- atom_style granular -
- fix nve/gran -
- fix gravity -
- thermo_style gran +
- fix nve/sphere +
- fix gravity
This compute +
+ +will calculate rotational kinetic energy which can then be output +with thermodynamic info. +
Use one of these 3 pair potentials:
- pair_style gran/history diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 416ed620f3..b2064dacac 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -315,9 +315,15 @@ To run a simulation of a granular model, you will want to use the following commands: "atom_style"_atom_style.html granular -"fix nve/gran"_fix_nve_gran.html -"fix gravity"_fix_gravity.html -"thermo_style"_thermo_style.html gran :ul +"fix nve/sphere"_fix_nve_sphere.html +"fix gravity"_fix_gravity.html :ul + +This compute + +"compute erotate/sphere"_compute_erotate_sphere.html :ul + +will calculate rotational kinetic energy which can then be "output +with thermodynamic info"_. Use one of these 3 pair potentials: diff --git a/doc/Section_intro.html b/doc/Section_intro.html index b138989dbb..0ff30903d1 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -128,8 +128,8 @@ commands)
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
- improper potentials: harmonic, cvff, class 2 (COMPASS) -
- hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simlulation -
- overlayed potentials: superposition of multiple pair potentials +
- hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation +
- overlaid potentials: superposition of multiple pair potentials
- polymer potentials: all-atom, united-atom, bead-spring, breakable
- water potentials: TIP3P, TIP4P, SPC
- implicit solvent potentials: hydrodynamic lubrication, Debye
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index bd68d38fe4..cfba53f6d7 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -129,8 +129,8 @@ commands)
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
- potentials can be used in one simlulation
- overlayed potentials: superposition of multiple pair potentials
+ potentials can be used in one simulation
+ overlaid potentials: superposition of multiple pair potentials
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
diff --git a/doc/Section_modify.html b/doc/Section_modify.html
index 77087e76ff..aaee85e949 100644
--- a/doc/Section_modify.html
+++ b/doc/Section_modify.html
@@ -14,7 +14,7 @@ Section
8. Modifying & extending LAMMPS
LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% if its source code +extend with new functionality. In fact, about 75% of its source code is files added in this fashion.
In this section, changes and additions users can make are listed along diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index 3b7be7822e..87acdb5344 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -11,7 +11,7 @@ Section"_Section_errors.html :c 8. Modifying & extending LAMMPS :h3 LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% if its source code +extend with new functionality. In fact, about 75% of its source code is files added in this fashion. In this section, changes and additions users can make are listed along diff --git a/doc/Section_tools.html b/doc/Section_tools.html index db0638824a..9e7c69d6c8 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -65,7 +65,7 @@ own sub-directories with their own Makefiles.
amber2lmp tool
-The amber2lmp sub-directory contain two Python scripts for converting +
The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information.
diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 17b84ddba4..3532f9c28a 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -61,7 +61,7 @@ own sub-directories with their own Makefiles. amber2lmp tool :h4,link(amber) -The amber2lmp sub-directory contain two Python scripts for converting +The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information. diff --git a/doc/angle_coeff.html b/doc/angle_coeff.html index db0e75636c..135862673e 100644 --- a/doc/angle_coeff.html +++ b/doc/angle_coeff.html @@ -32,7 +32,7 @@ Angle coefficients can also be set in the data file read by the 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 angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, then an asterisk with no numeric values means all types from 1 to N. A diff --git a/doc/angle_coeff.txt b/doc/angle_coeff.txt index 0eae25f22e..9ce03e49a0 100644 --- a/doc/angle_coeff.txt +++ b/doc/angle_coeff.txt @@ -29,7 +29,7 @@ Angle coefficients can also be set in the data file read by the "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 angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, then an asterisk with no numeric values means all types from 1 to N. A diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index ef7193ee0d..36449f7ab0 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -119,7 +119,7 @@ include that dimension. The default is 1 for all 3 dimensions. the specified factor for atoms of that type. This can be useful when different atom types have different sizes or masses. It can be used multiple times to adjust damp for several atom types. Note that -specifying a ratio of 2 increase the relaxation time which is +specifying a ratio of 2 increases the relaxation time which is equivalent to the the solvent's viscosity acting on particles with 1/2 the diameter. This is the opposite effect of scale factors used by the fix viscous command, since the damp factor in diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index e2be4640fd..cd0bbafb19 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -109,7 +109,7 @@ The keyword {scale} allows the damp factor to be scaled up or down by the specified factor for atoms of that type. This can be useful when different atom types have different sizes or masses. It can be used multiple times to adjust damp for several atom types. Note that -specifying a ratio of 2 increase the relaxation time which is +specifying a ratio of 2 increases the relaxation time which is equivalent to the the solvent's viscosity acting on particles with 1/2 the diameter. This is the opposite effect of scale factors used by the "fix viscous"_fix_viscous.html command, since the damp factor in diff --git a/doc/fix_poems.html b/doc/fix_poems.html index ffd8168496..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 diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt index cc96f7ed05..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 diff --git a/doc/jump.html b/doc/jump.html index 0fb42210c0..76c7c8d2ff 100644 --- a/doc/jump.html +++ b/doc/jump.html @@ -52,7 +52,7 @@ jump in.lj loop
If the jump file argument is a variable, the jump command can be used to cause different processor partitions to run different input scripts. In this example, LAMMPS is run on 40 processors, with 4 -partions of 10 procs each. An in.file containing the example variable +partitions of 10 procs each. An in.file containing the example variable and jump command will cause each partition to run a different simulation.
diff --git a/doc/jump.txt b/doc/jump.txt index 328c7935a1..b8b2d71d23 100644 --- a/doc/jump.txt +++ b/doc/jump.txt @@ -49,7 +49,7 @@ jump in.lj loop :pre If the jump {file} argument is a variable, the jump command can be used to cause different processor partitions to run different input scripts. In this example, LAMMPS is run on 40 processors, with 4 -partions of 10 procs each. An in.file containing the example variable +partitions of 10 procs each. An in.file containing the example variable and jump command will cause each partition to run a different simulation. diff --git a/doc/mass.html b/doc/mass.html index 960a66c059..24dca99fac 100644 --- a/doc/mass.html +++ b/doc/mass.html @@ -36,7 +36,7 @@ individual atoms, not types. Pair_style eam defin the masses of atom types in the EAM potential file.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 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 asterisk with no numeric values means all types from 1 to N. A leading @@ -46,7 +46,7 @@ types from m to n (inclusive).
A line in a data file that specifies mass uses the same format as the arguments of the mass command in an input script, except that no -wild-card asterik can be used. For example, under the "Masses" +wild-card asterisk can be used. For example, under the "Masses" section of a data file, the line that corresponds to the 1st example above would be listed as
diff --git a/doc/mass.txt b/doc/mass.txt index 18557e65b6..468aa742be 100644 --- a/doc/mass.txt +++ b/doc/mass.txt @@ -33,7 +33,7 @@ individual atoms, not types. "Pair_style eam"_pair_eam.html defines the masses of atom types in the EAM potential file. 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 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 asterisk with no numeric values means all types from 1 to N. A leading @@ -43,7 +43,7 @@ types from m to n (inclusive). A line in a data file that specifies mass uses the same format as the arguments of the mass command in an input script, except that no -wild-card asterik can be used. For example, under the "Masses" +wild-card asterisk can be used. For example, under the "Masses" section of a data file, the line that corresponds to the 1st example above would be listed as diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html index b0cb87c899..d89d11ea8b 100644 --- a/doc/pair_airebo.html +++ b/doc/pair_airebo.html @@ -80,9 +80,9 @@ LAMMPS atom types:- filename
- N element names = mapping of AIREBO elements to atom types
As an example, if your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be C, and the 4th to be H, you would use the -following pair_coeff command: +
As an example, if your LAMMPS simulation has 4 atom types and you want +the 1st 3 to be C, and the 4th to be H, you would use the following +pair_coeff command:
pair_coeff * * CH.airebo C C C H
diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt index d4fa1dd99f..e4e42b8603 100644 --- a/doc/pair_airebo.txt +++ b/doc/pair_airebo.txt @@ -77,9 +77,9 @@ LAMMPS atom types: filename N element names = mapping of AIREBO elements to atom types :ul -As an example, if your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be C, and the 4th to be H, you would use the -following pair_coeff command: +As an example, if your LAMMPS simulation has 4 atom types and you want +the 1st 3 to be C, and the 4th to be H, you would use the following +pair_coeff command: pair_coeff * * CH.airebo C C C H :pre diff --git a/doc/pair_gran.html b/doc/pair_gran.html index d90391ad5c..7dc342c208 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -44,7 +44,7 @@ apart when r is less than the contact distance d.
The 1st term is a normal force and the 2nd term is a tangential force. -The other quantites are as follows: +The other quantities are as follows:
- delta = d - r
- f(x) = 1 for Hookean contacts used in pair styles history and no_history
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt
index 7162f7af41..f91d0ef49a 100644
--- a/doc/pair_gran.txt
+++ b/doc/pair_gran.txt
@@ -34,7 +34,7 @@ apart when r is less than the contact distance d.
:c,image(Eqs/pair_granular.jpg)
The 1st term is a normal force and the 2nd term is a tangential force.
-The other quantites are as follows:
+The other quantities are as follows:
delta = d - r
f(x) = 1 for Hookean contacts used in pair styles {history} and {no_history}
diff --git a/doc/pair_soft.html b/doc/pair_soft.html
index a2d98aa767..d9de404e1a 100644
--- a/doc/pair_soft.html
+++ b/doc/pair_soft.html
@@ -65,7 +65,7 @@ always mixed via a geometric rule. The cutoff is mixed according to
the pair_modify mix value. The default mix value is geometric. See
the "pair_modify" command for details.
-
This pair styles does not support the pair_modify +
This pair style does not support the pair_modify shift option, since the pair interaction goes to 0.0 at the cutoff.
The pair_modify table and tail options are not diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt index c81adc9cce..6572583d59 100644 --- a/doc/pair_soft.txt +++ b/doc/pair_soft.txt @@ -62,7 +62,7 @@ always mixed via a {geometric} rule. The cutoff is mixed according to the pair_modify mix value. The default mix value is {geometric}. See the "pair_modify" command for details. -This pair styles does not support the "pair_modify"_pair_modify.html +This pair style does not support the "pair_modify"_pair_modify.html shift option, since the pair interaction goes to 0.0 at the cutoff. The "pair_modify"_pair_modify.html table and tail options are not diff --git a/doc/pair_sw.html b/doc/pair_sw.html index eda6de8b56..21198f81f1 100644 --- a/doc/pair_sw.html +++ b/doc/pair_sw.html @@ -85,19 +85,17 @@ 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 -tol that is used for -both two-body and three-body interactions. -In the Stillinger-Weber potential, the -interaction energies become negligibly small at atomic separations -substantially less than the theoretical cutoff -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 -entries so that they can be separately controlled. If tol = 0.0, then -the standard Stillinger-Weber cutoff is used. +
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 energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff 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 +provides 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.
The Stillinger-Weber potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt index 2c3d729916..3ee74af812 100644 --- a/doc/pair_sw.txt +++ b/doc/pair_sw.txt @@ -82,19 +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 -tol that is used for -both two-body and three-body interactions. -In the Stillinger-Weber potential, the -interaction energies become negligibly small at atomic separations -substantially less than the theoretical cutoff -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 -entries so that they can be separately controlled. If tol = 0.0, then -the standard Stillinger-Weber cutoff is used. +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 energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff 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 +provides 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. The Stillinger-Weber potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain