void lammps_open(int, char **, MPI_Comm, void **); void lammps_close(void *); void lammps_file(void *, char *); -char *lammps_command(doivd *, char *); +char *lammps_command(void *, char *);
The functions contain C++ code you could write in a C++ application that was invoking LAMMPS directly. Note that LAMMPS classes are -defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them +defined within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ application.
Two of the routines in library.cpp are of particular note. The lammps_open() function initiates LAMMPS and takes an MPI communicator as an argument. It returns a pointer to a LAMMPS "object". As with -C++, the lammps_open() function can be called mutliple times, to +C++, the lammps_open() function can be called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This @@ -604,7 +604,7 @@ create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized by the xmovie program, included with the LAMMPS package. This produces simple, fast 2d projections of 3d -systems, and can be useful for rapid debugging of simulation geoemtry +systems, and can be useful for rapid debugging of simulation geometry and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert @@ -613,7 +613,7 @@ native LAMMPS dump files to other formats. See the the ch2lmp tool, which contains a lammps2pdb Perl script which converts LAMMPS dump files into PDB files. The second is the lmp2arc tool which -converts LAMMPS dump files into Accelrys's Insight MD program files. +converts LAMMPS dump files into Accelrys' Insight MD program files. The third is the lmp2cfg tool which converts LAMMPS dump files into CFG files which can be read into the AtomEye visualizer. @@ -723,9 +723,9 @@ the xy, xz, and yz tilt factors as a simulation runs.
Non-equilibrium molecular dynamics or NEMD simulations are typically used to measure a fluid's rheological properties such as viscosity. In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceeding Howto section). +non-orthogonal simulation box (see the preceding Howto section).
-A shear strain can be applied to the simuaation box at a desired +
A shear strain can be applied to the simulation box at a desired strain rate by using the fix deform command. The fix nvt/sllod command can be used to thermostat the sheared fluid and integrate the SLLOD equations of motion for the @@ -765,7 +765,7 @@ The pair_style gayberne command can be used t define a Gay-Berne (GB) potential for how ellipsoidal particles interact with each other and with spherical particles. The GB potential is like a Lennard-Jones (LJ) potential, generalized for -orientiation-dependent interactions. +orientation-dependent interactions.
The orientation of ellipsoidal particles is stored as a quaternion. See the set command for a brief explanation of quaternions @@ -821,9 +821,9 @@ generate values that can be output with these commands.
The frequency and format of thermodynamic output is set by the thermo, thermo_style, and thermo_modify commands. The -thermo_style command also specifies what values are +thermo_style command also specifies what values are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three addtional kinds of keywords can also +(e.g. press, etotal, etc). Three additional kinds of keywords can also be specified (c_ID, f_ID, v_name), where a compute or fix or variable provides the value to be output. Each of these are described in turn. @@ -948,7 +948,7 @@ options for how it performs time averaging. The per-layer values it produces can be used in two ways. First, they can be written directly to a file. Note that the averaging parameters can be specified in such a way that time averaging is not done, in which case this is a -convenient means of simply outputting desired quanitities (summed over +convenient means of simply outputting desired quantities (summed over atoms within a 1d layer) directly to a separate file. Like other fixes that produce global quantities, the results of this fix can also be used as input by any command that accesses global quantities, diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index c075d47e57..416ed620f3 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -552,17 +552,17 @@ functions: void lammps_open(int, char **, MPI_Comm, void **); void lammps_close(void *); void lammps_file(void *, char *); -char *lammps_command(doivd *, char *); :pre +char *lammps_command(void *, char *); :pre The functions contain C++ code you could write in a C++ application that was invoking LAMMPS directly. Note that LAMMPS classes are -defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them +defined within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ application. Two of the routines in library.cpp are of particular note. The lammps_open() function initiates LAMMPS and takes an MPI communicator as an argument. It returns a pointer to a LAMMPS "object". As with -C++, the lammps_open() function can be called mutliple times, to +C++, the lammps_open() function can be called multiple times, to create multiple instances of LAMMPS. LAMMPS will run on the set of processors in the communicator. This @@ -600,7 +600,7 @@ create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized by the "xmovie"_Section_tools.html#xmovie program, included with the LAMMPS package. This produces simple, fast 2d projections of 3d -systems, and can be useful for rapid debugging of simulation geoemtry +systems, and can be useful for rapid debugging of simulation geometry and atom trajectories. Several programs included with LAMMPS as auxiliary tools can convert @@ -609,7 +609,7 @@ native LAMMPS dump files to other formats. See the the "ch2lmp tool"_Section_tools.html#charmm, which contains a lammps2pdb Perl script which converts LAMMPS dump files into PDB files. The second is the "lmp2arc tool"_Section_tools.html#arc which -converts LAMMPS dump files into Accelrys's Insight MD program files. +converts LAMMPS dump files into Accelrys' Insight MD program files. The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts LAMMPS dump files into CFG files which can be read into the "AtomEye"_atomeye visualizer. @@ -716,9 +716,9 @@ Another use of non-orthogonal boxes is to perform non-equilibrium MD Non-equilibrium molecular dynamics or NEMD simulations are typically used to measure a fluid's rheological properties such as viscosity. In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceeding Howto section). +non-orthogonal simulation box (see the preceding Howto section). -A shear strain can be applied to the simuaation box at a desired +A shear strain can be applied to the simulation box at a desired strain rate by using the "fix deform"_fix_deform.html command. The "fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat the sheared fluid and integrate the SLLOD equations of motion for the @@ -758,7 +758,7 @@ The "pair_style gayberne"_pair_gayberne.html command can be used to define a Gay-Berne (GB) potential for how ellipsoidal particles interact with each other and with spherical particles. The GB potential is like a Lennard-Jones (LJ) potential, generalized for -orientiation-dependent interactions. +orientation-dependent interactions. The orientation of ellipsoidal particles is stored as a quaternion. See the "set"_set.html command for a brief explanation of quaternions @@ -814,9 +814,9 @@ Thermodynamic output :h5 The frequency and format of thermodynamic output is set by the "thermo"_thermo.html, "thermo_style"_thermo_style.html, and "thermo_modify"_thermo_modify.html commands. The -"thermo_style"_themo_style.html command also specifies what values are +"thermo_style"_thermo_style.html command also specifies what values are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three addtional kinds of keywords can also +(e.g. press, etotal, etc). Three additional kinds of keywords can also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or "fix"_fix.html or "variable"_variable.html provides the value to be output. Each of these are described in turn. @@ -941,7 +941,7 @@ options for how it performs time averaging. The per-layer values it produces can be used in two ways. First, they can be written directly to a file. Note that the averaging parameters can be specified in such a way that time averaging is not done, in which case this is a -convenient means of simply outputting desired quanitities (summed over +convenient means of simply outputting desired quantities (summed over atoms within a 1d layer) directly to a separate file. Like other fixes that produce global quantities, the results of this fix can also be used as input by any command that accesses global quantities, diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 827a9031d6..b138989dbb 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -180,7 +180,7 @@ commands)
-Classes that compute long-range Coulombic interactions via K-space -represenations (Ewald, PPPM) are derived from the KSpace class. New +representations (Ewald, PPPM) are derived from the KSpace class. New styles can be created to add new K-space options to LAMMPS.
Ewald.cpp is an example of computing K-space interactions. @@ -469,7 +469,7 @@ thermodynamic info is output. See the quantities.
The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requies defining a new list of keywords. +Adding a new style thus only requires defining a new list of keywords. Search for the word "customize" with references to "thermo style" in thermo.cpp to see the two locations where code will need to be added.
@@ -503,7 +503,7 @@ group functions = mass(group), xcm(group,x), ... atom values = x123, y3, vx34, ... compute values = c_mytemp0, c_thermo_press3, ... -Adding keywords for the thermo_style custom command +
Adding keywords for the thermo_style custom command (which can then be accessed by variables) was discussed here on this page.
@@ -590,7 +590,7 @@ should indicate that your feature is only available if LAMMPS is built with the "user-foo" package. See other user package files for an example of how to do this. -Note that the more clear and self-exaplantory you make your doc and +
Note that the more clear and self-explanatory you make your doc and README files, the more likely it is that users will try out your new feature.
diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index b56580024f..3b7be7822e 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -85,7 +85,7 @@ in the LAMMPS distribution. "Bond, angle, dihedral, improper potentials"_#bond "Compute styles"_#compute "Dump styles"_#dump -"Dump custom output optoins"_#dump +"Dump custom output options"_#dump "Fix styles"_#fix which include integrators, \ temperature and pressure control, force constraints, \ boundary conditions, diagnostic output, etc @@ -358,7 +358,7 @@ needed. Kspace computations :link(kspace),h4 Classes that compute long-range Coulombic interactions via K-space -represenations (Ewald, PPPM) are derived from the KSpace class. New +representations (Ewald, PPPM) are derived from the KSpace class. New styles can be created to add new K-space options to LAMMPS. Ewald.cpp is an example of computing K-space interactions. @@ -446,7 +446,7 @@ thermodynamic info is output. See the quantities. The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requies defining a new list of keywords. +Adding a new style thus only requires defining a new list of keywords. Search for the word "customize" with references to "thermo style" in thermo.cpp to see the two locations where code will need to be added. @@ -480,7 +480,7 @@ group functions = mass(group), xcm(group,x), ... atom values = x[123], y[3], vx[34], ... compute values = c_mytemp[0], c_thermo_press[3], ... -Adding keywords for the "thermo_style custom"_themo_style.html command +Adding keywords for the "thermo_style custom"_thermo_style.html command (which can then be accessed by variables) was discussed "here"_Section_modify.html#thermo on this page. @@ -567,7 +567,7 @@ should indicate that your feature is only available if LAMMPS is built with the "user-foo" package. See other user package files for an example of how to do this. -Note that the more clear and self-exaplantory you make your doc and +Note that the more clear and self-explanatory you make your doc and README files, the more likely it is that users will try out your new feature. diff --git a/doc/Section_start.html b/doc/Section_start.html index 17fd7a8984..009450b408 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -191,7 +191,7 @@ support the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting is the default. If you compile with -DLAMMPS_XDR, the build will -include XDR compatability files for doing particle dumps in XTC +include XDR compatibility files for doing particle dumps in XTC format. This is only necessary if your platform does have its own XDR files available. See the Restrictions section of the dump command for details. diff --git a/doc/Section_start.txt b/doc/Section_start.txt index dbeab9469c..da31de42fd 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -186,7 +186,7 @@ support the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting is the default. If you compile with -DLAMMPS_XDR, the build will -include XDR compatability files for doing particle dumps in XTC +include XDR compatibility files for doing particle dumps in XTC format. This is only necessary if your platform does have its own XDR files available. See the Restrictions section of the "dump"_dump.html command for details. diff --git a/doc/Section_tools.html b/doc/Section_tools.html index 41b52135f7..db0638824a 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -153,8 +153,8 @@ produce are in the potentials directory.The lmp2arc sub-directory contains a tool for converting LAMMPS output -files to the format for Accelrys's Insight MD code (formerly -MSI/Biosysm and its Discover MD code). See the README file for more +files to the format for Accelrys' Insight MD code (formerly +MSI/Biosym and its Discover MD code). See the README file for more information.
This tool was written by John Carpenter (Cray), Michael Peachey @@ -228,7 +228,7 @@ definition file. This tool was used to create the system for the
The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from Accelrys's Insight MD code (formerly MSI/Biosysm and +data files from Accelrys' Insight MD code (formerly MSI/Biosym and its Discover MD code). See the README file for more information.
This tool was written by John Carpenter (Cray), Michael Peachey diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 6500b630e7..17b84ddba4 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -149,8 +149,8 @@ The source files and potentials were provided by Gerolf Ziegenhain lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output -files to the format for Accelrys's Insight MD code (formerly -MSI/Biosysm and its Discover MD code). See the README file for more +files to the format for Accelrys' Insight MD code (formerly +MSI/Biosym and its Discover MD code). See the README file for more information. This tool was written by John Carpenter (Cray), Michael Peachey @@ -224,7 +224,7 @@ definition file. This tool was used to create the system for the msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from Accelrys's Insight MD code (formerly MSI/Biosysm and +data files from Accelrys' Insight MD code (formerly MSI/Biosym and its Discover MD code). See the README file for more information. This tool was written by John Carpenter (Cray), Michael Peachey diff --git a/doc/angle_coeff.html b/doc/angle_coeff.html index 81eaba0e60..db0e75636c 100644 --- a/doc/angle_coeff.html +++ b/doc/angle_coeff.html @@ -15,7 +15,7 @@
angle_coeff N args-
Examples: @@ -35,9 +35,9 @@ Angle coefficients can also be set in the data file read by the be used, as in the 1st example above. Or a wild-card asterik can be used to set the coefficients for multiple angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, -then an asterik with no numeric values means all types from 1 to N. A -leading asterik means all types from 1 to n (inclusive). A trailing -asterik means all types from n to N (inclusive). A middle asterisk +then an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).
Note that using an angle_coeff command can override a previous setting diff --git a/doc/angle_coeff.txt b/doc/angle_coeff.txt index 1d6edb6597..0eae25f22e 100644 --- a/doc/angle_coeff.txt +++ b/doc/angle_coeff.txt @@ -12,7 +12,7 @@ angle_coeff command :h3 angle_coeff N args :pre -N = angle type (see asterik form below) +N = angle type (see asterisk form below) args = coefficients for one or more angle types :ul [Examples:] @@ -32,9 +32,9 @@ N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterik can be used to set the coefficients for multiple angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, -then an asterik with no numeric values means all types from 1 to N. A -leading asterik means all types from 1 to n (inclusive). A trailing -asterik means all types from n to N (inclusive). A middle asterisk +then an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that using an angle_coeff command can override a previous setting diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html index b5c5fcc793..cffa22d665 100644 --- a/doc/bond_quartic.html +++ b/doc/bond_quartic.html @@ -51,7 +51,7 @@ you will need to choose them carefully so they form a suitable bond potential.
Rc is the cutoff length at which the bond potential goes smoothly to a -local maximium. If a bond length ever becomes > Rc, LAMMPS "breaks" +local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" the bond, which means two things. First, the bond potential is turned off by setting its type to 0, and is no longer computed. Second, a pairwise interaction between the two atoms is turned on, since they diff --git a/doc/bond_quartic.txt b/doc/bond_quartic.txt index fc7afa2b9e..887abc6afc 100644 --- a/doc/bond_quartic.txt +++ b/doc/bond_quartic.txt @@ -48,7 +48,7 @@ you will need to choose them carefully so they form a suitable bond potential. Rc is the cutoff length at which the bond potential goes smoothly to a -local maximium. If a bond length ever becomes > Rc, LAMMPS "breaks" +local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" the bond, which means two things. First, the bond potential is turned off by setting its type to 0, and is no longer computed. Second, a pairwise interaction between the two atoms is turned on, since they diff --git a/doc/change_box.html b/doc/change_box.html index 0ec0bd2a6c..0cc459a9f4 100644 --- a/doc/change_box.html +++ b/doc/change_box.html @@ -52,7 +52,7 @@ orthogonal box. ave/spatial or fix deform be active. This is because these commands test whether the simulation box is orthogonal when they are first issued. Note that these -commmands can appear in your script before a change_box command is +commands can appear in your script before a change_box command is issued, so long as an undump or unfix command is also used to turn them off.
diff --git a/doc/change_box.txt b/doc/change_box.txt index fd07707f19..fc0ff37b2c 100644 --- a/doc/change_box.txt +++ b/doc/change_box.txt @@ -48,7 +48,7 @@ At the point in the input script when this command is issued, no ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be active. This is because these commands test whether the simulation box is orthogonal when they are first issued. Note that these -commmands can appear in your script before a change_box command is +commands can appear in your script before a change_box command is issued, so long as an "undump"_undump.html or "unfix"_unfix.html command is also used to turn them off. diff --git a/doc/compute_pe.html b/doc/compute_pe.html index c0c7f5413f..a48aa247ae 100644 --- a/doc/compute_pe.html +++ b/doc/compute_pe.html @@ -33,7 +33,7 @@ entire system of atoms. The specified group must be "all". See the energies. These per-atom values could be summed for a group of atoms via the compute reduce command. -The energy is calulated by the various pair, bond, etc potentials +
The energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are listed, then the potential energy is the sum of pair, bond, angle, dihedral, improper, and kspace (long-range) energy. If any extra keywords are listed, diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt index 71e37a5f06..fcb9c146e3 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -30,7 +30,7 @@ entire system of atoms. The specified group must be "all". See the energies. These per-atom values could be summed for a group of atoms via the "compute reduce"_compute_reduce.html command. -The energy is calulated by the various pair, bond, etc potentials +The energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are listed, then the potential energy is the sum of pair, bond, angle, dihedral, improper, and kspace (long-range) energy. If any extra keywords are listed, diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html index 66c4a8d6cc..d640320256 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -48,7 +48,7 @@ and long-range interactions. Fixes that impose constra virial term.
A 6-component pressure tensor is also calculated by this compute whose -componenents can be output by the thermo_style +components can be output by the thermo_style custom command or accessed by other compute and fix commands. The equation for the components of the tensor is the same as in above formula, except @@ -95,7 +95,7 @@ the simulation.
compute temp, compute stress/atom, -thermo_style, +thermo_style,
Default: none
diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index ea9ec60fa2..4b9ae520d2 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -45,7 +45,7 @@ and long-range interactions. "Fixes"_fix.html that impose constraints virial term. A 6-component pressure tensor is also calculated by this compute whose -componenents can be output by the "thermo_style +components can be output by the "thermo_style custom"_thermo_style.html command or accessed by other "compute"_compute.html and "fix"_fix.html commands. The equation for the components of the tensor is the same as in above formula, except @@ -92,6 +92,6 @@ the simulation. "compute temp"_compute_temp.html, "compute stress/atom"_compute_stress_atom.html, -"thermo_style"_themo_style.html, +"thermo_style"_thermo_style.html, [Default:] none diff --git a/doc/compute_temp_dipole.html b/doc/compute_temp_dipole.html index 216b83afa3..eed280d0fd 100644 --- a/doc/compute_temp_dipole.html +++ b/doc/compute_temp_dipole.html @@ -28,7 +28,7 @@ compute myTemp mobile temp/dipoleDefine a computation that calculates the temperature of a group of particles that include a point dipole. The computation is similar to compute_temp, however, additional degrees of -freedom are include to account for the rotational state of the +freedom are included to account for the rotational state of the particles. The associated kinetic energy includes a rotational term KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is the angular velocity. diff --git a/doc/compute_temp_dipole.txt b/doc/compute_temp_dipole.txt index 5a64eba47b..626015edc7 100755 --- a/doc/compute_temp_dipole.txt +++ b/doc/compute_temp_dipole.txt @@ -25,7 +25,7 @@ compute myTemp mobile temp/dipole :pre Define a computation that calculates the temperature of a group of particles that include a point dipole. The computation is similar to "compute_temp"_compute_temp.html, however, additional degrees of -freedom are include to account for the rotational state of the +freedom are included to account for the rotational state of the particles. The associated kinetic energy includes a rotational term KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is the angular velocity. diff --git a/doc/displace_box.html b/doc/displace_box.html index 8ca06c2f4b..d589e686c1 100644 --- a/doc/displace_box.html +++ b/doc/displace_box.html @@ -87,7 +87,7 @@ styles and values.
For style final, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. -See the discsussion of the units keyword below. +See the discussion of the units keyword below.
For style delta, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box @@ -134,7 +134,7 @@ units keyword below.
For style delta, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See -the discsussion of the units keyword below. +the discussion of the units keyword below.
All of these styles change the xy, xz, yz tilt factors. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half diff --git a/doc/displace_box.txt b/doc/displace_box.txt index 069c05c72e..263c53d0ae 100644 --- a/doc/displace_box.txt +++ b/doc/displace_box.txt @@ -79,7 +79,7 @@ styles and values. For style {final}, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. -See the discsussion of the units keyword below. +See the discussion of the units keyword below. For style {delta}, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box @@ -126,7 +126,7 @@ units keyword below. For style {delta}, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See -the discsussion of the units keyword below. +the discussion of the units keyword below. All of these styles change the xy, xz, yz tilt factors. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half diff --git a/doc/dump_modify.html b/doc/dump_modify.html index 2c183eb14d..6f5fcd7d6f 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -34,7 +34,7 @@ attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operation = "<" or "<=" or ">" or ">=" or "==" or "!=" value = numeric value to compare to - these 3 args can be replaced by the word "none" to turn off threshholding + these 3 args can be replaced by the word "none" to turn off thresholding @@ -105,15 +105,15 @@ shape, and it can be the "union" or "intersection" of a series of simpler regions.
The thresh keyword only applies to the dump custom style. -Multiple threshholds can be specified. Specifying "none" turns off -all threshhold criteria. If theshholds are specified, only atoms -whose attributes meet all the threshhold criteria are written to the +Multiple thresholds can be specified. Specifying "none" turns off +all threshold criteria. If thresholds are specified, only atoms +whose attributes meet all the threshold criteria are written to the dump file. The possible attributes that can be tested for are the same as those that can be specified in the dump custom command. Note that different attributes can be output by the dump -custom command than are used as threshhold criteria by the dump_modify +custom command than are used as threshold criteria by the dump_modify command. E.g. you can output the coordinates and stress of atoms -whose energy is above some threshhold. +whose energy is above some threshold.
Restrictions: none
diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index 1eb62faa08..4dcf1ad76f 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -28,7 +28,7 @@ keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {p attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operation = "<" or "<=" or ">" or ">=" or "==" or "!=" value = numeric value to compare to - these 3 args can be replaced by the word "none" to turn off threshholding + these 3 args can be replaced by the word "none" to turn off thresholding :pre :ule @@ -98,15 +98,15 @@ shape, and it can be the "union" or "intersection" of a series of simpler regions. The {thresh} keyword only applies to the dump {custom} style. -Multiple threshholds can be specified. Specifying "none" turns off -all threshhold criteria. If theshholds are specified, only atoms -whose attributes meet all the threshhold criteria are written to the +Multiple thresholds can be specified. Specifying "none" turns off +all threshold criteria. If thresholds are specified, only atoms +whose attributes meet all the threshold criteria are written to the dump file. The possible attributes that can be tested for are the same as those that can be specified in the "dump custom"_dump.html command. Note that different attributes can be output by the dump -custom command than are used as threshhold criteria by the dump_modify +custom command than are used as threshold criteria by the dump_modify command. E.g. you can output the coordinates and stress of atoms -whose energy is above some threshhold. +whose energy is above some threshold. [Restrictions:] none diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index 7c9e9b7c25..56aebd88d4 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -53,7 +53,7 @@ filename = file to write results to ave args = one or running or window M one = output 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 @@ -99,13 +99,13 @@ produce global quantities. timesteps the layer values will be generated in order to contribute to the average. The final averaged quantities are generated every Nfreq timesteps. The average is over Nrepeat quantities, computed -in the preceeding portion of the simulation every Nevery timesteps. +in the preceding portion of the simulation every Nevery timesteps. Nfreq must be a multiple of Nevery and Nevery must be non-zero even if Nrepeat is 1.For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similary for timesteps 190,192,194,196,198,200 on +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. @@ -117,7 +117,7 @@ where the layers are in a particular dim and have a thickness given by delta. Every Nfreq steps, when an averaging is being performed and the per-atom property is calculated for the first time, the number of layers and the layer boundaries are computed. Thus if the -simlation box changes size during a simulation, the number of layers +simulation box changes size during a simulation, the number of layers and their boundaries may also change. Layers are defined relative to a specified origin, which may be the lower/upper edge of the box (in dim) or its center point, or a specified coordinate value. Starting @@ -232,15 +232,15 @@ quantities. If the value of the units keyword is box or steps that were multiples of Nfreq, before they are accessed by another output command or written to a file.
-If the ave setting is one, then the layuer values produced on +
If the ave setting is one, then the layer values produced on timesteps that are multiples of Nfreq are independent of each other; they are output as-is without further averaging.
If the ave setting is running, then the layer values produced on timesteps that are multiples of Nfreq are summed and averaged in a -cummulative sense before being output. Each output layer value is +cumulative sense before being output. Each output layer value is thus the average of the layer value produced on that timestep with all -preceeding values for the same layer. This running average begins +preceding values for the same layer. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the unfix command, or re-defining the fix by re-specifying it. diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 1324cf08d2..12c54f7ca9 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -38,7 +38,7 @@ keyword = {norm} or {units} or {file} or {ave} :l filename = file to write results to {ave} args = {one} or {running} or {window M} one = output 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 :pre :ule @@ -83,13 +83,13 @@ The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what timesteps the layer values will be generated in order to contribute to the average. The final averaged quantities are generated every {Nfreq} timesteps. The average is over {Nrepeat} quantities, computed -in the preceeding portion of the simulation every {Nevery} timesteps. +in the preceding portion of the simulation every {Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similary for timesteps 190,192,194,196,198,200 on +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. @@ -101,7 +101,7 @@ where the layers are in a particular {dim} and have a thickness given by {delta}. Every Nfreq steps, when an averaging is being performed and the per-atom property is calculated for the first time, the number of layers and the layer boundaries are computed. Thus if the -simlation box changes size during a simulation, the number of layers +simulation box changes size during a simulation, the number of layers and their boundaries may also change. Layers are defined relative to a specified {origin}, which may be the lower/upper edge of the box (in {dim}) or its center point, or a specified coordinate value. Starting @@ -216,15 +216,15 @@ The {ave} keyword determines how the layer values produced every steps that were multiples of {Nfreq}, before they are accessed by another output command or written to a file. -If the {ave} setting is {one}, then the layuer values produced on +If the {ave} setting is {one}, then the layer values produced on timesteps that are multiples of {Nfreq} are independent of each other; they are output as-is without further averaging. If the {ave} setting is {running}, then the layer values produced on timesteps that are multiples of {Nfreq} are summed and averaged in a -cummulative sense before being output. Each output layer value is +cumulative sense before being output. Each output layer value is thus the average of the layer value produced on that timestep with all -preceeding values for the same layer. This running average begins +preceding values for the same layer. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the "unfix"_unfix.html command, or re-defining the fix by re-specifying it. diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 4460d1f0b9..77bc98d5e0 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -43,7 +43,7 @@ filename = name of file to output time averages to 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 @@ -94,13 +94,13 @@ since they produce per-atom values. timesteps the values will be generated in order to contribute to the average. The final averaged quantities are generated every Nfreq timesteps. The average is over Nrepeat quantities, computed in the -preceeding portion of the simulation every Nevery timesteps. +preceding portion of the simulation every Nevery timesteps. Nfreq must be a multiple of Nevery and Nevery must be non-zero even if Nrepeat is 1.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similary for timesteps 190,192,194,196,198,200 on +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. @@ -158,8 +158,8 @@ 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 -average of the value produced on that timestep with all preceeding +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 command, or by re-defining the fix by re-specifying it. diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 38ebfa89ef..0192370931 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -31,7 +31,7 @@ keyword = {file} or {ave} :l filename = name of file to output time averages to {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 :pre :ule @@ -81,13 +81,13 @@ The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what timesteps the values will be generated in order to contribute to the average. The final averaged quantities are generated every {Nfreq} timesteps. The average is over {Nrepeat} quantities, computed in the -preceeding portion of the simulation every {Nevery} timesteps. +preceding portion of the simulation every {Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similary for timesteps 190,192,194,196,198,200 on +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. @@ -145,8 +145,8 @@ 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 -average of the value produced on that timestep with all preceeding +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 command, or by re-defining the fix by re-specifying it. diff --git a/doc/fix_deform.html b/doc/fix_deform.html index 8c8f83aab2..8f09660e6d 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -126,7 +126,7 @@ value.
For style final, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. -See the discsussion of the units keyword below. +See the discussion of the units keyword below.
For style delta, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box @@ -233,13 +233,13 @@ units keyword below.
For style delta, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See -the discsussion of the units keyword below. +the discussion of the units keyword below.
For style vel, a velocity at which the tilt factor changes is specified in units of distance/time. This is effectively an "engineering shear strain rate", where rate = V/L0 and L0 is the initial box length perpendicular to the direction of shear. The -distance can be in lattice or box distance units. See the discsussion +distance can be in lattice or box distance units. See the discussion of the units keyword below. For example, if the initial tilt factor is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the tilt factor will be 15 Angstroms. After 2 psec, it will be 25 @@ -304,7 +304,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
To obey this constraint and allow for large shear deformations to be -applied via the xy, xz, or yz parameters, the folloiwng +applied via the xy, xz, or yz parameters, the following algorithm is used. If prd is the associated parallel box length (10 in the example above), then if the tilt factor exceeds the accepted range of -5 to 5 during the simulation, then the box is re-shaped to diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index 63c988d89c..c40ebf0670 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -116,7 +116,7 @@ value. For style {final}, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. -See the discsussion of the units keyword below. +See the discussion of the units keyword below. For style {delta}, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box @@ -223,13 +223,13 @@ units keyword below. For style {delta}, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See -the discsussion of the units keyword below. +the discussion of the units keyword below. For style {vel}, a velocity at which the tilt factor changes is specified in units of distance/time. This is effectively an "engineering shear strain rate", where rate = V/L0 and L0 is the initial box length perpendicular to the direction of shear. The -distance can be in lattice or box distance units. See the discsussion +distance can be in lattice or box distance units. See the discussion of the units keyword below. For example, if the initial tilt factor is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the tilt factor will be 15 Angstroms. After 2 psec, it will be 25 @@ -294,7 +294,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent. To obey this constraint and allow for large shear deformations to be -applied via the {xy}, {xz}, or {yz} parameters, the folloiwng +applied via the {xy}, {xz}, or {yz} parameters, the following algorithm is used. If {prd} is the associated parallel box length (10 in the example above), then if the tilt factor exceeds the accepted range of -5 to 5 during the simulation, then the box is re-shaped to diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index b8eba1b533..2cfe2f1117 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -78,7 +78,7 @@ normalizing factor each time temperature is computed.
Care must be taken that inserted particles are not too near existing particles, using the options described below. When inserting -particles above a surface in a non-perioidic box (see the +particles above a surface in a non-periodic box (see the boundary command), the possibility of a particle escaping the surface and flying upward should be considered, since the particle may be lost or the box size may grow infinitely large. A diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt index 169df751cb..4d86ba93fb 100644 --- a/doc/fix_deposit.txt +++ b/doc/fix_deposit.txt @@ -66,7 +66,7 @@ normalizing factor each time temperature is computed. Care must be taken that inserted particles are not too near existing particles, using the options described below. When inserting -particles above a surface in a non-perioidic box (see the +particles above a surface in a non-periodic box (see the "boundary"_boundary.html command), the possibility of a particle escaping the surface and flying upward should be considered, since the particle may be lost or the box size may grow infinitely large. A diff --git a/doc/fix_dt_reset.html b/doc/fix_dt_reset.html index 615bab6e9d..e5beec65c5 100644 --- a/doc/fix_dt_reset.html +++ b/doc/fix_dt_reset.html @@ -68,7 +68,7 @@ files. None of the fix_modify options are relevant to this fix.
The current timestep size is stored as a scalar quantity by this fix. -The cummulative simulation time (in time units) is stored as the first +The cumulative simulation time (in time units) is stored as the first element of a vector. Both these quantities can be accessed by various output commands. The scalar and vector values calculated by this fix are "intensive", meaning they are @@ -80,7 +80,7 @@ minimization.
Restrictions:
-The cummulative time is zeroed when the fix is created and +
The cumulative time is zeroed when the fix is created and continuously accrues thereafter. Using the reset_timestep command while this fix is defined will mess up the time accumulation. diff --git a/doc/fix_dt_reset.txt b/doc/fix_dt_reset.txt index d2b9d1b146..992a5dc7e0 100644 --- a/doc/fix_dt_reset.txt +++ b/doc/fix_dt_reset.txt @@ -64,7 +64,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. The current timestep size is stored as a scalar quantity by this fix. -The cummulative simulation time (in time units) is stored as the first +The cumulative simulation time (in time units) is stored as the first element of a vector. Both these quantities can be accessed by various "output commands"_Section_howto.html#4_15. The scalar and vector values calculated by this fix are "intensive", meaning they are @@ -76,7 +76,7 @@ minimization"_minimize.html. [Restrictions:] -The cummulative time is zeroed when the fix is created and +The cumulative time is zeroed when the fix is created and continuously accrues thereafter. Using the "reset_timestep"_reset_timestep.html command while this fix is defined will mess up the time accumulation. diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index 30f367ec32..28865d7ada 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -51,7 +51,7 @@ fix 1 all gravity 100.0 vector 1 1 0 fix is typically used with granular systems to include a "gravity" term acting on the macroscopic particles. More generally, it can represent any kind of driving field, e.g. a pressure gradient inducing -a Poisselle flow in a fluid. Note that this fix operates differently +a Poiseuille flow in a fluid. Note that this fix operates differently than the fix addforce command. The addforce fix adds the same force to each atom, independent of its mass. This command imparts the same acceleration to each atom (force/mass). diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index cd2680ce8b..86cff8cc07 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -43,7 +43,7 @@ Impose an additional acceleration on each particle in the group. This fix is typically used with granular systems to include a "gravity" term acting on the macroscopic particles. More generally, it can represent any kind of driving field, e.g. a pressure gradient inducing -a Poisselle flow in a fluid. Note that this fix operates differently +a Poiseuille flow in a fluid. Note that this fix operates differently than the "fix addforce"_fix_addforce.html command. The addforce fix adds the same force to each atom, independent of its mass. This command imparts the same acceleration to each atom (force/mass). diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 408079e261..115d29f77c 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -67,7 +67,7 @@ user.
Fr is a force due to solvent atoms at a temperature T randomly bumping into the particle. As derived from the fluctuation/dissipation -theorum, its magnitude is proportional to sqrt(T m / dt damp), where T +theorem, its magnitude is proportional to sqrt(T m / dt damp), where T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index 866e0c03bb..4068c44974 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -57,7 +57,7 @@ user. Fr is a force due to solvent atoms at a temperature T randomly bumping into the particle. As derived from the fluctuation/dissipation -theorum, its magnitude is proportional to sqrt(T m / dt damp), where T +theorem, its magnitude is proportional to sqrt(T m / dt damp), where T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as diff --git a/doc/fix_modify.html b/doc/fix_modify.html index 7dd8d7482e..3205eca03c 100644 --- a/doc/fix_modify.html +++ b/doc/fix_modify.html @@ -57,7 +57,7 @@ default method for computing P.
For fixes that calculate a contribution to the potential energy of the system, the energy keyword will include that contribution in -thermodyanmic output of potential energy. See the +thermodynamic output of potential energy. See the thermo_style command for info on how potential energy is output. The contribution by itself can be printed by using the keyword f_ID in the thermo_style custom command, where ID is the diff --git a/doc/fix_modify.txt b/doc/fix_modify.txt index 08a3e9a49f..25c26cd967 100644 --- a/doc/fix_modify.txt +++ b/doc/fix_modify.txt @@ -50,7 +50,7 @@ default method for computing P. For fixes that calculate a contribution to the potential energy of the system, the {energy} keyword will include that contribution in -thermodyanmic output of potential energy. See the +thermodynamic output of potential energy. See the "thermo_style"_thermo_style.html command for info on how potential energy is output. The contribution by itself can be printed by using the keyword f_ID in the thermo_style custom command, where ID is the diff --git a/doc/fix_nph.html b/doc/fix_nph.html index 9e2b3354ae..63c71e3f64 100644 --- a/doc/fix_nph.html +++ b/doc/fix_nph.html @@ -142,7 +142,7 @@ the thermo_style command) with ID = thermo_ and thermo_press. This means you can change the attributes of this fix's temperature or pressure via the compute_modify command or print this temperature -or pressure during thermodyanmic output via the thermo_style +or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix. diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt index 0acd1c2c79..bcc1731846 100644 --- a/doc/fix_nph.txt +++ b/doc/fix_nph.txt @@ -132,7 +132,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} and {thermo_press}. This means you can change the attributes of this fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodyanmic output via the "thermo_style +or pressure 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} or {thermo_press} will have no effect on this fix. diff --git a/doc/fix_npt.html b/doc/fix_npt.html index 355f98575e..2c90b51440 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -146,7 +146,7 @@ the thermo_style command) with ID = thermo_ and thermo_press. This means you can change the attributes of this fix's temperature or pressure via the compute_modify command or print this temperature -or pressure during thermodyanmic output via the thermo_style +or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix. diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 77d9cff9ae..e7aa0ec604 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -135,7 +135,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} and {thermo_press}. This means you can change the attributes of this fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodyanmic output via the "thermo_style +or pressure 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} or {thermo_press} will have no effect on this fix. diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index 56da54ee97..12634a1a3e 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -145,7 +145,7 @@ the thermo_style command) with ID = thermo_ and thermo_press. This means you can change the attributes of this fix's temperature or pressure via the compute_modify command or print this temperature -or pressure during thermodyanmic output via the thermo_style +or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix. diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 484cd2a49a..3876b35273 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -134,7 +134,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} and {thermo_press}. This means you can change the attributes of this fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodyanmic output via the "thermo_style +or pressure 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} or {thermo_press} will have no effect on this fix. diff --git a/doc/fix_nve_limit.html b/doc/fix_nve_limit.html index 271340b1d9..4402aaeaba 100644 --- a/doc/fix_nve_limit.html +++ b/doc/fix_nve_limit.html @@ -61,7 +61,7 @@ updates of atom's velocity/position were limited by the maximum distance criterion. This should be roughly the number of atoms so affected, except that updates occur at both the beginning and end of a timestep in a velocity Verlet timestepping algorithm. This is a -cummulative quantity for the current run, but is re-initialized to +cumulative quantity for the current run, but is re-initialized to zero each time a run is performed. This value can be accessed by various output commands. The scalar value calculated by this fix is "extensive", meaning it scales with the diff --git a/doc/fix_nve_limit.txt b/doc/fix_nve_limit.txt index da44909c0b..83a2f7c88d 100644 --- a/doc/fix_nve_limit.txt +++ b/doc/fix_nve_limit.txt @@ -58,7 +58,7 @@ updates of atom's velocity/position were limited by the maximum distance criterion. This should be roughly the number of atoms so affected, except that updates occur at both the beginning and end of a timestep in a velocity Verlet timestepping algorithm. This is a -cummulative quantity for the current run, but is re-initialized to +cumulative quantity for the current run, but is re-initialized to zero each time a run is performed. This value can be accessed by various "output commands"_Section_howto.html#4_15. The scalar value calculated by this fix is "extensive", meaning it scales with the diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index 79019b75b4..469ff8e371 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -77,7 +77,7 @@ the thermo_style command) with ID = thermo_ This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the compute_modify command or print this temperature -during thermodyanmic output via the thermo_style +during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix. diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index 5ec9bb0de7..599b8772e4 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -68,7 +68,7 @@ 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. diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index c263b7251d..95808278ab 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -103,7 +103,7 @@ the thermo_style command) with ID = thermo_ This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the compute_modify command or print this temperature -during thermodyanmic output via the thermo_style +during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix. diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt index b155272861..740cf141de 100644 --- a/doc/fix_nvt_sllod.txt +++ b/doc/fix_nvt_sllod.txt @@ -94,7 +94,7 @@ 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. diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html index 58cb3ac95d..6649708795 100644 --- a/doc/fix_orient_fcc.html +++ b/doc/fix_orient_fcc.html @@ -61,19 +61,19 @@ and RIj is a vector in the reference (perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an atom coord from file 0/1. Equation (2) gives the expected value of the order parameter XiIJ in the other grain. Hi and lo cutoffs are defined in equations (3) and -(4), using the input parameters cutlo and cuthi as threshholds to +(4), using the input parameters cutlo and cuthi as thresholds to avoid adding grain boundary energy when the deviation in the order parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a perfect crystal). The added potential energy Ui for atom I is given in equation (6) where it is interpolated between 0 and dE using the -two threshhold Xi values and the Wi value of equation (5). +two threshold Xi values and the Wi value of equation (5).
The derivative of this energy expression gives the force on each atom which thus depends on the orientation of its neighbors relative to the 2 grain orientations. Only atoms near the grain boundary feel a net force which tends to drive them to one of the two grain orientations.
-In equation (1), the reference vector used for each neigbbor is the +
In equation (1), the reference vector used for each neighbor is the reference vector closest to the actual neighbor position. This means it is possible two different neighbors will use the same reference vector. In such cases, the atom in question is far from a perfect diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt index d8b18fd26c..c1af022cc6 100644 --- a/doc/fix_orient_fcc.txt +++ b/doc/fix_orient_fcc.txt @@ -58,19 +58,19 @@ and RIj is a vector in the reference (perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an atom coord from file 0/1. Equation (2) gives the expected value of the order parameter XiIJ in the other grain. Hi and lo cutoffs are defined in equations (3) and -(4), using the input parameters {cutlo} and {cuthi} as threshholds to +(4), using the input parameters {cutlo} and {cuthi} as thresholds to avoid adding grain boundary energy when the deviation in the order parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a perfect crystal). The added potential energy Ui for atom I is given in equation (6) where it is interpolated between 0 and dE using the -two threshhold Xi values and the Wi value of equation (5). +two threshold Xi values and the Wi value of equation (5). The derivative of this energy expression gives the force on each atom which thus depends on the orientation of its neighbors relative to the 2 grain orientations. Only atoms near the grain boundary feel a net force which tends to drive them to one of the two grain orientations. -In equation (1), the reference vector used for each neigbbor is the +In equation (1), the reference vector used for each neighbor is the reference vector closest to the actual neighbor position. This means it is possible two different neighbors will use the same reference vector. In such cases, the atom in question is far from a perfect diff --git a/doc/fix_poems.html b/doc/fix_poems.html index bd5320a5b5..ffd8168496 100644 --- a/doc/fix_poems.html +++ b/doc/fix_poems.html @@ -59,7 +59,7 @@ a constant-energy time integration, so you should not update the same atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-collinear atoms. Which atoms are in which +must contain at least 3 non-colinear atoms. Which atoms are in which bodies can be defined via several options.
For option group, each of the listed groups is treated as a rigid diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt index 4b7e660dd0..cc96f7ed05 100644 --- a/doc/fix_poems.txt +++ b/doc/fix_poems.txt @@ -52,7 +52,7 @@ a constant-energy time integration, so you should not update the same atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-collinear atoms. Which atoms are in which +must contain at least 3 non-colinear atoms. Which atoms are in which bodies can be defined via several options. For option {group}, each of the listed groups is treated as a rigid diff --git a/doc/fix_print.html b/doc/fix_print.html index 3e1a1f3e92..7a8b597beb 100644 --- a/doc/fix_print.html +++ b/doc/fix_print.html @@ -52,7 +52,7 @@ style variables which are the most useful ones to use with the fix print command, since they are evaluated afresh each timestep that the fix print line is output. Equal-style variables calculate formulas involving mathematical operations, atom properties, group properties, -thermodyanimc properties, global values calculated by a +thermodynamic properties, global values calculated by a compute or fix, or references to other variables.
diff --git a/doc/fix_print.txt b/doc/fix_print.txt index 0c81dc352c..a8c4dd43c9 100644 --- a/doc/fix_print.txt +++ b/doc/fix_print.txt @@ -42,7 +42,7 @@ style variables which are the most useful ones to use with the fix print command, since they are evaluated afresh each timestep that the fix print line is output. Equal-style variables calculate formulas involving mathematical operations, atom properties, group properties, -thermodyanimc properties, global values calculated by a +thermodynamic properties, global values calculated by a "compute"_compute.html or "fix"_fix.html, or references to other "variables"_variable.html. diff --git a/doc/fix_rdf.html b/doc/fix_rdf.html index c5a1ab22ad..4729297fbb 100644 --- a/doc/fix_rdf.html +++ b/doc/fix_rdf.html @@ -18,7 +18,7 @@IMPORTANT NOTE: After equilibration, if the velocity profile you @@ -73,7 +73,7 @@ the Nevery parameter.
An alternative method for calculating a viscosity is to run a NEMD simulation, as described in this section of -the manual. NEMD simulations deform the simmulation box via the fix +the manual. NEMD simulations deform the simulation box via the fix deform command. Thus they cannot be run on a charged system using a PPPM solver since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the @@ -85,10 +85,10 @@ box orthogonal; thus it does not suffer from this limitation. files. None of the fix_modify options are relevant to this fix.
-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. This quantity can be accessed by various output commands, such as thermo_style custom. The scalar value calculated @@ -115,7 +115,7 @@ See the Maginn paper for an example of using this algori 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/fix_viscosity.txt b/doc/fix_viscosity.txt index 4bca45e258..5507bb6a22 100644 --- a/doc/fix_viscosity.txt +++ b/doc/fix_viscosity.txt @@ -59,7 +59,7 @@ swaps is computed by the fix and can be output. Dividing this quantity by time and the cross-sectional area of the simulation box yields a momentum flux. The ratio of momentum flux to the slope of the shear velocity profile is the viscosity of the fluid, in -appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for +appropriate units. See the "Muller-Plathe paper"_#Muller-Plathe for details. IMPORTANT NOTE: After equilibration, if the velocity profile you @@ -70,7 +70,7 @@ the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD simulation, as described in "this section"_Section_howto.html#4_13 of -the manual. NEMD simulations deform the simmulation box via the "fix +the manual. NEMD simulations deform the simulation box via the "fix deform"_fix_deform.html command. Thus they cannot be run on a charged system using a "PPPM solver"_kspace_style.html since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the @@ -82,10 +82,10 @@ 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. -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. This quantity can be accessed by various "output commands"_Section_howto.html#4_15, such as "thermo_style custom"_thermo_style.html. The scalar value calculated @@ -112,7 +112,7 @@ 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/fix_viscous.html b/doc/fix_viscous.html index 24add7af27..d67854d2d5 100644 --- a/doc/fix_viscous.html +++ b/doc/fix_viscous.html @@ -56,7 +56,7 @@ optional keyword scale is used, gamma can scaled up or down by the specified factor for atoms of that type. It can be used multiple times to adjust gamma for several atom types.
-In a Brownian dynamics context, gamma = kT / mD, where k = Bolztmann's +
In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's constant, T = temperature, m = particle mass, and D = particle diffusion coefficient. D can be written as kT / (6 pi eta d), where eta = viscosity of the frictional fluid and d = diameter of particle. diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt index 718b6269b6..37d5459989 100644 --- a/doc/fix_viscous.txt +++ b/doc/fix_viscous.txt @@ -46,7 +46,7 @@ optional keyword {scale} is used, gamma can scaled up or down by the specified factor for atoms of that type. It can be used multiple times to adjust gamma for several atom types. -In a Brownian dynamics context, gamma = kT / mD, where k = Bolztmann's +In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's constant, T = temperature, m = particle mass, and D = particle diffusion coefficient. D can be written as kT / (6 pi eta d), where eta = viscosity of the frictional fluid and d = diameter of particle. diff --git a/doc/improper_class2.html b/doc/improper_class2.html index 2a4e0408c3..ccd5f828da 100644 --- a/doc/improper_class2.html +++ b/doc/improper_class2.html @@ -56,7 +56,7 @@ the data file or restart files read by the read_data< or read_restart commands:
For this style, coefficients for the Ei formula can be specified in -eiher the input script or data file. These are the 2 coefficients: +either the input script or data file. These are the 2 coefficients:
variable a loop 10 diff --git a/doc/jump.txt b/doc/jump.txt index 981b6685bc..328c7935a1 100644 --- a/doc/jump.txt +++ b/doc/jump.txt @@ -35,7 +35,7 @@ be used to loop over a portion of the input script, as in this example. These commands perform 10 runs, each of 10000 steps, and create 10 dump files named file.1, file.2, etc. The "next"_next.html command is used to exit the loop after 10 iterations. When the "a" -variable has been incremented for the 10th time, it will cause the +variable has been incremented for the tenth time, it will cause the next jump command to be skipped. variable a loop 10 diff --git a/doc/label.html b/doc/label.html index 863b441278..70030e6d3c 100644 --- a/doc/label.html +++ b/doc/label.html @@ -30,7 +30,7 @@ command was used previously, this does nothing. But if a invoking this script file, then all command lines in the script prior to this line will be ignored. I.e. execution of the script will begin at this line. This is useful for looping over a section of the input -script as discussed in the jump commmand. +script as discussed in the jump command.Restrictions: none
diff --git a/doc/label.txt b/doc/label.txt index d0da373c63..c6a573141b 100644 --- a/doc/label.txt +++ b/doc/label.txt @@ -27,7 +27,7 @@ command was used previously, this does nothing. But if a invoking this script file, then all command lines in the script prior to this line will be ignored. I.e. execution of the script will begin at this line. This is useful for looping over a section of the input -script as discussed in the "jump"_jump.html commmand. +script as discussed in the "jump"_jump.html command. [Restrictions:] none diff --git a/doc/lattice.html b/doc/lattice.html index 5921fc3d6e..b18f4bea4e 100644 --- a/doc/lattice.html +++ b/doc/lattice.html @@ -81,7 +81,7 @@ either 2d or 3d problems. cell, and a set of transformation parameters (scale, origin, orient) that map the unit cell into the simulation box. The vectors a1,a2,a3 are the edge vectors of the unit cell. This is the nomenclature for -"primitive" vectors in solid-state crytallography, but in LAMMPS the +"primitive" vectors in solid-state crystallography, but in LAMMPS the unit cell they determine does not have to be a "primitive cell" of minimum volume. @@ -191,7 +191,7 @@ in the min/max of the y and z coordinates.Note that if the unit cell is orthogonal with axis-aligned edges (not rotated via the orient keyword), then the lattice spacings in each -dimension are simply the scale factor (descibed above) multiplied by +dimension are simply the scale factor (described above) multiplied by the length of a1,a2,a3. Thus a hex style lattice with a scale factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and 3*sqrt(3.0) in y. diff --git a/doc/lattice.txt b/doc/lattice.txt index 531161d954..2a0686e327 100644 --- a/doc/lattice.txt +++ b/doc/lattice.txt @@ -73,7 +73,7 @@ A lattice consists of a unit cell, a set of basis atoms within that cell, and a set of transformation parameters (scale, origin, orient) that map the unit cell into the simulation box. The vectors a1,a2,a3 are the edge vectors of the unit cell. This is the nomenclature for -"primitive" vectors in solid-state crytallography, but in LAMMPS the +"primitive" vectors in solid-state crystallography, but in LAMMPS the unit cell they determine does not have to be a "primitive cell" of minimum volume. @@ -183,7 +183,7 @@ in the min/max of the y and z coordinates. Note that if the unit cell is orthogonal with axis-aligned edges (not rotated via the {orient} keyword), then the lattice spacings in each -dimension are simply the scale factor (descibed above) multiplied by +dimension are simply the scale factor (described above) multiplied by the length of a1,a2,a3. Thus a {hex} style lattice with a scale factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and 3*sqrt(3.0) in y. diff --git a/doc/mass.html b/doc/mass.html index aff3ecd24d..960a66c059 100644 --- a/doc/mass.html +++ b/doc/mass.html @@ -15,7 +15,7 @@
mass I value-
Examples: @@ -39,9 +39,9 @@ the masses of atom types in the EAM potential file. be used, as in the 1st example above. Or a wild-card asterik can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an -asterik with no numeric values means all types from 1 to N. A leading -asterik means all types from 1 to n (inclusive). A trailing asterik -means all types from n to N (inclusive). A middle asterik means all +asterisk with no numeric values means all types from 1 to N. A leading +asterisk means all types from 1 to n (inclusive). A trailing asterisk +means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).
A line in a data file that specifies mass uses the same format as the diff --git a/doc/mass.txt b/doc/mass.txt index 617c470be9..18557e65b6 100644 --- a/doc/mass.txt +++ b/doc/mass.txt @@ -12,7 +12,7 @@ mass command :h3 mass I value :pre -I = atom type (see asterik form below) +I = atom type (see asterisk form below) value = mass :ul [Examples:] @@ -36,9 +36,9 @@ I can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterik can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an -asterik with no numeric values means all types from 1 to N. A leading -asterik means all types from 1 to n (inclusive). A trailing asterik -means all types from n to N (inclusive). A middle asterik means all +asterisk with no numeric values means all types from 1 to N. A leading +asterisk means all types from 1 to n (inclusive). A trailing asterisk +means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). A line in a data file that specifies mass uses the same format as the diff --git a/doc/min_modify.html b/doc/min_modify.html index 8a258fc06d..11bfbb021c 100644 --- a/doc/min_modify.html +++ b/doc/min_modify.html @@ -37,7 +37,7 @@ min_modify lineiter 5
This command sets parameters that affect the minimization algorithms. The various settings may effect the convergence rate and overall -number of force evaulations required by a minimization, so users can +number of force evaluations required by a minimization, so users can experiment with these parameters to tune their minimizations.
The linestyle sets the algorithm used for 1d line searches at each diff --git a/doc/min_modify.txt b/doc/min_modify.txt index 1919a4be1b..2fe6075ef9 100644 --- a/doc/min_modify.txt +++ b/doc/min_modify.txt @@ -32,7 +32,7 @@ min_modify lineiter 5 :pre This command sets parameters that affect the minimization algorithms. The various settings may effect the convergence rate and overall -number of force evaulations required by a minimization, so users can +number of force evaluations required by a minimization, so users can experiment with these parameters to tune their minimizations. The {linestyle} sets the algorithm used for 1d line searches at each diff --git a/doc/minimize.html b/doc/minimize.html index ae73fd916b..e601c3361a 100644 --- a/doc/minimize.html +++ b/doc/minimize.html @@ -103,7 +103,7 @@ contribute to the potential energy which is probably not what is desired.
The volume of the simulation domain is not allowed to change during a -minimzation. Ideally we would allow a fix such as npt to impose an +minimization. Ideally we would allow a fix such as npt to impose an external pressure that would be included in the minimization (i.e. allow the box dimensions to change), but this has not yet been implemented. diff --git a/doc/minimize.txt b/doc/minimize.txt index 7e853731f9..3157bd8c47 100644 --- a/doc/minimize.txt +++ b/doc/minimize.txt @@ -100,7 +100,7 @@ contribute to the potential energy which is probably not what is desired. The volume of the simulation domain is not allowed to change during a -minimzation. Ideally we would allow a fix such as {npt} to impose an +minimization. Ideally we would allow a fix such as {npt} to impose an external pressure that would be included in the minimization (i.e. allow the box dimensions to change), but this has not yet been implemented. diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html index 0fdcc1fd57..39f2275e6b 100644 --- a/doc/neigh_modify.html +++ b/doc/neigh_modify.html @@ -104,7 +104,7 @@ both atoms are in the specified group and in the same molecule, as determined by their molecule ID.
Each of the exclude options can be specified multiple times. The -exclude type option is the most efficient option to use; it requries +exclude type option is the most efficient option to use; it requires only a single check, no matter how many times it has been specified. The other exclude options are more expensive if specified multiple times; they require one check for each time they have been specified. @@ -120,7 +120,7 @@ long cutoff is being used, these parameters can be tuned. The indices of neighboring atoms are stored in "pages", which are allocated one after another as they fill up. The size of each page is set by the page value. A new page is allocated when the next atom's neighbors -could potentially overflow the list. This threshhold is set by the +could potentially overflow the list. This threshold is set by the one value which tells LAMMPS the maximum number of neighbor's one atom can have.
diff --git a/doc/neigh_modify.txt b/doc/neigh_modify.txt index e9a7efb451..9b4b84db31 100644 --- a/doc/neigh_modify.txt +++ b/doc/neigh_modify.txt @@ -98,7 +98,7 @@ both atoms are in the specified group and in the same molecule, as determined by their molecule ID. Each of the exclude options can be specified multiple times. The -{exclude type} option is the most efficient option to use; it requries +{exclude type} option is the most efficient option to use; it requires only a single check, no matter how many times it has been specified. The other exclude options are more expensive if specified multiple times; they require one check for each time they have been specified. @@ -114,7 +114,7 @@ long cutoff is being used, these parameters can be tuned. The indices of neighboring atoms are stored in "pages", which are allocated one after another as they fill up. The size of each page is set by the {page} value. A new page is allocated when the next atom's neighbors -could potentially overflow the list. This threshhold is set by the +could potentially overflow the list. This threshold is set by the {one} value which tells LAMMPS the maximum number of neighbor's one atom can have. diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html index c496a40328..b0cb87c899 100644 --- a/doc/pair_airebo.html +++ b/doc/pair_airebo.html @@ -69,7 +69,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff would be 10.2 Angstroms.The E_TORSION term is an explicit 4-body potential that describes -various diheadral angle preferences in hydrocarbon configurations. +various dihedral angle preferences in hydrocarbon configurations.
Only a single pair_coeff command is used with the airebo style which specifies an AIREBO potential file with parameters for C and H. These diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt index bfab494cbf..d4fa1dd99f 100644 --- a/doc/pair_airebo.txt +++ b/doc/pair_airebo.txt @@ -66,7 +66,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff would be 10.2 Angstroms. The E_TORSION term is an explicit 4-body potential that describes -various diheadral angle preferences in hydrocarbon configurations. +various dihedral angle preferences in hydrocarbon configurations. Only a single pair_coeff command is used with the {airebo} style which specifies an AIREBO potential file with parameters for C and H. These diff --git a/doc/pair_buck_coul.html b/doc/pair_buck_coul.html index 1b5dfc36f2..7d54244ccd 100644 --- a/doc/pair_buck_coul.html +++ b/doc/pair_buck_coul.html @@ -25,7 +25,7 @@
long = use Kspace long-range summation for the Coulombic term 1/r off = omit the Coulombic term-
Funcfl files in the potentials directory of the LAMMPS @@ -127,7 +127,7 @@ cutoff used by LAMMPS for the potential. The units of dr are Angstroms; I'm not sure of the units for drho - some measure of electron density.
-Following the 3 header lines are 3 arrays of tabulated values: +
Following the three header lines are three arrays of tabulated values:
The units for the embedding function F are eV. The units for the density function rho are the same as for drho (see above, electron density). The units for the effective charge Z are "atomic charge" or -sqrt(Hartree * Bohr-radii). For 2 interacting atoms i,j this is used +sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used by LAMMPS to compute the pair potential term in the EAM energy expression as r*phi, in units of eV-Angstroms, via the formula
diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt index 728d7fe363..c597067c40 100644 --- a/doc/pair_eam.txt +++ b/doc/pair_eam.txt @@ -98,7 +98,7 @@ F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs LAMMPS be Cu atoms. Different single-element files can be assigned to different atom types to model an alloy system. The mixing to create alloy potentials for type pairs with I != J is done automatically the -same way that the serial DYANMO code originally did it; you do not +same way that the serial DYNAMO code originally did it; you do not need to specify coefficients for these type pairs. {Funcfl} files in the {potentials} directory of the LAMMPS @@ -119,7 +119,7 @@ cutoff used by LAMMPS for the potential. The units of dr are Angstroms; I'm not sure of the units for drho - some measure of electron density. -Following the 3 header lines are 3 arrays of tabulated values: +Following the three header lines are three arrays of tabulated values: embedding function F(rho) (Nrho values) effective charge function Z(r) (Nr values) @@ -132,7 +132,7 @@ individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr. The units for the embedding function F are eV. The units for the density function rho are the same as for drho (see above, electron density). The units for the effective charge Z are "atomic charge" or -sqrt(Hartree * Bohr-radii). For 2 interacting atoms i,j this is used +sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used by LAMMPS to compute the pair potential term in the EAM energy expression as r*phi, in units of eV-Angstroms, via the formula diff --git a/doc/pair_gran.html b/doc/pair_gran.html index 547ea99545..d90391ad5c 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -9,7 +9,7 @@Because this poential computes forces and torques on particles, the +
Because this potential computes forces and torques on particles, the atom style must support particles whose size is set via the shape command. This is atom_style ellipsoid and dipole. Since only spherical mono-disperse particles diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt index 892af1bf90..6d904714b4 100644 --- a/doc/pair_lubricate.txt +++ b/doc/pair_lubricate.txt @@ -103,7 +103,7 @@ This style is part of the "colloid" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. -Because this poential computes forces and torques on particles, the +Because this potential computes forces and torques on particles, the atom style must support particles whose size is set via the "shape"_shape.html command. This is "atom_style"_atom_style.html ellipsoid and dipole. Since only spherical mono-disperse particles diff --git a/doc/pair_modify.html b/doc/pair_modify.html index 6d887880fa..1110cdf0ff 100644 --- a/doc/pair_modify.html +++ b/doc/pair_modify.html @@ -42,7 +42,7 @@ parameters are relevant to all pair styles.
The mix keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not -explicity set in the input script. Note that coefficients for I = J +explicitly set in the input script. Note that coefficients for I = J must be set explicitly, either in the input script via the "pair_coeff" command or in the "Pair Coeffs" section of the data file. For some pair styles is is not necessary to diff --git a/doc/pair_modify.txt b/doc/pair_modify.txt index ddde445e8e..e206d5e3cb 100644 --- a/doc/pair_modify.txt +++ b/doc/pair_modify.txt @@ -36,7 +36,7 @@ parameters are relevant to all pair styles. The {mix} keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not -explicity set in the input script. Note that coefficients for I = J +explicitly set in the input script. Note that coefficients for I = J must be set explicitly, either in the input script via the "pair_coeff" command or in the "Pair Coeffs" section of the "data file"_read_data.html. For some pair styles is is not necessary to diff --git a/doc/pair_none.html b/doc/pair_none.html index 32152c8784..d6d1fedead 100644 --- a/doc/pair_none.html +++ b/doc/pair_none.html @@ -32,7 +32,7 @@ bonds, angles, etc.
A pair style of none will also prevent pairwise neighbor lists from being built. However if the neighbor style is bin, data structures for binning are still allocated. If the neighbor skin -distance is small, then these data structues can consume a large +distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to nsq or set the skin distance to a larger value.
diff --git a/doc/pair_none.txt b/doc/pair_none.txt index 83f8eef996..14aa9db2b0 100644 --- a/doc/pair_none.txt +++ b/doc/pair_none.txt @@ -29,7 +29,7 @@ bonds, angles, etc. A pair style of {none} will also prevent pairwise neighbor lists from being built. However if the "neighbor"_neighbor.html style is {bin}, data structures for binning are still allocated. If the neighbor skin -distance is small, then these data structues can consume a large +distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to {nsq} or set the skin distance to a larger value. diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html index 90308ec4e0..e0b6b619df 100644 --- a/doc/pair_resquared.html +++ b/doc/pair_resquared.html @@ -33,7 +33,7 @@ size sigma. The distinction is made to allow the pair style to make efficient calculations of ellipsoid/solvent interactions.Details for the equations used are given in the references below and -in this supplementary document. +in this supplementary document.
Use of this pair style requires the NVE, NVT, or NPT fixes with the asphere extension (e.g. fix nve/asphere) in @@ -137,7 +137,7 @@ and cutoff distance can be mixed, but only for LJ sphere pairs. The default mix value is geometric. See the "pair_modify" command for details. Other type pairs cannot be mixed, due to the different meanings of the energy prefactors used to calculate the interactions -and the implicit dependance of the ellipsoid-LJ sphere interaction on +and the implicit dependence of the ellipsoid-LJ sphere interaction on the equation for the Hamaker constant presented here. Mixing of sigma and epsilon followed by calculation of the energy prefactors using the equations above is recommended. diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt index 6bcc5f209a..89b1cbb5ff 100755 --- a/doc/pair_resquared.txt +++ b/doc/pair_resquared.txt @@ -30,7 +30,7 @@ size sigma. The distinction is made to allow the pair style to make efficient calculations of ellipsoid/solvent interactions. Details for the equations used are given in the references below and -in "this supplementary document"_Eqs/pair_resquqred_extra.pdf. +in "this supplementary document"_Eqs/pair_resquared_extra.pdf. Use of this pair style requires the NVE, NVT, or NPT fixes with the {asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in @@ -134,7 +134,7 @@ and cutoff distance can be mixed, but only for LJ sphere pairs. The default mix value is {geometric}. See the "pair_modify" command for details. Other type pairs cannot be mixed, due to the different meanings of the energy prefactors used to calculate the interactions -and the implicit dependance of the ellipsoid-LJ sphere interaction on +and the implicit dependence of the ellipsoid-LJ sphere interaction on the equation for the Hamaker constant presented here. Mixing of sigma and epsilon followed by calculation of the energy prefactors using the equations above is recommended. diff --git a/doc/pair_style.html b/doc/pair_style.html index 3eb1357d91..8c9f241d70 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -92,11 +92,11 @@ the pair_style command, and coefficients specified by the associated
Lammps introduces an additional performance-optimization parameter +
LAMMPS introduces an additional performance-optimization parameter tol that is used for both two-body and three-body interactions. In the Stillinger-Weber potential, the -interaction enrgies become negligibly small at atomic separations +interaction energies become negligibly small at atomic separations substantially less than the theoretical cutoff -distances. Lammps therefore defines a virtual cutoff distance +distances. LAMMPS therefore defines a virtual cutoff distance based on a user defined tolerance tol. The use of the virtual cutoff distance in constructing atom neighbor lists can significantly reduce the neighbor list sizes and therefore the -computational cost. Lammps provide a tol value for each of the three-body +computational cost. LAMMPS provide a tol value for each of the three-body entries so that they can be separately controlled. If tol = 0.0, then the standard Stillinger-Weber cutoff is used.
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt index ef3dac514f..2c3d729916 100644 --- a/doc/pair_sw.txt +++ b/doc/pair_sw.txt @@ -82,17 +82,17 @@ for both two-body and three-body interactions. gamma is used only in the three-body interactions, but is defined for pairs of atoms. The non-annotated parameters are unitless. -Lammps introduces an additional performance-optimization parameter +LAMMPS introduces an additional performance-optimization parameter tol that is used for both two-body and three-body interactions. In the Stillinger-Weber potential, the -interaction enrgies become negligibly small at atomic separations +interaction energies become negligibly small at atomic separations substantially less than the theoretical cutoff -distances. Lammps therefore defines a virtual cutoff distance +distances. LAMMPS therefore defines a virtual cutoff distance based on a user defined tolerance tol. The use of the virtual cutoff distance in constructing atom neighbor lists can significantly reduce the neighbor list sizes and therefore the -computational cost. Lammps provide a tol value for each of the three-body +computational cost. LAMMPS provide a tol value for each of the three-body entries so that they can be separately controlled. If tol = 0.0, then the standard Stillinger-Weber cutoff is used. diff --git a/doc/pair_table.html b/doc/pair_table.html index e834e416c9..b5d566d5c3 100644 --- a/doc/pair_table.html +++ b/doc/pair_table.html @@ -70,7 +70,7 @@ commands: values. The keyword specifies a section of the file. The cutoff is an optional coefficient. If not specified, the outer cutoff in the table itself (see below) will be used to build an interpolation table -that extend to the largest tablulated distance. If specified, only +that extend to the largest tabulated distance. If specified, only file values up to the cutoff are used to create the interpolation table. diff --git a/doc/pair_table.txt b/doc/pair_table.txt index 2b4d96d18f..d7e694cbd4 100644 --- a/doc/pair_table.txt +++ b/doc/pair_table.txt @@ -67,7 +67,7 @@ The filename specifies a file containing tabulated energy and force values. The keyword specifies a section of the file. The cutoff is an optional coefficient. If not specified, the outer cutoff in the table itself (see below) will be used to build an interpolation table -that extend to the largest tablulated distance. If specified, only +that extend to the largest tabulated distance. If specified, only file values up to the cutoff are used to create the interpolation table. diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html index f47939dc34..0747a170bc 100644 --- a/doc/pair_tersoff.html +++ b/doc/pair_tersoff.html @@ -139,7 +139,7 @@ Tersoff_2 parameters.In the potentials directory, the file SiCGe.tersoff provides the LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy paramters for Si, C, and Ge. This file can be used for pure Si, +alloy parameters for Si, C, and Ge. This file can be used for pure Si, (three different versions), pure C, pure Ge, binary SiC, and binary SiGe. LAMMPS will generate an error if this file is used with any combination involving C and Ge, since there are no entries for the GeC @@ -202,7 +202,7 @@ appropriate units if your simulation doesn't use "metal" units.
-(Albe) J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: +
(Albe) J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt index 2fd533c62a..2b1fde8449 100644 --- a/doc/pair_tersoff.txt +++ b/doc/pair_tersoff.txt @@ -136,7 +136,7 @@ Tersoff_2 parameters. In the potentials directory, the file SiCGe.tersoff provides the LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy paramters for Si, C, and Ge. This file can be used for pure Si, +alloy parameters for Si, C, and Ge. This file can be used for pure Si, (three different versions), pure C, pure Ge, binary SiC, and binary SiGe. LAMMPS will generate an error if this file is used with any combination involving C and Ge, since there are no entries for the GeC @@ -197,7 +197,7 @@ appropriate units if your simulation doesn't use "metal" units. [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). :link(Albe) -[(Albe)] J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: +[(Albe)] J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). :link(Tersoff_2) diff --git a/doc/print.html b/doc/print.html index 8cac8ee8c9..227e8cbd4e 100644 --- a/doc/print.html +++ b/doc/print.html @@ -42,7 +42,7 @@ input script that is looped over (see the jump and style variables which are typically the most useful ones to use with the print command. Equal-style variables can calculate formulas involving mathematical operations, atom properties, group properties, -thermodyanimc properties, global values calculated by a +thermodynamic properties, global values calculated by a compute or fix, or references to other variables. diff --git a/doc/print.txt b/doc/print.txt index 71c8301561..d622afb6f4 100644 --- a/doc/print.txt +++ b/doc/print.txt @@ -39,7 +39,7 @@ See the "variable"_variable.html command for a description of {equal} style variables which are typically the most useful ones to use with the print command. Equal-style variables can calculate formulas involving mathematical operations, atom properties, group properties, -thermodyanimc properties, global values calculated by a +thermodynamic properties, global values calculated by a "compute"_compute.html or "fix"_fix.html, or references to other "variables"_variable.html. diff --git a/doc/read_data.html b/doc/read_data.html index 9491d9559a..56e300f1d8 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -139,7 +139,7 @@ back inside the box.These are the section keywords for the body of the file.
The lo/hi values for block or cylinder or prism styles can be specified as EDGE or INF. EDGE means they extend all the way to the global simulation box boundary. Note that this is the current box -boundary; if the box changes size during a simlation the region does +boundary; if the box changes size during a simulation the region does not. INF means a large negative or positive number (1.0e20), so it should encompass the simulation box even if it changes size. If a region is defined before the simulation box has been created (via @@ -85,12 +85,12 @@ parameter cannot be used.
For style cylinder, the c1,c2 params are coordinates in the 2 other dimensions besides the cylinder axis dimension. For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. Thus the -third example above specifes a cylinder with its axis in the +third example above specifies a cylinder with its axis in the y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and extending in the y-direction from -5.0 to the upper box boundary.
For style prism, a parallelepiped is defined (it's too hard to spell -parallelepiped in an input script!). Think of the parallelepided as +parallelepiped in an input script!). Think of the parallelepiped as initially an axis-aligned orthogonal box with the same xyz lo/hi parameters as region style block would define. Then, while holding the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted" @@ -114,7 +114,7 @@ configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
The union style creates a region consisting of the volume of all the -listed regions combined. The intesect style creates a region +listed regions combined. The intersect style creates a region consisting of the volume that is common to all the listed regions.
The side keyword determines whether the region is considered to be diff --git a/doc/region.txt b/doc/region.txt index 37d3f959a6..0bc4bc051c 100644 --- a/doc/region.txt +++ b/doc/region.txt @@ -65,7 +65,7 @@ command, or deleted via the "delete_atoms"_delete_atoms.html command. The lo/hi values for {block} or {cylinder} or {prism} styles can be specified as EDGE or INF. EDGE means they extend all the way to the global simulation box boundary. Note that this is the current box -boundary; if the box changes size during a simlation the region does +boundary; if the box changes size during a simulation the region does not. INF means a large negative or positive number (1.0e20), so it should encompass the simulation box even if it changes size. If a region is defined before the simulation box has been created (via @@ -76,12 +76,12 @@ parameter cannot be used. For style {cylinder}, the c1,c2 params are coordinates in the 2 other dimensions besides the cylinder axis dimension. For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. Thus the -third example above specifes a cylinder with its axis in the +third example above specifies a cylinder with its axis in the y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and extending in the y-direction from -5.0 to the upper box boundary. For style {prism}, a parallelepiped is defined (it's too hard to spell -parallelepiped in an input script!). Think of the parallelepided as +parallelepiped in an input script!). Think of the parallelepiped as initially an axis-aligned orthogonal box with the same xyz lo/hi parameters as region style {block} would define. Then, while holding the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted" @@ -105,7 +105,7 @@ configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent. The {union} style creates a region consisting of the volume of all the -listed regions combined. The {intesect} style creates a region +listed regions combined. The {intersect} style creates a region consisting of the volume that is common to all the listed regions. The {side} keyword determines whether the region is considered to be diff --git a/doc/replicate.html b/doc/replicate.html index 0be94e19c9..aa93423db5 100644 --- a/doc/replicate.html +++ b/doc/replicate.html @@ -36,7 +36,7 @@ topology interactions are created between pairs of new atoms as well as between old and new atoms. This is done by using the image flag for each atom to "unwrap" it out of the periodic box before replicating it. This means that molecular bonds you specify in the -orignal data file that span the periodic box should be between two +original data file that span the periodic box should be between two atoms with image flags that differ by 1. This will allow them to be unwrapped appropriately.
diff --git a/doc/replicate.txt b/doc/replicate.txt index 68e81b3b28..dcab5c59e1 100644 --- a/doc/replicate.txt +++ b/doc/replicate.txt @@ -33,7 +33,7 @@ topology interactions are created between pairs of new atoms as well as between old and new atoms. This is done by using the image flag for each atom to "unwrap" it out of the periodic box before replicating it. This means that molecular bonds you specify in the -orignal data file that span the periodic box should be between two +original data file that span the periodic box should be between two atoms with image flags that differ by 1. This will allow them to be unwrapped appropriately. diff --git a/doc/restart.html b/doc/restart.html index 46302836e7..3c95f5b271 100644 --- a/doc/restart.html +++ b/doc/restart.html @@ -71,7 +71,7 @@ file is binary (to enable exact restarts), it may not be readable on another machine. In this case, the restart2data program in the tools directory can be used to convert a restart file to an ASCII data file. Both the -read_restart commmand and restart2data tool can read in a restart file +read_restart command and restart2data tool can read in a restart file that was written with the "%" character so that multiple files were created. diff --git a/doc/restart.txt b/doc/restart.txt index 9cd822f5cf..92aa5b977a 100644 --- a/doc/restart.txt +++ b/doc/restart.txt @@ -68,7 +68,7 @@ file is binary (to enable exact restarts), it may not be readable on another machine. In this case, the "restart2data program"_Section_tools.html#restart in the tools directory can be used to convert a restart file to an ASCII data file. Both the -read_restart commmand and restart2data tool can read in a restart file +read_restart command and restart2data tool can read in a restart file that was written with the "%" character so that multiple files were created. diff --git a/doc/run.html b/doc/run.html index 5dbbf9246b..08a3297cfc 100644 --- a/doc/run.html +++ b/doc/run.html @@ -152,7 +152,7 @@ each time the command is invoked.IMPORTANT NOTE: For the every option, the command should be listed exactly as it would be if it appeared on a line by itself. Thus all -remaining arguments after the M value are considerd part of the LAMMPS +remaining arguments after the M value are considered part of the LAMMPS command (e.g. print "Protein Rg = $r" as in the example above). This means that, if specified, the every option must be the last keyword used. diff --git a/doc/run.txt b/doc/run.txt index 7fb06bc076..5d71dc481f 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -145,7 +145,7 @@ each time the command is invoked. IMPORTANT NOTE: For the {every} option, the command should be listed exactly as it would be if it appeared on a line by itself. Thus all -remaining arguments after the M value are considerd part of the LAMMPS +remaining arguments after the M value are considered part of the LAMMPS command (e.g. print "Protein Rg = $r" as in the example above). This means that, if specified, the {every} option must be the last keyword used. diff --git a/doc/run_style.html b/doc/run_style.html index a438522e84..bb6e3951bb 100644 --- a/doc/run_style.html +++ b/doc/run_style.html @@ -20,7 +20,7 @@
verlet args = none
respa args = N n1 n2 ... keyword values ...
N = # of levels of rRESPA
- n1, n2, ... = loop factor bewteen rRESPA levels (N-1 values)
+ n1, n2, ... = loop factor between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = bond or angle or dihedral or improper or
pair or inner or middle or outer or kspace
@@ -142,7 +142,7 @@ simulations using the CHARMM or similar all-atom force field, bonds
involving hydrogen atoms exhibit high frequency vibrations and require
a time step on the order of 0.5 fmsec in order to conserve energy.
These high frequency modes also limit the outer time step sizes since
-the modes are coupled. It is therefore desireable to use SHAKE with
+the modes are coupled. It is therefore desirable to use SHAKE with
respa in order to freeze out these high frequency motions and increase
the size of the time steps in the respa hierarchy. The following
settings can be used for biomolecular simulations with SHAKE and
diff --git a/doc/run_style.txt b/doc/run_style.txt
index e3a2433b40..f27a4b54eb 100644
--- a/doc/run_style.txt
+++ b/doc/run_style.txt
@@ -16,7 +16,7 @@ style = {verlet} or {respa} :ulb,l
{verlet} args = none
{respa} args = N n1 n2 ... keyword values ...
N = # of levels of rRESPA
- n1, n2, ... = loop factor bewteen rRESPA levels (N-1 values)
+ n1, n2, ... = loop factor between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = {bond} or {angle} or {dihedral} or {improper} or
{pair} or {inner} or {middle} or {outer} or {kspace}
@@ -137,7 +137,7 @@ simulations using the CHARMM or similar all-atom force field, bonds
involving hydrogen atoms exhibit high frequency vibrations and require
a time step on the order of 0.5 fmsec in order to conserve energy.
These high frequency modes also limit the outer time step sizes since
-the modes are coupled. It is therefore desireable to use SHAKE with
+the modes are coupled. It is therefore desirable to use SHAKE with
respa in order to freeze out these high frequency motions and increase
the size of the time steps in the respa hierarchy. The following
settings can be used for biomolecular simulations with SHAKE and
diff --git a/doc/set.html b/doc/set.html
index 744ac883f4..7c64f4bd5c 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -42,7 +42,7 @@
quat/random value = seed
seed = random # seed (positive integer) for quaternion orientations
bond value = bond type for all bonds between selected atoms
- angle value = angle type for all angles bewteen selected atoms
+ angle value = angle type for all angles between selected atoms
dihedral value = dihedral type for all dihedrals between selected atoms
improper value = improper type for all impropers between selected atoms
@@ -90,7 +90,7 @@ command.
Keyword type/fraction sets the atom type for a fraction of the selected atoms. The actual number of atoms changed is not guaranteed -to be exactly the requested fraction, but should be statisticaly +to be exactly the requested fraction, but should be statistically close. Random numbers are used in such a way that a particular atom is changed or not changed, regardless of how many processors are being used. diff --git a/doc/set.txt b/doc/set.txt index 9b42c2d177..ac6c7b71d8 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -38,7 +38,7 @@ keyword = {type} or {type/fraction} or {mol} or \ {quat/random} value = seed seed = random # seed (positive integer) for quaternion orientations {bond} value = bond type for all bonds between selected atoms - {angle} value = angle type for all angles bewteen selected atoms + {angle} value = angle type for all angles between selected atoms {dihedral} value = dihedral type for all dihedrals between selected atoms {improper} value = improper type for all impropers between selected atoms :pre :ule @@ -85,7 +85,7 @@ command. Keyword {type/fraction} sets the atom type for a fraction of the selected atoms. The actual number of atoms changed is not guaranteed -to be exactly the requested fraction, but should be statisticaly +to be exactly the requested fraction, but should be statistically close. Random numbers are used in such a way that a particular atom is changed or not changed, regardless of how many processors are being used. diff --git a/doc/shape.html b/doc/shape.html index f3dee20e73..603534bf8d 100644 --- a/doc/shape.html +++ b/doc/shape.html @@ -15,7 +15,7 @@
mass I x y z-
The I index can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card -asterik can be used to set the mass for multiple atom types. This +asterisk can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterik with no numeric values means all types -from 1 to N. A leading asterik means all types from 1 to n -(inclusive). A trailing asterik means all types from n to N -(inclusive). A middle asterik means all types from m to n +atom types, then an asterisk with no numeric values means all types +from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n (inclusive).
A line in a data file that specifies shape uses the same format as the arguments of the shape command in an input script, except that no -wild-card asterik can be used. For example, under the "Shapes" +wild-card asterisk can be used. For example, under the "Shapes" section of a data file, the line that corresponds to the 1st example above would be listed as
diff --git a/doc/shape.txt b/doc/shape.txt index 05bccb9597..f32474b370 100644 --- a/doc/shape.txt +++ b/doc/shape.txt @@ -12,7 +12,7 @@ shape command :h3 mass I x y z :pre -I = atom type (see asterik form below) +I = atom type (see asterisk form below) x = x diameter y = y diameter z = z diameter :ul @@ -47,17 +47,17 @@ components the same. The I index can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card -asterik can be used to set the mass for multiple atom types. This +asterisk can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterik with no numeric values means all types -from 1 to N. A leading asterik means all types from 1 to n -(inclusive). A trailing asterik means all types from n to N -(inclusive). A middle asterik means all types from m to n +atom types, then an asterisk with no numeric values means all types +from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n (inclusive). A line in a data file that specifies shape uses the same format as the arguments of the shape command in an input script, except that no -wild-card asterik can be used. For example, under the "Shapes" +wild-card asterisk can be used. For example, under the "Shapes" section of a data file, the line that corresponds to the 1st example above would be listed as diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 077bf2574b..3e4e268425 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -179,7 +179,7 @@ attributes of this computation via the directly assign a new compute which you have defined, to be used for drot. This is done via the thermo_modify command. For example, this could be useful if you wish to exclude -certain particles from the compuation. +certain particles from the computation.The grot keyword requires a rotational energy to be computed for granular particles. To do this, a compute of style "rotate/gran" is @@ -194,7 +194,7 @@ computation via the compute_modify command. Alternatively, you can directly assign a new compute which you have defined, to be used for grot. This is done via the thermo_modify command. For example, this could -be useful if you wish to exclude frozen particles from the compuation. +be useful if you wish to exclude frozen particles from the computation.
See this section for information on how to add new compute and fix styles to LAMMPS to calculate quantities that -could then be output with these keywords as part of thermodyanmic +could then be output with these keywords as part of thermodynamic information.
Description:
This command sets the style of units used for a simulation. It -detemines the units of all quantities specified in the input script +determines the units of all quantities specified in the input script and data file, as well as quantities output to the screen, log file, and dump files. Typically, this command is used at the very beginning of an input script. diff --git a/doc/units.txt b/doc/units.txt index 81783ed175..8ba25f9421 100644 --- a/doc/units.txt +++ b/doc/units.txt @@ -22,7 +22,7 @@ units lj :pre [Description:] This command sets the style of units used for a simulation. It -detemines the units of all quantities specified in the input script +determines the units of all quantities specified in the input script and data file, as well as quantities output to the screen, log file, and dump files. Typically, this command is used at the very beginning of an input script. diff --git a/doc/variable.html b/doc/variable.html index ed4c36ae95..601ffd75a9 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -106,7 +106,7 @@ be used for such settings instead, as in bench/in.lj.
Second, as described below, if a variable is iterated on to the end of its list of strings via the next command, it is removed -from the list of active varaibles, and is thus available to be +from the list of active variables, and is thus available to be re-defined in a subsequent variable command.
The thermo keywords allowed in a formula are those defined by the -"thermo_style custom" command. Since many thermodyanmic quantities +"thermo_style custom" command. Since many thermodynamic quantities are only computable after the a simulation has begun, these keywords cannot be used if a variable is evaluated before the first simulation begins. @@ -311,7 +311,7 @@ by "f_", and the word "compute" is replaced by "fix".
The current values of other variables can be accessed by prepending a "v_" to the variable name. This will cause that variable to be -evaulated. Atom-style variables generate per-atom values; all other +evaluated. Atom-style variables generate per-atom values; all other styles of variables generate a single scalar value.
The different kinds of variable references are as follows. N is a @@ -341,7 +341,7 @@ immediately when the line is read from the input script, just as it would be in other input script command. This could be the desired behavior if a static value is desired. Or it could be the desired behavior for an equal-style variable if the variable command appears -in a loop (see the jump and next commmands), +in a loop (see the jump and next commands), since the substitution will be performed anew each time thru the loop as the command is re-read. Note that if the variable formula is enclosed in double quotes, this prevents variable substitution and @@ -366,7 +366,7 @@ variable y equal 2*$x
variable x equal vol variable y equal 2*v_x-
wlll associate the equation string "2*v_x" with variable y. +
will associate the equation string "2*v_x" with variable y.
Thus if the variable y were evaluated periodically during a run where the box volume changed, the resulting value would always be 2000.0 for diff --git a/doc/variable.txt b/doc/variable.txt index 668963a709..71d9a38f24 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -100,7 +100,7 @@ be used for such settings instead, as in bench/in.lj. Second, as described below, if a variable is iterated on to the end of its list of strings via the "next"_next.html command, it is removed -from the list of active varaibles, and is thus available to be +from the list of active variables, and is thus available to be re-defined in a subsequent variable command. :line @@ -227,7 +227,7 @@ can use formula elements that produce either global values or per-atom values. The thermo keywords allowed in a formula are those defined by the -"thermo_style custom" command. Since many thermodyanmic quantities +"thermo_style custom" command. Since many thermodynamic quantities are only computable after the a simulation has begun, these keywords cannot be used if a variable is evaluated before the first simulation begins. @@ -304,7 +304,7 @@ by "f_", and the word "compute" is replaced by "fix". The current values of other variables can be accessed by prepending a "v_" to the variable name. This will cause that variable to be -evaulated. Atom-style variables generate per-atom values; all other +evaluated. Atom-style variables generate per-atom values; all other styles of variables generate a single scalar value. The different kinds of variable references are as follows. N is a @@ -332,7 +332,7 @@ immediately when the line is read from the input script, just as it would be in other input script command. This could be the desired behavior if a static value is desired. Or it could be the desired behavior for an equal-style variable if the variable command appears -in a loop (see the "jump"_jump.html and "next"_next.html commmands), +in a loop (see the "jump"_jump.html and "next"_next.html commands), since the substitution will be performed anew each time thru the loop as the command is re-read. Note that if the variable formula is enclosed in double quotes, this prevents variable substitution and @@ -357,7 +357,7 @@ By contrast, these lines: variable x equal vol variable y equal 2*v_x :pre -wlll associate the equation string "2*v_x" with variable y. +will associate the equation string "2*v_x" with variable y. Thus if the variable y were evaluated periodically during a run where the box volume changed, the resulting value would always be 2000.0 for diff --git a/doc/write_restart.html b/doc/write_restart.html index 960ea8e0ca..076070efde 100644 --- a/doc/write_restart.html +++ b/doc/write_restart.html @@ -49,7 +49,7 @@ command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, the restart2data program in the tools directory can be used to convert a restart file to an ASCII data file. -Both the read_restart commmand and restart2data tool can read in a +Both the read_restart command and restart2data tool can read in a restart file that was written with the "%" character so that multiple files were created.
diff --git a/doc/write_restart.txt b/doc/write_restart.txt index 13045a0842..064cdb4f63 100644 --- a/doc/write_restart.txt +++ b/doc/write_restart.txt @@ -46,7 +46,7 @@ command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, the restart2data program in the tools directory can be used to convert a restart file to an ASCII data file. -Both the read_restart commmand and restart2data tool can read in a +Both the read_restart command and restart2data tool can read in a restart file that was written with the "%" character so that multiple files were created.