From aa58c14f809ec8e5e7e28dfcd04e799262e60366 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 19 Feb 2008 21:47:37 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1543 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute.html | 2 +- doc/compute.txt | 2 +- doc/compute_pe_atom.html | 2 +- doc/compute_pe_atom.txt | 2 +- doc/compute_temp_dipole.html | 2 +- doc/compute_temp_dipole.txt | 2 +- doc/dump.html | 4 ++-- doc/dump.txt | 4 ++-- doc/fix_ave_atom.html | 10 +++++----- doc/fix_ave_atom.txt | 10 +++++----- doc/fix_msd.html | 2 +- doc/fix_msd.txt | 2 +- doc/fix_nvt.html | 2 +- doc/fix_nvt.txt | 2 +- doc/fix_poems.html | 4 ++-- doc/fix_poems.txt | 4 ++-- doc/fix_recenter.html | 4 ++-- doc/fix_recenter.txt | 4 ++-- doc/pair_charmm.html | 2 +- doc/pair_charmm.txt | 2 +- doc/pair_coeff.html | 24 ++++++++++++------------ doc/pair_coeff.txt | 24 ++++++++++++------------ doc/pair_dipole.html | 2 +- doc/pair_dipole.txt | 2 +- doc/pair_dpd.html | 6 +++--- doc/pair_dpd.txt | 6 +++--- doc/pair_hybrid.html | 6 +++--- doc/pair_hybrid.txt | 6 +++--- doc/velocity.html | 2 +- doc/velocity.txt | 2 +- 30 files changed, 74 insertions(+), 74 deletions(-) diff --git a/doc/compute.html b/doc/compute.html index d3bd0a15c2..db09256bce 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -102,7 +102,7 @@ via the compute_modify command.

Computes can be deleted with the uncompute command.

Code for new computes can be added to LAMMPS (see this -section of the manaul) and the results of their +section of the manual) and the results of their calculations accessed in the various ways described above.

Each compute style has its own doc page which describes its arguments diff --git a/doc/compute.txt b/doc/compute.txt index 3504bdee82..d334639211 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -99,7 +99,7 @@ via the "compute_modify"_compute_modify.html command. Computes can be deleted with the "uncompute"_uncompute.html command. Code for new computes can be added to LAMMPS (see "this -section"_Section_modify.html of the manaul) and the results of their +section"_Section_modify.html of the manual) and the results of their calculations accessed in the various ways described above. Each compute style has its own doc page which describes its arguments diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index bf6569abb8..7da6a9cd6a 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -37,7 +37,7 @@ ave/spatial command or fix ave/atom command. See this section for an overview.

-

The per-atom energy is calulated by the various pair, bond, etc +

The per-atom 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, and improper energy. If any extra keywords are listed, then diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 61da999004..c2ea738ae8 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -34,7 +34,7 @@ ave/spatial"_fix_ave_spatial.html command or "fix ave/atom"_fix_ave_atom.html command. See "this section"_Section_howto.html#4_15 for an overview. -The per-atom energy is calulated by the various pair, bond, etc +The per-atom 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, and improper energy. If any extra keywords are listed, then diff --git a/doc/compute_temp_dipole.html b/doc/compute_temp_dipole.html index 5579838c60..216b83afa3 100644 --- a/doc/compute_temp_dipole.html +++ b/doc/compute_temp_dipole.html @@ -28,7 +28,7 @@ compute myTemp mobile temp/dipole

Define 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 inlclude to account for the rotational state of the +freedom are include 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 dd7305b4ac..5a64eba47b 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 inlclude to account for the rotational state of the +freedom are include 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/dump.html b/doc/dump.html index 2ebf962971..0125741c01 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -248,7 +248,7 @@ the atom's dipole.

The quatw, quati, quatj, quatk, tqx, tqy, tqz keywords are specific to aspherical particles defined with an atom style of ellipsoid. The first 4 are the components of the quaternion that -define the orientiation of the particle. The final 3 give the +define the orientation of the particle. The final 3 give the rotational torque on the particle.

The c_ID and c_ID[N] keywords allow scalar or vector per-atom @@ -329,7 +329,7 @@ and associated functions, which should be a suitable substitute on machines that do not have the appropriate native header files. This option can be invoked at build time by adding -DLAMMPS_XDR to the CCFLAGS variable in the appropriate lo-level Makefile, -e.g. src/MAKE/Makefile.foo. This compatability mode has been tested +e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested successfully on Cray XT3 and IBM BlueGene/L machines and should also work on the Cray XT4, IBM BG/P, and Windows XP machines.

diff --git a/doc/dump.txt b/doc/dump.txt index 0234c62526..d2cf4dfad7 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -238,7 +238,7 @@ the atom's dipole. The {quatw}, {quati}, {quatj}, {quatk}, {tqx}, {tqy}, {tqz} keywords are specific to aspherical particles defined with an atom style of {ellipsoid}. The first 4 are the components of the quaternion that -define the orientiation of the particle. The final 3 give the +define the orientation of the particle. The final 3 give the rotational torque on the particle. The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom @@ -319,7 +319,7 @@ and associated functions, which should be a suitable substitute on machines that do not have the appropriate native header files. This option can be invoked at build time by adding -DLAMMPS_XDR to the CCFLAGS variable in the appropriate lo-level Makefile, -e.g. src/MAKE/Makefile.foo. This compatability mode has been tested +e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested successfully on Cray XT3 and IBM BlueGene/L machines and should also work on the Cray XT4, IBM BG/P, and Windows XP machines. diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html index 53eb8a967b..49e05c733f 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -65,7 +65,7 @@ variable, then see the fix ave/time command.

Computes that produce per-atom quantities are those which have the word atom in their style name. See the doc pages for -inidividual fixes to determine which ones produce per-atom +individual fixes to determine which ones produce per-atom quantities. Variables of style atom are the only ones that can be used with this fix since all other styles of variable produce global quantities. @@ -76,13 +76,13 @@ produce global quantities. 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. -Nfreq must be a multiple of Nevery and Nevery must be non-zero -even if Nrepeat is 1. +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.

diff --git a/doc/fix_ave_atom.txt b/doc/fix_ave_atom.txt index d52fecd722..f20b2e608d 100644 --- a/doc/fix_ave_atom.txt +++ b/doc/fix_ave_atom.txt @@ -54,7 +54,7 @@ variable, then see the "fix ave/time"_fix_ave_time.html command. "Computes"_compute.html that produce per-atom quantities are those which have the word {atom} in their style name. See the doc pages for -inidividual "fixes"_fix.html to determine which ones produce per-atom +individual "fixes"_fix.html to determine which ones produce per-atom quantities. "Variables"_variable.html of style {atom} are the only ones that can be used with this fix since all other styles of variable produce global quantities. @@ -65,13 +65,13 @@ 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. -{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero -even if {Nrepeat} is 1. +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. :line diff --git a/doc/fix_msd.html b/doc/fix_msd.html index 244d8ed136..01084d7a2d 100644 --- a/doc/fix_msd.html +++ b/doc/fix_msd.html @@ -40,7 +40,7 @@ and the computed MSD will not reflect its true displacement. See the fix rigid command for details. Thus, to compute the MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a dump file containing coordinates of the -atomss in the bodies. +atoms in the bodies.

Restart, fix_modify, output, run start/stop, minimize info:

diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt index 13ae6ba80a..d8bbc5e04d 100644 --- a/doc/fix_msd.txt +++ b/doc/fix_msd.txt @@ -37,7 +37,7 @@ and the computed MSD will not reflect its true displacement. See the "fix rigid"_fix_rigid.html command for details. Thus, to compute the MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a "dump file"_dump.html containing coordinates of the -atomss in the bodies. +atoms in the bodies. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index 44ea50ac1d..07026a1033 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -75,7 +75,7 @@ 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.txt b/doc/fix_nvt.txt index c4203492d5..1534ed89cb 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -66,7 +66,7 @@ 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_poems.html b/doc/fix_poems.html index bc0a79b9c9..bd5320a5b5 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-colinear atoms. Which atoms are in which +must contain at least 3 non-collinear 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 @@ -105,7 +105,7 @@ which includes all the desired rigid bodies. LAMMPS will allow multiple poems fixes to be defined, but it is more expensive.

The degrees-of-freedom removed by coupled rigid bodies are accounted -for in temperature and pressure computations. Similary, the rigid +for in temperature and pressure computations. Similarly, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt index 605daf5600..4b7e660dd0 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-colinear atoms. Which atoms are in which +must contain at least 3 non-collinear 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 @@ -98,7 +98,7 @@ which includes all the desired rigid bodies. LAMMPS will allow multiple poems fixes to be defined, but it is more expensive. The degrees-of-freedom removed by coupled rigid bodies are accounted -for in temperature and pressure computations. Similary, the rigid +for in temperature and pressure computations. Similarly, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html index 7433b3241d..b14b01f64a 100644 --- a/doc/fix_recenter.html +++ b/doc/fix_recenter.html @@ -51,7 +51,7 @@ do not drift during the simulation due to random perturbations the units keyword, as discussed below. One or more x,y,z values can also be specified as NULL, which means exclude that dimension from this operation. Or it can be specified as INIT which means to -constain the center-of-mass to its initial value at the beginning of +constrain the center-of-mass to its initial value at the beginning of the run.

The center-of-mass (COM) is computed for the group specified by the @@ -110,7 +110,7 @@ This fix is not invoked during energy minimization

This fix should not be used with an x,y,z setting that causes a large shift in the system on the 1st timestep, due to the requested COM being very different from the initial COM. This could cause atoms to -be lost,especially in parallel. Instead, use the +be lost, especially in parallel. Instead, use the displace_atoms command, which can be used to move atoms a large distance.

diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt index 033ff17159..17fa345772 100644 --- a/doc/fix_recenter.txt +++ b/doc/fix_recenter.txt @@ -43,7 +43,7 @@ Distance units for the x,y,z values are determined by the setting of the {units} keyword, as discussed below. One or more x,y,z values can also be specified as NULL, which means exclude that dimension from this operation. Or it can be specified as INIT which means to -constain the center-of-mass to its initial value at the beginning of +constrain the center-of-mass to its initial value at the beginning of the run. The center-of-mass (COM) is computed for the group specified by the @@ -102,7 +102,7 @@ This fix is not invoked during "energy minimization"_minimize.html. This fix should not be used with an x,y,z setting that causes a large shift in the system on the 1st timestep, due to the requested COM being very different from the initial COM. This could cause atoms to -be lost,especially in parallel. Instead, use the +be lost, especially in parallel. Instead, use the "displace_atoms"_displace_atoms.html command, which can be used to move atoms a large distance. diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index dc1e2815cf..9c95db13c1 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -56,7 +56,7 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5

The lj/charmm styles compute LJ and Coulombic interactions with an additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cuoff. It is a widely +smoothly to zero between an inner and outer cutoff. It is a widely used potential in the CHARMM MD code. See (MacKerell) for a description of the CHARMM force field. diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt index 3c141de4d5..5b890dc093 100644 --- a/doc/pair_charmm.txt +++ b/doc/pair_charmm.txt @@ -49,7 +49,7 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre The {lj/charmm} styles compute LJ and Coulombic interactions with an additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cuoff. It is a widely +smoothly to zero between an inner and outer cutoff. It is a widely used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code. See "(MacKerell)"_#MacKerell for a description of the CHARMM force field. diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index dd76f7f500..cd09581b6e 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -15,7 +15,7 @@ 

pair_coeff I J args
-