+| asphere | aspherical particles |
| class2 | class 2 force fields |
| dpd | dissipative particle dynamics (DPD) force field |
| granular | force fields and boundary conditions for granular systems |
@@ -293,7 +294,7 @@ This will produce a smaller executable which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
-editing of your machine Makefile.
+editing of your src/MAKE/Makefile.machine.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@@ -316,33 +317,19 @@ overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
-To use the "poems" package you must build LAMMPS with the POEMS
-library, which computes the constrained rigid-body motion of
-articulated (jointed) multibody systems. POEMS was written and is
-distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
-Institute (RPI) and a version is included in the LAMMPS distribution
-under the "lib" directory. To build LAMMPS with POEMS, you must use a
-low-level LAMMPS Makefile that includes the POEMS directory in its
-paths. See Makefile.g++_poems as an example. You must also build
-POEMS itself as a library before building LAMMPS, so that LAMMPS can
-link against it. The POEMS library is built by typing "make" from
-within the poems directory with the appropriate Makefile, e.g. "make
--f Makefile.g++". If one of the provided Makefiles is not appropriate
-for your system you can edit or add one as needed.
-
-To use the "meam" package you must build LAMMPS with the MEAM library,
-which computes the modified embedded atom method potential, which is a
-generalization of EAM potentials that can be used to model a wider
-variety of materials. This MEAM implementation was written by Greg
-Wagner at Sandia and is included under the "lib" directory. To build
-LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
-includes the MEAM directory in its paths. See Makefile.linux_meam as
-an example. You must also build MEAM itself as a library before
-building LAMMPS, so that LAMMPS can link against it. This requires a
-F90 compiler. The library is built by typing "make" from within the
-meam directory with the appropriate Makefile, e.g. "make -f
-Makefile.icc". If one of the provided Makefiles is not appropriate
-for your system you can edit or add one as needed.
+
To use the "meam" package you must build LAMMPS with the MEAM library
+in lib/meam, which computes the modified embedded atom method
+potential, which is a generalization of EAM potentials that can be
+used to model a wider variety of materials. This MEAM implementation
+was written by Greg Wagner at Sandia. To build LAMMPS with MEAM, you
+must use a low-level LAMMPS Makefile that includes the MEAM directory
+in its paths. See Makefile.linux_meam as an example. You must also
+build MEAM itself as a library before building LAMMPS, so that LAMMPS
+can link against it. This requires a F90 compiler. The library is
+built by typing "make" from within the meam directory with the
+appropriate Makefile, e.g. "make -f Makefile.icc". If one of the
+provided Makefiles is not appropriate for your system you can edit or
+add one as needed.
Note that linking a Fortran library to a C++ code can be problematic
(e.g. Fortran routine names can't be found due to non-standard
@@ -350,6 +337,19 @@ underscore rules) and typically requires additional C++ or F90
libraries be included in the link. You may need to read documentation
for your compiler about how to do this correctly.
+To use the "poems" package you must build LAMMPS with the POEMS
+library in lib/poems, which computes the constrained rigid-body motion
+of articulated (jointed) multibody systems. POEMS was written and is
+distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
+Institute (RPI). To build LAMMPS with POEMS, you must use a low-level
+LAMMPS Makefile that includes the POEMS directory in its paths. See
+Makefile.g++_poems as an example. You must also build POEMS itself as
+a library before building LAMMPS, so that LAMMPS can link against it.
+The POEMS library is built by typing "make" from within the poems
+directory with the appropriate Makefile, e.g. "make -f Makefile.g++".
+If one of the provided Makefiles is not appropriate for your system
+you can edit or add one as needed.
+
2.4 Building LAMMPS as a library
LAMMPS can be built as a library, which can then be called from
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index 5bbb6f6ae1..a0b6de21af 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -266,6 +266,7 @@ fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
+asphere : aspherical particles
class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
@@ -286,7 +287,7 @@ This will produce a smaller executable which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
-editing of your machine Makefile.
+editing of your src/MAKE/Makefile.machine.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@@ -309,33 +310,19 @@ overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
-To use the "poems" package you must build LAMMPS with the POEMS
-library, which computes the constrained rigid-body motion of
-articulated (jointed) multibody systems. POEMS was written and is
-distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
-Institute (RPI) and a version is included in the LAMMPS distribution
-under the "lib" directory. To build LAMMPS with POEMS, you must use a
-low-level LAMMPS Makefile that includes the POEMS directory in its
-paths. See Makefile.g++_poems as an example. You must also build
-POEMS itself as a library before building LAMMPS, so that LAMMPS can
-link against it. The POEMS library is built by typing "make" from
-within the poems directory with the appropriate Makefile, e.g. "make
--f Makefile.g++". If one of the provided Makefiles is not appropriate
-for your system you can edit or add one as needed.
-
-To use the "meam" package you must build LAMMPS with the MEAM library,
-which computes the modified embedded atom method potential, which is a
-generalization of EAM potentials that can be used to model a wider
-variety of materials. This MEAM implementation was written by Greg
-Wagner at Sandia and is included under the "lib" directory. To build
-LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
-includes the MEAM directory in its paths. See Makefile.linux_meam as
-an example. You must also build MEAM itself as a library before
-building LAMMPS, so that LAMMPS can link against it. This requires a
-F90 compiler. The library is built by typing "make" from within the
-meam directory with the appropriate Makefile, e.g. "make -f
-Makefile.icc". If one of the provided Makefiles is not appropriate
-for your system you can edit or add one as needed.
+To use the "meam" package you must build LAMMPS with the MEAM library
+in lib/meam, which computes the modified embedded atom method
+potential, which is a generalization of EAM potentials that can be
+used to model a wider variety of materials. This MEAM implementation
+was written by Greg Wagner at Sandia. To build LAMMPS with MEAM, you
+must use a low-level LAMMPS Makefile that includes the MEAM directory
+in its paths. See Makefile.linux_meam as an example. You must also
+build MEAM itself as a library before building LAMMPS, so that LAMMPS
+can link against it. This requires a F90 compiler. The library is
+built by typing "make" from within the meam directory with the
+appropriate Makefile, e.g. "make -f Makefile.icc". If one of the
+provided Makefiles is not appropriate for your system you can edit or
+add one as needed.
Note that linking a Fortran library to a C++ code can be problematic
(e.g. Fortran routine names can't be found due to non-standard
@@ -343,6 +330,19 @@ underscore rules) and typically requires additional C++ or F90
libraries be included in the link. You may need to read documentation
for your compiler about how to do this correctly.
+To use the "poems" package you must build LAMMPS with the POEMS
+library in lib/poems, which computes the constrained rigid-body motion
+of articulated (jointed) multibody systems. POEMS was written and is
+distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
+Institute (RPI). To build LAMMPS with POEMS, you must use a low-level
+LAMMPS Makefile that includes the POEMS directory in its paths. See
+Makefile.g++_poems as an example. You must also build POEMS itself as
+a library before building LAMMPS, so that LAMMPS can link against it.
+The POEMS library is built by typing "make" from within the poems
+directory with the appropriate Makefile, e.g. "make -f Makefile.g++".
+If one of the provided Makefiles is not appropriate for your system
+you can edit or add one as needed.
+
2.4 Building LAMMPS as a library :h4,link(2_4)
LAMMPS can be built as a library, which can then be called from
diff --git a/doc/atom_style.html b/doc/atom_style.html
index 3007f047b4..554e27102e 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -15,7 +15,7 @@
atom_style style args
-- style = angle or atomic or bond or charge or dpd or full or granular or molecular or hybrid
+
- style = angle or atomic or bond or charge or dpd or ellipsoid or full or granular or molecular or hybrid
args = none for any style except hybrid
hybrid args = list of one or more sub-styles
@@ -53,18 +53,23 @@ velocities, atom IDs and types.
- bond = bonds - e.g. bead-spring polymers
- charge = charge
- dpd = default values, also communicates velocities
+
- ellipsoid = quaternion for particle orientation, angular velocity/momentum
- molecular = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
- full = molecular + charge - e.g. biomolecules, charged polymers
- granular = granular atoms with rotational properties
-Typical simulations with a single pair potential will use only one of
-these styles. For cases where multiple pair potentials will be used
-(see the pair_style hybrid command), it may be
-necessary to use multiple atom styles. Another example is doing a DPD
-simulations with bonds or angles. In these cases the hybrid style
-can be used to list multiple atom styles. Atoms will then store and
-communicate the union of all quantities implied by the individual
-styles.
+
Typically, simulations require only a single (non-hybrid) atom style.
+If some atoms in the simulation do not have all the properties defined
+by a particular style, use the simplest style that defines all the
+needed properties by any atom. For example, if some atoms in a
+simulation are charged, but others are not, use the charge style.
+If some atoms have bonds, but others do not, use the bond style.
+The only scenario where the hybrid style is needed is if there is no
+single style which defines all needed properties of all atoms.
+E.g. if you want charged DPD particles, you would need to use
+"atom_style hybrid dpd charge". When a hybrid style is used, atoms
+store and communicate the union of all quantities implied by the
+individual styles.
LAMMPS can be extended with new atom styles; see this
section.
diff --git a/doc/atom_style.txt b/doc/atom_style.txt
index a1f2b13436..229970c100 100644
--- a/doc/atom_style.txt
+++ b/doc/atom_style.txt
@@ -12,7 +12,7 @@ atom_style command :h3
atom_style style args :pre
-style = {angle} or {atomic} or {bond} or {charge} or {dpd} or \
+style = {angle} or {atomic} or {bond} or {charge} or {dpd} or {ellipsoid} or \
{full} or {granular} or {molecular} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@@ -50,18 +50,23 @@ velocities, atom IDs and types.
{bond} = bonds - e.g. bead-spring polymers
{charge} = charge
{dpd} = default values, also communicates velocities
+{ellipsoid} = quaternion for particle orientation, angular velocity/momentum
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
{full} = molecular + charge - e.g. biomolecules, charged polymers
{granular} = granular atoms with rotational properties :ul
-Typical simulations with a single pair potential will use only one of
-these styles. For cases where multiple pair potentials will be used
-(see the "pair_style"_pair_style.html {hybrid} command), it may be
-necessary to use multiple atom styles. Another example is doing a DPD
-simulations with bonds or angles. In these cases the {hybrid} style
-can be used to list multiple atom styles. Atoms will then store and
-communicate the union of all quantities implied by the individual
-styles.
+Typically, simulations require only a single (non-hybrid) atom style.
+If some atoms in the simulation do not have all the properties defined
+by a particular style, use the simplest style that defines all the
+needed properties by any atom. For example, if some atoms in a
+simulation are charged, but others are not, use the {charge} style.
+If some atoms have bonds, but others do not, use the {bond} style.
+The only scenario where the {hybrid} style is needed is if there is no
+single style which defines all needed properties of all atoms.
+E.g. if you want charged DPD particles, you would need to use
+"atom_style hybrid dpd charge". When a hybrid style is used, atoms
+store and communicate the union of all quantities implied by the
+individual styles.
LAMMPS can be extended with new atom styles; see "this
section"_Section_modify.html.
diff --git a/doc/compute.html b/doc/compute.html
index 1ced3d2f53..a1bbe342a6 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -75,6 +75,7 @@ defined in LAMMPS:
temp/partial - temperature excluding one or more dimensions of velocity
temp/ramp - temperature after subtracting a ramped velocity component
temp/region - temperature of a region of atoms
+variable - calculate a scalar value from a variable
variable/atom - calculate a formula for each atom
Restrictions: none
diff --git a/doc/compute.txt b/doc/compute.txt
index 7d624a7b4c..dd20ec69af 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -72,6 +72,7 @@ defined in LAMMPS:
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/ramp"_compute_temp_ramp.html - temperature after subtracting a ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
+"variable"_compute_variable.html - calculate a scalar value from a variable
"variable/atom"_compute_variable_atom.html - calculate a formula for each atom :ul
[Restrictions:] none
diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html
new file mode 100644
index 0000000000..d5b3cb8780
--- /dev/null
+++ b/doc/compute_temp_asphere.html
@@ -0,0 +1,47 @@
+
+
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
+
+
+
+
+
+
+
+
+
+compute temp/asphere command
+
+Syntax:
+
+compute ID group-ID temp/asphere
+
+- ID, group-ID are documented in compute command
+
- temp/asphere = style name of this compute command
+
+Examples:
+
+compute 1 all temp/asphere
+compute myTemp mobile temp/asphere
+
+Description:
+
+Define a computation that calculates the temperature of a group of
+aspherical or ellipsoidal particles. The computation is similar to
+compute_temp, however, additional degrees of
+freedom (2 or 3) are incorporated for particles where the principal
+moments of inertia are unequal. The associated kinetic energy thus
+includes a rotational term KE_rotational = 1/2 I w^2, where I is the
+moment of inertia and w is the angular velocity.
+
+Restrictions:
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with atom_style ellipsoid.
+
+Related commands:
+
+compute temp
+
+Default: none
+
+
diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt
new file mode 100755
index 0000000000..c59f7dfb26
--- /dev/null
+++ b/doc/compute_temp_asphere.txt
@@ -0,0 +1,42 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute temp/asphere command :h3
+
+[Syntax:]
+
+compute ID group-ID temp/asphere :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+temp/asphere = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all temp/asphere
+compute myTemp mobile temp/asphere :pre
+
+[Description:]
+
+Define a computation that calculates the temperature of a group of
+aspherical or ellipsoidal particles. The computation is similar to
+"compute_temp"_compute_temp.html, however, additional degrees of
+freedom (2 or 3) are incorporated for particles where the principal
+moments of inertia are unequal. The associated kinetic energy thus
+includes a rotational term KE_rotational = 1/2 I w^2, where I is the
+moment of inertia and w is the angular velocity.
+
+[Restrictions:]
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with atom_style ellipsoid.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html
+
+[Default:] none
diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html
index 7a311bc188..88bcd60d9b 100644
--- a/doc/compute_temp_region.html
+++ b/doc/compute_temp_region.html
@@ -36,7 +36,7 @@ temp/rescale, etc.
Note that a region-style temperature can be used to thermostat with
fix temp/rescale or fix
langevin, but should probably not be used with
-Nose/Hoover style fixes (>fix nvt, fix
+Nose/Hoover style fixes (fix nvt, fix
npt, or fix nph), if the
degrees-of-freedom included in the computed T varies with time.
diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt
index a3d1bbfbe3..738fc98fba 100644
--- a/doc/compute_temp_region.txt
+++ b/doc/compute_temp_region.txt
@@ -33,7 +33,7 @@ temp/rescale"_fix_temp_rescale.html, etc.
Note that a {region}-style temperature can be used to thermostat with
"fix temp/rescale"_fix_temp_rescale.html or "fix
langevin"_fix_langevin.html, but should probably not be used with
-Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, fix
+Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, "fix
npt"_fix_npt.html, or "fix nph"_fix_nph.html), if the
degrees-of-freedom included in the computed T varies with time.
diff --git a/doc/compute_variable.html b/doc/compute_variable.html
new file mode 100644
index 0000000000..56b9ec01b2
--- /dev/null
+++ b/doc/compute_variable.html
@@ -0,0 +1,55 @@
+
+LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
+
+
+
+
+
+
+
+
+
+compute variable command
+
+Syntax:
+
+compute ID group-ID variable name
+
+- ID, group-ID are documented in compute command
+
- variable/atom = style name of this compute command
+
- name = variable name to invoke to compute a scalar quantity
+
+Examples:
+
+compute 1 all variable myTemp
+
+Description:
+
+Define a computation that calculates a formula that returns a scalar
+quantity. This quantity can be time averaged and output via the fix
+ave/time command. It could also be output via the
+thermo_style custom command, although it makes
+more sense to access the variable directly in this case.
+
+The formula is defined by the variable equal command.
+A variable of style equal can access properties of the system, such
+as volume or temperature, and also reference individual atom
+attributes, such as its coordinates or velocity.
+
+For example, these 3 commands would time average the system density
+(assuming the volume fluctuates) temperature and output the average
+value periodically to the file den.profile:
+
+variable den equal div(atoms,vol)
+compute density all variable den
+fix 1 all ave/time 1 1000 density 0 den.profile
+
+Restrictions: none
+
+Related commands:
+
+fix ave/time, variable
+
+Default: none
+
+
diff --git a/doc/compute_variable.txt b/doc/compute_variable.txt
new file mode 100644
index 0000000000..5b13a12388
--- /dev/null
+++ b/doc/compute_variable.txt
@@ -0,0 +1,50 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute variable command :h3
+
+[Syntax:]
+
+compute ID group-ID variable name :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+variable/atom = style name of this compute command
+name = variable name to invoke to compute a scalar quantity :ul
+
+[Examples:]
+
+compute 1 all variable myTemp :pre
+
+[Description:]
+
+Define a computation that calculates a formula that returns a scalar
+quantity. This quantity can be time averaged and output via the "fix
+ave/time"_fix_ave_time.html command. It could also be output via the
+"thermo_style custom"_thermo_style.html command, although it makes
+more sense to access the variable directly in this case.
+
+The formula is defined by the "variable equal"_variable.html command.
+A variable of style {equal} can access properties of the system, such
+as volume or temperature, and also reference individual atom
+attributes, such as its coordinates or velocity.
+
+For example, these 3 commands would time average the system density
+(assuming the volume fluctuates) temperature and output the average
+value periodically to the file den.profile:
+
+variable den equal div(atoms,vol)
+compute density all variable den
+fix 1 all ave/time 1 1000 density 0 den.profile :pre
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix ave/time"_fix_ave_time.html, "variable"_variable.html
+
+[Default:] none
diff --git a/doc/dump.html b/doc/dump.html
index bcd6013a0d..dd1f336ca3 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -37,7 +37,8 @@
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, tqx, tqy, tqz,
+ q, mux, muy, muz,
+ quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID[N]
@@ -52,7 +53,8 @@
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
- tqx,tqy,tqz = torque on dipolar atoms
+ quatw,quati,quatj,quatk = quaternion components for aspherical particles
+ tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
@@ -228,10 +230,15 @@ directly using the ix, iy, iz keywords. The
dump_modify command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
-The mux, muy, muz, tqy, tqx, tqy keywords are specific
-to dipolar systems defined with an atom style of dipole. The first
-3 give the orientation of the atom's dipole. The latter 3 give the
-torque on the dipolar atoms.
+
The mux, muy, muz keywords are specific to dipolar systems
+defined with an atom style of dipole. They give the orientation of
+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
+rotational torque on the particle.
The epair, ke, etotal, centro, and sxx, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
diff --git a/doc/dump.txt b/doc/dump.txt
index bfec5c466b..e7953c5f09 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -28,7 +28,8 @@ args = list of arguments for a particular style :l
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, tqx, tqy, tqz,
+ q, mux, muy, muz,
+ quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID\[N\]
@@ -43,7 +44,8 @@ args = list of arguments for a particular style :l
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
- tqx,tqy,tqz = torque on dipolar atoms
+ quatw,quati,quatj,quatk = quaternion components for aspherical particles
+ tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
@@ -218,10 +220,15 @@ directly using the {ix}, {iy}, {iz} keywords. The
"dump_modify"_dump_modify.html command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
-The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} keywords are specific
-to dipolar systems defined with an atom style of {dipole}. The first
-3 give the orientation of the atom's dipole. The latter 3 give the
-torque on the dipolar atoms.
+The {mux}, {muy}, {muz} keywords are specific to dipolar systems
+defined with an atom style of {dipole}. They give the orientation of
+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
+rotational torque on the particle.
The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html
new file mode 100644
index 0000000000..78e1ebc6fb
--- /dev/null
+++ b/doc/fix_nve_asphere.html
@@ -0,0 +1,43 @@
+
+
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
+
+
+
+
+
+
+
+
+
+fix nve/asphere command
+
+Syntax:
+
+fix ID group-ID nve/asphere
+
+- ID, group-ID are documented in fix command
+
- nve/asphere = style name of this fix command
+
+Examples:
+
+fix 1 all nve/asphere
+
+Description:
+
+Perform constant NVE updates of position, velocity, and angular
+velocity for aspherical or ellipsoidal particles in the group each
+timestep. V is volume; E is energy. This creates a system trajectory
+consistent with the microcanonical ensemble.
+
+Restrictions:
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with atom_style ellipsoid.
+
+Related commands:
+
+fix nve
+
+Default: none
+
+
diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt
new file mode 100755
index 0000000000..bd85d44bec
--- /dev/null
+++ b/doc/fix_nve_asphere.txt
@@ -0,0 +1,38 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nve/asphere command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/asphere :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nve/asphere = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nve/asphere :pre
+
+[Description:]
+
+Perform constant NVE updates of position, velocity, and angular
+velocity for aspherical or ellipsoidal particles in the group each
+timestep. V is volume; E is energy. This creates a system trajectory
+consistent with the microcanonical ensemble.
+
+[Restrictions:]
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with atom_style ellipsoid.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html
+
+[Default:] none
diff --git a/doc/next.html b/doc/next.html
index d2a0b201b9..0f66dc0240 100644
--- a/doc/next.html
+++ b/doc/next.html
@@ -77,7 +77,7 @@ finished.
Jump and next commands can also be nested to enable multi-level loops.
For example, this script will run 15 simulations in a double loop.
-variable i loop 3
+
variable i loop 3
variable j loop 5
clear
...
@@ -87,8 +87,8 @@ run 10000
next j
jump in.script
next i
-jump in.script
-
+jump in.script
+
Restrictions: none
Related commands:
diff --git a/doc/next.txt b/doc/next.txt
index 0125ca9e93..07e888c00d 100644
--- a/doc/next.txt
+++ b/doc/next.txt
@@ -84,7 +84,7 @@ run 10000
next j
jump in.script
next i
-jump in.script
+jump in.script :pre
[Restrictions:] none
diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html
index 6890064dc2..2cf3321726 100644
--- a/doc/pair_charmm.html
+++ b/doc/pair_charmm.html
@@ -113,6 +113,12 @@ because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all CHARMM potentials is to use the arithmetic formulas documented
+by the pair_modify command. The pair_modify
+mix setting is thus ignored for CHARMM potentials.
+
Restrictions:
The lj/charmm/coul/charmm and lj/charmm/coul/charmm/implicit
diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt
index 3ed6b22804..abc291acae 100644
--- a/doc/pair_charmm.txt
+++ b/doc/pair_charmm.txt
@@ -106,6 +106,12 @@ because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all CHARMM potentials is to use the {arithmetic} formulas documented
+by the "pair_modify"_pair_modify.html command. The "pair_modify
+mix"_pair_modify.html setting is thus ignored for CHARMM potentials.
+
[Restrictions:]
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
diff --git a/doc/pair_class2.html b/doc/pair_class2.html
index f744574b98..3688e7cfb4 100644
--- a/doc/pair_class2.html
+++ b/doc/pair_class2.html
@@ -86,6 +86,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all class2 potentials is to use the sixthpower formulas documented
+by the pair_modify command. The pair_modify
+mix setting is thus ignored for class2 potentials
+for epsilon and sigma. However it is still followed for mixing the
+cutoff distance.
+
Restrictions:
These styles are part of the "class2" package. They are only enabled
diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt
index d2da005415..10deb96488 100644
--- a/doc/pair_class2.txt
+++ b/doc/pair_class2.txt
@@ -80,6 +80,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all class2 potentials is to use the {sixthpower} formulas documented
+by the "pair_modify"_pair_modify.html command. The "pair_modify
+mix"_pair_modify.html setting is thus ignored for class2 potentials
+for epsilon and sigma. However it is still followed for mixing the
+cutoff distance.
+
[Restrictions:]
These styles are part of the "class2" package. They are only enabled
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 98d3fab476..2f7931a59c 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -93,6 +93,7 @@ the pair_style command, and coefficients specified by the associated
pair_style eam - embedded atom method (EAM)
pair_style eam/alloy - alloy EAM
pair_style eam/fs - Finnis-Sinclair EAM
+pair_style gayberne - Gay-Berne ellipsoidal potential
pair_style gran/hertzian - granular potential with Hertizain interactions
pair_style gran/history - granular potential with history effects
pair_style gran/no_history - granular potential without history effects
diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt
index 63e4758a7a..a3279f5580 100644
--- a/doc/pair_coeff.txt
+++ b/doc/pair_coeff.txt
@@ -90,6 +90,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
+"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html
new file mode 100644
index 0000000000..995043589d
--- /dev/null
+++ b/doc/pair_gayberne.html
@@ -0,0 +1,125 @@
+
+LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
+
+
+
+
+
+
+
+
+
+pair_style gayberne command
+
+Syntax:
+
+pair_style gayberne gamma upsilon mu cutoff
+
+- gamma = shift for potential minimum (typically 1)
+
- upsilon = exponent for eta orientation-dependent energy function
+
- mu = exponent for chi orientation-dependent energy function
+
- cutoff = global cutoff for interactions (distance units)
+
+Examples:
+
+pair_style gayberne 1.0 1.0 1.0 10.0
+pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
+
+Description:
+
+Style gayberne computes a Gay-Berne anisotropic LJ interaction
+(Beradi) between pairs of ellipsoidal particles via the
+formulas
+
+
+
+where A1 and A2 are the transformation matrices from the simulation
+box frame to the body frame and r12 is the center to center vector
+between the particles. Ur controls the shifted distance dependent
+interaction based on the distance of closest approach of the two
+particles (h12) and the user-specified shift parameter gamma.
+
+For large uniform molecules it has been shown that the energy
+parameters are approximately representable in terms of local contact
+curvatures (Everaers):
+
+
+
+The variable names utilized as potential parameters are for the most
+part taken from (Everaers) in order to be consistent with
+its RE-squared potential fix. Details on the upsilon and mu
+parameters are given here.
+Use of this pair style requires the
+fix nve/asphere in order to integrate particle
+rotation. Additionally, atom_style ellipsoid should
+be used since it defines the rotation state of the ellipsoidal
+particles.
+
+More details of the Gay-Berne formulation are given in the references
+listed below and in this document.
+
+The following coefficients must be defined for each pair of atoms
+types via the pair_coeff command as in the examples
+above, or in the data file or restart files read by the
+read_data or read_restart
+commands:
+
+- epsilon = well depth (energy units)
+
- sigma = minimum effective particle radii (distance units)
+
- a = ellipsoid radius in x dimension (distance units)
+
- b = ellipsoid radius in y dimension (distance units)
+
- c = ellipsoid radius in z dimension (distance units)
+
- epsilon_a = relative well depth for side-to-side interactions
+
- epsilon_b = relative well depth for face-to-face interactions
+
- epsilon_c = relative well depth for end-to-end interactions
+
- cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global
+cutoff specified in the pair_style command is used.
+
+The epsilon and sigma parameters are mixed for I != J atom pairings
+the same as Lennard-Jones parameters; see the pair_modify
+mix documentation for details. The other parameters
+(except cutoff) are really specific to a single atom type, and not a
+pair of atoms. Thus they are applied to atom type I only.
+
+Restrictions:
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with atom_style ellipsoid.
+
+The use of this potential requires additional fixes as described
+above. The "shift yes" option currently cannot be used with this
+potential to shift energies to 0 at the cutoff due to the anisotropic
+dependence of the interaction. Angular velocities are all set to zero
+initially. The Gay-Berne potential does not become isotropic as r
+increases (Everaers). The distance of closest approach
+approximation becomes less accurate as the shape of ellipsoids becomes
+more dissimilar (high aspect ratio particles).
+
+Related commands:
+
+pair_coeff, fix nve/asphere,
+compute temp/asphere
+
+Default: none
+
+
+
+
+
+(Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+
+
+
+(Berardi) Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
+
+
+
+(Perram) Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
+
+
+
+(Allen) Allen and Germano, Mol Phys 104, 3225-3235 (2006).
+
+
diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt
new file mode 100755
index 0000000000..9a14e855e0
--- /dev/null
+++ b/doc/pair_gayberne.txt
@@ -0,0 +1,116 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style gayberne command :h3
+
+[Syntax:]
+
+pair_style gayberne gamma upsilon mu cutoff :pre
+
+gamma = shift for potential minimum (typically 1)
+upsilon = exponent for eta orientation-dependent energy function
+mu = exponent for chi orientation-dependent energy function
+cutoff = global cutoff for interactions (distance units) :ul
+
+[Examples:]
+
+pair_style gayberne 1.0 1.0 1.0 10.0
+pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
+
+[Description:]
+
+Style {gayberne} computes a Gay-Berne anisotropic LJ interaction
+"(Beradi)"_#Beradi between pairs of ellipsoidal particles via the
+formulas
+
+:c,image(Eqs/pair_gayberne.jpg)
+
+where A1 and A2 are the transformation matrices from the simulation
+box frame to the body frame and r12 is the center to center vector
+between the particles. Ur controls the shifted distance dependent
+interaction based on the distance of closest approach of the two
+particles (h12) and the user-specified shift parameter gamma.
+
+For large uniform molecules it has been shown that the energy
+parameters are approximately representable in terms of local contact
+curvatures "(Everaers)"_#Everaers:
+
+:c,image(Eqs/pair_gayberne2.jpg)
+
+The variable names utilized as potential parameters are for the most
+part taken from "(Everaers)"_#Everaers in order to be consistent with
+its RE-squared potential fix. Details on the upsilon and mu
+parameters are given "here"_Eqs/pair_gayberne_extra.pdf.
+Use of this pair style requires the
+"fix nve/asphere"_fix_nve_asphere.html in order to integrate particle
+rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
+be used since it defines the rotation state of the ellipsoidal
+particles.
+
+More details of the Gay-Berne formulation are given in the references
+listed below and in "this document"_Eqs/pair_gayberne_extra.pdf.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+epsilon = well depth (energy units)
+sigma = minimum effective particle radii (distance units)
+a = ellipsoid radius in x dimension (distance units)
+b = ellipsoid radius in y dimension (distance units)
+c = ellipsoid radius in z dimension (distance units)
+epsilon_a = relative well depth for side-to-side interactions
+epsilon_b = relative well depth for face-to-face interactions
+epsilon_c = relative well depth for end-to-end interactions
+cutoff (distance units) :ul
+
+The last coefficient is optional. If not specified, the global
+cutoff specified in the pair_style command is used.
+
+The epsilon and sigma parameters are mixed for I != J atom pairings
+the same as Lennard-Jones parameters; see the "pair_modify
+mix"_pair_modify.html documentation for details. The other parameters
+(except cutoff) are really specific to a single atom type, and not a
+pair of atoms. Thus they are applied to atom type I only.
+
+[Restrictions:]
+
+Can only be used if LAMMPS was built with the "asphere" package. Can
+only be used with "atom_style ellipsoid"_atom_style.html.
+
+The use of this potential requires additional fixes as described
+above. The "shift yes" option currently cannot be used with this
+potential to shift energies to 0 at the cutoff due to the anisotropic
+dependence of the interaction. Angular velocities are all set to zero
+initially. The Gay-Berne potential does not become isotropic as r
+increases "(Everaers)"_#Everaers. The distance of closest approach
+approximation becomes less accurate as the shape of ellipsoids becomes
+more dissimilar (high aspect ratio particles).
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html,
+"compute temp/asphere"_compute_temp_asphere.html
+
+[Default:] none
+
+:line
+
+:link(Everaers)
+[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+
+:link(Berardi)
+[(Berardi)] Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
+
+:link(Perram)
+[(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
+
+:link(Allen)
+[(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006).
diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html
index 9422b776c8..89604c17de 100644
--- a/doc/pair_lj_expand.html
+++ b/doc/pair_lj_expand.html
@@ -49,6 +49,13 @@ commands:
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule is set by the
+pair_modify command. Additionally, the delta
+coefficient is always mixed by the rule
+
+delta_ij = (delta_i + delta_j) / 2
+
Restrictions: none
Related commands:
diff --git a/doc/pair_lj_expand.txt b/doc/pair_lj_expand.txt
index 8572c5916e..ed8885294a 100644
--- a/doc/pair_lj_expand.txt
+++ b/doc/pair_lj_expand.txt
@@ -46,6 +46,13 @@ cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule is set by the
+"pair_modify"_pair_modify.html command. Additionally, the delta
+coefficient is always mixed by the rule
+
+delta_ij = (delta_i + delta_j) / 2 :pre
+
[Restrictions:] none
[Related commands:]
diff --git a/doc/pair_modify.html b/doc/pair_modify.html
index 08770f185f..2f2c0b975b 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -49,13 +49,15 @@ not affected by this setting.
The mix keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
-J, when I != J. (I = J coefficients are set explicitly in the data
-file or input script.) The pair_coeff command can
-be used in the input script to specify epilon/sigma for a specific I,J
-pairing, which overrides the setting of the mix keyword. In each
-case, the LJ cutoff is mixed the same way as sigma.
+J, when I != J. Coefficients for I = J are set explicitly in the data
+file or input script. The pair_coeff command can be
+used in the input script to specify epilon/sigma for a specific I != J
+pairing, which overrides the setting of the mix keyword.
-These are the formulas used by the 3 mix options:
+
These are the formulas used by the 3 mix options. In each case, the
+LJ cutoff is mixed the same way as sigma. Note that some of these
+options are not available for certain pair styles. See the doc page
+for individual pair styles for those restrictions.
geometric
@@ -71,17 +73,7 @@ sigma_ij = (sigma_i + sigma_j) / 2
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
-sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
-
-Style soft only uses a pre-factor coefficient, which is always mixed
-geometrically, regardless of the mix setting. The charmm styles
-are always mixed arithmetically, regardless of the mix setting. The
-class2 styles are always mixed as a sixthpower, regardless of the
-mix setting, except that the cutoff is mixed according to the mix
-setting. Style lj/expand always mixes its delta coefficient using
-the rule
-
-delta_ij = (delta_i + delta_j) / 2
+sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
The table keyword applies to pair styles with a long-range Coulombic
term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
diff --git a/doc/pair_modify.txt b/doc/pair_modify.txt
index f08dbaef66..bab52c22d8 100644
--- a/doc/pair_modify.txt
+++ b/doc/pair_modify.txt
@@ -43,13 +43,15 @@ not affected by this setting.
The {mix} keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
-J, when I != J. (I = J coefficients are set explicitly in the data
-file or input script.) The "pair_coeff"_pair_coeff.html command can
-be used in the input script to specify epilon/sigma for a specific I,J
-pairing, which overrides the setting of the {mix} keyword. In each
-case, the LJ cutoff is mixed the same way as sigma.
+J, when I != J. Coefficients for I = J are set explicitly in the data
+file or input script. The "pair_coeff"_pair_coeff.html command can be
+used in the input script to specify epilon/sigma for a specific I != J
+pairing, which overrides the setting of the {mix} keyword.
-These are the formulas used by the 3 {mix} options:
+These are the formulas used by the 3 {mix} options. In each case, the
+LJ cutoff is mixed the same way as sigma. Note that some of these
+options are not available for certain pair styles. See the doc page
+for individual pair styles for those restrictions.
{geometric}
@@ -65,17 +67,7 @@ sigma_ij = (sigma_i + sigma_j) / 2 :pre
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
-sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
-
-Style {soft} only uses a pre-factor coefficient, which is always mixed
-geometrically, regardless of the {mix} setting. The {charmm} styles
-are always mixed arithmetically, regardless of the {mix} setting. The
-{class2} styles are always mixed as a sixthpower, regardless of the
-{mix} setting, except that the cutoff is mixed according to the mix
-setting. Style {lj/expand} always mixes its delta coefficient using
-the rule
-
-delta_ij = (delta_i + delta_j) / 2 :pre
+sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
The {table} keyword applies to pair styles with a long-range Coulombic
term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
diff --git a/doc/pair_soft.html b/doc/pair_soft.html
index 0a7ae109c2..92a970717e 100644
--- a/doc/pair_soft.html
+++ b/doc/pair_soft.html
@@ -54,6 +54,12 @@ or switch to a new pair style.
The last coefficient is optional. If not specified, the global soft
cutoff is used.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for Astart and Astop is
+as follows:
+
+A_ij = sqrt(A_i * A_j)
+
Restrictions: none
Related commands:
diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt
index 255d642124..5f1f21b895 100644
--- a/doc/pair_soft.txt
+++ b/doc/pair_soft.txt
@@ -51,6 +51,12 @@ or switch to a new pair style.
The last coefficient is optional. If not specified, the global soft
cutoff is used.
+If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for Astart and Astop is
+as follows:
+
+A_ij = sqrt(A_i * A_j) :pre
+
[Restrictions:] none
[Related commands:]
diff --git a/doc/pair_style.html b/doc/pair_style.html
index a3ff4bbc73..132e9dc050 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -99,6 +99,7 @@ the pair_style command, and coefficients specified by the associated
pair_style eam - embedded atom method (EAM)
pair_style eam/alloy - alloy EAM
pair_style eam/fs - Finnis-Sinclair EAM
+pair_style gayberne - Gay-Berne ellipsoidal potential
pair_style gran/hertzian - granular potential with Hertizain interactions
pair_style gran/history - granular potential with history effects
pair_style gran/no_history - granular potential without history effects
diff --git a/doc/pair_style.txt b/doc/pair_style.txt
index 58169b70bf..68bdf4fe25 100644
--- a/doc/pair_style.txt
+++ b/doc/pair_style.txt
@@ -96,6 +96,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
+"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
diff --git a/doc/read_data.html b/doc/read_data.html
index b37cde6500..dd076a27d8 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -253,6 +253,7 @@ line formats for each atom style in LAMMPS:
| bond | atom-ID molecule-ID atom-type x y z |
| charge | atom-ID atom-type q x y z |
| dpd | atom-ID atom-type x y z |
+| ellipsoid | atom-ID atom-type x y z quatw quati quatj quatk |
| full | atom-ID molecule-ID atom-type q x y z |
| granular | atom-ID atom-type diameter density x y z |
| molecular | atom-ID molecule-ID atom-type x y z
@@ -266,7 +267,8 @@ line formats for each atom style in LAMMPS:
q = charge on atom
diameter = diameter of atom
density = density of atom
-x,y,z = coordinates of atom
+x,y,z = coordinates of atom
+quatw,quati,quatj,quatk = quaternion components for orientation of atom
The units for these quantities depend on the unit style; see the
units command for details.
@@ -575,15 +577,25 @@ script.
line syntax: depends on atom style
-| all styles except granular | atom-ID vx vy vz |
-| granular | atom-ID vx vy vz phix phiy phiz
+ | | all styles except those listed | atom-ID vx vy vz |
+| ellipsoid | atom-ID vx vy vz lx ly lz |
+| granular | atom-ID vx vy vz wx wy wz
| where the keywords have these meanings:
+
+- vx,vy,vz = translational velocity of atom
+
- lx,ly,lz = angular momentum of aspherical atom
+
- wx,wy,wz = angular velocity of granular atom
+
The velocity lines can appear in any order. This section can only be
-used after an Atoms section. The Atoms section must have assigned
-a unique atom ID to each atom so that velocities can be assigned in
-this way. Vx,vy,vz are in units of velocity.
-Phix,phiy,phiz are in units of angular velocity (radians/time).
+used after an Atoms section. This is because the Atoms section
+must have assigned a unique atom ID to each atom so that velocities
+can be assigned to them.
+
+Vx,vy,vz are in units of velocity. Lx, ly, lz are in
+units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
+units of angular velocity (radians/time).
Translational velocities can also be set by the
velocity command in the input script.
diff --git a/doc/read_data.txt b/doc/read_data.txt
index c2842839d7..8917f55eef 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -231,6 +231,7 @@ atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dpd: atom-ID atom-type x y z
+ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
molecular: atom-ID molecule-ID atom-type x y z :tb(s=:)
@@ -243,7 +244,8 @@ type-ID = type of atom (1-Ntype)
q = charge on atom
diameter = diameter of atom
density = density of atom
-x,y,z = coordinates of atom :ul
+x,y,z = coordinates of atom
+quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
@@ -491,14 +493,24 @@ script.
one line per atom
line syntax: depends on atom style :ul
-all styles except granular: atom-ID vx vy vz
-granular: atom-ID vx vy vz phix phiy phiz :tb(s=:)
+all styles except those listed: atom-ID vx vy vz
+ellipsoid: atom-ID vx vy vz lx ly lz
+granular: atom-ID vx vy vz wx wy wz :tb(s=:)
+
+where the keywords have these meanings:
+
+vx,vy,vz = translational velocity of atom
+lx,ly,lz = angular momentum of aspherical atom
+wx,wy,wz = angular velocity of granular atom :ul
The velocity lines can appear in any order. This section can only be
-used after an {Atoms} section. The {Atoms} section must have assigned
-a unique atom ID to each atom so that velocities can be assigned in
-this way. Vx,vy,vz are in "units"_units.html of velocity.
-Phix,phiy,phiz are in units of angular velocity (radians/time).
+used after an {Atoms} section. This is because the {Atoms} section
+must have assigned a unique atom ID to each atom so that velocities
+can be assigned to them.
+
+Vx,vy,vz are in "units"_units.html of velocity. Lx, ly, lz are in
+units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
+units of angular velocity (radians/time).
Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.
|