Note that using a angle_coeff command can override a previous setting +
Note that using an angle_coeff command can override a previous setting for the same angle type. For example, these commands set the coeffs for all angle types, then overwrite the coeffs for just angle type 2:
@@ -49,7 +49,7 @@A line in a data file that specifies angle coefficients uses the exact same format as the arguments of the angle_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Angle Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-2Oct06/doc/angle_coeff.txt lammps-3Oct06/doc/angle_coeff.txt --- lammps-2Oct06/doc/angle_coeff.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/angle_coeff.txt 2006-09-28 13:22:09.000000000 -0600 @@ -34,10 +34,10 @@ 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 asterik +asterik means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that using a angle_coeff command can override a previous setting +Note that using an angle_coeff command can override a previous setting for the same angle type. For example, these commands set the coeffs for all angle types, then overwrite the coeffs for just angle type 2: @@ -46,7 +46,7 @@ A line in a data file that specifies angle coefficients uses the exact same format as the arguments of the angle_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Angle Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-2Oct06/doc/bond_coeff.html lammps-3Oct06/doc/bond_coeff.html --- lammps-2Oct06/doc/bond_coeff.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/bond_coeff.html 2006-09-28 13:47:07.000000000 -0600 @@ -15,7 +15,7 @@
bond_coeff N args-
Examples: @@ -33,12 +33,12 @@ read_data command or in a restart file.
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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple bond types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of bond 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 +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 a bond_coeff command can override a previous setting @@ -50,7 +50,7 @@
A line in a data file that specifies bond coefficients uses the exact same format as the arguments of the bond_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Bond Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-2Oct06/doc/bond_coeff.txt lammps-3Oct06/doc/bond_coeff.txt --- lammps-2Oct06/doc/bond_coeff.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/bond_coeff.txt 2006-09-28 13:47:07.000000000 -0600 @@ -12,7 +12,7 @@ bond_coeff N args :pre -N = bond type (see asterik form below) +N = bond type (see asterisk form below) args = coefficients for one or more bond types :ul [Examples:] @@ -30,12 +30,12 @@ "read_data"_read_data.html command or in a restart file. 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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple bond types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of bond 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 +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 a bond_coeff command can override a previous setting @@ -47,7 +47,7 @@ A line in a data file that specifies bond coefficients uses the exact same format as the arguments of the bond_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Bond Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-2Oct06/doc/delete_atoms.html lammps-3Oct06/doc/delete_atoms.html --- lammps-2Oct06/doc/delete_atoms.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/delete_atoms.html 2006-09-28 13:55:36.000000000 -0600 @@ -36,7 +36,7 @@
Description:
-Delete the specfied atoms. This command can be used to carve out +
Delete the specified atoms. This command can be used to carve out voids from a block of material or to delete created atoms that are too close to each other (e.g. at a grain boundary).
@@ -73,7 +73,7 @@If the special_bonds command is used with a setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not appear in the neighbor list, and thus will not be considered for -deltion by the overlap style. You probably don't want to be +deletion by the overlap style. You probably don't want to be deleting one atom in a bonded pair anyway.
Related commands: diff -Naur lammps-2Oct06/doc/delete_atoms.txt lammps-3Oct06/doc/delete_atoms.txt --- lammps-2Oct06/doc/delete_atoms.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/delete_atoms.txt 2006-09-28 13:55:36.000000000 -0600 @@ -31,7 +31,7 @@ [Description:] -Delete the specfied atoms. This command can be used to carve out +Delete the specified atoms. This command can be used to carve out voids from a block of material or to delete created atoms that are too close to each other (e.g. at a grain boundary). @@ -68,7 +68,7 @@ If the "special_bonds"_special_bonds.html command is used with a setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not appear in the neighbor list, and thus will not be considered for -deltion by the {overlap} style. You probably don't want to be +deletion by the {overlap} style. You probably don't want to be deleting one atom in a bonded pair anyway. [Related commands:] diff -Naur lammps-2Oct06/doc/dielectric.html lammps-3Oct06/doc/dielectric.html --- lammps-2Oct06/doc/dielectric.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dielectric.html 2006-09-28 14:12:14.000000000 -0600 @@ -26,7 +26,7 @@
Set the dielectric constant for Coulombic interactions (pairwise and long-range) to this value. The constant is unitless, since it is used to reduce the strength of the interactions. The value is used in the -denominator of the formulas for Coulombic interations - e.g. a value +denominator of the formulas for Coulombic interactions - e.g. a value of 4.0 reduces the Coulombic interactions to 25% of their default strength. See the pair_style command for more details. diff -Naur lammps-2Oct06/doc/dielectric.txt lammps-3Oct06/doc/dielectric.txt --- lammps-2Oct06/doc/dielectric.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dielectric.txt 2006-09-28 14:12:14.000000000 -0600 @@ -23,7 +23,7 @@ Set the dielectric constant for Coulombic interactions (pairwise and long-range) to this value. The constant is unitless, since it is used to reduce the strength of the interactions. The value is used in the -denominator of the formulas for Coulombic interations - e.g. a value +denominator of the formulas for Coulombic interactions - e.g. a value of 4.0 reduces the Coulombic interactions to 25% of their default strength. See the "pair_style"_pair_style.html command for more details. diff -Naur lammps-2Oct06/doc/dihedral_coeff.html lammps-3Oct06/doc/dihedral_coeff.html --- lammps-2Oct06/doc/dihedral_coeff.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dihedral_coeff.html 2006-09-28 14:27:30.000000000 -0600 @@ -15,7 +15,7 @@
dihedral_coeff N args-
Examples: @@ -34,12 +34,12 @@ read_data command or in a restart file.
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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple dihedral types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral 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 +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 a dihedral_coeff command can override a previous setting @@ -51,7 +51,7 @@
A line in a data file that specifies dihedral coefficients uses the exact same format as the arguments of the dihedral_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Dihedral Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as @@ -82,7 +82,7 @@ read_data, read_restart, or create_box command.
-An dihedral style must be defined before any dihedral coefficients are +
A dihedral style must be defined before any dihedral coefficients are set, either in the input script or in a data file.
Related commands: diff -Naur lammps-2Oct06/doc/dihedral_coeff.txt lammps-3Oct06/doc/dihedral_coeff.txt --- lammps-2Oct06/doc/dihedral_coeff.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dihedral_coeff.txt 2006-09-28 14:27:30.000000000 -0600 @@ -12,7 +12,7 @@ dihedral_coeff N args :pre -N = dihedral type (see asterik form below) +N = dihedral type (see asterisk form below) args = coefficients for one or more dihedral types :ul [Examples:] @@ -31,12 +31,12 @@ "read_data"_read_data.html command or in a restart file. 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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple dihedral types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral 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 +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 a dihedral_coeff command can override a previous setting @@ -48,7 +48,7 @@ A line in a data file that specifies dihedral coefficients uses the exact same format as the arguments of the dihedral_coeff command in an input -script, except that wild-card asteriks should not be used since +script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Dihedral Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as @@ -79,7 +79,7 @@ "read_data"_read_data.html, "read_restart"_read_restart.html, or "create_box"_create_box.html command. -An dihedral style must be defined before any dihedral coefficients are +A dihedral style must be defined before any dihedral coefficients are set, either in the input script or in a data file. [Related commands:] diff -Naur lammps-2Oct06/doc/dihedral_style.html lammps-3Oct06/doc/dihedral_style.html --- lammps-2Oct06/doc/dihedral_style.html 2006-09-27 13:12:31.000000000 -0600 +++ lammps-3Oct06/doc/dihedral_style.html 2006-09-28 14:48:33.000000000 -0600 @@ -40,7 +40,7 @@
In the formulas listed for each dihedral style, phi is the torsional angle defined by the quadruplet of atoms.
-Note that when both an dihedral and pair style is defined, the +
Note that when both a dihedral and pair style is defined, the special_bond command often needs to be used to turn off (or weight) the pairwise interactions that would otherwise exist between the 4 bonded atoms. diff -Naur lammps-2Oct06/doc/dihedral_style.txt lammps-3Oct06/doc/dihedral_style.txt --- lammps-2Oct06/doc/dihedral_style.txt 2006-09-27 13:12:31.000000000 -0600 +++ lammps-3Oct06/doc/dihedral_style.txt 2006-09-28 14:48:33.000000000 -0600 @@ -38,7 +38,7 @@ In the formulas listed for each dihedral style, {phi} is the torsional angle defined by the quadruplet of atoms. -Note that when both an dihedral and pair style is defined, the +Note that when both a dihedral and pair style is defined, the "special_bond"_special_bond.html command often needs to be used to turn off (or weight) the pairwise interactions that would otherwise exist between the 4 bonded atoms. diff -Naur lammps-2Oct06/doc/dipole.html lammps-3Oct06/doc/dipole.html --- lammps-2Oct06/doc/dipole.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dipole.html 2006-09-28 14:54:07.000000000 -0600 @@ -15,7 +15,7 @@
dipole I value-
Examples: @@ -34,17 +34,17 @@ units command for a discussion of dipole units.
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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the dipole moment 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 +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 a dipole moement uses the exact +
A line in a data file that specifies a dipole moment uses the exact same format as the arguments of the dipole command in an input script, -except that no wild-card asterik can be used. For example, under the +except that no wild-card asterisk can be used. For example, under the "Dipoles" section of a data file, the line that corresponds to the 1st example above would be listed as
diff -Naur lammps-2Oct06/doc/dipole.txt lammps-3Oct06/doc/dipole.txt --- lammps-2Oct06/doc/dipole.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/dipole.txt 2006-09-28 14:54:07.000000000 -0600 @@ -12,7 +12,7 @@ dipole I value :pre -I = atom type (see asterik form below) +I = atom type (see asterisk form below) value = dipole :ul [Examples:] @@ -31,17 +31,17 @@ "units"_units.html command for a discussion of dipole units. 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 +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the dipole moment 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 +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 a dipole moement uses the exact +A line in a data file that specifies a dipole moment uses the exact same format as the arguments of the dipole command in an input script, -except that no wild-card asterik can be used. For example, under the +except that no wild-card asterisk can be used. For example, under the "Dipoles" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-2Oct06/doc/fix_momentum.html lammps-3Oct06/doc/fix_momentum.html --- lammps-2Oct06/doc/fix_momentum.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/fix_momentum.html 2006-10-02 14:21:36.000000000 -0600 @@ -19,7 +19,8 @@Examples:
-fix 1 all momentum 1 linear 1 1 0 angular +fix 1 all momentum 1 linear 1 1 0 +fix 1 all momentum 100 linear 1 1 1 angularDescription:
Zero the linear and/or angular momentum of the group of atoms every N -timesteps by adjusting the velocities of the atoms. +timesteps by adjusting the velocities of the atoms. One (or both) of +the linear or angular keywords must be specified.
If the linear keyword is used, the linear momentum is zeroed by subtracting the center-of-mass velocity of the group from each atom. @@ -53,7 +56,7 @@ thermostatting).
Note that the velocity command can be used to create -velocities with zero aggregate linear and/or angular momentum. +initial velocities with zero aggregate linear and/or angular momentum.
Restrictions: none
diff -Naur lammps-2Oct06/doc/fix_momentum.txt lammps-3Oct06/doc/fix_momentum.txt --- lammps-2Oct06/doc/fix_momentum.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/fix_momentum.txt 2006-10-02 14:21:36.000000000 -0600 @@ -14,7 +14,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l momentum = style name of this fix command :l - +N = adjust the momentum every this many timesteps one or more keyword/value pairs may be appended to the args :l keyword = {linear} or {angular} :l {linear} values = xflag yflag zflag @@ -24,12 +24,14 @@ [Examples:] -fix 1 all momentum 1 linear 1 1 0 angular :pre +fix 1 all momentum 1 linear 1 1 0 +fix 1 all momentum 100 linear 1 1 1 angular :pre [Description:] Zero the linear and/or angular momentum of the group of atoms every N -timesteps by adjusting the velocities of the atoms. +timesteps by adjusting the velocities of the atoms. One (or both) of +the {linear} or {angular} keywords must be specified. If the {linear} keyword is used, the linear momentum is zeroed by subtracting the center-of-mass velocity of the group from each atom. @@ -46,7 +48,7 @@ thermostatting). Note that the "velocity"_velocity.html command can be used to create -velocities with zero aggregate linear and/or angular momentum. +initial velocities with zero aggregate linear and/or angular momentum. [Restrictions:] none diff -Naur lammps-2Oct06/doc/fix_recenter.html lammps-3Oct06/doc/fix_recenter.html --- lammps-2Oct06/doc/fix_recenter.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/fix_recenter.html 2006-10-02 14:53:54.000000000 -0600 @@ -33,7 +33,9 @@
Examples:
-fix 1 all recenter 1 1 1 0 +fix 1 all recenter 0.0 0.5 0.0 +fix 1 all recenter INIT INIT NULL +fix 1 all recenter INIT 0.0 0.0 units boxDescription:
diff -Naur lammps-2Oct06/doc/fix_recenter.txt lammps-3Oct06/doc/fix_recenter.txt --- lammps-2Oct06/doc/fix_recenter.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-3Oct06/doc/fix_recenter.txt 2006-10-02 14:53:54.000000000 -0600 @@ -25,7 +25,9 @@ [Examples:] -fix 1 all recenter 1 1 1 0 :pre +fix 1 all recenter 0.0 0.5 0.0 +fix 1 all recenter INIT INIT NULL +fix 1 all recenter INIT 0.0 0.0 units box :pre [Description:] diff -Naur lammps-2Oct06/src/fix_momentum.cpp lammps-3Oct06/src/fix_momentum.cpp --- lammps-2Oct06/src/fix_momentum.cpp 2006-09-27 13:51:33.000000000 -0600 +++ lammps-3Oct06/src/fix_momentum.cpp 2006-10-02 14:21:36.000000000 -0600 @@ -27,7 +27,7 @@ FixMomentum::FixMomentum(int narg, char **arg) : Fix(narg, arg) { - if (narg != 7) error->all("Illegal fix momentum command"); + if (narg < 4) error->all("Illegal fix momentum command"); nevery = atoi(arg[3]); if (nevery <= 0) error->all("Illegal fix momentum command"); diff -Naur lammps-2Oct06/src/group.cpp lammps-3Oct06/src/group.cpp --- lammps-2Oct06/src/group.cpp 2006-09-27 13:51:33.000000000 -0600 +++ lammps-3Oct06/src/group.cpp 2006-10-02 14:21:36.000000000 -0600 @@ -699,7 +699,7 @@ dy = (x[i][1] + ybox*yprd) - cm[1]; dz = (x[i][2] + zbox*zprd) - cm[2]; if (mass_require) massone = mass[type[i]]; - massone = rmass[i]; + else massone = rmass[i]; p[0] += massone * (dy*v[i][2] - dz*v[i][1]); p[1] += massone * (dz*v[i][0] - dx*v[i][2]); p[2] += massone * (dx*v[i][1] - dy*v[i][0]); diff -Naur lammps-2Oct06/src/pppm.cpp lammps-3Oct06/src/pppm.cpp --- lammps-2Oct06/src/pppm.cpp 2006-09-27 13:51:33.000000000 -0600 +++ lammps-3Oct06/src/pppm.cpp 2006-10-02 14:21:36.000000000 -0600 @@ -18,6 +18,7 @@ #include "mpi.h" #include "string.h" #include "stdio.h" +#include "stdlib.h" #include "math.h" #include "pppm.h" #include "atom.h"