replace :l,ule and :l,ole with :l :ule or :l :ole

This commit is contained in:
Axel Kohlmeyer
2016-09-07 02:11:59 -04:00
parent 0d491d483c
commit 55022d1263
32 changed files with 110 additions and 56 deletions

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@ -2276,7 +2276,8 @@ molecule diffusion rates. :l
As input to special functions of "equal-style As input to special functions of "equal-style
variables"_variable.html, like sum() and max(). E.g. to find the variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l,ule largest cluster or fastest diffusing molecule. :l
:ule
Example calculations with chunks :h5 Example calculations with chunks :h5
@ -2432,7 +2433,8 @@ package, :ulb,l
the adiabatic core-shell method, implemented in the the adiabatic core-shell method, implemented in the
"CORESHELL"_#howto_26 package, :l "CORESHELL"_#howto_26 package, :l
the thermalized Drude dipole method, implemented in the the thermalized Drude dipole method, implemented in the
"USER-DRUDE"_#howto_27 package. :l,ule "USER-DRUDE"_#howto_27 package. :l
:ule
The fluctuating charge method calculates instantaneous charges on The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization interacting atoms based on the electronegativity equalization
@ -2739,7 +2741,8 @@ too much. To avoid this, damping at short range can be done by Thole
functions (for which there are physical grounds). This Thole damping functions (for which there are physical grounds). This Thole damping
is applied to the point charges composing the induced dipole (the is applied to the point charges composing the induced dipole (the
charge of the Drude particle and the opposite charge on the core, not charge of the Drude particle and the opposite charge on the core, not
to the total charge of the core atom). :l,ule to the total charge of the core atom). :l
:ule
A detailed tutorial covering the usage of Drude induced dipoles in A detailed tutorial covering the usage of Drude induced dipoles in
LAMMPS is "available here"_tutorial_drude.html. LAMMPS is "available here"_tutorial_drude.html.

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@ -241,7 +241,8 @@ Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis, "Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza. :l,ule Pizza.py WWW site"_pizza. :l
:ule
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org) :link(python,http://www.python.org)

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@ -130,7 +130,8 @@ If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the LAMMPS performance when it isn't used, send an email to the
"developers"_http://lammps.sandia.gov/authors.html. We might be "developers"_http://lammps.sandia.gov/authors.html. We might be
interested in adding it to the LAMMPS distribution. See further interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page. :l,ule details on this at the bottom of this page. :l
:ule
:line :line
:line :line

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@ -761,7 +761,8 @@ Add a wrapper method to python/lammps.py for this interface
function. :l function. :l
You should now be able to invoke the new interface function from a You should now be able to invoke the new interface function from a
Python script. Isn't ctypes amazing? :l,ule Python script. Isn't ctypes amazing? :l
:ule
:line :line
:line :line

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@ -1208,7 +1208,8 @@ Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents"). :l (e.g. by typing: cd "Documents"). :l
At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
with the name of your LAMMPS input script. :l,ule with the name of your LAMMPS input script. :l
:ule
For the MPI version, which allows you to run LAMMPS under Windows on For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps: multiple processors, follow these steps:
@ -1237,7 +1238,8 @@ In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something use this executable to run on a single processor by typing something
like: "lmp_win_mpi -in in.lj". :l,ule like: "lmp_win_mpi -in in.lj". :l
:ule
:line :line

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@ -42,7 +42,8 @@ LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU same functionality can eventually be supported on a variety of GPU
hardware. :l,ule hardware. :l
:ule
Here is a quick overview of how to enable and use the GPU package: Here is a quick overview of how to enable and use the GPU package:
@ -245,7 +246,8 @@ regardless of asynchronous CPU calculations. :l
The output section "GPU Time Info (average)" reports "Max Mem / Proc". The output section "GPU Time Info (average)" reports "Max Mem / Proc".
This is the maximum memory used at one time on the GPU for data This is the maximum memory used at one time on the GPU for data
storage by a single MPI process. :l,ule storage by a single MPI process. :l
:ule
[Restrictions:] [Restrictions:]

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@ -31,7 +31,8 @@ Fixes: nve, npt, nvt, nvt/sllod :l
Improper Styles: cvff, harmonic :l Improper Styles: cvff, harmonic :l
Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne, Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
K-Space Styles: pppm :l,ule K-Space Styles: pppm :l
:ule
[Speed-ups to expect:] [Speed-ups to expect:]
@ -70,7 +71,8 @@ For Intel Xeon CPUs:
Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
performance. :l performance. :l
"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l,ule "-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
:ule
For Intel Xeon Phi CPUs for simulations without {kspace_style For Intel Xeon Phi CPUs for simulations without {kspace_style
pppm} in the input script : pppm} in the input script :
@ -79,7 +81,8 @@ Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
Runs should be performed using MCDRAM. :l Runs should be performed using MCDRAM. :l
"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel" "-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
should be added to the LAMMPS command-line. Choice for best should be added to the LAMMPS command-line. Choice for best
performance will depend on the simulation. :l,ule performance will depend on the simulation. :l
:ule
For Intel Xeon Phi CPUs for simulations with {kspace_style For Intel Xeon Phi CPUs for simulations with {kspace_style
pppm} in the input script: pppm} in the input script:
@ -93,13 +96,15 @@ performance. :l
export KMP_AFFINITY=none :l export KMP_AFFINITY=none :l
"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes "-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
-sf intel" added to LAMMPS command-line. Choice for best performance -sf intel" added to LAMMPS command-line. Choice for best performance
will depend on the simulation. :l,ule will depend on the simulation. :l
:ule
For Intel Xeon Phi coprocessors (Offload): For Intel Xeon Phi coprocessors (Offload):
Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
"-pk intel N omp 1" added to command-line where N is the number of "-pk intel N omp 1" added to command-line where N is the number of
coprocessors per node. :l,ule coprocessors per node. :l
:ule
:line :line
@ -463,7 +468,8 @@ Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Krake
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l,ule Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
:ule

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@ -381,7 +381,8 @@ When running large number of atoms per GPU, KOKKOS is typically faster
than the GPU package. :l than the GPU package. :l
When running on Intel Xeon Phi, KOKKOS is not as fast as When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware. :l,ule the USER-INTEL package, which is optimized for that hardware. :l
:ule
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the KOKKOS package on different LAMMPS web site for performance of the KOKKOS package on different

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@ -163,7 +163,8 @@ sometimes be achived by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the and thus reducing the work done by the long-range solver. Using the
"run_style verlet/split"_run_style.html command, which is compatible "run_style verlet/split"_run_style.html command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation. :l,ule of MPI tasks assigned to the KSpace calculation. :l
:ule
Additional performance tips are as follows: Additional performance tips are as follows:
@ -178,7 +179,8 @@ NOTE: By default, several current MPI implementations use a processor
affinity setting that restricts each MPI task to a single CPU core. affinity setting that restricts each MPI task to a single CPU core.
Using multi-threading in this mode will force all threads to share the Using multi-threading in this mode will force all threads to share the
one core and thus is likely to be counterproductive. Instead, binding one core and thus is likely to be counterproductive. Instead, binding
MPI tasks to a (multi-core) socket, should solve this issue. :l,ule MPI tasks to a (multi-core) socket, should solve this issue. :l
:ule
[Restrictions:] [Restrictions:]

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@ -108,7 +108,8 @@ variable"_variable.html. :l
Local values can be reduced by the "compute Local values can be reduced by the "compute
reduce"_compute_reduce.html command, or histogrammed by the "fix reduce"_compute_reduce.html command, or histogrammed by the "fix
ave/histo"_fix_ave_histo.html command, or output by the "dump ave/histo"_fix_ave_histo.html command, or output by the "dump
local"_dump.html command. :l,ule local"_dump.html command. :l
:ule
The results of computes that calculate global quantities can be either The results of computes that calculate global quantities can be either
"intensive" or "extensive" values. Intensive means the value is "intensive" or "extensive" values. Intensive means the value is

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@ -130,7 +130,8 @@ variable"_variable.html. :l
Local values can be reduced by the "compute Local values can be reduced by the "compute
reduce"_compute_reduce.html command, or histogrammed by the "fix reduce"_compute_reduce.html command, or histogrammed by the "fix
ave/histo"_fix_ave_histo.html command. :l,ule ave/histo"_fix_ave_histo.html command. :l
:ule
See this "howto section"_Section_howto.html#howto_15 for a summary of See this "howto section"_Section_howto.html#howto_15 for a summary of
various LAMMPS output options, many of which involve fixes. various LAMMPS output options, many of which involve fixes.

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@ -61,7 +61,8 @@ It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system. :ulb,l instead of scaling all the charges in the system. :ulb,l
There is a new option {after} for better compatibility with "fix There is a new option {after} for better compatibility with "fix
ave/time". :l,ule ave/time". :l
:ule
This version is suited for free energy calculations using This version is suited for free energy calculations using
"compute ti"_compute_ti.html or "compute fep"_compute_fep.html. "compute ti"_compute_ti.html or "compute fep"_compute_fep.html.

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@ -32,7 +32,8 @@ the components of the total torque applied on the group (around its
center of mass) are Tx,Ty,Tz :ulb,l center of mass) are Tx,Ty,Tz :ulb,l
the group would move as a rigid body in the absence of other the group would move as a rigid body in the absence of other
forces. :l,ule forces. :l
:ule
This command can be used to drive a group of atoms into rotation. This command can be used to drive a group of atoms into rotation.

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@ -19,7 +19,8 @@ type = {thermal} or {two_temperature} or {hardy} or {field} :l
{two_temperature} = electron-phonon coupling with field: temperature and electron_temperature {two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l
:ule
[Examples:] [Examples:]

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@ -232,7 +232,8 @@ so Npair = N*(N+1)/2. :l
If {type} is set to {full} then each input value is correlated with If {type} is set to {full} then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2. :l,ule Npair = N^2. :l
:ule
The {ave} keyword determines what happens to the accumulation of The {ave} keyword determines what happens to the accumulation of
correlation samples every {Nfreq} timesteps. If the {ave} setting is correlation samples every {Nfreq} timesteps. If the {ave} setting is
@ -342,7 +343,8 @@ CNN. :l
For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12, For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN. :l,ule CNN. :l
:ule
The array values calculated by this fix are treated as intensive. If The array values calculated by this fix are treated as intensive. If
you need to divide them by the number of atoms, you must do this in a you need to divide them by the number of atoms, you must do this in a

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@ -229,7 +229,8 @@ computes the global pressure even if its group is {ATOMS}. This is
what we want. If we thermostated {ATOMS} using {npt}, the pressure what we want. If we thermostated {ATOMS} using {npt}, the pressure
should be the global one, but the temperature should be only that of should be the global one, but the temperature should be only that of
the cores. That's why the command {fix_modify} should be called in the cores. That's why the command {fix_modify} should be called in
that case. :l,ule that case. :l
:ule
:line :line

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@ -621,7 +621,8 @@ rigid styles for the rigid bodies. :l
Use "fix press/berendsen"_fix_press_berendsen.html to compute the Use "fix press/berendsen"_fix_press_berendsen.html to compute the
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any
other thermostat) for the non-rigid particles. :l,ule other thermostat) for the non-rigid particles. :l
:ule
In all case, the rigid bodies and non-rigid particles both contribute In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the to the global pressure and the box is scaled the same by any of the

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@ -16,7 +16,8 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
temp/berendsen = style name of this fix command :l temp/berendsen = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l Tstart,Tstop = desired temperature at start/end of run :l
Tstart can be a variable (see below) :pre Tstart can be a variable (see below) :pre
Tdamp = temperature damping parameter (time units) :l,ule Tdamp = temperature damping parameter (time units) :l
:ule
[Examples:] [Examples:]

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@ -19,7 +19,8 @@ temp/csvr or temp/csld = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l Tstart,Tstop = desired temperature at start/end of run :l
Tstart can be a variable (see below) :pre Tstart can be a variable (see below) :pre
Tdamp = temperature damping parameter (time units) :l Tdamp = temperature damping parameter (time units) :l
seed = random number seed to use for white noise (positive integer) :l,ule seed = random number seed to use for white noise (positive integer) :l
:ule
[Examples:] [Examples:]

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@ -18,7 +18,8 @@ N = perform rescaling every N steps :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
Tstart can be a variable (see below) :pre Tstart can be a variable (see below) :pre
window = only rescale if temperature is outside this window (temperature units) :l window = only rescale if temperature is outside this window (temperature units) :l
fraction = rescale to target temperature by this fraction :l,ule fraction = rescale to target temperature by this fraction :l
:ule
[Examples:] [Examples:]

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@ -123,7 +123,8 @@ to freeze a wall or portion of a bio-molecule. :l
When one or more rigid bodies are specified, interactions within each When one or more rigid bodies are specified, interactions within each
body can be turned off to save needless computation. See the "fix body can be turned off to save needless computation. See the "fix
rigid"_fix_rigid.html command for more details. :l,ule rigid"_fix_rigid.html command for more details. :l
:ule
The {exclude type} option turns off the pairwise interaction if one The {exclude type} option turns off the pairwise interaction if one
atom is of type M and the other of type N. M can equal N. The atom is of type M and the other of type N. M can equal N. The

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@ -162,7 +162,8 @@ Line 1: nr, nBOt (nr is the number of divisions the radius is broken
into for function tables and MUST be a factor of 5; nBOt is the number into for function tables and MUST be a factor of 5; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij) :ulb,l of divisions for the tabulated values of THETA_(S,ij) :ulb,l
Line 2: delta_1-delta_7 (if all are not used in the particular :l Line 2: delta_1-delta_7 (if all are not used in the particular :l
formulation, set unused values to 0.0) :l,ule formulation, set unused values to 0.0) :l
:ule
Following this N lines for e_1-e_N containing p_pi. Following this N lines for e_1-e_N containing p_pi.
@ -176,7 +177,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 2: c_sigma, a_sigma, c_pi, a_pi :l
Line 3: delta_sigma, delta_pi :l Line 3: delta_sigma, delta_pi :l
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent) :l,ule the previous section but is interaction type dependent) :l
:ule
The next section contains a line for each three body interaction type The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@ -185,7 +187,8 @@ Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for
g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward
contains the full expressions for the constants as functions of contains the full expressions for the constants as functions of
b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l
Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l,ule Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l
:ule
The next section contains a block for each interaction type for the The next section contains a block for each interaction type for the
phi_ij(r_ij). Each block has nr entries with 5 entries per line. phi_ij(r_ij). Each block has nr entries with 5 entries per line.
@ -196,7 +199,8 @@ Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
until nr) :l until nr) :l
... :l ... :l
Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
e_1-e_1 interaction type) :l,ule e_1-e_1 interaction type) :l
:ule
The next section contains a block for each interaction type for the The next section contains a block for each interaction type for the
beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per
@ -208,7 +212,8 @@ Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9),
beta_sigma(r10) (this continues until nr) :l beta_sigma(r10) (this continues until nr) :l
... :l ... :l
Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3),
beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l,ule beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l
:ule
The next section contains a block for each interaction type for The next section contains a block for each interaction type for
beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line.
@ -219,7 +224,8 @@ Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9),
beta_pi(r10) (this continues until nr) :l beta_pi(r10) (this continues until nr) :l
... :l ... :l
Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4),
beta_pi(r5) (for the e_1-e_2 interaction type) :l,ule beta_pi(r5) (for the e_1-e_2 interaction type) :l
:ule
The next section contains a block for each interaction type for the The next section contains a block for each interaction type for the
THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has
@ -231,7 +237,8 @@ Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8),
THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l
... :l ... :l
Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l,ule THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l
:ule
The next section contains a block of N lines for e_1-e_N The next section contains a block of N lines for e_1-e_N
@ -266,7 +273,8 @@ into for function tables and MUST be a factor of 5; ntheta is the power of the
power of the spline used to fit the angular function; nBOt is the number power of the spline used to fit the angular function; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij) :ulb,l of divisions for the tabulated values of THETA_(S,ij) :ulb,l
Line 2: delta_1-delta_7 (if all are not used in the particular :l Line 2: delta_1-delta_7 (if all are not used in the particular :l
formulation, set unused values to 0.0) :l,ule formulation, set unused values to 0.0) :l
:ule
Following this N lines for e_1-e_N containing p_pi. Following this N lines for e_1-e_N containing p_pi.
@ -280,7 +288,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 2: c_sigma, a_sigma, c_pi, a_pi :l
Line 3: delta_sigma, delta_pi :l Line 3: delta_sigma, delta_pi :l
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent) :l,ule the previous section but is interaction type dependent) :l
:ule
The next section contains a line for each three body interaction type The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@ -292,7 +301,8 @@ can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The terms the second line will contain the remaining constants The
following lines will then contain the constants for the remainaing g0, following lines will then contain the constants for the remainaing g0,
g1, g2... (for e_1-e_1-e_2) and the other three body g1, g2... (for e_1-e_1-e_2) and the other three body
interactions :l,ule interactions :l
:ule
The rest of the table has the same structure as the previous section The rest of the table has the same structure as the previous section
(see above). (see above).
@ -319,7 +329,8 @@ into for function tables and MUST be a factor of 5; ntheta is the number of
divisions for the tabulated values of the g angular function; nBOt is the number divisions for the tabulated values of the g angular function; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij) :ulb,l of divisions for the tabulated values of THETA_(S,ij) :ulb,l
Line 2: delta_1-delta_7 (if all are not used in the particular :l Line 2: delta_1-delta_7 (if all are not used in the particular :l
formulation, set unused values to 0.0) :l,ule formulation, set unused values to 0.0) :l
:ule
Following this N lines for e_1-e_N containing p_pi. Following this N lines for e_1-e_N containing p_pi.
@ -333,7 +344,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 2: c_sigma, a_sigma, c_pi, a_pi :l
Line 3: delta_sigma, delta_pi :l Line 3: delta_sigma, delta_pi :l
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent) :l,ule the previous section but is interaction type dependent) :l
:ule
The next section contains a line for each three body interaction type The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@ -344,7 +356,8 @@ Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
until ntheta) :l until ntheta) :l
... :l ... :l
Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
e_1-e_1-e_2 interaction type) :l,ule e_1-e_1-e_2 interaction type) :l
:ule
The rest of the table has the same structure as the previous section (see above). The rest of the table has the same structure as the previous section (see above).

View File

@ -20,7 +20,8 @@ flag_coul = {long} or {off} :l
{long} = use Kspace long-range summation for the Coulombic term 1/r {long} = use Kspace long-range summation for the Coulombic term 1/r
{off} = omit the Coulombic term :pre {off} = omit the Coulombic term :pre
cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule cutoff2 = global cutoff for Coulombic (optional) (distance units) :l
:ule
[Examples:] [Examples:]

View File

@ -23,7 +23,8 @@ Kt = elastic constant for tangential contact (force/distance units or pressure u
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
dampflag = 0 or 1 if tangential damping force is excluded or included :l,ule dampflag = 0 or 1 if tangential damping force is excluded or included :l
:ule
NOTE: Versions of LAMMPS before 9Jan09 had different style names for NOTE: Versions of LAMMPS before 9Jan09 had different style names for
granular force fields. This is to emphasize the fact that the granular force fields. This is to emphasize the fact that the

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@ -187,7 +187,8 @@ enabled will not be thermodynamically consistent with the truncated
force-field that was used. In other words, atoms do not feel any LJ force-field that was used. In other words, atoms do not feel any LJ
pair interactions beyond the cutoff, but the energy and pressure pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from reported by the simulation include an estimated contribution from
those interactions. :l,ule those interactions. :l
:ule
The {compute} keyword allows pairwise computations to be turned off, The {compute} keyword allows pairwise computations to be turned off,
even though a "pair_style"_pair_style.html is defined. This is not even though a "pair_style"_pair_style.html is defined. This is not

View File

@ -118,7 +118,8 @@ consistent (dE/dr = -F) over the entire range of r values. LAMMPS
will warn if this is not the case. :l will warn if this is not the case. :l
Use as large an inner cutoff as possible. This avoids fitting splines Use as large an inner cutoff as possible. This avoids fitting splines
to very steep parts of the potential. :l,ule to very steep parts of the potential. :l
:ule
:line :line

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@ -111,7 +111,8 @@ Make sure that your tabulated forces and tabulated energies are consistent
(dE/dr = -F) along the entire range of r values. :l (dE/dr = -F) along the entire range of r values. :l
Use as large an inner cutoff as possible. This avoids fitting splines Use as large an inner cutoff as possible. This avoids fitting splines
to very steep parts of the potential. :l,ule to very steep parts of the potential. :l
:ule
:line :line

View File

@ -698,7 +698,8 @@ atoms in such a bond. :l
If you plan to "dump"_dump.html image flags and perform post-analysis If you plan to "dump"_dump.html image flags and perform post-analysis
that will unwrap atom coordinates, it may be important that a that will unwrap atom coordinates, it may be important that a
continued run (restarted from a data file) begins with image flags continued run (restarted from a data file) begins with image flags
that are consistent with the previous run. :l,ule that are consistent with the previous run. :l
:ule
NOTE: If your system is an infinite periodic crystal with bonds then NOTE: If your system is an infinite periodic crystal with bonds then
it is impossible to have fully consistent image flags. This is because it is impossible to have fully consistent image flags. This is because

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@ -243,7 +243,8 @@ to yz. :l
For style {sphere}, the lattice spacing in dimensions x,y,z are For style {sphere}, the lattice spacing in dimensions x,y,z are
applied to the sphere center x,y,z. The spacing in dimension x is applied to the sphere center x,y,z. The spacing in dimension x is
applied to the sphere radius. :l,ule applied to the sphere radius. :l
:ule
:line :line

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@ -60,7 +60,8 @@ Calculate the portion of per-atom forces resulting from a subset of
the potential. E.g. compute only Coulombic forces. This can be done the potential. E.g. compute only Coulombic forces. This can be done
by only defining only a Coulombic pair style in the rerun script. by only defining only a Coulombic pair style in the rerun script.
Doing this in the original script would result in different (bad) Doing this in the original script would result in different (bad)
dynamics. :l,ule dynamics. :l
:ule
Conceptually, using the rerun command is like running an input script Conceptually, using the rerun command is like running an input script
that has a loop in it (see the "next"_next.html and "jump"_jump.html that has a loop in it (see the "next"_next.html and "jump"_jump.html

View File

@ -332,8 +332,8 @@ For the {thole} pair style the coefficients are
the atom polarizability in units of cubic length :olb,l the atom polarizability in units of cubic length :olb,l
the screening factor of the Thole function (optional, default value the screening factor of the Thole function (optional, default value
specified by the pair_style command) :l specified by the pair_style command) :l
the cutoff (optional, default value defined by the pair_style command) the cutoff (optional, default value defined by the pair_style command) :l
:l,ole :ole
The special neighbors have charge-charge and charge-dipole The special neighbors have charge-charge and charge-dipole
interactions screened by the {coul} factors of the {special_bonds} interactions screened by the {coul} factors of the {special_bonds}

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@ -17,7 +17,8 @@ style = any of the supported "dump styles"_dump.html :l
file = name of file to write dump info to :l file = name of file to write dump info to :l
dump-args = any additional args needed for a particular "dump style"_dump.html :l dump-args = any additional args needed for a particular "dump style"_dump.html :l
modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l
dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l,ule dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l
:ule
[Examples:] [Examples:]