374,857838,1000000). After compresion, these will be +(27,4982,58374,857838,1000000). After compression, these will be renumbered to (1,2,3,4,5). The original values (27,...,1000000) can be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command, or by using the "fix ave/time"_fix_ave_time.html command in @@ -538,7 +538,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to to the first or last bin in both the radial and axis dimensions. If {discard} is set to {mixed}, which is the default, the radial dimension is treated the same as for {discard} = no. But for the axis -dimensinon, it will only have its chunk ID set to the first or last +dimension, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in the axis dimension. This is the case if the {bound} keyword settings are {lower} and {upper}, which is the default. If the {bound} keyword diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 0367b2fe95..854a5778ec 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -70,7 +70,7 @@ The ID of the previously specified "compute orientorder/atom"_compute_orientorder/atom command is specified as {orientorderID}. The compute must invoke its {components} option to calculate components of the {Ybar_lm} vector for each atoms, as -described in its documenation. Note that orientorder/atom compute +described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the orientorder/atom compute is larger than the specified {threshold}, diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index d1ebd72ae5..69532f1154 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -14,7 +14,7 @@ compute ID group-ID event/displace threshold :pre ID, group-ID are documented in "compute"_compute.html command event/displace = style name of this compute command -threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul +threshold = minimum distance any particle must move to trigger an event (distance units) :ul [Examples:] diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index f62efcff2e..3136b1fd18 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -55,7 +55,7 @@ M is the actual length of the input vector, then an output value of 0.0 is assigned to the atom. An example of how this command is useful, is in the context of -"chunks" which are static or dyanmic subsets of atoms. The "compute +"chunks" which are static or dynamic subsets of atoms. The "compute chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs to each atom. It's output can be used as the {index} parameter for this command. Various other computes with "chunk" in their style @@ -192,7 +192,7 @@ reference thermodynamic keywords and various other attributes of atoms, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating a vector of global quantities which the {index} parameter will reference for -assignement of global values to atoms. +assignment of global values to atoms. :line @@ -207,7 +207,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the -corresponsing input values are in. +corresponding input values are in. [Restrictions:] none diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 720d26ce76..e8adac3deb 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -38,7 +38,7 @@ subtracted to a group of atoms. The compute takes three arguments which are IDs of other "computes"_compute.html. One calculates per-atom kinetic energy ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the -third calcualtes per-atom stress ({stress-ID}). +third calculates per-atom stress ({stress-ID}). NOTE: These other computes should provide values for all the atoms in the group this compute specifies. That means the other computes could @@ -83,7 +83,7 @@ The heat flux can be output every so many timesteps (e.g. via the post-processing operation, an autocorrelation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. -The "fix ave/correlate"_fix_ave_correlate.html command can calclate +The "fix ave/correlate"_fix_ave_correlate.html command can calculate the autocorrelation. The trap() function in the "variable"_variable.html command can calculate the integral. diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index 59a459b0d7..b0dbb12aea 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section defined and examples of how they can be used to measure properties of a system. -This compute calculates the 6 components of the symmetric intertia +This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The calculation includes all effects due to atoms passing thru periodic boundaries. diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index b92ceaacde..11a51229c7 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -48,7 +48,7 @@ others. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calcluated. +displacment of each atom is calculated. See the "compute msd"_compute_msd.html doc page for further important NOTEs, which also apply to this compute. diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index d2b34ed110..7a98709f89 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -52,7 +52,7 @@ corrections, even if they are enabled via the Some pair styles tally additional quantities, e.g. a breakdown of potential energy into a dozen or so components is tallied by the -"pair_style reax"_pair_reax.html commmand. These values (1 or more) +"pair_style reax"_pair_reax.html command. These values (1 or more) are stored as a global vector by this compute. See the doc page for "individual pair styles"_pair_style.html for info on these values. diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 0d420b2202..0121210994 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -47,7 +47,7 @@ force cutoff distance for that interaction, as defined by the "pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html commands. -The value {dist} is the distance bewteen the pair of atoms. +The value {dist} is the distance between the pair of atoms. The value {eng} is the interaction energy for the pair of atoms. diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index 8e2fd17f24..6de3a79e5b 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -51,7 +51,7 @@ these terms is included in the pair energy, not the dihedral energy. The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, as specified by the "kspace_style pppm"_kspace_style.html command. -For PPPM, the calcluation requires 1 extra FFT each timestep that +For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This "document"_PDF/kspace.pdf describes how the long-range per-atom energy calculation is performed. diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 9e8c2a3b46..ae62859b17 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias. Also note that the N in the first formula above is really degrees-of-freedom divided by d = dimensionality, where the DOF value -is calcluated by the temperature compute. See the various "compute +is calculated by the temperature compute. See the various "compute temperature"_compute.html styles for details. A compute of this style with the ID of "thermo_press" is created when diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index 3bed9c0677..b9d4944b30 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -64,7 +64,7 @@ can only be used if the {compress} keyword was set to {yes} for the "compute chunk/atom"_compute_chunk_atom.html command referenced by chunkID. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compresed chunk ID of 3 may correspond to an original +to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID (molecule ID in this case) of 415. The {id} attribute will then be 415 for the 3rd chunk. diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 5cdd58fbc2..077ad57d81 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -123,7 +123,7 @@ The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of the COM velocity and force on the COM of the body. The {omegax}, {omegay}, and {omegaz} attributes are the angular -velocity componennts of the body around its COM. +velocity components of the body around its COM. The {angmomx}, {angmomy}, and {angmomz} attributes are the angular momentum components of the body around its COM. diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index 95af1b2163..adece93343 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -35,7 +35,7 @@ any command that uses per-particle values from a compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle values will be given dimentionless, see "units"_units.html. +The per-particle values will be given dimensionless, see "units"_units.html. [Restrictions:] diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 3dc642da32..d09c8069cc 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -92,7 +92,7 @@ The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and by the methodology described in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified by the "kspace_style pppm"_kspace_style.html command. Note that for -PPPM, the calcluation requires 6 extra FFTs each timestep that +PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the cost of the PPPM calculation if it is needed on a large fraction of the simulation timesteps. diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index d565c95134..2e205a370b 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -44,7 +44,7 @@ compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre Define a computation that calculates the temperature of a group of atoms that are also in chunks, after optionally subtracting out the center-of-mass velocity of each chunk. By specifying optional values, -it can also calulate the per-chunk temperature or energies of the +it can also calculate the per-chunk temperature or energies of the multiple chunks of atoms. In LAMMPS, chunks are collections of atoms defined by a "compute @@ -122,7 +122,7 @@ concept is somewhat ill-defined. In some cases, you can use the {adof} and {cdof} keywords to adjust the calculated degress of freedom appropriately, as explained below. -Note that the per-chunk temperature calulated by this compute and the +Note that the per-chunk temperature calculated by this compute and the "fix ave/chunk temp"_fix_ave_chunk.html command can be different. This compute calculates the temperature for each chunk for a single snapshot. Fix ave/chunk can do that but can also time average those diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 5f8ee1ee88..5898f4ed03 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -545,7 +545,7 @@ that the coordinate values may be far outside the box bounds printed with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will -have the corresponding cooordinate increased or decreased by 1.0. +have the corresponding coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt index b84817327b..f15d20f849 100644 --- a/doc/src/dump_custom_vtk.txt +++ b/doc/src/dump_custom_vtk.txt @@ -211,7 +211,7 @@ charge. There are several options for outputting atom coordinates. The {x}, {y}, {z} attributes are used to write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). -Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the +Additionally, you can use {xs}, {ys}, {zs} if you want to also save the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you @@ -224,7 +224,7 @@ values may be far outside the box bounds printed with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will have the corresponding -cooordinate increased or decreased by 1.0. +coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 819cdbd36c..a1fc527ec4 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -99,7 +99,7 @@ included in the image or movie and how it appears. A series of such images can easily be manually converted into an animated movie of your simulation or the process can be automated without writing the intermediate files using the dump movie style; see further details -below. Other dump styles store snapshots of numerical data asociated +below. Other dump styles store snapshots of numerical data associated with atoms in various formats, as discussed on the "dump"_dump.html doc page. @@ -261,7 +261,7 @@ the input script defines, e.g. Angstroms. The {bond} keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being in the specified group and due to other selection criteria -(e.g. region, threshhold settings of the +(e.g. region, threshold settings of the "dump_modify"_dump_modify.html command). By default, bonds are drawn if they are defined in the input data file as read by the "read_data"_read_data.html command. Using {none} for both the bond @@ -356,7 +356,7 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent and how they are drawn by this dump image command. For all the body styles, individual atoms can be either a diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 0cf30e3c92..7eafffa24c 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold. If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values -which may be useful for the comparision operator. Boolean values can +which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the "variable"_variable.html command doc page for details. diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 0238d9b4f2..a1fe6ae6d0 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -67,7 +67,7 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre [NOTE:] -If you are trying to replace a deprectated fix ave/spatial command +If you are trying to replace a deprecated fix ave/spatial command with the newer, more flexible fix ave/chunk and "compute chunk/atom"_compute_chunk_atom.html commands, you simply need to split the fix ave/spatial arguments across the two new commands. For @@ -189,7 +189,7 @@ chunk/atom"_compute_chunk_atom.html command must remain constant. If the {ave} keyword is set to {running} or {window} then {Nchunk} must remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold {Nchunk} constant -for the appropriate time windows, by not allowing it to re-calcualte +for the appropriate time windows, by not allowing it to re-calculate {Nchunk}, which can also affect how it assigns chunk IDs to atoms. More details are given on the "compute chunk/atom"_compute_chunk_atom.html doc page. @@ -410,7 +410,7 @@ chunk/atom"_compute_chunk_atom.html command supports them. The OrigID column is only used if the {compress} keyword was set to {yes} for the "compute chunk/atom"_compute_chunk_atom.html command. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed -to remove chunk IDs with no atoms assigned to them. Thus a compresed +to remove chunk IDs with no atoms assigned to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID or molecule ID of 415. The OrigID column will list 415 for the 3rd chunk. diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index bd097f291a..6ae9fe53b6 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -64,7 +64,7 @@ fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\] [Description:] Use one or more global scalar values as inputs every few timesteps, -calculate time correlations bewteen them at varying time intervals, +calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 569cdc96cf..b04f17e460 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -33,7 +33,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title vector = all input values are global vectors or global arrays {ave} args = {one} or {running} or {window M} one = output a new average value every Nfreq steps - running = output cummulative average of all previous Nfreq steps + running = output cumulative average of all previous Nfreq steps window M = output average of M most recent Nfreq steps {start} args = Nstart Nstart = start averaging on this timestep @@ -223,7 +223,7 @@ output as-is without further averaging. If the {ave} setting is {running}, then the values produced on timesteps that are multiples of {Nfreq} are summed and averaged in a -cummulative sense before being output. Each output value is thus the +cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the "unfix"_unfix.html diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 8473fa8152..16ea1d39f9 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -15,12 +15,12 @@ fix ID group-ID balance Nfreq thresh style args keyword args ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l balance = style name of this fix command :l Nfreq = perform dynamic load balancing every this many steps :l -thresh = imbalance threshhold that must be exceeded to perform a re-balance :l +thresh = imbalance threshold that must be exceeded to perform a re-balance :l style = {shift} or {rcb} :l shift args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -78,7 +78,7 @@ The balancing can be performed with or without per-particle weighting. With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically inducces a different number of atoms assigned to each processor. NOTE: The weighting options listed above are documented with the @@ -249,7 +249,7 @@ typically be positioned to better than 1 part in 1000 accuracy be accurate to better than 1 part in a million. Thus there is no need to set {Niter} to a large value. This is especially true if you are rebalancing often enough that each time you expect only an incremental -adjustement in the cutting planes is necessary. LAMMPS will check if +adjustment in the cutting planes is necessary. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than {Niter} and exit early. diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 98ba472327..d27246872c 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -122,7 +122,7 @@ by this fix are "intensive". These are the 2 quantities: (1) # of bonds broken on the most recent breakage timestep -(2) cummulative # of bonds broken :ul +(2) cumulative # of bonds broken :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index 3d00b60844..949eb7e7e3 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -218,7 +218,7 @@ by this fix are "intensive". These are the 2 quantities: (1) # of bonds created on the most recent creation timestep -(2) cummulative # of bonds created :ul +(2) cumulative # of bonds created :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 38c5e17c60..5290abe185 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -81,7 +81,7 @@ by this processor on this timestep. The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the "read_data"_read_data.html comand. +in the data file, read by the "read_data"_read_data.html command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then swaps will conserve chain length. For a particular momoner there will @@ -124,7 +124,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the "compute_modify"_compute_modify.html command or print this temperature -during thermodyanmic output via the "thermo_style +during thermodynamic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. @@ -151,8 +151,8 @@ the Boltzmann criterion. This fix computes two statistical quantities as a global 2-vector of output, which can be accessed by various "output commands"_Section_howto.html#howto_15. The first component of the -vector is the cummulative number of swaps performed by all processors. -The second component of the vector is the cummulative number of swaps +vector is the cumulative number of swaps performed by all processors. +The second component of the vector is the cumulative number of swaps attempted (whether accepted or rejected). Note that a swap "attempt" only occurs when swap partners meeting the criteria described above are found on a particular timestep. The vector values calculated by diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 96701b170e..e775074bcc 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -103,7 +103,7 @@ far. In all cases, the particle positions at each iteration are unaffected by the chosen value, except that all particles are displaced by the same amount, different on each iteration. -NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz} +NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz} can sometimes result in arbitrarily large values of the tilt factors, i.e. a dramatically deformed simulation box. This typically indicates that there is something badly wrong with how the simulation was diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index e2be03f46b..e48dedacd9 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -59,7 +59,7 @@ always apply to the entire system and there can only be one instance of the colvars fix at a time. The colvars fix will only communicate the minimum information necessary and the colvars library supports multiple, completely independent collective variables, so there is -no restriction to functionaliry by limiting the number of colvars fixes. +no restriction to functionality by limiting the number of colvars fixes. The {input} keyword allows to specify a state file that would contain the restart information required in order to continue a calculation from @@ -100,7 +100,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index a19f42c77c..3d590cd3e1 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -175,7 +175,7 @@ equal-style versus internal-style variable interchangeably. [Restart, fix_modify, output, run start/stop, minimize info:] -Currenlty, no information about this fix is written to "binary restart +Currently, no information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 8fc72bbdad..42778d7978 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -17,7 +17,7 @@ eos/table = style name of this fix command style = {linear} = method of interpolation file = filename containing the tabulated equation of state N = use N values in {linear} tables -keyword = name of table keyword correponding to table file :ul +keyword = name of table keyword corresponding to table file :ul [Examples:] diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 749642f57c..e8d515e1f3 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -17,7 +17,7 @@ eos/table/rx = style name of this fix command style = {linear} = method of interpolation file1 = filename containing the tabulated equation of state N = use N values in {linear} tables -keyword = name of table keyword correponding to table file +keyword = name of table keyword corresponding to table file file2 = filename containing the heats of formation of each species (optional) deltaHf = heat of formation for a single species in energy units (optional) energyCorr = energy correction in energy units (optional) diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index 0243cbe977..ace1fae63a 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -74,7 +74,7 @@ are relevant to this fix. This fix computes a global scalar, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative number of deleted atoms. The scalar value calculated by +cumulative number of deleted atoms. The scalar value calculated by this fix is "intensive". No parameter of this fix can be used with the {start/stop} keywords of diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index b6a1a7500a..ca7625e2d0 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -116,7 +116,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index b387117d83..a3d0fb7eaa 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -307,7 +307,7 @@ setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index 4b09d695b9..d3112d529d 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -80,7 +80,7 @@ setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 9bbe252c1f..83af5b273a 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -58,7 +58,7 @@ nve"_fix_nve.html command). It is up to you to decide whether periodic boundaries are appropriate with the kind of atom motion you are prescribing with this fix. -NOTE: As dicsussed below, atoms are moved relative to their initial +NOTE: As discussed below, atoms are moved relative to their initial position at the time the fix is specified. These initial coordinates are stored by the fix in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index c613a598fe..6bd0876537 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. The MS-CG library uses C++11, which may not be supported by older compilers. The MS-CG library also has some additional numeric library -dependencies, which are describd in its documentation. +dependencies, which are described in its documentation. Currently, the MS-CG library is not setup to run in parallel with MPI, so this fix can only be used in a serial LAMMPS build and run diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt index 98cf75999b..5f1b271546 100644 --- a/doc/src/fix_nve_asphere_noforce.txt +++ b/doc/src/fix_nve_asphere_noforce.txt @@ -25,7 +25,7 @@ Perform updates of position and orientation, but not velocity or angular momentum for atoms in the group each timestep. In other words, the force and torque on the atoms is ignored and their velocity and angular momentum are not updated. The atom velocities and -angularm momenta are used to update their positions and orientation. +angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index 2d772ba6be..e92d1640cd 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -35,7 +35,7 @@ radial velocity of electrons are also updated and thermostatted. Likewise the temperature calculated by the fix, using the compute it creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc page), is performed with a "compute -temp/deform/eff"_compute_temp_deform_eff.html commmand that includes +temp/deform/eff"_compute_temp_deform_eff.html command that includes the eFF contribution to the temperature from the electron radial velocity. diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 10a0c95c80..0f399f187b 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -183,7 +183,7 @@ This fix requires LAMMPS be built with an FFT library. See the [Default:] -The option defaults are sysdim = the same dimemsion as specified by +The option defaults are sysdim = the same dimension as specified by the "dimension"_dimension.html command, and nasr = 20. :line diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index 90ed84a8bf..f1487c3aa7 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -175,7 +175,7 @@ some other way. The {vol} option specifies what volume fraction of the insertion volume will be filled with particles. For particles with a size specified by the {diam range} keyword, they are assumed to all be of -maximum diamter {Dhi} for purposes of computing their contribution to +maximum diameter {Dhi} for purposes of computing their contribution to the volume fraction. The higher the volume fraction value, the more particles are inserted diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index 951a82709e..049c3d8e2a 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -71,7 +71,7 @@ or AMBER, can have a strong effect on energies and forces, and produces a different model than the published versions. NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used -to perform charge equliibration with the "COMB +to perform charge equilibration with the "COMB potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html command can be used to perform charge equilibration with the "ReaxFF force field"_pair_reax_c.html, although fix qeq/shielded yields the diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index 74f944db66..a26934dfb4 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -33,7 +33,7 @@ typically used in conjunction with the ReaxFF force field model as implemented in the "pair_style reax/c"_pair_reax_c.html command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html -command should be used to perform charge equliibration with the "COMB +command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the "(Aktulga)"_#Aktulga paper. diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index a85e140b62..1fd1b3ca5a 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,7 +34,7 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. -The format of the output file should be self-explantory. +The format of the output file should be self-explanatory. :line diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 335d3a78e9..a860aad128 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -119,7 +119,7 @@ contribution to the pressure of the system (virial) is also accounted for. NOTE: This command works by using the current forces on atoms to -caculate an additional constraint force which when added will leave +calculate an additional constraint force which when added will leave the atoms in positions that satisfy the SHAKE constraints (e.g. bond length) after the next time integration step. If you define fixes (e.g. "fix efield"_fix_efield.html) that add additional force to the @@ -133,7 +133,7 @@ forces (to atoms that fix shake operates on). The {mol} keyword should be used when other commands, such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules -on-the-fly during a simulation, and you wish to contrain the new +on-the-fly during a simulation, and you wish to constrain the new molecules via SHAKE. You specify a {template-ID} previously defined using the "molecule"_molecule.html command, which reads a file that defines the molecule. You must use the same {template-ID} that the @@ -210,7 +210,7 @@ which can lead to poor energy conservation. You can test for this in your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time. -SHAKE or RATTLE should not be used to contrain an angle at 180 degrees +SHAKE or RATTLE should not be used to constrain an angle at 180 degrees (e.g. linear CO2 molecule). This causes numeric difficulties. [Related commands:] none diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 13519ecfad..a432b511d1 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -182,7 +182,7 @@ can be used to scale down their effective collision radius by an amount {rfactor}, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation -bewteen two big particles is as small as about 0.88 sigma. Thus an +between two big particles is as small as about 0.88 sigma. Thus an {rfactor} value of 0.85 should prevent dual collisions. The {bounce} keyword can be used to limit the maximum number of @@ -241,7 +241,7 @@ box shape changes. This re-binning is always done so as to fit an integer number of bins in the current box dimension, whether it be a fixed, shrink-wrapped, or periodic boundary, as set by the "boundary"_boundary.html command. If the box size or shape changes, -then the size of the search bins must be recalculated avery +then the size of the search bins must be recalculated every reneighboring. Note that changing the SRD bin size may alter the properties of the SRD fluid, such as its viscosity. @@ -345,15 +345,15 @@ commands"_Section_howto.html#howto_15. The vector values calculated by this fix are "intensive", meaning they do not scale with the size of the simulation. Technically, the first 8 do scale with the size of the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodyanmic output. +scaled when printed as part of thermodynamic output. These are the 12 quantities. All are values for the current timestep, except for quantity 5 and the last three, each of which are -cummulative quantities since the beginning of the run. +cumulative quantities since the beginning of the run. (1) # of SRD/big collision checks performed (2) # of SRDs which had a collision -(3) # of SRD/big colllisions (including multiple bounces) +(3) # of SRD/big collisions (including multiple bounces) (4) # of SRD particles inside a big particle (5) # of SRD particles whose velocity was rescaled to be < Vmax (6) # of bins for collision searching diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 177591d8e7..9c1dd538da 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -127,7 +127,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 7e53926516..c356070038 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -136,7 +136,7 @@ These fixes are not invoked during "energy minimization"_minimize.html. These fixes compute a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to the fix. The scalar value +cumulative energy change due to the fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index f38d20d0d7..7369fca184 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -134,7 +134,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt index c39651e05c..f87c1a2192 100644 --- a/doc/src/fix_temp_rescale_eff.txt +++ b/doc/src/fix_temp_rescale_eff.txt @@ -52,7 +52,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 9038a12709..a807feaec7 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -109,10 +109,10 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative kinetic energy transferred between the bottom and middle +cumulative kinetic energy transferred between the bottom and middle of the simulation box (in the {edim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are energy; see the "units"_units.html command for details. The scalar value calculated by this fix is "intensive". @@ -141,7 +141,7 @@ of this idea. When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange kinetic energy -bewteen solvent particles. +between solvent particles. [Related commands:] diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 8b9c0d3cb6..520d8b593a 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -116,10 +116,10 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative momentum transferred between the bottom and middle of the +cumulative momentum transferred between the bottom and middle of the simulation box (in the {pdim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are momentum = mass*velocity. The scalar value calculated by this fix is "intensive". @@ -147,7 +147,7 @@ See the "Maginn paper"_#Maginn for an example of using this algorithm in a computation of alcohol molecule properties. When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange momenta bewteen +in a background solvent, you may want to only exchange momenta between solvent particles. [Related commands:] diff --git a/doc/src/group.txt b/doc/src/group.txt index ab975af756..afa218c5a3 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -144,7 +144,7 @@ or exclude from a group. For example, these lines define a variable "eatom" that calculates the potential energy of each atom and includes it in the group if its -potential energy is above the threshhold value -3.0. +potential energy is above the threshold value -3.0. compute 1 all pe/atom compute 2 all reduce sum c_1 @@ -165,7 +165,7 @@ group command invokes it. Because the eatom variable computes the per-atom energy via the pe/atom compute, it will only be current if a run has been performed which evaluated pairwise energies, and the pe/atom compute was actually invoked during the run. Printing the -thermodyanmic info for compute 2 insures that this is the case, since +thermodynamic info for compute 2 insures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the "Variable Accuracy" section of the "variable"_variable.html doc page for more details on insuring that diff --git a/doc/src/if.txt b/doc/src/if.txt index aa93c73790..c678f4aa77 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -37,7 +37,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre [Description:] This command provides an if-then-else capability within an input -script. A Boolean expression is evaluted and the result is TRUE or +script. A Boolean expression is evaluated and the result is TRUE or FALSE. Note that as in the examples above, the expression can contain variables, as defined by the "variable"_variable.html command, which will be evaluated as part of the expression. Thus a user-defined diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index d1eca6d5d9..705b1cf742 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -36,7 +36,7 @@ j,k, and l. The "ring" improper style implements the improper potential introduced by Destree et al., in Equation (9) of "(Destree)"_#Destree. This potential does not affect small amplitude vibrations but is used in an -ad-hoc way to prevent the onset of accidentially large amplitude +ad-hoc way to prevent the onset of accidentally large amplitude fluctuations leading to the occurrence of a planar conformation of the three bonds i-j, j-k and j-l, an intermediate conformation toward the chiral inversion of a methine carbon. In the "Impropers" section of diff --git a/doc/src/info.txt b/doc/src/info.txt index 605dafa851..0b761ccc15 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -94,7 +94,7 @@ The {time} category prints the accumulated CPU and wall time for the process that writes output (usually MPI rank 0). The {configuration} command prints some information about the LAMMPS -version and architection and OS it is run on. Where supported, also +version and architecture and OS it is run on. Where supported, also information about the memory consumption provided by the OS is reported. diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 013e61965f..cb57863ad0 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -98,7 +98,7 @@ Coulombics. The {overlap} keyword can be used in conjunction with the {minorder} keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchangeed between +that occurs when values on the FFT grid are exchanged between processors. This communication is distinct from the communication inherent in the parallel FFTs themselves, and is required because processors interpolate charge and field values using grid point values @@ -122,7 +122,7 @@ neighbor processors. The {minorder} keyword limits how small the {order} setting can become. The minimum allowed value for PPPM is 2, which is the default. If {minorder} is set to the same value as {order} then no reduction is allowed, and LAMMPS will generate an -error if the grid communcation is non-nearest-neighbor and {overlap} +error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. @@ -284,7 +284,7 @@ of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal performance and accuracy in the results is obtained when these values are different. -The {disp/auto} option controlls whether the pppm/disp is allowed to +The {disp/auto} option controls whether the pppm/disp is allowed to generate PPPM parameters automatically. If set to {no}, parameters have to be specified using the {gewald/disp}, {mesh/disp}, {force/disp/real} or {force/disp/kspace} keywords, or diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 492d1d88e7..e523c91d41 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -131,7 +131,7 @@ reduce force aliasing errors and increase the accuracy of the method for a given mesh size. Or a coarser mesh can be used for the same target accuracy, which saves CPU time. However, there is a trade-off since FFTs on two meshes are now performed which increases the -compuation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, +computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, and "(Hockney)"_#Hockney for details of the method. For high relative accuracy, using staggered PPPM allows the mesh size @@ -174,7 +174,7 @@ using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your lo-level Makefile. This setting also changes some of the PPPM operations (e.g. mapping charge to mesh and interpolating electric fields to particles) to be performed in single precision. This option -can speed-up long-range calulations, particularly in parallel or on +can speed-up long-range calculations, particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag is discussed in "this section"_Section_start.html#start_2_4 of the manual. MSM does not currently support the -DFFT_SINGLE compiler switch. @@ -233,7 +233,7 @@ simulation cell. One way to handle this issue if you have a long simulation where the box size changes dramatically, is to break it into shorter simulations (multiple "run"_run.html commands). This works because the grid size is re-computed at the beginning of each -run. Another way to ensure the descired accuracy requirement is met +run. Another way to ensure the described accuracy requirement is met is to run a short simulation at the maximum expected tilt or length, note the required grid size, and then use the "kspace_modify"_kspace_modify.html {mesh} command to manually set the @@ -255,7 +255,7 @@ are estimated using equations 33 and 46 of "(Wang)"_#Wang. See the "kspace_modify"_kspace_modify.html command for additional options of the K-space solvers that can be set, including a {force} -option for setting an absoulte RMS error in forces, as opposed to a +option for setting an absolute RMS error in forces, as opposed to a relative RMS error. :line diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 2de23310b8..52701b3f54 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -48,7 +48,7 @@ soft"_pair_soft.html potential can be used to un-overlap atoms while running dynamics. Note that you can minimize some atoms in the system while holding the -coordiates of other atoms fixed by applying "fix +coordinates of other atoms fixed by applying "fix setforce"_fix_setforce.html to the other atoms. See a fuller discussion of using fixes while minimizing below. @@ -58,7 +58,7 @@ which atom coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search typically evaluates forces and energies several times to set new coordinates. Currently, a backtracking algorithm is used which may not be optimal -in terms of the number of force evaulations performed, but appears to +in terms of the number of force evaluations performed, but appears to be more robust than previous line searches we've tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). diff --git a/doc/src/package.txt b/doc/src/package.txt index de7e0f5c22..cfb663d4b1 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -166,7 +166,7 @@ neighbor list building is performed on the CPU. GPU neighbor list building currently cannot be used with a triclinic box. GPU neighbor list calculation currently cannot be used with "hybrid"_pair_hybrid.html pair styles. GPU neighbor lists are not -compatible with comannds that are not GPU-enabled. When a non-GPU +compatible with commands that are not GPU-enabled. When a non-GPU enabled command requires a neighbor list, it will also be built on the CPU. In these cases, it will typically be more efficient to only use CPU neighbor list builds. diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index c9dd31d57b..457a797d95 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -68,7 +68,7 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the -potentials directory of the LAMMPS distrbution, is an extended {setfl} +potentials directory of the LAMMPS distribution, is an extended {setfl} file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 08490c601a..27fb6c10fe 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -34,7 +34,7 @@ non-linear regression model. The method implements the recently proposed machine learning access to atomic forces as discussed extensively in the following publications - "(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise -of the method is to map the atomic enviornment numerically into a +of the method is to map the atomic environment numerically into a fingerprint, and use machine learning methods to create a mapping to the vectorial atomic forces. diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index 49c6c8db62..4e792754b8 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively. [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html shift diff --git a/doc/src/pair_body.txt b/doc/src/pair_body.txt index 622cc88f88..7899da832b 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body.txt @@ -59,7 +59,7 @@ computed and summed. If the distance is not within the cutoff, no interactions between the body and point particle are computed. The interaction between two sub-particles, or a sub-particle and point -particle, or betwee two point particles is computed as a Lennard-Jones +particle, or between two point particles is computed as a Lennard-Jones interaction, using the standard formula :c,image(Eqs/pair_lj.jpg) diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 0dbd1fc5dd..795d847fa6 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -78,8 +78,8 @@ levels of the recursive representations for both the sigma and the pi bond-orders. Bond-order terms can be understood in terms of molecular orbital hopping paths based upon the Cyrot-Lackmann theorem ("Pettifor_1"_#Pettifor_1). The sigma bond-order with a half-full -valence shell is used to interpolate the bond-order expressiont that -incorporated explicite valance band filling. This pi bond-order +valence shell is used to interpolate the bond-order expression that +incorporated explicit valance band filling. This pi bond-order expression also contains also contains a three-member ring term that allows implementation of an asymmetric density of states, which helps to either stabilize or destabilize close-packed structures. The pi diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index b3d5fdef27..c598225e35 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -127,7 +127,7 @@ summation method, described in "Wolf"_#Wolf, given by: :c,image(Eqs/pair_coul_wolf.jpg) where {alpha} is the damping parameter, and erc() and erfc() are -error-fuction and complementary error-function terms. This potential +error-function and complementary error-function terms. This potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, pairwise {1/r} summation. With a manipulation of adding and substracting a self term (for i = j) to the @@ -135,7 +135,7 @@ first and second term on the right-hand-side, respectively, and a small enough {alpha} damping parameter, the second term shrinks and the potential becomes a rapidly-converging real-space summation. With a long enough cutoff and small enough alpha parameter, the energy and -forces calcluated by the Wolf summation method approach those of the +forces calculated by the Wolf summation method approach those of the Ewald sum. So it is a means of getting effective long-range interactions with a short-range potential. diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index 498e1873df..9bd3b51c80 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -48,7 +48,7 @@ Examples of the use of this type of Coulomb interaction include implicit solvent simulations of salt ions "(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi. Note that this potential is only reasonable for implicit solvent simulations -and in combiantion with coul/cut or coul/long. It is also usually combined +and in combination with coul/cut or coul/long. It is also usually combined with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi. The following coefficients must be defined for each pair of atom diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 7072b1702d..62a5faffed 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -88,7 +88,7 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), where T is the temperature set by the "pair_style"_pair_style.html command so it does not need to be specified. -For style {dpd/tstat}, the coefficiencts defined for each pair of +For style {dpd/tstat}, the coefficients defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command is the same, except that A is not included. diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index ed09ce4d99..4d3c2b2dea 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -273,7 +273,7 @@ style. However the DYNAMO {setfl} file must has two lines added to it, at the end of the file: line 1: Comment line (ignored) -line 2: N Coefficient0 Coefficient1 ... CoeffincientN :ul +line 2: N Coefficient0 Coefficient1 ... CoefficientN :ul The last line begins with the degree {N} of the polynomial function {h(x)} that modifies the cross interaction between A and B elements. diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 47078f9a8f..8744d6d93e 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -107,7 +107,7 @@ This can be used when an {eim} potential is used as part of the that will be used with other potentials. The ffield.eim file in the {potentials} directory of the LAMMPS -distribution is formated as follows: +distribution is formatted as follows: Lines starting with # are comments and are ignored by LAMMPS. Lines starting with "global:" include three global values. The first value diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index b3c9b5b5d5..f83f37657f 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -107,7 +107,7 @@ hydrogen types to be assigned to the same donor/acceptor type pair. For other pair_styles, if the pair_coeff command is re-used for the same I.J type pair, the settings for that type pair are overwritten. For the hydrogen bond potentials this is not the case; the settings -are cummulative. This means the only way to turn off a previous +are cumulative. This means the only way to turn off a previous setting, is to re-use the pair_style command and start over. For the {hbond/dreiding/lj} style the list of coefficients is as diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 47451cf14a..b7e46b9566 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -189,7 +189,7 @@ potentials. Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise -interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4 +interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the "special_bonds"_special_bonds.html command. Different weights can be assigned to different pair hybrid sub-styles via the "pair_modify diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 04d8d23dba..5a623e5ece 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -46,7 +46,7 @@ model. You should get an error or warning message from either LAMMPS or KIM if there is an incompatibility. The argument {printflag} is optional. If it is set to a non-zero -value then a KIM dsecriptor file is printed when KIM is invoked. This +value then a KIM descriptor file is printed when KIM is invoked. This can be useful for debugging. The default is to not print this file. Only a single pair_coeff command is used with the {kim} style which diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index bb1146b64e..44cfeb48e9 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -39,7 +39,7 @@ function of the line segment length and the specified sub-particle size for that particle type. If a line segment has a length L and is of type I, then the number of spheres N that represent the segment is calculated as N = L/sizeI, rounded up to an integer value. Thus if L -is not evenly divisibly by sizeI, N is incremented to include one +is not evenly divisible by sizeI, N is incremented to include one extra sphere. The centers of the spheres are spaced equally along the line segment. Imagine N+1 equally-space points, which include the 2 end points of the segment. The sphere centers are halfway between @@ -48,7 +48,7 @@ each pair of points. The LJ interaction between 2 spheres on different line segments (or a sphere on a line segment and a point particles) is computed with sub-particle epsilon, sigma, and cutoff values that are set by the -pair_coeff command, as described below. If the distance bewteen the 2 +pair_coeff command, as described below. If the distance between the 2 spheres is greater than the sub-particle cutoff, there is no interaction. This means that some pairs of sub-particles on 2 line segments may interact, but others may not. @@ -90,7 +90,7 @@ The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for line particles of type I and type J. They are used to define the N sub-particles per segment as described above. These coefficients are actually stored on a per-type basis. Thus if there are multiple -pair_coeff commmands that involve type I, as either the first or +pair_coeff commands that involve type I, as either the first or second atom type, you should use consistent values for sizeI or sizeJ in all of them. If you do not do this, the last value specified for sizeI will apply to all segments of type I. If typeI or typeJ refers @@ -112,7 +112,7 @@ cutoff is used. [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 784f1f7f52..95aa58ed37 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -106,7 +106,7 @@ pair_coeff 1 1 1.0 9.5 :pre The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones and Coulomb potential modified by a soft core, in order to avoid singularities during free energy calculations when sites are created -or anihilated "(Beutler)"_#Beutler, +or annihilated "(Beutler)"_#Beutler, :c,image(Eqs/pair_lj_soft.jpg) @@ -124,7 +124,7 @@ pair potentiel is identical to a Lennard-Jones term or a Coulomb term or a combination of both. When lambda = 0 the interactions are deactivated. The transition between these two extrema is smoothed by a soft repulsive core in order to avoid singularities in potential -energy and forces when sites are created or anihilated and can overlap +energy and forces when sites are created or annihilated and can overlap "(Beutler)"_#Beutler. The paratemers n, alpha_LJ and alpha_C are set in the @@ -192,7 +192,7 @@ in several water models). NOTES: When using the core-softed Coulomb potentials with long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free energy calculation in which sites holding electrostatic charges are -being created or anihilated (using "fix adapt/fep"_fix_adapt_fep.html +being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html) it is important to adapt both the lambda activation parameter (from 0 to 1, or the reverse) and the value of the charge (from 0 to its final value, or the reverse). This diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index ba46a135a2..08e53cb38c 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -140,5 +140,5 @@ for more info. :link(Lenosky) [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modelling Simulation Materials Science Enginerring, 8, 825 +Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt index fec00ed44c..ad602db9f1 100644 --- a/doc/src/pair_mie.txt +++ b/doc/src/pair_mie.txt @@ -57,7 +57,7 @@ cutoff specified in the pair_style command is used. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the mie/cut pair styles can be mixed. -If not explicity defined, both the repulsive and attractive gamma +If not explicitly defined, both the repulsive and attractive gamma exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is {geometric}. See the "pair_modify" command for details. diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 73bc1a314f..c5e3a3c399 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -80,7 +80,7 @@ the {morse} and {morse/smooth/linear} styles. The {morse/soft} variant is similar to the {lj/cut/soft} pair style in that it modifies the potential at short range to have a soft core. This helps to avoid singularities during free energy calculation in -which sites are created or anihilated. The formula differs from that +which sites are created or annihilated. The formula differs from that of {lj/cut/soft}, and is instead given by: :c,image(Eqs/pair_morse_soft.jpg) diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index f404fa4181..53737d2274 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -68,7 +68,7 @@ A12 specifies the energy prefactor which depends on the types of the two interacting particles. For ellipsoid/ellipsoid interactions, the interaction is computed by -the formulas in the supplementary docuement referenced above. A12 is +the formulas in the supplementary document referenced above. A12 is the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ units: @@ -79,7 +79,7 @@ composing the ellipsoids and epsilon_LJ determines the interaction strength of the spherical particles. For ellipsoid/LJ sphere interactions, the interaction is also computed -by the formulas in the supplementary docuement referenced above. A12 +by the formulas in the supplementary document referenced above. A12 has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for details): diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index c70af68b30..714188de32 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -36,7 +36,7 @@ atoms. This interactions depend on interatomic distance The parameters appearing in the upper expressions are set in the ffield.SMTBQ.Syst file where Syst corresponds to the selected system -(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +(e.g. field.SMTBQ.Al2O3). Examples for TiO2, Al2O3 are provided. A single pair_coeff command is used with the SMTBQ styles which provides the path to the potential file with parameters for needed elements. These are mapped to LAMMPS diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt index d25debe91b..2387056a1b 100644 --- a/doc/src/pair_sph_heatconduction.txt +++ b/doc/src/pair_sph_heatconduction.txt @@ -20,7 +20,7 @@ pair_coeff * * 1.0 2.4 :pre [Description:] The sph/heatconduction style computes heat transport between SPH particles. -The transport model is the diffusion euqation for the internal energy. +The transport model is the diffusion equation for the internal energy. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index a951cccbc3..c1eff12cbf 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -86,7 +86,7 @@ the beginning of a run. This means you must specify the number of types in your system accordingly; usually to be one larger than what would normally be the case, e.g. via the "create_box"_create_box.html or by changing the header in your "data file"_read_data.html. The -ficitious "bond particles" are inserted at the beginning of the run, +fictitious "bond particles" are inserted at the beginning of the run, and serve as placeholders that define the position of the bonds. This allows neighbor lists to be constructed and pairwise interactions to be computed in almost the same way as is done for actual particles. diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index 6504edb2a5..fa694f2177 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -180,7 +180,7 @@ NOTE: If you use "R" or "RSQ", the tabulated distance values in the file are effectively ignored, and replaced by new values as described in the previous paragraph. If the distance value in the table is not very close to the new value (i.e. round-off difference), then you will -be assingning energy/force values to a different distance, which is +be assigning energy/force values to a different distance, which is probably not what you want. LAMMPS will warn if this is occurring. If used, the parameter "BITMAP" is also followed by 2 values {rlo} and diff --git a/doc/src/partition.txt b/doc/src/partition.txt index ccef359050..9c1d560c83 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -39,7 +39,7 @@ such a variable is used in a "jump"_jump.html command. The "partition" command is another mechanism for having as input script operate differently on different partitions. It is basically a -prefix on any LAMMPS command. The commmand will only be invoked on +prefix on any LAMMPS command. The command will only be invoked on the partition(s) specified by the {style} and {N} arguments. If the {style} is {yes}, the command will be invoked on any partition diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 1ad66ee441..607c367afd 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -133,7 +133,7 @@ event. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -PRD commmand, which is the "compute +PRD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -230,7 +230,7 @@ files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For the PRD command, these contain the thermodynamic output for each replica. You will see short runs and minimizations corresponding to the dynamics and quench operations of the loop listed above. The -timestep will be reset aprpopriately depending on whether the +timestep will be reset appropriately depending on whether the operation advances time or not. After the PRD command completes, timing statistics for the PRD run are diff --git a/doc/src/processors.txt b/doc/src/processors.txt index adf2a0920f..854d41ba49 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -179,7 +179,7 @@ The first non-blank, non-comment line should have Px Py Py :pre These must be compatible with the total number of processors -and the Px, Py, Pz settings of the processors commmand. +and the Px, Py, Pz settings of the processors command. This line should be immediately followed by P = Px*Py*Pz lines of the form: @@ -244,7 +244,7 @@ The {part} keyword affects the factorization of P into Px,Py,Pz. It can be useful when running in multi-partition mode, e.g. with the "run_style verlet/split"_run_style.html command. It specifies a -dependency bewteen a sending partition {Psend} and a receiving +dependency between a sending partition {Psend} and a receiving partition {Precv} which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of {Psend} and {Precv} must be integers from 1 to Np, where Np is the number of diff --git a/doc/src/python.txt b/doc/src/python.txt index 7da69a0319..db379d425f 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -143,7 +143,7 @@ numeric or string value, as specified by the {format} keyword. As explained on the "variable"_variable.html doc page, the definition of a python-style variable associates a Python function name with the variable. This must match the {func} setting for this command. For -exampe these two commands would be self-consistent: +example these two commands would be self-consistent: variable foo python myMultiply python myMultiply return v_foo format f file funcs.py :pre @@ -356,7 +356,7 @@ python loop invoke :pre This has the effect of looping over a series of 10 short runs (10 timesteps each) where the pair style cutoff is increased from a value of 1.0 in distance units, in increments of 0.1. The looping stops -when the per-atom potential energy falls below a threshhold of -4.0 in +when the per-atom potential energy falls below a threshold of -4.0 in energy units. More generally, Python can be used to implement a loop with complex logic, much more so than can be created using the LAMMPS "jump"_jump.html and "if"_if.html commands. @@ -384,7 +384,7 @@ file() functions, so long as the command would work if it were executed in the LAMMPS input script directly at the same point. However, a Python function can also be invoked during a run, whenever -an associated LAMMPS variable it is assigned to is evaluted. If the +an associated LAMMPS variable it is assigned to is evaluated. If the variable is an input argument to another LAMMPS command (e.g. "fix setforce"_fix_setforce.html), then the Python function will be invoked inside the class for that command, in one of its methods that is diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 9ddc9d8921..b860fef848 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -180,7 +180,7 @@ used appropriately when each data file is read, the values in those sections will be stored correctly in the larger data structures allocated by the use of the {extra} keywords. E.g. the substrate file can list mass and pair coefficients for type 1 silicon atoms. The -water file can list mass and pair coeffcients for type 1 and type 2 +water file can list mass and pair coefficients for type 1 and type 2 hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords will store those mass and pair coefficient values appropriately in data structures that allow for 3 atom types (Si, H, O). Of course, diff --git a/doc/src/region.txt b/doc/src/region.txt index c4798a035b..7b5c9e36d4 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -283,7 +283,7 @@ velocity: variable dx equal ramp(0,10) region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre -Note that the initial displacemet is 0.0, though that is not required. +Note that the initial displacement is 0.0, though that is not required. Either of these variables would "wiggle" the region back and forth in the y direction: diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 2e7153e38c..291558e0e5 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -53,7 +53,7 @@ top of each other. NOTE: You cannot use the replicate command on a system which has a molecule that spans the box and is bonded to itself across a periodic -boundary, so that the molecule is efffectively a loop. A simple +boundary, so that the molecule is effectively a loop. A simple example would be a linear polymer chain that spans the simulation box and bonds back to itself across the periodic boundary. More realistic examples would be a CNT (meant to be an infinitely long CNT) or a diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 2dafabebb5..f487de2831 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -112,16 +112,16 @@ partition yes 1 processors 3 4 5 partition yes 2 processors 3 1 5 :pre When you run in 2-partition mode with the {verlet/split} style, the -thermodyanmic data for the entire simulation will be output to the log +thermodynamic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and screen.0 by default; see the "-plog and -pscreen command-line switches"_Section_start.html#start_7 to change this. The log and screen file for the 2nd partition will not contain thermodynamic -output beyone the 1st timestep of the run. +output beyond the 1st timestep of the run. See "Section 5"_Section_accelerate.html of the manual for performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignemnt of +style. One important performance consideration is the assignment of logical processors in the 2 partitions to the physical cores of a parallel machine. The "processors"_processors.html command has options to support this, and strategies are discussed in diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 70c6a3031b..127719cdb5 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -91,7 +91,7 @@ a disabled suffix is turned back on. The use of these 2 commands lets your input script use a standard LAMMPS style (i.e. a non-accelerated variant), which can be useful for testing or benchmarking purposes. Of course this is also possible by not using any suffix commands, and -explictly appending or not appending the suffix to the relevant +explicitly appending or not appending the suffix to the relevant commands in your input script. NOTE: The default "run_style"_run_style.html verlet is invoked prior to diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 5b0f5a006c..04c7d708f6 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -130,7 +130,7 @@ transition event. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -TAD commmand, which is the "compute +TAD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -144,7 +144,7 @@ NEB is determined by the {neb_style} keyword and must be a damped dynamics minimizer. The tolerances and limits for each NEB calculation can be set by the {neb} keyword. As discussed on the "neb"_neb.html, it is often advantageous to use a larger timestep for -NEB than for normal dyanmics. Since the size of the timestep set by +NEB than for normal dynamics. Since the size of the timestep set by the "timestep"_timestep.html command is used by TAD for performing dynamics, there is a {neb_step} keyword which can be used to set a larger timestep for each NEB calculation if desired. @@ -258,7 +258,7 @@ number of replicas or processors. Note that within a single state, the dynamics will typically temporarily continue beyond the event that is ultimately chosen, until -the stopping criterionis satisfied. When the event is eventually +the stopping criterion is satisfied. When the event is eventually executed, the timestep counter is reset to the value when the event was detected. Similarly, after each quench and NEB minimization, the timestep counter is reset to the value at the start of the diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 6cdb8a3cc8..37b58618a6 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -226,7 +226,7 @@ simulation time, also in time "units"_units.html, which is simply not been reset. If the timestep has changed (e.g. via "fix dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via the "reset_timestep" command), then the simulation time is effectively -a cummulative value up to the current point. +a cumulative value up to the current point. The {cpu} keyword is elapsed CPU seconds since the beginning of this run. The {tpcpu} and {spcpu} keywords are measures of how fast your @@ -289,7 +289,7 @@ The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See "this section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic periodic cells, including a precise defintion +description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, {lz}, {yz}, {xz}, {xy}. diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 358ec75a53..c148a9dce1 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -52,7 +52,7 @@ procsessors. The {full} setting adds information about CPU utilization and thread utilization, when multi-threading is enabled. With the {sync} setting, all MPI tasks are synchronized at each timer -call which measures load imbalance for each section more accuractly, +call which measures load imbalance for each section more accurately, though it can also slow down the simulation by prohibiting overlapping independent computations on different MPI ranks Using the {nosync} setting (which is the default) turns this synchronization off. diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index c2f4a16207..a350521f6c 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -75,7 +75,7 @@ The motion of of the Drude particles can be calculated by minimizing the energy of the induced dipoles at each timestep, by an interative, self-consistent procedure. The Drude particles can be massless and therefore do not contribute to the kinetic energy. However, the -relaxed method is computationall slow. An extended-lagrangian method +relaxed method is computational slow. An extended-lagrangian method can be used to calculate the positions of the Drude particles, but this requires them to have mass. It is important in this case to decouple the degrees of freedom associated with the Drude oscillators @@ -270,7 +270,7 @@ be stable, for example if the atomic polarizability is too high for instance, a DP can escape from its DC and be captured by another DC, which makes the force and energy diverge and the simulation crash. Even without reaching this extreme case, the correlation -between nearby dipoles on the same molecule may be exagerated. Often, +between nearby dipoles on the same molecule may be exaggerated. Often, special bond relations prevent bonded neighboring atoms to see the charge of each other's DP, so that the problem does not always appear. It is possible to use screened dipole dipole interactions by using the diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index 6966bb90b9..5d3491782e 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -328,7 +328,7 @@ IPyLammps Examples :h2 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this directory and navigate to one of them. If you compiled and installed -a LAMMPS shared library with execeptions, PNG, JPEG and FFMPEG support +a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. Validating a dihedral potential :h3 diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 29d50a2b8e..a46030b162 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -781,7 +781,7 @@ is for a vector-style variable where "name" is replaced by the name of the variable. These functions operate on a global vector of inputs and reduce it to -a single scalar value. This is analagous to the operation of the +a single scalar value. This is analogous to the operation of the "compute reduce"_compute_reduce.html command, which performs similar operations on per-atom and local vectors. diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index ae32a94e84..6e99d75460 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -53,7 +53,7 @@ support optional arguments and thus LAMMPS needs to be able to cleanly separate the two sets of args. Note that if the specified filename uses wildcard characters "*" or -"%", as supported by the "dump"_dump.html commmand, they will operate +"%", as supported by the "dump"_dump.html command, they will operate in the same fashion to create the new filename(s). Normally, "dump image"_dump_image.html files require a filename with a "*" character for the timestep. That is not the case for the write_dump command; no