| born |
@@ -315,7 +315,7 @@ each, as in the 1st example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
-types. This takes the form “*” or “n” or “n” or “m*n”. If N = the
+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 asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
@@ -341,10 +341,10 @@ details.
For example, these commands would change the prefactor coefficient of
the pair_style soft potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:
-variable prefactor equal ramp(10,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor
-
-
+variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+
The kspace keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
@@ -380,14 +380,12 @@ constant).
For example, these commands would shrink the diameter of all granular
particles in the “center” group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:
-variable size equal ramp(1.0,0.1)
-fix 1 center adapt 10 atom diameter v_size
-
-
+variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter v_size
+
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_addforce.html b/doc/html/fix_addforce.html
index 2e773e8d92..0d70f117d5 100644
--- a/doc/html/fix_addforce.html
+++ b/doc/html/fix_addforce.html
@@ -154,11 +154,11 @@
Examples
-
fix kick flow addforce 1.0 0.0 0.0
-fix kick flow addforce 1.0 0.0 v_oscillate
-fix ff boundary addforce 0.0 0.0 v_push energy v_espace
-
-
+
+fix kick flow addforce 1.0 0.0 0.0
+fix kick flow addforce 1.0 0.0 v_oscillate
+fix ff boundary addforce 0.0 0.0 v_push energy v_espace
+
Description
@@ -221,7 +221,7 @@ converge properly.
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
@@ -230,12 +230,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this
fix to add the potential “energy” inferred by the added force to the
diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html
index d53243c00f..c15d2330aa 100644
--- a/doc/html/fix_append_atoms.html
+++ b/doc/html/fix_append_atoms.html
@@ -197,10 +197,8 @@ A box value selects standard distance units as defined by the
A lattice value means the distance units are in lattice spacings.
The lattice command must have been previously used to
define the lattice spacings.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_aveforce.html b/doc/html/fix_aveforce.html
index b5d312fdc6..dc0690a91d 100644
--- a/doc/html/fix_aveforce.html
+++ b/doc/html/fix_aveforce.html
@@ -150,11 +150,11 @@
Examples
-
fix pressdown topwall aveforce 0.0 -1.0 0.0
-fix 2 bottomwall aveforce NULL -1.0 0.0 region top
-fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
-
-
+
+fix pressdown topwall aveforce 0.0 -1.0 0.0
+fix 2 bottomwall aveforce NULL -1.0 0.0 region top
+fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
+
Description
@@ -187,7 +187,7 @@ to it.
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
@@ -196,12 +196,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify respa option is supported by this
fix. This allows to set at which level of the r-RESPA
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index d23425a85b..9bf14204bc 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -621,7 +621,7 @@ command if you want to include lattice spacings in a variable formula.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -631,7 +631,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
diff --git a/doc/html/fix_dt_reset.html b/doc/html/fix_dt_reset.html
index 9d7eaee03a..a6e011a7ac 100644
--- a/doc/html/fix_dt_reset.html
+++ b/doc/html/fix_dt_reset.html
@@ -182,9 +182,7 @@ outer loop (largest) timestep, which is the same timestep that the
Note that the cumulative simulation time (in time units), which
accounts for changes in the timestep size as a simulation proceeds,
can be accessed by the thermo_style time keyword.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_enforce2d.html b/doc/html/fix_enforce2d.html
index 3b70700e85..2790632437 100644
--- a/doc/html/fix_enforce2d.html
+++ b/doc/html/fix_enforce2d.html
@@ -151,7 +151,7 @@ not move from their initial z coordinate.
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
@@ -160,12 +160,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_evaporate.html b/doc/html/fix_evaporate.html
index 2f9d6f8aba..929f36c037 100644
--- a/doc/html/fix_evaporate.html
+++ b/doc/html/fix_evaporate.html
@@ -187,9 +187,7 @@ count is changing due to evaporation, you typically should use the
compute_modify dynamic yes command for the
temperature compute you are using.
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global scalar, which can be accessed by various
diff --git a/doc/html/fix_flow_gauss.html b/doc/html/fix_flow_gauss.html
index ca10c2d38d..7c5defac59 100644
--- a/doc/html/fix_flow_gauss.html
+++ b/doc/html/fix_flow_gauss.html
@@ -219,10 +219,8 @@ work on the system must have fix_modify energy yes set as well. This
includes thermostat fixes and any constraints that hold the positions
of wall atoms fixed, such as fix spring/self.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the Making LAMMPS section for more info.
No information about this fix is written to binary restart files.
diff --git a/doc/html/fix_freeze.html b/doc/html/fix_freeze.html
index 0d285a3709..36a0b3c6fa 100644
--- a/doc/html/fix_freeze.html
+++ b/doc/html/fix_freeze.html
@@ -155,7 +155,7 @@ using
f
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
@@ -164,12 +164,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index f10e0f3416..84a652448b 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -208,7 +208,7 @@ field.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -218,7 +218,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html
index 366694bd8a..92dafa1af5 100644
--- a/doc/html/fix_indent.html
+++ b/doc/html/fix_indent.html
@@ -163,11 +163,11 @@
Examples
-
fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
-fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
-fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
-
-
+
+fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
+fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
+fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
+
Description
@@ -179,9 +179,9 @@ constraining wall around a simulation; see the discussion of the
The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.
A spherical indenter exerts a force of magnitude
-
+
+F(r) = - K (r - R)^2
+
on each atom where K is the specified force constant, r is the
distance from the atom to the center of the indenter, and R is the
radius of the indenter. The force is repulsive and F(r) = 0 for r >
@@ -226,23 +226,23 @@ fashion. For the latter, see the start and stop keywords of t
then this variable definition will keep it’s center at a relative
position in the simulation box, 1/4 of the way from the left edge to
the right edge, even if the box size changes:
-
variable x equal "xlo + 0.25*lx"
-
-
+
+variable x equal "xlo + 0.25*lx"
+
Similarly, either of these variable definitions will move the indenter
from an initial position at 2.5 at a constant velocity of 5:
-
variable x equal "2.5 + 5*elaplong*dt"
-variable x equal vdisplace(2.5,5)
-
-
+
+variable x equal "2.5 + 5*elaplong*dt"
+variable x equal vdisplace(2.5,5)
+
If a spherical indenter’s radius is specified as v_r, then these
variable definitions will grow the size of the indenter at a specfied
rate.
-
variable r0 equal 0.0
-variable rate equal 1.0
-variable r equal "v_r0 + step*dt*v_rate"
-
-
+
+variable r0 equal 0.0
+variable rate equal 1.0
+variable r equal "v_r0 + step*dt*v_rate"
+
If the side keyword is specified as out, which is the default,
then particles outside the indenter are pushded away from its outer
surface, as described above. This only applies to spherical or
@@ -275,9 +275,7 @@ contains xlat, ylat, zlat keywords of the
fix 1 all indent $k sphere ...
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this
fix to add the energy of interaction between atoms and the indenter to
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html
index bf67a0e983..b9c5e56f09 100644
--- a/doc/html/fix_langevin.html
+++ b/doc/html/fix_langevin.html
@@ -363,7 +363,7 @@ generates an average temperature of 220 K, instead of 300 K.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -373,7 +373,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_manifoldforce.html b/doc/html/fix_manifoldforce.html
index bba7854a61..fa64343002 100644
--- a/doc/html/fix_manifoldforce.html
+++ b/doc/html/fix_manifoldforce.html
@@ -147,10 +147,8 @@
This can be used in combination with
minimize to remove overlap between particles while
keeping them (roughly) constrained to the given manifold, e.g. to set up a run with
fix nve/manifold/rattle.
I have found that only
hftn and
quickmin with a very small time step perform adequately though.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_meso.html b/doc/html/fix_meso.html
index a3727a2590..0ad7f8f622 100644
--- a/doc/html/fix_meso.html
+++ b/doc/html/fix_meso.html
@@ -150,9 +150,7 @@ needed to time-integrate mesoscopic systems where particles carry
internal variables such as SPH or DPDE.
See this PDF guide to using SPH in
LAMMPS.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_meso_stationary.html b/doc/html/fix_meso_stationary.html
index 42106fb5c2..b4fb2d708c 100644
--- a/doc/html/fix_meso_stationary.html
+++ b/doc/html/fix_meso_stationary.html
@@ -151,9 +151,7 @@ fixed boundary particles which constrain a fluid to a given region in
space.
See this PDF guide to using SPH in
LAMMPS.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_modify.html b/doc/html/fix_modify.html
index 7e3b41240e..2af8e6a5be 100644
--- a/doc/html/fix_modify.html
+++ b/doc/html/fix_modify.html
@@ -128,9 +128,9 @@
fix_modify command
Syntax
-
fix_modify fix-ID keyword value ...
-
-
+
+fix_modify fix-ID keyword value ...
+
- fix-ID = ID of the fix to modify
- one or more keyword/value pairs may be appended
@@ -145,11 +145,11 @@
Examples
-
fix_modify 3 temp myTemp press myPress
-fix_modify 1 energy yes
-fix_modify tether respa 2
-
-
+
+fix_modify 3 temp myTemp press myPress
+fix_modify 1 energy yes
+fix_modify tether respa 2
+
Description
diff --git a/doc/html/fix_momentum.html b/doc/html/fix_momentum.html
index 8329e21764..c5388609c5 100644
--- a/doc/html/fix_momentum.html
+++ b/doc/html/fix_momentum.html
@@ -175,9 +175,7 @@ thermostatting).
of atoms by rescaling the velocities after the momentum was removed.
Note that the velocity command can be used to create
initial velocities with zero aggregate linear and/or angular momentum.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html
index 1e50f393e0..77ce3e40aa 100644
--- a/doc/html/fix_neb.html
+++ b/doc/html/fix_neb.html
@@ -149,7 +149,7 @@
simulation run via the neb command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the neb command and in
-Section_howto 5 of the manual. The fix
+Section 6.5 of the manual. The fix
neb command must be used with the “neb” command to define how
inter-replica forces are computed.
Only the N atoms in the fix group experience inter-replica forces.
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index 8cbee0b46f..5b4e907f36 100644
--- a/doc/html/fix_nh.html
+++ b/doc/html/fix_nh.html
@@ -594,7 +594,7 @@ the various ways to do this.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -604,7 +604,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html
index 2c2d1a4d0a..f32f344a7d 100644
--- a/doc/html/fix_nph_asphere.html
+++ b/doc/html/fix_nph_asphere.html
@@ -195,7 +195,7 @@ It also means that changing attributes of
thermo_temp or
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -205,7 +205,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_nph_body.html b/doc/html/fix_nph_body.html
index 891af950d5..314d162346 100644
--- a/doc/html/fix_nph_body.html
+++ b/doc/html/fix_nph_body.html
@@ -172,10 +172,10 @@ unchanged and controlling the pressure of a surrounding fluid.
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/body” and
“pressure”, as if these commands had been issued:
-
compute fix-ID_temp all temp/body
-compute fix-ID_press all pressure fix-ID_temp
-
-
+
+compute fix-ID_temp all temp/body
+compute fix-ID_press all pressure fix-ID_temp
+
See the compute temp/body and compute pressure commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -192,7 +192,7 @@ It also means that changing attributes of thermo_temp or
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -202,11 +202,9 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html
index ec7a15a0cd..ce7e1a82fc 100644
--- a/doc/html/fix_nph_sphere.html
+++ b/doc/html/fix_nph_sphere.html
@@ -195,7 +195,7 @@ It also means that changing attributes of thermo_temp or
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -205,7 +205,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html
index 85dd234fe3..4297f3c953 100644
--- a/doc/html/fix_nphug.html
+++ b/doc/html/fix_nphug.html
@@ -254,7 +254,7 @@ It also means that changing attributes of thermo_temp or
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -264,7 +264,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html
index 2216a34678..f0514cc211 100644
--- a/doc/html/fix_npt_asphere.html
+++ b/doc/html/fix_npt_asphere.html
@@ -215,7 +215,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -225,7 +225,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat and barostat
diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html
index b037898463..b5b4b2c806 100644
--- a/doc/html/fix_npt_body.html
+++ b/doc/html/fix_npt_body.html
@@ -212,7 +212,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -222,7 +222,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat and barostat
diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html
index f05e786221..6e17faf4a1 100644
--- a/doc/html/fix_npt_sphere.html
+++ b/doc/html/fix_npt_sphere.html
@@ -214,7 +214,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -224,7 +224,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat and barostat
diff --git a/doc/html/fix_nve.html b/doc/html/fix_nve.html
index bda99e1820..049b4aea64 100644
--- a/doc/html/fix_nve.html
+++ b/doc/html/fix_nve.html
@@ -161,7 +161,7 @@ ensemble.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -171,12 +171,10 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html
index 88dbabd521..76b01445dc 100644
--- a/doc/html/fix_nve_asphere.html
+++ b/doc/html/fix_nve_asphere.html
@@ -163,7 +163,7 @@ This fix is not invoked during Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -173,7 +173,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/fix_nve_eff.html b/doc/html/fix_nve_eff.html
index d7e486fe39..cb8c7c772f 100644
--- a/doc/html/fix_nve_eff.html
+++ b/doc/html/fix_nve_eff.html
@@ -149,9 +149,7 @@ nuclei and electrons in the group for the
fix nve command, except that the radius and radial velocity
of electrons are also updated.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html
index ede833982c..febff4c671 100644
--- a/doc/html/fix_nve_limit.html
+++ b/doc/html/fix_nve_limit.html
@@ -178,9 +178,7 @@ strategy is to turn off fix shake when performing initial dynamics
that need this fix, then turn fix shake on when doing normal dynamics
with a fixed-size timestep.
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html
index 5b6a9bb8ab..4ace7ccd77 100644
--- a/doc/html/fix_nve_line.html
+++ b/doc/html/fix_nve_line.html
@@ -148,8 +148,8 @@
orientation, and angular velocity for line segment particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble. See
-Section_howto 14 of the manual for an overview of
-using line segment particles.
+
Section 6.14 of the manual for an
+overview of using line segment particles.
This fix differs from the fix nve command, which
assumes point particles and only updates their position and velocity.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 149e6de046..de2190636f 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -159,7 +159,7 @@ keyword =
every
atoms constrained to a curved surface (manifold) in the group each
timestep. The constraint is handled by RATTLE
(Andersen)
written out for the special case of single-particle constraints as
-explained in
(Paquay). V is volume; E is energy. This way,
+explained in
(Paquay). V is volume; E is energy. This way,
the dynamics of particles constrained to curved surfaces can be
studied. If combined with
fix langevin, this
generates Brownian motion of particles constrained to a curved
diff --git a/doc/html/fix_nve_noforce.html b/doc/html/fix_nve_noforce.html
index 495a804493..ddde5961c0 100644
--- a/doc/html/fix_nve_noforce.html
+++ b/doc/html/fix_nve_noforce.html
@@ -155,9 +155,7 @@ command, but with fix nve/noforce, the forces on the wall atoms are
unchanged, and can thus be printed by the
dump command or
queried with an equal-style
variable that uses the
fcm() group function to compute the total force on the group of atoms.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html
index 2a70998598..5874f2a8e2 100644
--- a/doc/html/fix_nve_sphere.html
+++ b/doc/html/fix_nve_sphere.html
@@ -177,7 +177,7 @@ at only a small additional computational cost.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -187,7 +187,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html
index 1462555ef2..407af506f5 100644
--- a/doc/html/fix_nve_tri.html
+++ b/doc/html/fix_nve_tri.html
@@ -146,10 +146,10 @@
Description
Perform constant NVE integration to update position, velocity,
orientation, and angular momentum for triangular particles in the
-group each timestep. V is volume; E is energy. This creates a system
-trajectory consistent with the microcanonical ensemble. See
-Section_howto 14 of the manual for an overview of
-using triangular particles.
+group each timestep. V is volume; E is energy. This creates a
+system trajectory consistent with the microcanonical ensemble. See
+
Section 6.14 of the manual for an
+overview of using triangular particles.
This fix differs from the fix nve command, which
assumes point particles and only updates their position and velocity.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html
index 473db13d7f..ffa5445676 100644
--- a/doc/html/fix_nvt_asphere.html
+++ b/doc/html/fix_nvt_asphere.html
@@ -201,7 +201,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -211,7 +211,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html
index 57ba66659d..0ad3a20fb6 100644
--- a/doc/html/fix_nvt_body.html
+++ b/doc/html/fix_nvt_body.html
@@ -198,7 +198,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -208,7 +208,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index bcb049ebeb..d20d96a113 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/doc/html/fix_nvt_manifold_rattle.html
@@ -160,10 +160,8 @@ keyword = temp or tchain or every
This fix combines the RATTLE-based (Andersen) time integrator of fix nve/manifold/rattle (Paquay) with a Nose-Hoover-chain thermostat to sample the
canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
For a list of currently supported manifolds and their parameters, see manifolds
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html
index 09875bceb8..a7e91fc5f5 100644
--- a/doc/html/fix_nvt_sllod.html
+++ b/doc/html/fix_nvt_sllod.html
@@ -226,7 +226,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -236,7 +236,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html
index 6a27b967ed..b79b7c419a 100644
--- a/doc/html/fix_nvt_sphere.html
+++ b/doc/html/fix_nvt_sphere.html
@@ -201,7 +201,7 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -211,7 +211,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart
diff --git a/doc/html/fix_oneway.html b/doc/html/fix_oneway.html
index 8d22f6f62f..bb5b2a052e 100644
--- a/doc/html/fix_oneway.html
+++ b/doc/html/fix_oneway.html
@@ -156,10 +156,8 @@ dimension. The effect is that the particle moves in one direction
only.
This can be used, for example, as a simple model of a semi-permeable
membrane, or as an implementation of Maxwell’s demon.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_planeforce.html b/doc/html/fix_planeforce.html
index 9adcd39dda..83c023cc9e 100644
--- a/doc/html/fix_planeforce.html
+++ b/doc/html/fix_planeforce.html
@@ -151,9 +151,7 @@ components of force in the plane specified by the normal vector
force perpendicular to the plane.
If the initial velocity of the atom is 0.0 (or in the plane), then it
should continue to move in the plane thereafter.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_poems.html b/doc/html/fix_poems.html
index d7308971fb..f1dc2c297e 100644
--- a/doc/html/fix_poems.html
+++ b/doc/html/fix_poems.html
@@ -208,9 +208,7 @@ for in temperature and pressure computations. Similarly, the rigid
body contribution to the pressure virial is also accounted for. The
latter is only correct if forces within the bodies have been turned
off, and there is only a single fix poems defined.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_press_berendsen.html b/doc/html/fix_press_berendsen.html
index ffd58394b6..5afff5a4f3 100644
--- a/doc/html/fix_press_berendsen.html
+++ b/doc/html/fix_press_berendsen.html
@@ -275,10 +275,10 @@ these 4 keywords:
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp” and “pressure”,
as if these commands had been issued:
-
compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
-
+
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+
See the compute temp and compute pressure commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is the same
@@ -291,9 +291,7 @@ fix’s temperature or pressure via the
or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID.
It also means that changing attributes of thermo_temp or
thermo_press will have no effect on this fix.
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify temp and press options are
supported by this fix. You can use them to assign a
diff --git a/doc/html/fix_print.html b/doc/html/fix_print.html
index 68739849fc..85cd254494 100644
--- a/doc/html/fix_print.html
+++ b/doc/html/fix_print.html
@@ -186,9 +186,7 @@ keyword was used. By default, the title line is as follows:
where ID is replaced with the fix-ID.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands. No parameter of this fix can
diff --git a/doc/html/fix_property_atom.html b/doc/html/fix_property_atom.html
index 474600ad06..81dc2b6611 100644
--- a/doc/html/fix_property_atom.html
+++ b/doc/html/fix_property_atom.html
@@ -153,11 +153,11 @@
Examples
-
fix 1 all property/atom mol
-fix 1 all property/atom i_myflag1 i_myflag2
-fix 1 all property/atom d_sx d_sy d_sz
-
-
+
+fix 1 all property/atom mol
+fix 1 all property/atom i_myflag1 i_myflag2
+fix 1 all property/atom d_sx d_sy d_sz
+
Description
@@ -246,10 +246,10 @@ you need to initialize them explicitly. This can be done by the
read_data command, using its
fix keyword and
passing it the fix-ID of this fix.
Thus these commands:
-
fix prop all property/atom mol d_flag
-read_data data.txt fix prop NULL Molecules
-
-
+
+fix prop all property/atom mol d_flag
+read_data data.txt fix prop NULL Molecules
+
would allow a data file to have a section like this:
@@ -271,11 +271,11 @@ per-atom properties can be in any order.
set command. For example, if you wanted molecules
defined for every set of 10 atoms, based on their atom-IDs,
these commands could be used:
-
fix prop all property/atom mol
-variable cluster atom ((id-1)/10)+1
-set id * mol v_cluster
-
-
+
+fix prop all property/atom mol
+variable cluster atom ((id-1)/10)+1
+set id * mol v_cluster
+
The atom-style variable will create values for atoms
with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
set commands assigns them to the molecule ID for each atom,
@@ -292,11 +292,11 @@ properties in a completely general fashion.
their values. This means that the values can be output via the
dump custom command, accessed by fixes like
fix ave/atom, accessed by other computes like
compute reduce, or used in
atom-style variables.
For example, these commands will output two new properties to a custom
dump file:
-
fix prop all property/atom i_flag1 d_flag2
-compute 1 all property/atom i_flag1 d_flag2
-dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
-
-
+
+fix prop all property/atom i_flag1 d_flag2
+compute 1 all property/atom i_flag1 d_flag2
+dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
+
If you wish to add new pair styles,
fixes, or computes that use the per-atom
@@ -324,10 +324,10 @@ command, there will be a new section named with the fix-ID
existing data file and just add this Isotopes section with
one line per atom containing atom-ID and mass. Either way, the
extended data file can be read back with:
-
fix Isotopes all property/atom rmass ghost yes
-read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
-
-
+
+fix Isotopes all property/atom rmass ghost yes
+read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
+
Please note that the first Isotopes refers to the fix-ID
and the second to the name of the section. The following input
script code will now change the first 100 water molecules in this
@@ -337,10 +337,8 @@ example to heavy water:
set group hwat mass 2.0141018
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the per-atom values it stores to binary restart files, so that the values can be restored when a
simulation is restarted. See the read_restart
command for info on how to re-specify a fix in an input script that
diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html
index 3bf7a12a5c..13a0577b28 100644
--- a/doc/html/fix_qeq_comb.html
+++ b/doc/html/fix_qeq_comb.html
@@ -183,7 +183,7 @@ equilibration calculation is written to the specifed file.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html
index 665de2e845..a973e86218 100644
--- a/doc/html/fix_qeq_reax.html
+++ b/doc/html/fix_qeq_reax.html
@@ -189,7 +189,7 @@ be used with the
start/stop keywords of the
Section_accelerate
+hardware, as discussed in
Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -199,7 +199,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html
index 6428f2b3a3..59a3c11e74 100644
--- a/doc/html/fix_recenter.html
+++ b/doc/html/fix_recenter.html
@@ -208,9 +208,7 @@ solvent would be cooled to compensate. A better solution for this
simulation scenario is to use the fix spring command
to tether the molecule in place.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html
index 3dc4ef9053..aced61874e 100644
--- a/doc/html/fix_rigid.html
+++ b/doc/html/fix_rigid.html
@@ -733,7 +733,7 @@ rigid/nvt.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -743,7 +743,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_setforce.html b/doc/html/fix_setforce.html
index 35b7f76194..dd03b992f6 100644
--- a/doc/html/fix_setforce.html
+++ b/doc/html/fix_setforce.html
@@ -149,11 +149,11 @@
Examples
-
fix freeze indenter setforce 0.0 0.0 0.0
-fix 2 edge setforce NULL 0.0 0.0
-fix 2 edge setforce NULL 0.0 v_oscillate
-
-
+
+fix freeze indenter setforce 0.0 0.0 0.0
+fix 2 edge setforce NULL 0.0 0.0
+fix 2 edge setforce NULL 0.0 v_oscillate
+
Description
@@ -187,7 +187,7 @@ to it.
Styles with a r kk suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
The region keyword is also supported by Kokkos, but a Kokkos-enabled
@@ -198,12 +198,10 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify respa option is supported by
this fix. This allows to set at which level of the r-RESPA
diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html
index 6c279062d0..8622c1515e 100644
--- a/doc/html/fix_shake.html
+++ b/doc/html/fix_shake.html
@@ -262,7 +262,7 @@ info of atoms in the molecule.
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
-Section_accelerate of the manual. The
+Section 5 of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
@@ -271,7 +271,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
RATTLE:
diff --git a/doc/html/fix_srd.html b/doc/html/fix_srd.html
index 10de92548e..8ee372d9d4 100644
--- a/doc/html/fix_srd.html
+++ b/doc/html/fix_srd.html
@@ -207,9 +207,9 @@ rotations every N timesteps.
SRD particles have a mass, temperature, characteristic timestep
dt_SRD, and mean free path between collisions (lamda). The
fundamental equation relating these 4 quantities is
-
lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
-
-
+
+lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
+
The mass of SRD particles is set by the mass command
elsewhere in the input script. The SRD timestep dt_SRD is N times the
step dt defined by the timestep command. Big
@@ -419,10 +419,8 @@ epsilon or cutoff length to 0.0.
The “delete_atoms overlap” command may be useful in setting up an SRD
simulation to insure there are no initial overlaps between big and SRD
particles.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix tabulates several SRD statistics which are stored in a vector
diff --git a/doc/html/fix_store_force.html b/doc/html/fix_store_force.html
index 30ced5f810..43d5848e79 100644
--- a/doc/html/fix_store_force.html
+++ b/doc/html/fix_store_force.html
@@ -168,9 +168,7 @@ i.e. before other fixes that apply constraints. However, if you wish
to include certain constraints (e.g. fix shake) in the stored force,
then it could be specified after some fixes and before others.
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix produces a per-atom array which can be accessed by various
diff --git a/doc/html/fix_tmd.html b/doc/html/fix_tmd.html
index c8e628825e..a6a826dd62 100644
--- a/doc/html/fix_tmd.html
+++ b/doc/html/fix_tmd.html
@@ -128,9 +128,9 @@
fix tmd command
Syntax
-
fix ID group-ID tmd rho_final file1 N file2
-
-
+
+fix ID group-ID tmd rho_final file1 N file2
+
- ID, group-ID are documented in fix command
- tmd = style name of this fix command
@@ -142,10 +142,10 @@
Examples
-
fix 1 all nve
-fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
-
-
+
+fix 1 all nve
+fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
+
Description
@@ -199,9 +199,7 @@ restarted runs, the name of the TMD statistics file should be changed
to prevent it being overwritten.
For more information about TMD, see (Schlitter1) and
(Schlitter2).
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various output commands.
diff --git a/doc/html/fix_vector.html b/doc/html/fix_vector.html
index 87d0a0ebd7..17b80b0202 100644
--- a/doc/html/fix_vector.html
+++ b/doc/html/fix_vector.html
@@ -138,21 +138,21 @@
one or more input values can be listed
value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
-
c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID
-v_name = value calculated by an equal-style variable with name
-v_name[I] = Ith component of vector-style variable with name
-
-
+
+c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = value calculated by an equal-style variable with name
+v_name[I] = Ith component of vector-style variable with name
+
Examples
-
fix 1 all vector 100 c_myTemp
-fix 1 all vector 5 c_myTemp v_integral
-
-
+
+fix 1 all vector 100 c_myTemp
+fix 1 all vector 5 c_myTemp v_integral
+
Description
@@ -166,12 +166,12 @@ rows is growing. The resulting vector or array can be used by other
time-integrated using the
variable trap() function.
For example the velocity auto-correlation function (VACF) can be
time-integrated, to yield a diffusion coefficient, as follows:
-
compute 2 all vacf
-fix 5 all vector 1 c_2[4]
-variable diff equal dt*trap(f_5)
-thermo_style custom step v_diff
-
-
+
+compute 2 all vacf
+fix 5 all vector 1 c_2[4]
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff
+
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own “group” definitions.
@@ -197,7 +197,7 @@ command with a timestep value that encompasses all the runs. This is
so that the vector or array stored by this fix can be allocated to a
sufficient size.
-
If a value begins with “c_”, a compute ID must follow which has been
+
If a value begins with “c_”, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
@@ -209,7 +209,7 @@ not in your input script, but by fix temp/rescale. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and add them to LAMMPS.
-
If a value begins with “f_”, a fix ID must follow which has been
+
If a value begins with “f_”, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
@@ -217,7 +217,7 @@ calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with Nevery, else an error will result.
Users can also write code for their own fix styles and add them to LAMMPS.
-
If a value begins with “v_”, a variable name must follow which has
+
If a value begins with “v_”, a variable name must follow which has
been previously defined in the input script. An equal-style or
vector-style variable can be referenced; the latter requires a
bracketed term to specify the Ith element of the vector calculated by
@@ -227,10 +227,8 @@ which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to be stored by fix vector.
-
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix produces a global vector or global array which can be
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html
index 9df5dfe8ef..31e0ed2501 100644
--- a/doc/html/fix_wall_reflect.html
+++ b/doc/html/fix_wall_reflect.html
@@ -252,7 +252,7 @@ position = c0 + A (1 - cos(omega*delta))
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -262,7 +262,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html
index c72f90b6bb..d244f4b0cb 100644
--- a/doc/html/fix_wall_srd.html
+++ b/doc/html/fix_wall_srd.html
@@ -159,11 +159,11 @@
Examples
-
fix xwalls all wall/srd xlo EDGE xhi EDGE
-fix walls all wall/srd xlo 0.0 ylo 10.0 units box
-fix top all wall/srd zhi v_pressdown
-
-
+
+fix xwalls all wall/srd xlo EDGE xhi EDGE
+fix walls all wall/srd xlo 0.0 ylo 10.0 units box
+fix top all wall/srd zhi v_pressdown
+
Description
@@ -249,22 +249,22 @@ define the lattice spacings.
Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
variables.
-
variable ramp equal ramp(0,10)
-fix 1 all wall/srd xlo v_ramp
-
-
-
variable linear equal vdisplace(0,20)
-fix 1 all wall/srd xlo v_linear
-
-
-
variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle
-
-
-
variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle
-
-
+
+variable ramp equal ramp(0,10)
+fix 1 all wall/srd xlo v_ramp
+
+
+variable linear equal vdisplace(0,20)
+fix 1 all wall/srd xlo v_linear
+
+
+variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+
+
+variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+
The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The displace(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
@@ -272,20 +272,18 @@ where delta is the elapsed time.
The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:
-
position = c0 + A sin(omega*delta)
-
-
+
+position = c0 + A sin(omega*delta)
+
The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:
-
position = c0 + A (1 - cos(omega*delta))
-
-
-
+
+position = c0 + A (1 - cos(omega*delta))
+
-
-
Restart, fix_modify, output, run start/stop, minimize info
+
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
diff --git a/doc/html/group.html b/doc/html/group.html
index 009ce0deea..29c9364e48 100644
--- a/doc/html/group.html
+++ b/doc/html/group.html
@@ -329,7 +329,7 @@ per-atom values are 0.0, are removed from the dynamic group.
each run and on every timestep that is a multiple of
N, which is the
argument for the
every keyword (N = 1 is the default). For an
energy minimization, via the
minimize command, an
-assignement is made at the beginning of the minimization, but not
+assignment is made at the beginning of the minimization, but not
during the iterations of the minimizer.
The point in the timestep at which atoms are assigned to a dynamic
group is after the initial stage of velocity Verlet time integration
diff --git a/doc/html/if.html b/doc/html/if.html
index fe0350f9d5..b6fa9347b2 100644
--- a/doc/html/if.html
+++ b/doc/html/if.html
@@ -186,7 +186,7 @@ above.
If a command itself requires a quoted argument (e.g. a
print command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
-See Section_commands 2 of the manual for
+See Section 3.2 of the manual for
more details on using quotes in arguments. Only one of level of
nesting is allowed, but that should be sufficient for most use cases.
diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html
index 0d39e5935a..281b2e7a45 100644
--- a/doc/html/improper_class2.html
+++ b/doc/html/improper_class2.html
@@ -199,7 +199,7 @@ radians internally; hence the units of M are in energy/radian^2.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -209,7 +209,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_coeff.html b/doc/html/improper_coeff.html
index bad06f5d5e..a457db6736 100644
--- a/doc/html/improper_coeff.html
+++ b/doc/html/improper_coeff.html
@@ -128,9 +128,9 @@
improper_coeff command
Syntax
-
+
+improper_coeff N args
+
- N = improper type (see asterisk form below)
- args = coefficients for one or more improper types
@@ -138,11 +138,11 @@
Examples
-
improper_coeff 1 300.0 0.0
-improper_coeff * 80.2 -1 2
-improper_coeff *4 80.2 -1 2
-
-
+
+improper_coeff 1 300.0 0.0
+improper_coeff * 80.2 -1 2
+improper_coeff *4 80.2 -1 2
+
Description
@@ -154,7 +154,7 @@ 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 asterisk can be
used to set the coefficients for multiple improper types. This takes
-the form “*” or “n” or “n” or “m*n”. If N = the number of improper
+the form “*” or “*n” or “n*” or “m*n”. If N = the number of improper
types, then an asterisk with no numeric values means all types from 1
to N. A leading asterisk means all types from 1 to n (inclusive). A
trailing asterisk means all types from n to N (inclusive). A middle
@@ -163,10 +163,10 @@ asterisk means all types from m to n (inclusive).
setting for the same improper type. For example, these commands set
the coeffs for all improper types, then overwrite the coeffs for just
improper type 2:
-
improper_coeff * 300.0 0.0
-improper_coeff 2 50.0 0.0
-
-
+
+improper_coeff * 300.0 0.0
+improper_coeff 2 50.0 0.0
+
A line in a data file that specifies improper coefficients uses the
exact same format as the arguments of the improper_coeff command in an
input script, except that wild-card asterisks should not be used since
diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html
index 28c2370f09..7f477dd600 100644
--- a/doc/html/improper_cossq.html
+++ b/doc/html/improper_cossq.html
@@ -173,7 +173,7 @@ internally; hence the units of K are in energy/radian^2.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -183,7 +183,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html
index 461f02eeab..dfc56136b6 100644
--- a/doc/html/improper_cvff.html
+++ b/doc/html/improper_cvff.html
@@ -174,7 +174,7 @@ commands:
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -184,7 +184,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html
index be22144ccf..ea9ee9d225 100644
--- a/doc/html/improper_fourier.html
+++ b/doc/html/improper_fourier.html
@@ -166,7 +166,7 @@ commands:
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -176,7 +176,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html
index 11553c0187..cc024bb0f6 100644
--- a/doc/html/improper_harmonic.html
+++ b/doc/html/improper_harmonic.html
@@ -179,7 +179,7 @@ internally; hence the units of K are in energy/radian^2.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -189,7 +189,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_hybrid.html b/doc/html/improper_hybrid.html
index 438f01c690..742c0c785e 100644
--- a/doc/html/improper_hybrid.html
+++ b/doc/html/improper_hybrid.html
@@ -128,20 +128,20 @@
improper_style hybrid command
Syntax
-
improper_style hybrid style1 style2 ...
-
-
+
+improper_style hybrid style1 style2 ...
+
- style1,style2 = list of one or more improper styles
Examples
-
improper_style hybrid harmonic helix
-improper_coeff 1 harmonic 120.0 30
-improper_coeff 2 cvff 20.0 -1 2
-
-
+
+improper_style hybrid harmonic helix
+improper_coeff 1 harmonic 120.0 30
+improper_coeff 2 cvff 20.0 -1 2
+
Description
diff --git a/doc/html/improper_none.html b/doc/html/improper_none.html
index 5b3ddfa062..daeabe5196 100644
--- a/doc/html/improper_none.html
+++ b/doc/html/improper_none.html
@@ -128,15 +128,15 @@
improper_style none command
Syntax
-
+
+improper_style none
+
Examples
-
+
+improper_style none
+
Description
diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html
index 0e7e4330b0..c970326ef4 100644
--- a/doc/html/improper_ring.html
+++ b/doc/html/improper_ring.html
@@ -177,7 +177,7 @@ internally; hence the units of K are in energy/radian^2.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -187,7 +187,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_style.html b/doc/html/improper_style.html
index b21d0199f5..cd71f9a567 100644
--- a/doc/html/improper_style.html
+++ b/doc/html/improper_style.html
@@ -128,20 +128,20 @@
improper_style command
Syntax
-
+
+improper_style style
+
- style = none or hybrid or class2 or cvff or harmonic
Examples
-
improper_style harmonic
-improper_style cvff
-improper_style hybrid cvff harmonic
-
-
+
+improper_style harmonic
+improper_style cvff
+improper_style hybrid cvff harmonic
+
Description
@@ -208,9 +208,9 @@ a package.
Default
-
+
+improper_style none
+
diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html
index de79db67ef..f8fcfb706e 100644
--- a/doc/html/improper_umbrella.html
+++ b/doc/html/improper_umbrella.html
@@ -168,7 +168,7 @@ commands:
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -178,7 +178,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/improper_zero.html b/doc/html/improper_zero.html
index 35365943bc..8fcf52d50c 100644
--- a/doc/html/improper_zero.html
+++ b/doc/html/improper_zero.html
@@ -134,11 +134,11 @@ improper_style zero nocoeff
Examples
-
improper_style zero
-improper_style zero nocoeff
-improper_coeff *
-
-
+
+improper_style zero
+improper_style zero nocoeff
+improper_coeff *
+
Description
diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html
index 5cecc5b41d..68a9f47895 100644
--- a/doc/html/kspace_style.html
+++ b/doc/html/kspace_style.html
@@ -271,7 +271,7 @@ However, for low relative accuracy, the staggered PPPM mesh size may
be essentially the same as for regular PPPM, which means the method
will be up to 2x slower in the KSpace time (simply 2x more expensive).
For more details and timings, see
-
Section_accelerate.
+
Section 5.
Note
Using pppm/stagger may not give the same increase in the
@@ -374,7 +374,7 @@ relative RMS error.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -393,7 +393,7 @@ calculated on the CPU in non-threaded mode.
These accelerated styles are part of the GPU, USER-INTEL,
KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. See the Making LAMMPS section for more info.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/log.html b/doc/html/log.html
index d0aedd79d7..00b63cc6b8 100644
--- a/doc/html/log.html
+++ b/doc/html/log.html
@@ -155,7 +155,7 @@ be a variable, so that different processors do not attempt to write to
the same log file.
The file “log.lammps” is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
-switch -log. See Section_start 6 for
+switch -log. See Section 2.7 for
details.
diff --git a/doc/html/manifolds.html b/doc/html/manifolds.html
index 73f57ef600..5fec3a287f 100644
--- a/doc/html/manifolds.html
+++ b/doc/html/manifolds.html
@@ -139,9 +139,9 @@ to the relevant fixes.
-
-
-
+
+
+
@@ -159,7 +159,7 @@ to the relevant fixes.
| cylinder_dent |
R l a |
-x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise |
+x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise |
A cylinder with a dent around z = 0 |
|
@@ -195,7 +195,7 @@ to the relevant fixes.
| supersphere |
R q |
-|x|^q + |y|^q + |z|^q - R^q = 0 |
+|x|^q + |y|^q + |z|^q - R^q = 0 |
A supersphere of hyperradius R |
|
diff --git a/doc/html/mass.html b/doc/html/mass.html
index b52482445a..45725432bf 100644
--- a/doc/html/mass.html
+++ b/doc/html/mass.html
@@ -138,11 +138,11 @@
Examples
-
mass 1 1.0
-mass * 62.5
-mass 2* 62.5
-
-
+
+mass 1 1.0
+mass * 62.5
+mass 2* 62.5
+
Description
@@ -153,7 +153,7 @@ what mass units to use.
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
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
+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 asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
diff --git a/doc/html/neb.html b/doc/html/neb.html
index d820af07c5..38af41fdab 100644
--- a/doc/html/neb.html
+++ b/doc/html/neb.html
@@ -170,7 +170,7 @@ follows the discussion in these 3 papers: (Henkelman2), and (Nakano).
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see Section_start 7 of the
+switch; see Section 2.7 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on just
diff --git a/doc/html/pair_adp.html b/doc/html/pair_adp.html
index 5bc88ab7d0..759795cc8b 100644
--- a/doc/html/pair_adp.html
+++ b/doc/html/pair_adp.html
@@ -235,7 +235,7 @@ array tabulated with a scaling by r.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -245,7 +245,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html
index 6827568073..4624ba98c7 100644
--- a/doc/html/pair_airebo.html
+++ b/doc/html/pair_airebo.html
@@ -284,7 +284,7 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -294,7 +294,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_awpmd.html b/doc/html/pair_awpmd.html
index 5fb4a74c41..4b2dc24da3 100644
--- a/doc/html/pair_awpmd.html
+++ b/doc/html/pair_awpmd.html
@@ -128,9 +128,9 @@
pair_style awpmd/cut command
Syntax
-
pair_style awpmd/cut Rc keyword value ...
-
-
+
+pair_style awpmd/cut Rc keyword value ...
+
- Rc = global cutoff, -1 means cutoff of half the shortest box length
- zero or more keyword/value pairs may be appended
@@ -154,12 +154,12 @@
Examples
-
pair_style awpmd/cut -1
-pair_style awpmd/cut 40.0 uhf free
-pair_coeff * *
-pair_coeff 2 2 20.0
-
-
+
+pair_style awpmd/cut -1
+pair_style awpmd/cut 40.0 uhf free
+pair_coeff * *
+pair_coeff 2 2 20.0
+
Description
diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html
index baf69eecfa..e807bdb7aa 100644
--- a/doc/html/pair_beck.html
+++ b/doc/html/pair_beck.html
@@ -174,7 +174,7 @@ Rc is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -184,7 +184,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html
index 5f623fb0b7..f71c89bec2 100644
--- a/doc/html/pair_body.html
+++ b/doc/html/pair_body.html
@@ -145,7 +145,7 @@ pair_coeff 1 1 1.0 1.5 2.5
Description
Style body is for use with body particles and calculates pairwise
body/body interactions as well as interactions between body and
-point-particles. See Section_howto 14
+point-particles. See Section 6.14
of the manual and the body doc page for more details on
using body particles.
This pair style is designed for use with the “nparticle” body style,
diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html
index c73ca9761f..d3edfaaded 100644
--- a/doc/html/pair_born.html
+++ b/doc/html/pair_born.html
@@ -261,7 +261,7 @@ same global Coulombic cutoff specified in the pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -271,7 +271,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_buck.html b/doc/html/pair_buck.html
index fa537931bf..e24b875998 100644
--- a/doc/html/pair_buck.html
+++ b/doc/html/pair_buck.html
@@ -289,7 +289,7 @@ pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -299,7 +299,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_buck_long.html b/doc/html/pair_buck_long.html
index 82fc5d5641..5d8371e461 100644
--- a/doc/html/pair_buck_long.html
+++ b/doc/html/pair_buck_long.html
@@ -223,7 +223,7 @@ global Coulombic cutoff is allowed.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -233,7 +233,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html
index 93e44709ce..8fc752ddf6 100644
--- a/doc/html/pair_charmm.html
+++ b/doc/html/pair_charmm.html
@@ -260,7 +260,7 @@ the pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -270,7 +270,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html
index a2dee8a442..3efdc15034 100644
--- a/doc/html/pair_class2.html
+++ b/doc/html/pair_class2.html
@@ -238,7 +238,7 @@ cutoff distance.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -248,7 +248,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_coeff.html b/doc/html/pair_coeff.html
index 1689bf6047..c5bb770a91 100644
--- a/doc/html/pair_coeff.html
+++ b/doc/html/pair_coeff.html
@@ -128,9 +128,9 @@
pair_coeff command
Syntax
-
+
+pair_coeff I J args
+
- I,J = atom types (see asterisk form below)
- args = coefficients for one or more pairs of atom types
@@ -138,15 +138,15 @@
Examples
-
pair_coeff 1 2 1.0 1.0 2.5
-pair_coeff 2 * 1.0 1.0
-pair_coeff 3* 1*2 1.0 1.0 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff * * nialhjea 1 1 2
-pair_coeff * 3 morse.table ENTRY1
-pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
-
-
+
+pair_coeff 1 2 1.0 1.0 2.5
+pair_coeff 2 * 1.0 1.0
+pair_coeff 3* 1*2 1.0 1.0 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff * * nialhjea 1 1 2
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
+
Description
@@ -160,7 +160,7 @@ required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.
A wildcard asterisk can be used in place of or in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
-types. This takes the form “*” or “n” or “n” or “m*n”. If N = the
+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 asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
@@ -170,10 +170,10 @@ asterisks imply type pairs where J < I, they are ignored.
Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J
pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
-
pair_coeff * * 1.0 1.0 2.5
-pair_coeff 2 3 2.0 1.0 1.12
-
-
+
+pair_coeff * * 1.0 1.0 2.5
+pair_coeff 2 3 2.0 1.0 1.12
+
A line in a data file that specifies pair coefficients uses the exact
same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of
@@ -214,13 +214,13 @@ copying them into your working directory. Environment variables are
set in different ways for different shells. Here are example settings
for
csh, tcsh:
-
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
-
-
+
+% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
+
bash:
-
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
-
-
+
+% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
+
Windows:
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"
diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html
index a1520bc730..57ec62a36b 100644
--- a/doc/html/pair_colloid.html
+++ b/doc/html/pair_colloid.html
@@ -239,7 +239,7 @@ commands for efficiency: Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -249,7 +249,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html
index c0768ee36a..3fffa53753 100644
--- a/doc/html/pair_comb.html
+++ b/doc/html/pair_comb.html
@@ -230,7 +230,7 @@ nor file ffield.comb3 with style comb.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -240,7 +240,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html
index 98cba31724..252ace1d8a 100644
--- a/doc/html/pair_coul.html
+++ b/doc/html/pair_coul.html
@@ -415,7 +415,7 @@ command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -425,7 +425,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html
index 12d0c515ef..05c7ec567b 100644
--- a/doc/html/pair_cs.html
+++ b/doc/html/pair_cs.html
@@ -164,7 +164,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
Description
These pair styles are designed to be used with the adiabatic
core/shell model of (Mitchell and Finchham). See
-Section_howto 25 of the manual for an
+Section 6.25 of the manual for an
overview of the model as implemented in LAMMPS.
These pair styles are identical to the pair_style born/coul/long and pair_style buck/coul/long styles, except they correctly treat the
special case where the distance between two charged core and shell
diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
index 25e82fc6e3..bedd2387db 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -298,7 +298,7 @@ type pair.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -308,7 +308,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html
index 1275469c41..8ae775068a 100644
--- a/doc/html/pair_dpd.html
+++ b/doc/html/pair_dpd.html
@@ -235,7 +235,7 @@ random force.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -245,7 +245,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_eam.html b/doc/html/pair_eam.html
index 62a0305a0c..06a22a2d74 100644
--- a/doc/html/pair_eam.html
+++ b/doc/html/pair_eam.html
@@ -493,7 +493,7 @@ are listed.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -503,7 +503,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accerlate of the manual for more
+
See Section 5 of the manual for more
instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html
index 54a690dde1..0be43042ec 100644
--- a/doc/html/pair_edip.html
+++ b/doc/html/pair_edip.html
@@ -216,7 +216,7 @@ the EDIP package.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -226,7 +226,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html
index 831c9f00dc..235f487b3d 100644
--- a/doc/html/pair_eim.html
+++ b/doc/html/pair_eim.html
@@ -244,7 +244,7 @@ needs.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -254,7 +254,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html
index d90d449b83..086a35e74f 100644
--- a/doc/html/pair_gauss.html
+++ b/doc/html/pair_gauss.html
@@ -204,7 +204,7 @@ commands:
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -215,7 +215,7 @@ LAMMPS was built with those packages. See the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html
index 68e46bd2d8..9a5923113e 100644
--- a/doc/html/pair_gayberne.html
+++ b/doc/html/pair_gayberne.html
@@ -247,7 +247,7 @@ pair_coeff sigma to 1.0 as well.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -257,7 +257,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_gran.html b/doc/html/pair_gran.html
index 37946c96aa..2932d4e4bd 100644
--- a/doc/html/pair_gran.html
+++ b/doc/html/pair_gran.html
@@ -299,7 +299,7 @@ potential.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -309,7 +309,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html
index a58a10912a..a8a5ce03b2 100644
--- a/doc/html/pair_gromacs.html
+++ b/doc/html/pair_gromacs.html
@@ -217,7 +217,7 @@ cutoff(s) specified in the pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -227,7 +227,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html
index e639ba34e8..a2b9b14aed 100644
--- a/doc/html/pair_hbond_dreiding.html
+++ b/doc/html/pair_hbond_dreiding.html
@@ -287,7 +287,7 @@ optional parameters.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -297,7 +297,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html
index 60044d0faf..fc5db924e0 100644
--- a/doc/html/pair_hybrid.html
+++ b/doc/html/pair_hybrid.html
@@ -419,7 +419,7 @@ off C/C interaction, i.e. by setting the appropriate coefficients to
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual.
Since the hybrid and hybrid/overlay styles delegate computation to
the individual sub-styles, the suffix versions of the hybrid and
@@ -433,7 +433,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_kim.html b/doc/html/pair_kim.html
index 0465abb269..b3dd8684cb 100644
--- a/doc/html/pair_kim.html
+++ b/doc/html/pair_kim.html
@@ -128,9 +128,9 @@
pair_style kim command
Syntax
-
pair_style kim virialmode model printflag
-
-
+
+pair_style kim virialmode model printflag
+
- virialmode = KIMvirial or LAMMPSvirial
- model = name of KIM model (potential)
@@ -139,14 +139,14 @@
Examples
-
pair_style kim KIMvirial model_Ar_P_Morse
-pair_coeff * * Ar Ar
-
-
-
pair_style kim KIMvirial model_Ar_P_Morse 1
-pair_coeff * * Ar Ar
-
-
+
+pair_style kim KIMvirial model_Ar_P_Morse
+pair_coeff * * Ar Ar
+
+
+pair_style kim KIMvirial model_Ar_P_Morse 1
+pair_coeff * * Ar Ar
+
Description
@@ -177,9 +177,9 @@ pair_coeff command, where N is the number of LAMMPS atom types:
As an example, imagine the KIM model supports Si and C atoms. If your
LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair_coeff command:
-
pair_coeff * * Si Si Si C
-
-
+
+pair_coeff * * Si Si Si C
+
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
defined within KIM. The final C argument maps LAMMPS atom type 4 to C
diff --git a/doc/html/pair_lcbop.html b/doc/html/pair_lcbop.html
index 7e2e82ff4a..9f3f225455 100644
--- a/doc/html/pair_lcbop.html
+++ b/doc/html/pair_lcbop.html
@@ -128,16 +128,16 @@
pair_style lcbop command
Syntax
-
+
+pair_style lcbop
+
Examples
-
pair_style lcbop
-pair_coeff * * ../potentials/C.lcbop C
-
-
+
+pair_style lcbop
+pair_coeff * * ../potentials/C.lcbop C
+
Description
@@ -157,9 +157,9 @@ where N is the number of LAMMPS atom types:
to specify the path for the potential file.
As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C you would use the following pair_coeff command:
-
pair_coeff * * C.lcbop C C C NULL
-
-
+
+pair_coeff * * C.lcbop C C C NULL
+
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first C argument maps LAMMPS atom type 1 to the C element in the
LCBOP file. If a mapping value is specified as NULL, the mapping is
diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html
index 73f9948c27..881bf9c6aa 100644
--- a/doc/html/pair_lj.html
+++ b/doc/html/pair_lj.html
@@ -414,7 +414,7 @@ pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -424,7 +424,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html
index 3f7e8fdd9b..8db501bd12 100644
--- a/doc/html/pair_lj96.html
+++ b/doc/html/pair_lj96.html
@@ -171,7 +171,7 @@ cutoff specified in the pair_style command is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -181,7 +181,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html
index 6dad5de332..32b652937a 100644
--- a/doc/html/pair_lj_cubic.html
+++ b/doc/html/pair_lj_cubic.html
@@ -183,7 +183,7 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma =
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html
index 69fc39c046..0202b2e153 100644
--- a/doc/html/pair_lj_expand.html
+++ b/doc/html/pair_lj_expand.html
@@ -175,7 +175,7 @@ optional. If not specified, the global LJ cutoff is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -185,7 +185,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html
index 2256d2d48e..f72aad0384 100644
--- a/doc/html/pair_lj_long.html
+++ b/doc/html/pair_lj_long.html
@@ -275,7 +275,7 @@ specified in the pair_style command.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -285,7 +285,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html
index b09ff7e036..ded174264c 100644
--- a/doc/html/pair_lj_sf.html
+++ b/doc/html/pair_lj_sf.html
@@ -168,7 +168,7 @@ LJ cutoff specified in the pair_style command is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -178,7 +178,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html
index 0973d95ff9..e42ea25efd 100644
--- a/doc/html/pair_lj_smooth.html
+++ b/doc/html/pair_lj_smooth.html
@@ -183,7 +183,7 @@ specified, the global values for Rin and Rc are used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html
index edd6d68386..067334a27d 100644
--- a/doc/html/pair_lj_smooth_linear.html
+++ b/doc/html/pair_lj_smooth_linear.html
@@ -169,7 +169,7 @@ for Rc is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -179,7 +179,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html
index f67e200935..26592c9f94 100644
--- a/doc/html/pair_lj_soft.html
+++ b/doc/html/pair_lj_soft.html
@@ -353,7 +353,7 @@ directory tree, under examples/USER/fep.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -363,7 +363,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, tail correction, restart info:
diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html
index d0f57e43cb..1d5ef40828 100644
--- a/doc/html/pair_meam_spline.html
+++ b/doc/html/pair_meam_spline.html
@@ -199,7 +199,7 @@ MEAM potentials. It may be extended for alloy systems in the future.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -209,7 +209,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html
index bcf7271af0..f4844c2192 100644
--- a/doc/html/pair_morse.html
+++ b/doc/html/pair_morse.html
@@ -222,7 +222,7 @@ cutoff is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -232,7 +232,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html
index a24bb092e7..a05117a647 100644
--- a/doc/html/pair_nb3b_harmonic.html
+++ b/doc/html/pair_nb3b_harmonic.html
@@ -202,7 +202,7 @@ simulation; LAMMPS ignores those entries.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -212,7 +212,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html
index c7759721cf..97dea100ae 100644
--- a/doc/html/pair_nm.html
+++ b/doc/html/pair_nm.html
@@ -250,7 +250,7 @@ the
run_st
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -260,7 +260,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/pair_none.html b/doc/html/pair_none.html
index 1b294a15f5..84a0e71b67 100644
--- a/doc/html/pair_none.html
+++ b/doc/html/pair_none.html
@@ -128,15 +128,15 @@
pair_style none command
Syntax
-
+
+pair_style none
+
Examples
-
+
+pair_style none
+
Description
diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html
index c2fa31cce8..14fa845a22 100644
--- a/doc/html/pair_peri.html
+++ b/doc/html/pair_peri.html
@@ -258,7 +258,7 @@ details please see the description in “(Mtchell2011a)”.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -268,7 +268,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html
index 38e27022b9..ff0e1ee9ea 100644
--- a/doc/html/pair_reax_c.html
+++ b/doc/html/pair_reax_c.html
@@ -170,7 +170,7 @@ the
(Akt
The reax/c/kk style is a Kokkos version of the ReaxFF potential that is
derived from the reax/c style. The Kokkos version can run on GPUs and
can also use OpenMP multithreading. For more information about the Kokkos package,
-see Section_packages and Section_accelerate.
+see Section 4 and Section 5.3.3.
One important consideration when using the reax/c/kk style is the choice of either
half or full neighbor lists. This setting can be changed using the Kokkos package
command.
@@ -377,7 +377,7 @@ script that reads a restart file.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -387,7 +387,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the suffix command in your input script.
-See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
diff --git a/doc/html/pair_resquared.html b/doc/html/pair_resquared.html
index 70c4fd0ba0..dcba82a43e 100644
--- a/doc/html/pair_resquared.html
+++ b/doc/html/pair_resquared.html
@@ -247,7 +247,7 @@ specified in the pair_style command is used.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -257,7 +257,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html
index 21a9ded1a5..67ce57044a 100644
--- a/doc/html/pair_sdk.html
+++ b/doc/html/pair_sdk.html
@@ -215,7 +215,7 @@ pair_style command.
Styles with a gpu, intel, kk, omp or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -225,7 +225,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, and rRESPA info:
diff --git a/doc/html/pair_smd_tlsph.html b/doc/html/pair_smd_tlsph.html
index 69ea38dfa4..330e3c56f2 100644
--- a/doc/html/pair_smd_tlsph.html
+++ b/doc/html/pair_smd_tlsph.html
@@ -128,9 +128,9 @@
pair_style smd/tlsph command
Syntax
-
pair_style smd/tlsph args
-
-
+
+pair_style smd/tlsph args
+
Examples
@@ -140,11 +140,11 @@
Description
The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command:
-
pair_style smd/tlsph
-pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
- *END
-
-
+
+pair_style smd/tlsph
+pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
+ *END
+
Here, i and j denote the LAMMPS particle types for which this pair style is
defined. Note that i and j must be equal, i.e., no tlsph cross interactions
between different particle types are allowed.
@@ -152,7 +152,7 @@ In contrast to the usual LAMMPS pair coeff definitions, which
number of floats and integers, the tlsph pair coeff definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The pair coeff line must be terminated with
-the **END* keyword. The use the line continuation operator & is recommended. A typical
+the *END keyword. The use the line continuation operator & is recommended. A typical
invocation of the tlsph for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
diff --git a/doc/html/pair_smd_ulsph.html b/doc/html/pair_smd_ulsph.html
index a838c63e41..1e21539e51 100644
--- a/doc/html/pair_smd_ulsph.html
+++ b/doc/html/pair_smd_ulsph.html
@@ -128,27 +128,27 @@
pair_style smd/ulsph command
Syntax
-
pair_style smd/ulsph args
-
-
+
+pair_style smd/ulsph args
+
- these keywords must be given
-
keyword = **DENSITY_SUMMATION* or **DENSITY_CONTINUITY* and **VELOCITY_GRADIENT* or **NO_VELOCITY_GRADIENT* and **GRADIENT_CORRECTION* or **NO_GRADIENT_CORRECTION*
+
keyword = *DENSITY_SUMMATION or *DENSITY_CONTINUITY and *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT and *GRADIENT_CORRECTION or *NO_GRADIENT_CORRECTION
Examples
-
pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+
pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
Description
The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked similar to the following command:
-
pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
-pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
- *END
-
-
+
+pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
+ *END
+
Here, i and j denote the LAMMPS particle types for which this pair style is
defined. Note that i and j can be different, i.e., ulsph cross interactions
between different particle types are allowed. However, i–i respectively j–j pair_coeff lines have to preceed a cross interaction.
@@ -156,11 +156,11 @@ In contrast to the usual LAMMPS pair coeff definitions, which
number of floats and integers, the ulsph pair coeff definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The pair coeff line must be terminated with
-the **END* keyword. The use the line continuation operator & is recommended. A typical
+the *END keyword. The use the line continuation operator & is recommended. A typical
invocation of the ulsph for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor).
-
Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
+
Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
Please see the SMD user guide for a complete listing of the possible keywords and material models.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html
index 3443927106..0569003710 100644
--- a/doc/html/pair_soft.html
+++ b/doc/html/pair_soft.html
@@ -205,7 +205,7 @@ variables.
Styles with a gpu, intel, kk, omp, or opt suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -215,7 +215,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
use the
suffix command in your input script.
-
See Section_accelerate of the manual for
+
See Section 5 of the manual for
more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info:
diff --git a/doc/html/pair_sph_heatconduction.html b/doc/html/pair_sph_heatconduction.html
index b864553905..d4161616a4 100644
--- a/doc/html/pair_sph_heatconduction.html
+++ b/doc/html/pair_sph_heatconduction.html
@@ -128,16 +128,16 @@
pair_style sph/heatconduction command
Syntax
-
pair_style sph/heatconduction
-
-
+
+pair_style sph/heatconduction
+
Examples
-
pair_style sph/heatconduction
-pair_coeff * * 1.0 2.4
-
-
+
+pair_style sph/heatconduction
+pair_coeff * * 1.0 2.4
+