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more conversion of parsed-literal to code-block and a bunch of other issues

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This commit is contained in:
Axel Kohlmeyer
2020-03-12 08:04:26 -04:00
parent 524b37598f
commit 010b1f7434
64 changed files with 189 additions and 172 deletions
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2
doc/src/Errors_common.rst
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@ -71,7 +71,7 @@ Some commands allow for using variable references in place of numeric
constants so that the value can be evaluated and may change over the constants so that the value can be evaluated and may change over the
course of a run. This is typically done with the syntax *v\_name* for a course of a run. This is typically done with the syntax *v\_name* for a
parameter, where name is the name of the variable. On the other hand, parameter, where name is the name of the variable. On the other hand,
immediate variable expansion with the syntax $\ *name* is performed while immediate variable expansion with the syntax ${name} is performed while
reading the input and before parsing commands, reading the input and before parsing commands,
.. note:: .. note::

10
doc/src/Speed_intel.rst
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@ -192,7 +192,7 @@ will report every hardware thread as a separate core allowing one to
determine the number of hardware threads available. On Linux systems, determine the number of hardware threads available. On Linux systems,
this information can normally be obtained with: this information can normally be obtained with:
.. parsed-literal:: .. code-block:: bash
cat /proc/cpuinfo cat /proc/cpuinfo
@ -219,7 +219,7 @@ Phi x200 processors making it easier to cross-compile. For users with
recent installations of Intel Parallel Studio, the process can be as recent installations of Intel Parallel Studio, the process can be as
simple as: simple as:
.. parsed-literal:: .. code-block:: bash
make yes-user-intel make yes-user-intel
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
@ -334,7 +334,7 @@ desired.
Examples (see documentation for your MPI/Machine for differences in Examples (see documentation for your MPI/Machine for differences in
launching MPI applications): launching MPI applications):
.. parsed-literal:: .. code-block:: bash
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
@ -346,14 +346,14 @@ can be edited to enable the USER-INTEL package. This requires adding
the :doc:`package intel <package>` command to the top of the input the :doc:`package intel <package>` command to the top of the input
script. For the second example above, this would be: script. For the second example above, this would be:
.. parsed-literal:: .. code-block:: LAMMPS
package intel 0 omp 2 mode double package intel 0 omp 2 mode double
To enable the USER-INTEL package only for individual styles, you can To enable the USER-INTEL package only for individual styles, you can
add an "intel" suffix to the individual style, e.g.: add an "intel" suffix to the individual style, e.g.:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/cut/intel 2.5 pair_style lj/cut/intel 2.5

20
doc/src/Speed_kokkos.rst
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@ -71,7 +71,7 @@ Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
Here is a quick overview of how to use the KOKKOS package Here is a quick overview of how to use the KOKKOS package
for CPU acceleration, assuming one or more 16-core nodes. for CPU acceleration, assuming one or more 16-core nodes.
.. parsed-literal:: .. code-block:: bash
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading
mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
@ -119,7 +119,7 @@ below.
page for details and default settings. Experimenting with its options page for details and default settings. Experimenting with its options
can provide a speed-up for specific calculations. For example: can provide a speed-up for specific calculations. For example:
.. parsed-literal:: .. code-block:: bash
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm
@ -180,9 +180,9 @@ tasks.
Examples of mpirun commands that follow these rules are shown below. Examples of mpirun commands that follow these rules are shown below.
.. parsed-literal:: .. code-block:: bash
Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): # Running on an Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task
mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task
mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task
@ -205,7 +205,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
details and default settings. Experimenting with its options can provide details and default settings. Experimenting with its options can provide
a speed-up for specific calculations. For example: a speed-up for specific calculations. For example:
.. parsed-literal:: .. code-block:: bash
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
@ -246,7 +246,7 @@ then the number of MPI tasks/node should not exceed N.
Here are examples of how to use the KOKKOS package for GPUs, assuming Here are examples of how to use the KOKKOS package for GPUs, assuming
one or more nodes, each with two GPUs: one or more nodes, each with two GPUs:
.. parsed-literal:: .. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)
@ -266,7 +266,7 @@ one or more nodes, each with two GPUs:
default settings. Experimenting with its options can provide a speed-up default settings. Experimenting with its options can provide a speed-up
for specific calculations. For example: for specific calculations. For example:
.. parsed-literal:: .. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
@ -308,7 +308,7 @@ hardware options appropriate to your system, as documented above.
You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g. "kk" suffix to individual styles in your input script, e.g.
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/cut/kk 2.5 pair_style lj/cut/kk 2.5
@ -323,7 +323,7 @@ used together in a few special cases. In the Makefile, the
KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is
the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi
.. parsed-literal:: .. code-block:: bash
KOKKOS_DEVICES=Cuda,OpenMP KOKKOS_DEVICES=Cuda,OpenMP
@ -340,7 +340,7 @@ as "t Nt" and the number of GPUs as "g Ng"
For example, the command to run with 1 GPU and 8 OpenMP threads is then: For example, the command to run with 1 GPU and 8 OpenMP threads is then:
.. parsed-literal:: .. code-block:: bash
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk

4
doc/src/compute_dpd_atom.rst
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@ -16,7 +16,9 @@ Syntax
Examples Examples
"""""""" """"""""
compute 1 all dpd/atom .. code-block:: LAMMPS
compute 1 all dpd/atom
Description Description
""""""""""" """""""""""

16
doc/src/dump.rst
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@ -125,18 +125,18 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump myDump all atom 100 dump.atom dump myDump all atom 100 dump.atom
dump myDump all atom/mpiio 100 dump.atom.mpiio dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz dump myDump all atom/gz 100 dump.atom.gz
dump 2 subgroup atom 50 dump.run.bin dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.\* id type x y vx fx dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke
dump 2 inner cfg 10 dump.snap.\*.cfg mass type xs ys zs vx vy vz dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.\*.cfg mass type xs ys zs id type c_Stress[2] dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc dump 1 all xtc 1000 file.xtc
Description Description
@ -425,7 +425,7 @@ library, which is part of the MPI standard for versions 2.0 and above.
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, e.g. package installed, e.g.
.. parsed-literal:: .. code-block:: bash
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform make mpi # build LAMMPS for your platform
@ -481,10 +481,10 @@ had been listed one by one. E.g. these 2 dump commands are
equivalent, since the :doc:`compute stress/atom <compute_stress_atom>` equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
command creates a per-atom array with 6 columns: command creates a per-atom array with 6 columns:
.. parsed-literal:: .. code-block:: LAMMPS
compute myPress all stress/atom NULL compute myPress all stress/atom NULL
dump 2 all custom 100 tmp.dump id myPress[\*] dump 2 all custom 100 tmp.dump id myPress[*]
dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] & dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
myPress[4] myPress[5] myPress[6] myPress[4] myPress[5] myPress[6]
@ -537,7 +537,7 @@ values.
Here is an example of how to dump bond info for a system, including Here is an example of how to dump bond info for a system, including
the distance and energy of each bond: the distance and energy of each bond:
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/local batom1 batom2 btype compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng compute 2 all bond/local dist eng

4
doc/src/dump_molfile.rst
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@ -21,10 +21,10 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump mf1 all molfile 10 melt1.xml hoomd dump mf1 all molfile 10 melt1.xml hoomd
dump mf2 all molfile 10 melt2-\*.pdb pdb . dump mf2 all molfile 10 melt2-*.pdb pdb .
dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
Description Description

4
doc/src/dump_netcdf.rst
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@ -24,12 +24,12 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump 1 all netcdf 100 traj.nc type x y z vx vy vz dump 1 all netcdf 100 traj.nc type x y z vx vy vz
dump_modify 1 append yes at -1 thermo yes dump_modify 1 append yes at -1 thermo yes
dump 1 all netcdf/mpiio 1000 traj.nc id type x y z dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
dump 1 all netcdf 1000 traj.\*.nc id type x y z dump 1 all netcdf 1000 traj.*.nc id type x y z
Description Description
""""""""""" """""""""""

6
doc/src/dump_vtk.rst
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@ -20,10 +20,10 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump dmpvtk all vtk 100 dump\*.myforce.vtk id type vx fx dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx
dump dmpvtp flow vtk 100 dump\*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
Description Description
""""""""""" """""""""""

4
doc/src/echo.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
echo both echo both
echo log echo log
@ -40,6 +40,6 @@ Restrictions
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
echo log echo log

2
doc/src/fix.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 all nve fix 1 all nve
fix 3 all nvt temp 300.0 300.0 0.01 fix 3 all nvt temp 300.0 300.0 0.01

4
doc/src/fix_langevin_spin.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix 2 all langevin/spin 300.0 0.01 21 fix 2 all langevin/spin 300.0 0.01 21
@ -53,7 +53,7 @@ Note: due to the form of the sLLG equation, this fix has to be defined just
before the nve/spin fix (and after all other magnetic fixes). before the nve/spin fix (and after all other magnetic fixes).
As an example: As an example:
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
fix 2 all langevin/spin 300.0 0.01 21 fix 2 all langevin/spin 300.0 0.01 21

4
doc/src/fix_saed_vtk.rst
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@ -33,7 +33,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
@ -65,7 +65,7 @@ which store their own "group" definitions.
Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>` Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>`
values, e.g. values, e.g.
.. parsed-literal:: .. code-block:: LAMMPS
compute 3 top saed 0.0251 Al O compute 3 top saed 0.0251 Al O
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed

2
doc/src/fix_setforce.rst
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@ -31,7 +31,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix freeze indenter setforce 0.0 0.0 0.0 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 0.0

2
doc/src/fix_shake.rst
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@ -39,7 +39,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2 fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31

2
doc/src/fix_shardlow.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 all shardlow fix 1 all shardlow

2
doc/src/fix_smd.rst
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@ -37,7 +37,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0 fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0

4
doc/src/fix_smd_setvel.rst
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@ -25,9 +25,9 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
fix top_velocity top_group setvel 1.0 0.0 0.0 fix top_velocity top_group smd/setvel 1.0 0.0 0.0
Description Description
""""""""""" """""""""""

8
doc/src/group.rst
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@ -48,7 +48,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
group edge region regstrip group edge region regstrip
group water type 3 4 group water type 3 4
@ -155,7 +155,7 @@ For example, these lines define a variable "eatom" that calculates the
potential energy of each atom and includes it in the group if its potential energy of each atom and includes it in the group if its
potential energy is above the threshold value -3.0. potential energy is above the threshold value -3.0.
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pe/atom compute 1 all pe/atom
compute 2 all reduce sum c_1 compute 2 all reduce sum c_1
@ -167,7 +167,7 @@ potential energy is above the threshold value -3.0.
Note that these lines Note that these lines
.. parsed-literal:: .. code-block:: LAMMPS
compute 2 all reduce sum c_1 compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2 thermo_style custom step temp pe c_2
@ -266,7 +266,7 @@ used to model a quench of the system, freezing atoms outside the
shrinking sphere, then converting the remaining atoms to a static shrinking sphere, then converting the remaining atoms to a static
group and running further. group and running further.
.. parsed-literal:: .. code-block:: LAMMPS
variable nsteps equal 5000 variable nsteps equal 5000
variable rad equal 18-(step/v_nsteps)\*(18-5) variable rad equal 18-(step/v_nsteps)\*(18-5)

2
doc/src/group2ndx.rst
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@ -20,7 +20,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
group2ndx allindex.ndx group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile group2ndx someindex.ndx upper lower mobile

2
doc/src/hyper.rst
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@ -32,7 +32,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute event all event/displace 1.0 compute event all event/displace 1.0
fix HG mobile hyper/global 3.0 0.3 0.4 800.0 fix HG mobile hyper/global 3.0 0.3 0.4 800.0

18
doc/src/if.rst
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@ -21,7 +21,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
if "${steps} > 1000" then quit if "${steps} > 1000" then quit
if "${myString} == a10" then quit if "${myString} == a10" then quit
@ -75,7 +75,7 @@ above.
Note that by using the line continuation character "&", the if command Note that by using the line continuation character "&", the if command
can be spread across many lines, though it is still a single command: can be spread across many lines, though it is still a single command:
.. parsed-literal:: .. code-block:: LAMMPS
if "$a < $b" then & if "$a < $b" then &
"print 'Minimum value = $a'" & "print 'Minimum value = $a'" &
@ -99,7 +99,7 @@ checked, so long as it is current on the timestep when the run
completes. As explained on the :doc:`variable <variable>` doc page, completes. As explained on the :doc:`variable <variable>` doc page,
this can be insured by including the variable in thermodynamic output. this can be insured by including the variable in thermodynamic output.
.. parsed-literal:: .. code-block:: LAMMPS
variable myTemp equal temp variable myTemp equal temp
label loop label loop
@ -115,19 +115,19 @@ Here is an example of a double loop which uses the if and
:doc:`jump <jump>` commands to break out of the inner loop when a :doc:`jump <jump>` commands to break out of the inner loop when a
condition is met, then continues iterating through the outer loop. condition is met, then continues iterating through the outer loop.
.. parsed-literal:: .. code-block:: LAMMPS
label loopa label loopa
variable a loop 5 variable a loop 5
label loopb label loopb
variable b loop 5 variable b loop 5
print "A,B = $a,$b" print "A,B = $a,$b"
run 10000 run 10000
if "$b > 2" then "jump SELF break" if "$b > 2" then "jump SELF break"
next b next b
jump in.script loopb jump in.script loopb
label break label break
variable b delete variable b delete
next a next a
jump SELF loopa jump SELF loopa

2
doc/src/include.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
include newfile include newfile
include in.run2 include in.run2

2
doc/src/info.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
info system info system
info groups computes variables info groups computes variables

26
doc/src/jump.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
jump newfile jump newfile
jump in.run2 runloop jump in.run2 runloop
@ -39,7 +39,7 @@ script is re-opened and read again.
The SELF option is not guaranteed to work when the current input The SELF option is not guaranteed to work when the current input
script is being read through stdin (standard input), e.g. script is being read through stdin (standard input), e.g.
.. parsed-literal:: .. code-block:: bash
lmp_g++ < in.script lmp_g++ < in.script
@ -47,7 +47,7 @@ since the SELF option invokes the C-library rewind() call, which may
not be supported for stdin on some systems or by some MPI not be supported for stdin on some systems or by some MPI
implementations. This can be worked around by using the :doc:`-in command-line switch <Run_options>`, e.g. implementations. This can be worked around by using the :doc:`-in command-line switch <Run_options>`, e.g.
.. parsed-literal:: .. code-block:: bash
lmp_g++ -in in.script lmp_g++ -in in.script
@ -56,7 +56,7 @@ the script name as a variable to the input script. In the latter
case, a :doc:`variable <variable>` called "fname" could be used in place case, a :doc:`variable <variable>` called "fname" could be used in place
of SELF, e.g. of SELF, e.g.
.. parsed-literal:: .. code-block:: bash
lmp_g++ -var fname in.script < in.script lmp_g++ -var fname in.script < in.script
@ -70,7 +70,7 @@ etc. The :doc:`next <next>` command is used to exit the loop after 10
iterations. When the "a" variable has been incremented for the tenth iterations. When the "a" variable has been incremented for the tenth
time, it will cause the next jump command to be skipped. time, it will cause the next jump command to be skipped.
.. parsed-literal:: .. code-block:: LAMMPS
variable a loop 10 variable a loop 10
label loop label loop
@ -87,7 +87,7 @@ partitions of 10 procs each. An in.file containing the example
variable and jump command will cause each partition to run a different variable and jump command will cause each partition to run a different
simulation. simulation.
.. parsed-literal:: .. code-block:: LAMMPS
mpirun -np 40 lmp_ibm -partition 4x10 -in in.file mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
@ -101,7 +101,7 @@ checked, so long as it is current on the timestep when the run
completes. As explained on the :doc:`variable <variable>` doc page, completes. As explained on the :doc:`variable <variable>` doc page,
this can be insured by including the variable in thermodynamic output. this can be insured by including the variable in thermodynamic output.
.. parsed-literal:: .. code-block:: LAMMPS
variable myTemp equal temp variable myTemp equal temp
label loop label loop
@ -117,19 +117,19 @@ Here is an example of a double loop which uses the if and
:doc:`jump <jump>` commands to break out of the inner loop when a :doc:`jump <jump>` commands to break out of the inner loop when a
condition is met, then continues iterating through the outer loop. condition is met, then continues iterating through the outer loop.
.. parsed-literal:: .. code-block:: LAMMPS
label loopa label loopa
variable a loop 5 variable a loop 5
label loopb label loopb
variable b loop 5 variable b loop 5
print "A,B = $a,$b" print "A,B = $a,$b"
run 10000 run 10000
if "$b > 2" then "jump SELF break" if "$b > 2" then "jump SELF break"
next b next b
jump in.script loopb jump in.script loopb
label break label break
variable b delete variable b delete
next a next a
jump SELF loopa jump SELF loopa

2
doc/src/label.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
label xyz label xyz
label loop label loop

10
doc/src/lattice.rst
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@ -38,7 +38,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
lattice fcc 3.52 lattice fcc 3.52
lattice hex 0.85 lattice hex 0.85
@ -254,11 +254,11 @@ in commands that use the spacings should be decipherable.
Example commands for generating a Wurtzite crystal (courtesy Example commands for generating a Wurtzite crystal (courtesy
of Aidan Thompson), with its 8 atom unit cell. of Aidan Thompson), with its 8 atom unit cell.
.. parsed-literal:: .. code-block:: LAMMPS
variable a equal 4.340330 variable a equal 4.340330
variable b equal $a\*sqrt(3.0) variable b equal $a*sqrt(3.0)
variable c equal $a\*sqrt(8.0/3.0) variable c equal $a*sqrt(8.0/3.0)
variable 1_3 equal 1.0/3.0 variable 1_3 equal 1.0/3.0
variable 2_3 equal 2.0/3.0 variable 2_3 equal 2.0/3.0
@ -304,7 +304,7 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
lattice none 1.0 lattice none 1.0

2
doc/src/log.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
log log.equil log log.equil
log log.equil append log log.equil append

6
doc/src/mass.rst
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@ -16,11 +16,11 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
mass 1 1.0 mass 1 1.0
mass \* 62.5 mass * 62.5
mass 2\* 62.5 mass 2* 62.5
Description Description
""""""""""" """""""""""

21
doc/src/message.rst
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@ -28,7 +28,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
message client md file tmp.couple message client md file tmp.couple
message server md file tmp.couple message server md file tmp.couple
@ -95,7 +95,7 @@ code's machine. Support for socket messaging is provided by the
open-source `ZeroMQ library <http://zeromq.org>`_, which must be open-source `ZeroMQ library <http://zeromq.org>`_, which must be
installed on your system. The client specifies an IP address (IPv4 installed on your system. The client specifies an IP address (IPv4
format) or the DNS name of the machine the server code is running on, format) or the DNS name of the machine the server code is running on,
followed by a 4-digit port ID for the socket, separated by a colon. followed by a 4 or 5 digit port ID for the socket, separated by a colon.
E.g. E.g.
.. parsed-literal:: .. parsed-literal::
@ -110,7 +110,20 @@ what the client specifies.
.. note:: .. note::
What are allowed port IDs? On Linux or Unix machines port IDs below 1024 are reserved to the
superuser and thus not available. Other ports may already be in
use and cannot be opened by a second process. On a Linux machine
the commands "netstat -t4an" or "ss -t4an" will list all locally
used port IDs for IPv4 addresses.
.. note::
On many machines (and sometimes on local networks) also ports IDs
may be blocked by default through firewalls. In that case either
access to the required port (or a desired range of ports) has to
be selectively enabled to the firewall disabled (the latter is
usually not a good idea unless you are on a (small) local network
that is already protected from outside access.
.. note:: .. note::
@ -120,7 +133,7 @@ what the client specifies.
For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched
by the same mpirun command, e.g. with this syntax for OpenMPI: by the same mpirun command, e.g. with this syntax for OpenMPI:
.. parsed-literal:: .. code-block:: bash
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server

2
doc/src/minimize.rst
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@ -21,7 +21,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
minimize 1.0e-4 1.0e-6 100 1000 minimize 1.0e-4 1.0e-6 100 1000
minimize 0.0 1.0e-8 1000 100000 minimize 0.0 1.0e-8 1000 100000

2
doc/src/molecule.rst
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@ -39,7 +39,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
molecule 1 mymol.txt molecule 1 mymol.txt
molecule 1 co2.txt h2o.txt molecule 1 co2.txt h2o.txt

4
doc/src/neb.rst
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@ -34,7 +34,7 @@ keyword = *verbose*
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
neb 0.1 0.0 1000 500 50 final coords.final neb 0.1 0.0 1000 500 50 final coords.final
neb 0.0 0.001 1000 500 50 each coords.initial.$i neb 0.0 0.001 1000 500 50 each coords.initial.$i
@ -147,7 +147,7 @@ For a *file-style* setting of *each*\ , a filename is specified which is
assumed to be unique to each replica. This can be done by using a assumed to be unique to each replica. This can be done by using a
variable in the filename, e.g. variable in the filename, e.g.
.. parsed-literal:: .. code-block:: LAMMPS
variable i equal part variable i equal part
neb 0.0 0.001 1000 500 50 each coords.initial.$i neb 0.0 0.001 1000 500 50 each coords.initial.$i

2
doc/src/neb_spin.rst
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@ -38,7 +38,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
neb/spin 0.1 0.0 1000 500 50 final coords.final neb/spin 0.1 0.0 1000 500 50 final coords.final
neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i

2
doc/src/neighbor.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
neighbor 0.3 bin neighbor 0.3 bin
neighbor 2.0 nsq neighbor 2.0 nsq

4
doc/src/newton.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
newton off newton off
newton on off newton on off
@ -64,6 +64,6 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
newton on newton on

8
doc/src/next.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
next x next x
next a t x myTemp next a t x myTemp
@ -82,7 +82,7 @@ command with an *index*\ -style variable. If this input script is named
in.polymer, 8 simulations would be run using data files from in.polymer, 8 simulations would be run using data files from
directories run1 through run8. directories run1 through run8.
.. parsed-literal:: .. code-block:: LAMMPS
variable d index run1 run2 run3 run4 run5 run6 run7 run8 variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d shell cd $d
@ -103,7 +103,7 @@ finished.
Jump and next commands can also be nested to enable multi-level loops. Jump and next commands can also be nested to enable multi-level loops.
For example, this script will run 15 simulations in a double loop. For example, this script will run 15 simulations in a double loop.
.. parsed-literal:: .. code-block:: LAMMPS
variable i loop 3 variable i loop 3
variable j loop 5 variable j loop 5
@ -121,7 +121,7 @@ Here is an example of a double loop which uses the :doc:`if <if>` and
:doc:`jump <jump>` commands to break out of the inner loop when a :doc:`jump <jump>` commands to break out of the inner loop when a
condition is met, then continues iterating through the outer loop. condition is met, then continues iterating through the outer loop.
.. parsed-literal:: .. code-block:: LAMMPS
label loopa label loopa
variable a loop 5 variable a loop 5

6
doc/src/package.rst
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@ -102,7 +102,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
package gpu 1 package gpu 1
package gpu 1 split 0.75 package gpu 1 split 0.75
@ -230,7 +230,7 @@ As an example, if you have two GPUs per node and 8 CPU cores per node,
and would like to run on 4 nodes (32 cores) with dynamic balancing of and would like to run on 4 nodes (32 cores) with dynamic balancing of
force calculation across CPU and GPU cores, you could specify force calculation across CPU and GPU cores, you could specify
.. parsed-literal:: .. code-block:: bash
mpirun -np 32 -sf gpu -in in.script # launch command mpirun -np 32 -sf gpu -in in.script # launch command
package gpu 2 split -1 # input script command package gpu 2 split -1 # input script command
@ -566,7 +566,7 @@ performance.
Here are examples of how to set the environment variable when Here are examples of how to set the environment variable when
launching LAMMPS: launching LAMMPS:
.. parsed-literal:: .. code-block:: bash
env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script

6
doc/src/partition.rst
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@ -17,12 +17,12 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
partition yes 1 processors 4 10 6 partition yes 1 processors 4 10 6
partition no 5 print "Active partition" partition no 5 print "Active partition"
partition yes \*5 fix all nve partition yes *5 fix all nve
partition yes 6\* fix all nvt temp 1.0 1.0 0.1 partition yes 6* fix all nvt temp 1.0 1.0 0.1
Description Description
""""""""""" """""""""""

2
doc/src/prd.rst
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@ -39,7 +39,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
prd 5000 100 10 10 100 1 54982 prd 5000 100 10 10 100 1 54982
prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200 prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200

2
doc/src/print.rst
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@ -24,7 +24,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
print "Done with equilibration" file info.dat print "Done with equilibration" file info.dat
print Vol=$v append info.dat screen no print Vol=$v append info.dat screen no

14
doc/src/processors.rst
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@ -41,15 +41,15 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
processors \* \* 5 processors * * 5
processors 2 4 4 processors 2 4 4
processors \* \* 8 map xyz processors * * 8 map xyz
processors \* \* \* grid numa processors * * * grid numa
processors \* \* \* grid twolevel 4 \* \* 1 processors * * * grid twolevel 4 * * 1
processors 4 8 16 grid custom myfile processors 4 8 16 grid custom myfile
processors \* \* \* part 1 2 multiple processors * * * part 1 2 multiple
Description Description
""""""""""" """""""""""
@ -93,7 +93,7 @@ Px,Py,Pz values for different partitions.
You can use the :doc:`partition <partition>` command to specify You can use the :doc:`partition <partition>` command to specify
different processor grids for different partitions, e.g. different processor grids for different partitions, e.g.
.. parsed-literal:: .. code-block:: LAMMPS
partition yes 1 processors 4 4 4 partition yes 1 processors 4 4 4
partition yes 2 processors 2 3 2 partition yes 2 processors 2 3 2

2
doc/src/quit.rst
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@ -15,7 +15,7 @@ status = numerical exit status (optional)
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
quit quit
if "$n > 10000" then "quit 1" if "$n > 10000" then "quit 1"

8
doc/src/region.rst
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@ -72,7 +72,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
region 1 block -3.0 5.0 INF 10.0 INF INF region 1 block -3.0 5.0 INF 10.0 INF INF
region 2 sphere 0.0 0.0 0.0 5 side out region 2 sphere 0.0 0.0 0.0 5 side out
@ -289,7 +289,7 @@ For example, these commands would displace a region from its initial
position, in the positive x direction, effectively at a constant position, in the positive x direction, effectively at a constant
velocity: velocity:
.. parsed-literal:: .. code-block:: LAMMPS
variable dx equal ramp(0,10) variable dx equal ramp(0,10)
region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
@ -299,10 +299,10 @@ Note that the initial displacement is 0.0, though that is not required.
Either of these variables would "wiggle" the region back and forth in Either of these variables would "wiggle" the region back and forth in
the y direction: the y direction:
.. parsed-literal:: .. code-block:: LAMMPS
variable dy equal swiggle(0,5,100) variable dy equal swiggle(0,5,100)
variable dysame equal 5\*sin(2\*PI\*elaplong\*dt/100) variable dysame equal 5*sin(2*PI*elaplong*dt/100)
region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
The *rotate* keyword rotates the region around a rotation axis *R* = The *rotate* keyword rotates the region around a rotation axis *R* =

2
doc/src/replicate.rst
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@ -21,7 +21,7 @@ nx,ny,nz = replication factors in each dimension
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
replicate 2 3 2 replicate 2 3 2

2
doc/src/rerun.rst
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@ -33,7 +33,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
rerun dump.file dump x y z vx vy vz rerun dump.file dump x y z vx vy vz
rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z

8
doc/src/restart.rst
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@ -29,7 +29,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
restart 0 restart 0
restart 1000 poly.restart restart 1000 poly.restart
@ -85,7 +85,7 @@ file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First, versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g. build LAMMPS with its MPIIO package installed, e.g.
.. parsed-literal:: .. code-block:: bash
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform make mpi # build LAMMPS for your platform
@ -117,7 +117,7 @@ For example, the following commands will write restart files
every step from 1100 to 1200, and could be useful for debugging every step from 1100 to 1200, and could be useful for debugging
a simulation where something goes wrong at step 1163: a simulation where something goes wrong at step 1163:
.. parsed-literal:: .. code-block:: LAMMPS
variable s equal stride(1100,1200,1) variable s equal stride(1100,1200,1)
restart v_s tmp.restart restart v_s tmp.restart
@ -180,6 +180,6 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
restart 0 restart 0

12
doc/src/run.rst
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@ -31,7 +31,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
run 10000 run 10000
run 1000000 upto run 1000000 upto
@ -70,7 +70,7 @@ keywords.
For example, consider this fix followed by 10 run commands: For example, consider this fix followed by 10 run commands:
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 all nvt 200.0 300.0 1.0 fix 1 all nvt 200.0 300.0 1.0
run 1000 start 0 stop 10000 run 1000 start 0 stop 10000
@ -144,14 +144,14 @@ of M steps each. After each M-length run, the specified commands are
invoked. If only a single command is specified as NULL, then no invoked. If only a single command is specified as NULL, then no
command is invoked. Thus these lines: command is invoked. Thus these lines:
.. parsed-literal:: .. code-block:: LAMMPS
variable q equal x[100] variable q equal x[100]
run 6000 every 2000 "print 'Coord = $q'" run 6000 every 2000 "print 'Coord = $q'"
are the equivalent of: are the equivalent of:
.. parsed-literal:: .. code-block:: LAMMPS
variable q equal x[100] variable q equal x[100]
run 2000 run 2000
@ -169,7 +169,7 @@ Note that by using the line continuation character "&", the run every
command can be spread across many lines, though it is still a single command can be spread across many lines, though it is still a single
command: command:
.. parsed-literal:: .. code-block:: LAMMPS
run 100000 every 1000 & run 100000 every 1000 &
"print 'Minimum value = $a'" & "print 'Minimum value = $a'" &
@ -187,7 +187,7 @@ skipped for intermediate runs.
You might wish to specify a command that exits the run by You might wish to specify a command that exits the run by
jumping out of the loop, e.g. jumping out of the loop, e.g.
.. parsed-literal:: .. code-block:: LAMMPS
variable t equal temp variable t equal temp
run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"

2
doc/src/server.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
server md server md

2
doc/src/server_mc.rst
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@ -15,7 +15,7 @@ mc = the protocol argument to the :doc:`server <server>` command
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
server mc server mc

2
doc/src/server_md.rst
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@ -15,7 +15,7 @@ md = the protocol argument to the :doc:`server <server>` command
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
server md server md

8
doc/src/set.rst
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@ -120,16 +120,16 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
set group solvent type 2 set group solvent type 2
set group solvent type/fraction 2 0.5 12393 set group solvent type/fraction 2 0.5 12393
set group edge bond 4 set group edge bond 4
set region half charge 0.5 set region half charge 0.5
set type 3 charge 0.5 set type 3 charge 0.5
set type 1\*3 charge 0.5 set type 1*3 charge 0.5
set atom \* charge v_atomfile set atom * charge v_atomfile
set atom 100\*200 x 0.5 y 1.0 set atom 100*200 x 0.5 y 1.0
set atom 100 vx 0.0 vy 0.0 vz -1.0 set atom 100 vx 0.0 vy 0.0 vz -1.0
set atom 1492 type 3 set atom 1492 type 3

6
doc/src/shell.rst
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@ -32,7 +32,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
shell cd sub1 shell cd sub1
shell cd .. shell cd ..
@ -89,7 +89,7 @@ Any other cmd is passed as-is to the shell along with its arguments as
one string, invoked by the C-library system() call. For example, one string, invoked by the C-library system() call. For example,
these lines in your input script: these lines in your input script:
.. parsed-literal:: .. code-block:: LAMMPS
variable n equal 10 variable n equal 10
variable foo string file2 variable foo string file2
@ -97,7 +97,7 @@ these lines in your input script:
would be the same as invoking would be the same as invoking
.. parsed-literal:: .. code-block:: bash
% my_setup file1 10 file2 % my_setup file1 10 file2

2
doc/src/suffix.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
suffix off suffix off
suffix on suffix on

2
doc/src/tad.rst
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@ -41,7 +41,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
tad 2000 50 1800 2300 0.01 0.01 event tad 2000 50 1800 2300 0.01 0.01 event
tad 2000 50 1800 2300 0.01 0.01 event & tad 2000 50 1800 2300 0.01 0.01 event &

10
doc/src/temper.rst
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@ -21,7 +21,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
temper 100000 100 $t tempfix 0 58728 temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w temper 40000 100 $t tempfix 0 32285 $w
@ -50,7 +50,7 @@ variable previously set in the input script, so that each partition is
assigned a different temperature. See the :doc:`variable <variable>` assigned a different temperature. See the :doc:`variable <variable>`
command for more details. For example: command for more details. For example:
.. parsed-literal:: .. code-block:: LAMMPS
variable t world 300.0 310.0 320.0 330.0 variable t world 300.0 310.0 320.0 330.0
fix myfix all nvt temp $t $t 100.0 fix myfix all nvt temp $t $t 100.0
@ -102,10 +102,10 @@ screen.N files as time proceeds.
You can have each replica create its own dump file in the following You can have each replica create its own dump file in the following
manner: manner:
.. parsed-literal:: .. code-block:: LAMMPS
variable rep world 0 1 2 3 4 5 6 7 variable rep world 0 1 2 3 4 5 6 7
dump 1 all atom 1000 dump.temper.$\ *rep* dump 1 all atom 1000 dump.temper.${rep}
.. note:: .. note::
@ -143,7 +143,7 @@ log file listed the following for a simulation with 5 replicas:
then a setting of then a setting of
.. parsed-literal:: .. code-block:: LAMMPS
variable w world 2 4 0 1 3 variable w world 2 4 0 1 3

25
doc/src/temper_grem.rst
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@ -22,10 +22,10 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
temper/grem 100000 1000 $\ *lambda* fxgREM fxnvt 0 58728 temper/grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728
temper/grem 40000 100 $\ *lambda* fxgREM fxnpt 0 32285 $\ *walkers* temper/grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers}
Description Description
""""""""""" """""""""""
@ -47,17 +47,18 @@ has the same dependencies, restraints, and input variables which are
discussed there in greater detail. discussed there in greater detail.
Instead of temperature, this command performs replica exchanges in Instead of temperature, this command performs replica exchanges in
lambda as per the generalized ensemble enforced by :doc:`fix grem <fix_grem>`. The desired lambda is specified by *lambda*\ , lambda as per the generalized ensemble enforced by :doc:`fix grem
which is typically a variable previously set in the input script, so <fix_grem>`. The desired lambda is specified by *lambda*\ , which is
that each partition is assigned a different temperature. See the typically a variable previously set in the input script, so that each
:doc:`variable <variable>` command for more details. For example: partition is assigned a different temperature. See the :doc:`variable
<variable>` command for more details. For example:
.. parsed-literal:: .. code-block:: LAMMPS
variable lambda world 400 420 440 460 variable lambda world 400 420 440 460
fix fxnvt all nvt temp 300.0 300.0 100.0 fix fxnvt all nvt temp 300.0 300.0 100.0
fix fxgREM all grem $\ *lambda* -0.05 -50000 fxnvt fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt
temper 100000 100 $\ *lambda* fxgREM fxnvt 3847 58382 temper/grem 100000 100 ${lambda} fxgREM fxnvt 3847 58382
would define 4 lambdas with constant kinetic temperature but unique would define 4 lambdas with constant kinetic temperature but unique
generalized temperature, and assign one of them to :doc:`fix grem <fix_grem>` used by each replica, and to the grem command. generalized temperature, and assign one of them to :doc:`fix grem <fix_grem>` used by each replica, and to the grem command.
@ -87,12 +88,12 @@ a simulation with 5 replicas:
then a setting of then a setting of
.. parsed-literal:: .. code-block:: LAMMPS
variable walkers world 2 4 0 1 3 variable walkers world 2 4 0 1 3
would be used to restart the run with a grem command like the example would be used to restart the run with a grem command like the example
above with $\ *walkers* as the last argument. This functionality is above with ${walkers} as the last argument. This functionality is
identical to :doc:`temper <temper>`. identical to :doc:`temper <temper>`.
---------- ----------

2
doc/src/temper_npt.rst
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@ -22,7 +22,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
temper/npt 100000 100 $t nptfix 0 58728 1 temper/npt 100000 100 $t nptfix 0 58728 1
temper/npt 2500000 1000 300 nptfix 0 32285 $p temper/npt 2500000 1000 300 nptfix 0 32285 $p

6
doc/src/thermo.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
thermo 100 thermo 100
@ -45,7 +45,7 @@ options for :doc:`equal-style variables <variable>`.
For example, the following commands will output thermodynamic info at For example, the following commands will output thermodynamic info at
timesteps 0,10,20,30,100,200,300,1000,2000,etc: timesteps 0,10,20,30,100,200,300,1000,2000,etc:
.. parsed-literal:: .. code-block:: LAMMPS
variable s equal logfreq(10,3,10) variable s equal logfreq(10,3,10)
thermo v_s thermo v_s
@ -62,6 +62,6 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
thermo 0 thermo 0

4
doc/src/timer.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
timer full sync timer full sync
timer timeout 2:00:00 every 100 timer timeout 2:00:00 every 100
@ -125,7 +125,7 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
timer normal nosync timer normal nosync
timer timeout off timer timeout off

2
doc/src/timestep.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
timestep 2.0 timestep 2.0
timestep 0.003 timestep 0.003

2
doc/src/uncompute.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
uncompute 2 uncompute 2
uncompute lower-boundary uncompute lower-boundary

2
doc/src/undump.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
undump mine undump mine
undump 2 undump 2

2
doc/src/unfix.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
unfix 2 unfix 2
unfix lower-boundary unfix lower-boundary

1
doc/utils/sphinx-config/false_positives.txt
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@ -1929,6 +1929,7 @@ Nelement
Nelements Nelements
nemd nemd
netcdf netcdf
netstat
Nettleton Nettleton
Neumann Neumann
Nevent Nevent