diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 36391731d06c6bc651a2df236ef45edd8e8bbb56..359aa19edba33e45644d2ecae6ae64ea3a41f138 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -261,7 +261,6 @@ END_RST -->
:link(start_6,Section_start.html#start_6)
:link(start_7,Section_start.html#start_7)
:link(start_8,Section_start.html#start_8)
-:link(start_9,Section_start.html#start_9)
:link(cmd_1,Section_commands.html#cmd_1)
:link(cmd_2,Section_commands.html#cmd_2)
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
index 64b80c1a55b71ebdf0de29e845b110107fb21d7e..8812358886e5f867e7fa3e002130c74ad828d877 100644
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@@ -56,7 +56,7 @@ timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_8 of the manual has an overview.
+section"_Section_start.html#start_7 of the manual has an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
@@ -226,16 +226,16 @@ re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command, using the
src/Make.py tool. This tool is discussed in "Section
-2.4"_Section_start.html#start_4 of the manual, and its use is
+4"_Section_packages.html of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.
diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index 40e61a248e1945415a5bbf3a2c65f7a6a37f6519..408c01d52cf2dcbcee7fb1242dc01b74e2752734 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -71,7 +71,7 @@ style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_7. The installation
+command-line argument"_Section_start.html#start_6. The installation
and compilation of optional packages is explained in the "installation
instructions"_Section_start.html#start_3.
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index f2f2561af84cc944ad7635f10366f006e64ffbaf..6d699fe24be8d06956605689192b9bfb2ac1f4c6 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -54,7 +54,7 @@ restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_7 and read by a
+switch"_Section_start.html#start_6 and read by a
"read_data"_read_data.html command in a new script.
Here we give examples of 2 scripts that read either a binary restart
@@ -337,7 +337,7 @@ All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_7 of the manual.
+section"_Section_start.html#start_6 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
@@ -387,7 +387,7 @@ for more info on packages.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
-switch"_Section_start.html#start_7 to launch LAMMPS on multiple
+switch"_Section_start.html#start_6 to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
@@ -395,7 +395,7 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
-of the "-in command-line switch"_Section_start.html#start_7 to specify
+of the "-in command-line switch"_Section_start.html#start_6 to specify
the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
@@ -1872,7 +1872,7 @@ void lammps_free(void *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
-arguments"_Section_start.html#start_7 when LAMMPS is run in
+arguments"_Section_start.html#start_6 when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index a65e510654c64670230210da4139689871c09237..c7e6e84831018538630318fee79b53792581be99 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -369,7 +369,7 @@ suffix in their style name. "Section 5.3.1"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system,
and details on how to build and use this package. Its styles can be
invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_7. See also the "KOKKOS"_#KOKKOS
+switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
@@ -427,8 +427,8 @@ src/GPU/README
lib/gpu/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.1"_accelerate_gpu.html
-"Section 2.7 -sf gpu"_Section_start.html#start_7
-"Section 2.7 -pk gpu"_Section_start.html#start_7
+"Section 2.6 -sf gpu"_Section_start.html#start_6
+"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -553,7 +553,7 @@ style name. "Section 5.3.3"_accelerate_kokkos.html gives details of
what hardware and software is required on your system, and how to
build and use this package. Its styles can be invoked at run time via
the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_7. Also see the "GPU"_#GPU,
+switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs, KNLs, and GPUs.
@@ -621,9 +621,9 @@ src/KOKKOS/README
lib/kokkos/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.3"_accelerate_kokkos.html
-"Section 2.7 -k on ..."_Section_start.html#start_7
-"Section 2.7 -sf kk"_Section_start.html#start_7
-"Section 2.7 -pk kokkos"_Section_start.html#start_7
+"Section 2.6 -k on ..."_Section_start.html#start_6
+"Section 2.6 -sf kk"_Section_start.html#start_6
+"Section 2.6 -pk kokkos"_Section_start.html#start_6
"package kokkos"_package.html
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -950,7 +950,7 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. "Section 5.3.5"_accelerate_opt.html gives details
of how to build and use this package. Its styles can be invoked at
run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_7. See also the "KOKKOS"_#KOKKOS,
+switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
@@ -977,7 +977,7 @@ CCFLAGS: add -restrict :ul
src/OPT: filenames -> commands
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.5"_accelerate_opt.html
-"Section 2.7 -sf opt"_Section_start.html#start_7
+"Section 2.6 -sf opt"_Section_start.html#start_6
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -1887,7 +1887,7 @@ All of them have an "intel" in their style name. "Section
5.3.2"_accelerate_intel.html gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_7.
+"-suffix intel" "command-line switches"_Section_start.html#start_6.
Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs and KNLs.
@@ -1943,8 +1943,8 @@ src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.2"_accelerate_gpu.html
-"Section 2.7 -sf intel"_Section_start.html#start_7
-"Section 2.7 -pk intel"_Section_start.html#start_7
+"Section 2.6 -sf intel"_Section_start.html#start_6
+"Section 2.6 -pk intel"_Section_start.html#start_6
"package intel"_package.html
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
src/USER-INTEL/TEST
@@ -2217,7 +2217,7 @@ via OpenMP directives. All of them have an "omp" in their style name.
"Section 5.3.4"_accelerate_omp.html gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf omp" or
-"-suffix omp" "command-line switches"_Section_start.html#start_7.
+"-suffix omp" "command-line switches"_Section_start.html#start_6.
Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
CPUs.
@@ -2250,8 +2250,8 @@ src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.4"_accelerate_omp.html
-"Section 2.7 -sf omp"_Section_start.html#start_7
-"Section 2.7 -pk omp"_Section_start.html#start_7
+"Section 2.6 -sf omp"_Section_start.html#start_6
+"Section 2.6 -pk omp"_Section_start.html#start_6
"package omp"_package.html
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index 1e67fca321aa58a5fef7f71cb7d7b061e0326ae2..f4b6bdad9734b4f837a407e292944b330cea6130 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -198,7 +198,7 @@ file and the shared library.
11.3 Building LAMMPS as a shared library :link(py_3),h4
Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.5"_Section_start.html#start_5. A shared library is one
+"Section 2.4"_Section_start.html#start_4. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
@@ -217,7 +217,7 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
-"Section 2.5"_Section_start.html#start_5 for more details.
+"Section 2.4"_Section_start.html#start_4 for more details.
:line
@@ -439,7 +439,7 @@ first importing from the lammps.py file:
>>> CDLL("liblammps.so") :pre
If an error occurs, carefully go thru the steps in "Section
-2.5"_Section_start.html#start_5 and above about building a shared
+2.4"_Section_start.html#start_4 and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index b7a471c3fa44c1512e2b88bf89cd7f4af9a7e189..c798005f5e62aad3b13aa59aa0d778ca0a9f4598 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -14,11 +14,11 @@ experienced users.
2.1 "What's in the LAMMPS distribution"_#start_1
2.2 "Making LAMMPS"_#start_2
2.3 "Making LAMMPS with optional packages"_#start_3
-2.5 "Building LAMMPS as a library"_#start_4
-2.6 "Running LAMMPS"_#start_5
-2.7 "Command-line options"_#start_6
-2.8 "Screen output"_#start_7
-2.9 "Tips for users of previous versions"_#start_8 :all(b)
+2.4 "Building LAMMPS as a library"_#start_4
+2.5 "Running LAMMPS"_#start_5
+2.6 "Command-line options"_#start_6
+2.7 "Screen output"_#start_7
+2.8 "Tips for users of previous versions"_#start_8 :all(b)
:line
@@ -714,7 +714,7 @@ type
lmp_machine -h :pre
to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will list the styles and commands
+switch"_#start_6 for "help", which will list the styles and commands
known to your executable, and immediately exit.
:line
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt
index 2ac7d62f6c26cd0941e31ebdd578d7aa55ad562f..68e9fa477a2a6d52e4ab8db10f50b935bab37adf 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/accelerate_gpu.txt
@@ -54,7 +54,7 @@ specify the # of GPUs per node
use GPU styles in your input script :ul
The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_7 respectively. Or
+"command-line switches"_Section_start.html#start_6 respectively. Or
the effect of the "-pk" or "-sf" switches can be duplicated by adding
the "package gpu"_package.html or "suffix gpu"_suffix.html commands
respectively to your input script.
@@ -75,7 +75,7 @@ This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.
You can do both these steps in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
+described in "Section 4"_Section_packages.html of the manual.
Type "Make.py -h" for help. If run from the src directory, this
command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
starting Makefile.machine:
@@ -151,9 +151,9 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_7,
+Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
which will automatically append "gpu" to styles that support it. Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_7 to
+the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
set Ng = # of GPUs/node to use.
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
@@ -188,7 +188,7 @@ pair_style lj/cut/gpu 2.5 :pre
You must also use the "package gpu"_package.html command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_7 were used. It specifies the
+switches"_Section_start.html#start_6 were used. It specifies the
number of GPUs/node to use, as well as other options.
[Speed-ups to expect:]
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index 155e29e367241c02943c06eb674ddb7fffbb1cd2..74ae9d9a4249d825922d36d38ba71b798fbc1b95 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -226,7 +226,7 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
make intel_cpu_intelmpi :pre
Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 2.4"_Section_start.html#start_4 of the
+script, described in "Section 4"_Section_packages.html of the
manual. Type "Make.py -h" for help. For an example:
Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
@@ -301,7 +301,7 @@ Hyper-Threading technology disabled.
To enable USER-INTEL optimizations for all available styles used in
the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_7 can be used without
+"command-line switch"_Section_start.html#start_6 can be used without
any requirement for editing the input script. This switch will
automatically append "intel" to styles that support it. It also
invokes a default command: "package intel 1"_package.html. This
@@ -314,7 +314,7 @@ support, that 1 coprocessor per node will be used with automatic
balancing of work between the CPU and the coprocessor.
You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
+the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
with keyword/value pairs as specified in the documentation. Here,
Nphi = # of Xeon Phi coprocessors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
@@ -387,7 +387,7 @@ can performed automatically by using "-sf hybrid intel opt" or
and "omp" suffixes can be appended manually in the input script. For
the latter, the "package omp"_package.html command must be in the
input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7 must be used where Nt is the
+switch"_Section_start.html#start_6 must be used where Nt is the
number of OpenMP threads. The number of OpenMP threads should not be
set differently for the different packages. Note that the "suffix
hybrid intel omp"_suffix.html command can also be used within the
@@ -486,7 +486,7 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_7 is used to limit the coprocessor
+switch"_Section_start.html#start_6 is used to limit the coprocessor
threads per MPI task.
[Restrictions:]
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt
index 602c3191f65107d51f65f801a61b15faf40d7bd7..6ccd6958411523d0a6b958eab78b88ff4a32f72c 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@@ -136,7 +136,7 @@ You must choose at build time whether to build for CPUs (OpenMP),
GPUs, or Phi.
You can do any of these in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
+described in "Section 4"_Section_packages.html of the manual.
Type "Make.py -h" for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
@@ -144,7 +144,7 @@ src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_7
+"-sf kk" "command-line switches"_Section_start.html#start_6
respectively. Or the effect of the "-pk" or "-sf" switches can be
duplicated by adding the "package kokkos"_package.html or "suffix
kk"_suffix.html commands respectively to your input script.
@@ -280,10 +280,10 @@ specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.
You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package. It
+switch"_Section_start.html#start_6 to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are "documented
-here"_Section_start.html#start_7. The two most commonly used
+here"_Section_start.html#start_6. The two most commonly used
options are:
-k on t Nt g Ng :pre
@@ -304,12 +304,12 @@ The "-k on" switch also issues a "package kokkos" command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the "package"_package.html command doc page.
-Use the "-sf kk" "command-line switch"_Section_start.html#start_7,
+Use the "-sf kk" "command-line switch"_Section_start.html#start_6,
which will automatically append "kk" to styles that support it. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 if
+the "-pk kokkos" "command-line switch"_Section_start.html#start_6 if
you wish to change any of the default "package kokkos"_package.html
optionns set by the "-k on" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
@@ -323,7 +323,7 @@ However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. You can do this with the "-pk" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
[Or run with the KOKKOS package by editing an input script:]
@@ -332,7 +332,7 @@ appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.
You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
+switch"_Section_start.html#start_6 to enable the KOKKOS package, and
specify its additional arguments for hardware options appropriate to
your system, as documented above.
@@ -343,7 +343,7 @@ pair_style lj/cut/kk 2.5 :pre
You only need to use the "package kokkos"_package.html command if you
wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Section_start.html#start_6.
[Speed-ups to expect:]
@@ -389,7 +389,7 @@ If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the "t" keyword of the "-k" "command-line
-switch"_Section_start.html#start_7. If you do not change this, no
+switch"_Section_start.html#start_6. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).
@@ -429,7 +429,7 @@ details).
The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
+Use the "-k" "command-line switch"_Section_commands.html#start_6 to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of
diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt
index c8dd343861ed3acd5351bb282d028c3661e3076f..81b7a5adc28ac9740edea7b0f084e7547bf25fcc 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@@ -41,7 +41,7 @@ each MPI task running on a CPU.
The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the "make" command. Or how to do it with
one command via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for
+4"_Section_packages.html of the manual. Type "Make.py -h" for
help.
Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
@@ -62,14 +62,14 @@ threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
"omp" to styles that support it. The "-sf omp" switch also issues a
default "package omp 0"_package.html command, which will set the
number of threads per MPI task via the OMP_NUM_THREADS environment
variable.
You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7, to explicitly set Nt = # of OpenMP
+switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
threads per MPI task to use, as well as additional options. Its
syntax is the same as the "package omp"_package.html command whose doc
page gives details, including the default values used if it is not
diff --git a/doc/src/accelerate_opt.txt b/doc/src/accelerate_opt.txt
index 704321ca07fdaaa8b62da2d3047c2cb5c479d11d..5a2a5eac0a971be2ba5e2b0fc8a418bdba550d2b 100644
--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/accelerate_opt.txt
@@ -36,7 +36,7 @@ None.
The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the "make" command. Or how to do it with one command
via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for
+4"_Section_packages.html of the manual. Type "Make.py -h" for
help.
Note that if you use an Intel compiler to build with the OPT package,
@@ -46,7 +46,7 @@ The Make.py command will add this automatically.
[Run with the OPT package from the command line:]
As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
"opt" to styles that support it.
[Or run with the OPT package by editing an input script:]
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index a02e60425807db521855880ddaaa1aa51402738a..7ff7ef8fd417c1118951adcbc0f89b4c7d08540a 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index 74f2544cd4c71d096da8436713bc98a1b6b24f59..71a508d69198ae1b476f868768faf35e05748fe6 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -94,7 +94,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index 4fb2ccaf7cf5e4fcea86ed4a3d5d11a4ca438ad9..c0ce3c9301f735fc69fb1b239d30ddce3150c3b0 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index 6ab214508cbecf3e8d89866238361872d1693511..830fd6db584a67bf7c93082b971e3abb383e69d2 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index c6cd57e419aca9d435482b31839c94bd9df81237..b5c53b1b0fb5a81d8ab33d2ebbc8e2087fd26fab 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index dc1a29a86ba630ddca3ad59789c608144c5b91ce..6ed9fe2150b7d7bdcda19e55bc7ca852ceed4a88 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index 48af5ba76a7c32b310d9a4a662361690aa5735b3..44a68c1087582357c0d2b27a98ba21184a582531 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index 23e1b150a86eb8f87b60bd3c8c6abcb22bd54fd3..065cdad5421bf816fd6cb600a023d265e4bbfff8 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index f58ae8e4f4fc8950f22969148ba538250a3b5bc3..da39e7cf326b43afce171e0005c1ef93cde2d5c8 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -51,7 +51,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 9da8ffed284c610842ed82cab65dd71640237dbe..5adda6cb32f85a00310f5dc62ada7838e84d5715 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 12ee805218979c7af1f2f07de68a75e4de4a7afb..4c74763964832d98cfcae9443866e2db4293ca64 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index fea2eb9e03763f2da0d4ffc8fd427201e01e6da0..f7640bdfbc0f75af1170cb551220d846df1529a0 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index 61dd7b041eadefca56b123959d685dc9b618070c..bd6e167bd8f4dfccc84412c6597e1d2568a1daec 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -136,7 +136,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index 79728d6569b392606bdf0206949c2b10a692e606..da6f59900d69fb784ee8cdf91cc3bef60921aaa8 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -394,7 +394,7 @@ weights. It assigns the same weight to each particle owned by a
processor based on the total computational time spent by that
processor. See details below on what time window is used. It uses
the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_8, namely, for sections {Pair},
+breakdown"_Section_start.html#start_7, namely, for sections {Pair},
{Bond}, {Kspace}, and {Neigh}. The time spent in those portions of
the timestep are measured for each MPI rank, summed, then divided by
the number of particles owned by that processor. I.e. the weight is
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index aa0541238781f7268ced22ee07e074a5de4437a0..9687a6316805acb77298f74eeb84952e8f4243fe 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -56,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index 80d2a805c53124a72c95195e917a619cca399e11..9050c3bf5ccecdd8701f414ef0caea5e39a19c2c 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -59,7 +59,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 3908c16a7e9c43bdcb20ecfb7e0ed82e5f9d7b17..ff687444a97378373514442bda71a614b74bd821 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -62,7 +62,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index 1cbd897dacc79c33a958995f48133237cf4045a5..c18a7e0fd4d35a337a832255b64b4daf8f07392f 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -54,7 +54,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index 8cb2d2ce7d5cc938104d85855481e96845b79d1b..bf3b3c115adeb59fcbd0a7a51e36a4612e6c020d 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index 836d6afda4f53af8d464e9553b8f9b5ee2e003d7..1918ce00b6210468a119d332762ed85f8f2bad0e 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 12e51f9bef6f375a66f407721a0e323c7c98bc12..4f6a32e341b57a7977e4aaabc83d8dd1a1282137 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index ac9f3369c22b86e4c3c691e39d8a59542c016ad0..434af625061a45679e9f01630c3999743d6d77ee 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index e61f4f034364b1552824649e4b95df9fe2f36d2a..4dc7ad4a3693e8d0ed492514fbaaf5f15deaecd0 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -88,7 +88,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index cb096fba1116ac3e7ac486e1666ab5ce70b7734f..906d3e5d7639eb08e211554b2817195dd383bcf1 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -133,7 +133,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index 292e779f7231f80abc6387c85448d7ac4c6dc8d8..f0691ad20762758234828f976e7519ef47568d57 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index 0bd2d4b121756f5361c532e37eedfaebf31a595f..b88be79e20704a41482ad444668ca8b81d0c4b32 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index 163a00af52308368c464fec1c47e26e351a703c1..fe2420b4e40d8d28e0b824d8022b8322596877f6 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 73dc67cdefef9bf3d853be18e4f4032b62e767d7..06abe054e4819e7c7e9ea9e248e7f2285e423572 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -128,7 +128,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 91ab6f37380ebf92e948ce971633a89053ded5dd..cb9fc72c223b2293990764db4b0dffb59dc249b5 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -153,7 +153,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 89614a3fdb524282d76e89d3e2b221fc258a852f..715682affc010e657556ba9221ca68a093b5259a 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index 5682309b83df3c263374b1415685d64c084ae611..da892b59daaf8eda8e540f9a26f850e55877b4aa 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index c763dcce22c27c904332d42311beba49218e356a..d9a48ff384d9df3dd9228a05be3c523302b80362 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index fced983db034a7eb52d93fd612903a62154636ff..1e907557b28564f74e3f080160997a107941d4b5 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -58,7 +58,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 5774a67685e3e78fda3985ea847d9df57374a20c..7d3c2ea083d0ef78b7e275caa9ca51e1305e8e49 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -52,7 +52,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 0df28a05d461553231818882ee616d9bdaa15dba..8392d83899de8c41cd855e6a038f3e7a585ec08a 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -52,7 +52,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index afcc5d3514e6b19752ddca18beeabafdd9783849..d1a6ba3ff2865db905b97bf72b70d343f509e06e 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index 526b469f635626654f73535995bab5019319a028..ca2f5aed40f2f67512a255813689a50e35a4c7d7 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index 8ef8ad05f87f20ccd50be2b87de0efed22791f39..3141c7a719bcb0de5d39366183a269f761bd0230 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -26,7 +26,7 @@ command to the screen and/or log file as it is read and processed. If
an input script has errors, it can be useful to look at echoed output
to see the last command processed.
-The "command-line switch"_Section_start.html#start_5 -echo can be used
+The "command-line switch"_Section_start.html#start_6 -echo can be used
in place of this command.
[Restrictions:] none
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index da9f98a6dae5e993898f98a97f2fcd18a7e7070a..1cc0a1533206024aef0993ba8c8d57a131908bee 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index d980e9a2115097c04ada2dfef658c99d0aebed8b..5d7dec3e6aef7bb804f312546cb15bbe85b0e639 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index d3254eece6b1a8e8508b799196c628bb249477c5..63d872eded4d2e4c6a70a936e427d899115e3463 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -557,7 +557,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 1dce620033c74ca1389609484c545df6f6e4db1f..5d04e96677f2adc27c9622b84d97810b23748d7a 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -41,7 +41,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index 6a4f6c2fcf839cb7d50d13d37eb524ad28ce971c..a63ee4cb32688c286797292acbaa140fbed18101 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -45,7 +45,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 2cf1665c30ee07f93ca955bfa47176819e8e63a1..dae8ac5ed0910fc2c91b776339de840707bf5500 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -102,7 +102,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 534d83f6a94790425379b4391f8075a149daef50..93c73f5a5dd2390f93d80dfe7ce2d4efc7f53e69 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -276,7 +276,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index 4f94e2a85784ad330a5e2276503de77db8f16f69..bcf4465fb8f5c9bc30626cc3275f422fd2158e9e 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -73,7 +73,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index c1cc3e560a09aa1ce2f500df7adf654a738124b3..8fa30ac22289d7fe39ff6f1d0c314990dfb52c79 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -492,7 +492,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 3d151a724b10e915e147d64c02e5bd238853a4ac..8c35b6a1a7a4b8bbd2fc98573764f99f0995249c 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -93,7 +93,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 3a273be595321ebe793f7eb7896cb4aeffe0d2b5..1e590f1cb3f3d5a46724d86e657d805a6a1906e3 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -92,7 +92,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 9258f40c766df92f941958d4f54b3afa967a6b81..62b45edfd7cd5ffbd8fe8ab48d5aefc29d3417ee 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -102,7 +102,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index ef3ffc49558706482069f407c1aa7d70f400abd1..292e46f94af6fcfe8e8c8b5b1e04908c2c55c9bc 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -152,7 +152,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 8fe98f1818a7c2b513bbca698407c65417f668fc..5f3979e36ed9e586f2eee15750364641348c040c 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index 772920df61cc32cfdc1a0aa9c2f788507881323d..d89bf19db24fa7a988923a8cb5822cccc9641ed9 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -116,7 +116,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index 24a8fede57a095ba00781387906039eb3e5bafff..c4cf2cb08de85d8fe892f240473a0a90daa56de0 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -127,7 +127,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index 7ad83018777948930f6c071921da1724f8242255..c04c17858ebdf9b4166827a9cf5f52ed0f43e597 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -46,7 +46,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index 03846a2558196d1d4cafad7b77d563fc026ff053..1f31fb96792239de806f99e78744106b0b08c1f7 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index f91a41f515ed0557d86caef998e4f89dad8988f5..21dc6cba8a4aa7e067bcb9b0c066879e60b23479 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 77de1dea40af798aa0935aa84c7c9670316c848a..21b900f16ac69d3ef28b7b39fa90f232f43eb290 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -98,7 +98,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 1f04b85c8b749bbc0babd8bbbc0707cb88c3b0a0..6a5e09ba7fb57ef45a91b9bf764e1f2e821fc34f 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -97,7 +97,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 82631f22e3008cb2f5bcc4186b429ff43abbc17d..392dbc281c6f5eee0fc164f4ed8eb6670bfbcbef 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -121,7 +121,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index fa1c97bcce2fd266f82bfdf2c1c96ce8baf53699..ecf0922b7901a154f0728579b41d6e9502b2f3d0 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 30c5003e7288d70d38bdb8f34e3a81c6e5083e2e..7f82404127fc61f6c3225f1c0d9b960bad470e27 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -74,7 +74,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index a1a19b73686e642d06bd75667c7c2ffb0df29f92..18450c7cd5c0852c30e2324f3c683d84a2b63479 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -92,7 +92,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index aadb0a9cbc297e735d92971325a588cd73abd1ca..54aa7faef802f3061f795c54a7449d6d93265d0b 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 9a588356e0b294cf6c4b3f9f317280b9fa79b6d3..7c920791f7b10bd923da0402c35a8215a15bf650 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -151,7 +151,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 87021b855112fd7ea4b5145d3c479d8bd6d86971..62969112f7b7963b66ff99a387cb3183eb3894cb 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -676,7 +676,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index 90766fc5bc8837293531dc93f901aa3a0c7f35aa..f5be0f93a54c459ead80c691dd4905df678760c4 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 8b26aaa874ddc127c0799aabb11c5fcacc6f645e..c187b17c6cf7405a7ebb387c358424b313927b3e 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -159,7 +159,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 5b425316e047b348c2c1ff9e22655f4f2e7ef6d6..954ec65bf6a1c059226c1beac58bea86fab0fb84 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -142,7 +142,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index 0b41afe2db6c43d4fefd6120453e4a5c18102506..14ec6258de654a466ec429328014f420e81cb999 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -99,7 +99,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index e238063a8f07b248a13de71d01a6305b76b93150..138a6a16503b125003b15ec1ceb394f18963e1eb 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index 72f346ba04ce1792c54f9f9b518bd3d9596c253b..5f69eccc60a1d060b894c89f487d591fa1a8b0b8 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index 3a5354b1fe6b03e299c518bd7b2b924022a32f06..f9062da207b329cb7616ca38420e8878675252b4 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index b47b0ca41f16aa796e0d7a47273ee48aa30e1b15..bb17e5a641e8da1b4b92f3e1b5ecfe8245fddf1a 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -70,7 +70,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index cba59399e715aac6e1550e5fb2c9ecf86e4344f8..c02d39247403622fe51e1ffbc4e47df43e11db77 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -69,7 +69,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index fafa2e7e4cf29acf51fdb899963a0c49df51433c..d6df9ee6cccc8ec2f391a2583ac495caa0ad07e9 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index 1b1a209511309d3538d6125a78f0dcc642434348..4e3799f7b1c48fafa179454b458c2eff588c4453 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -40,12 +40,12 @@ lmp_g++ < in.script :pre
since the SELF option invokes the C-library rewind() call, which may
not be supported for stdin on some systems or by some MPI
implementations. This can be worked around by using the "-in
-command-line argument"_Section_start.html#start_7, e.g.
+command-line argument"_Section_start.html#start_6, e.g.
lmp_g++ -in in.script :pre
or by using the "-var command-line
-argument"_Section_start.html#start_7 to pass the script name as a
+argument"_Section_start.html#start_6 to pass the script name as a
variable to the input script. In the latter case, a
"variable"_variable.html called "fname" could be used in place of
SELF, e.g.
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 460482ea1e350ec9092b5d052badc71e5e054c3d..92bb12e6dbccf42c9c8d1b80d587088e91bf88c7 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -34,7 +34,7 @@ the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
-switch -log. See "Section 2.7"_Section_start.html#start_7 for
+switch -log. See "Section 2.6"_Section_start.html#start_6 for
details.
[Restrictions:] none
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index d2e8be3f03298e9bfd9bde20f56ede4ed7675277..144fe8bdefcf350ad0d8a4170b2d443f67904f0f 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -51,7 +51,7 @@ follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
+switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on just one or two
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 7b8f499ba897868c9118739bdb6cb32984afbfc0..062f79a5bbba0bc7e9042145dd03cebbf1ceebe3 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -66,7 +66,7 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See "this
-section"_Section_start.html#start_8 for details.
+section"_Section_start.html#start_7 for details.
[Restrictions:] none
diff --git a/doc/src/next.txt b/doc/src/next.txt
index fe9dc975423858269a8fbb3f7f776be83ad7c033..08f73b896cb7ef13f74c5dd982f07d021fe44eea 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -71,7 +71,7 @@ next value (for each variable) is assigned to whichever processor
partition executes the command first. All processors in the partition
are assigned the same value(s). Running LAMMPS on multiple partitions
of processors via the "-partition" command-line switch is described in
-"this section"_Section_start.html#start_7 of the manual. {Universe}-
+"this section"_Section_start.html#start_6 of the manual. {Universe}-
and {uloop}-style variables are incremented using the files
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
see in your directory during and after such a LAMMPS run.
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 18a26bd55c0f6cbf83c144bdc8835b2b314f7d9c..1b9092644fd4d3bea73eb7b16829056c2bf6a91c 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -115,7 +115,7 @@ their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
-switch"_Section_start.html#start_7. The syntax is exactly the same as
+switch"_Section_start.html#start_6. The syntax is exactly the same as
when used in an input script.
Note that all of the accelerator packages require the package command
@@ -126,18 +126,18 @@ a default version of the command is typically invoked by other
accelerator settings.
The KOKKOS package requires a "-k on" "command-line
-switch"_Section_start.html#start_7 respectively, which invokes a
+switch"_Section_start.html#start_6 respectively, which invokes a
"package kokkos" command with default settings.
For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Section_start.html#start_7
+intel" or "-sf omp" "command-line switch"_Section_start.html#start_6
is used to auto-append accelerator suffixes to various styles in the
input script, then those switches also invoke a "package gpu",
"package intel", or "package omp" command with default settings.
NOTE: A package command for a particular style can be invoked multiple
times when a simulation is setup, e.g. by the "-c on", "-k on", "-sf",
-and "-pk" "command-line switches"_Section_start.html#start_7, and by
+and "-pk" "command-line switches"_Section_start.html#start_6, and by
using this command in an input script. Each time it is used all of
the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist
@@ -305,7 +305,7 @@ value via their package commands, but there is only a single global
invoked, you should insure the two values are consistent. If they are
not, the last one invoked will take precedence, for both packages.
Also note that if the "-sf hybrid intel omp" "command-line
-switch"_"_Section_start.html#start_7 is used, it invokes a "package
+switch"_"_Section_start.html#start_6 is used, it invokes a "package
intel" command, followed by a "package omp" command, both with a
setting of {Nthreads} = 0.
@@ -550,7 +550,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"suffix"_suffix.html, "-pk" "command-line
-setting"_Section_start.html#start_7
+setting"_Section_start.html#start_6
[Default:]
@@ -558,9 +558,9 @@ For the GPU package, the default is Ngpu = 1 and the option defaults
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
to Ngpu-1, tpa = 1, and device = not used. These settings are made
automatically if the "-sf gpu" "command-line
-switch"_Section_start.html#start_7 is used. If it is not used, you
+switch"_Section_start.html#start_6 is used. If it is not used, you
must invoke the package gpu command in your input script or via the
-"-pk gpu" "command-line switch"_Section_start.html#start_7.
+"-pk gpu" "command-line switch"_Section_start.html#start_6.
For the USER-INTEL package, the default is Nphi = 1 and the option
defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
@@ -569,21 +569,21 @@ style being used. This value is output to the screen in the offload
report at the end of each run. Note that all of these settings,
except "omp" and "mode", are ignored if LAMMPS was not built with
Xeon Phi coprocessor support. These settings are made automatically
-if the "-sf intel" "command-line switch"_Section_start.html#start_7
+if the "-sf intel" "command-line switch"_Section_start.html#start_6
is used. If it is not used, you must invoke the package intel
command in your input script or or via the "-pk intel" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
For the KOKKOS package, the option defaults neigh = full,
neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
These settings are made automatically by the required "-k on" "command-line
-switch"_Section_start.html#start_7. You can change them bu using the
+switch"_Section_start.html#start_6. You can change them bu using the
package kokkos command in your input script or via the "-pk kokkos"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Section_start.html#start_6.
For the OMP package, the default is Nthreads = 0 and the option
defaults are neigh = yes. These settings are made automatically if
-the "-sf omp" "command-line switch"_Section_start.html#start_7 is
+the "-sf omp" "command-line switch"_Section_start.html#start_6 is
used. If it is not used, you must invoke the package omp command in
your input script or via the "-pk omp" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 457a797d95d32342519ff9954aef3aff1fa0b3ec..9d2a48dcbca399bc00f09458c56941cf3f622b5e 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -137,7 +137,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 06dcccb9d9fc932b3e7664b1fffbdcc466ce7894..402e537dadf39bc5728d6001d32a0709d17e54c0 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -70,7 +70,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated style explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 0c03eb32673146d0f9ecf314cd04c978ca003f80..e66ecb637f7714fd2e41c89ffc8a4c88414bee3c 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -185,7 +185,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index 4e792754b832d408c16042193060a319a91431da..e160f09b3d6fc5764c24bdd367d284e93db55622 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index d38d9e3191d196fb41c17d495b0a655407a41f55..a3cc744a2203cd92ae8314dca242a0e76f70d8cb 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -152,7 +152,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index 33eed7762992575a98b2ce703d2854e98d696242..79b71e91c73e3d6a99b129472cea4831e6905324 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -85,7 +85,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index e705e735fb78340795c8e1b2c6b9364e47322aec..d18b39d5d92b0bf7882f51a3a32149ed5d9e56d6 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -152,7 +152,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index ba18738e4d6e70b97d5b92bd4a55dc0dca0a6c66..05e760e1b22b44c5901f9160b9fa4f3eaaa44c5c 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -114,7 +114,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 1e78607c084e6b4ac07bca1cc8ec39a5a6585d80..ef4ef41c954db0aef17b2998012f85adab936830 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -195,7 +195,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 23b90aae2dad9bb43c173b908cc2dba86843ba93..36fae5068b6e055adac9b7a2fb475e0df513968c 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -114,7 +114,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index a0df1d464eb8466a8eebe25a17cb89585cdf300e..83b15b358bf532f6725853f8fc7e7b2329419ac5 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -139,7 +139,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index 3a2f380bfa747fd748365d9fc6c1fcb02c677218..f5461b1cbc208ca0c5cd01583416f1821b0a6ec8 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -124,7 +124,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index 4a601e90c0aa1493ef86805ddb62b8caddeae28d..29e5beed3c755f9e85b2b5d49f3fcbcdd4095470 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -274,7 +274,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 985581cac8b227ad8ee3a75ec187ef13c985068b..2516e5eae4d00113892dd8e97558b59ca13b97e3 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -198,7 +198,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 62a5faffedd9d7096d82e7a1e8618df313d5d147..9dd204ad2db7d580daa79d7c4d4bb5649de9349a 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -121,7 +121,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 4d3c2b2deae20ae1b31141d3fe9a44cfbca3a7b0..ce8495affd006b014dba20fe6732051b0fa34faa 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -381,7 +381,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for more
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index 86453859d3a72db5719918f0f605ac415623c61c..e5b1420b5938eed1008b780fc226e1258d0c3fa5 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -121,7 +121,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 3f068d4040a7e230f4e003ec3c4dc5bb7892af70..75ad2d4683ee64716ebc003ca5267d5733302760 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -148,7 +148,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index 8639f220a478448b803550fa719d40857a080725..c9235785866f6856ad438fb934afdcc64d4ba781 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -145,7 +145,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 62a58b350412d1fb64ca71b9faba94aa2973f8a2..d7e87af013f002a6e6472a4ae45e3f5c27fd3de5 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -191,7 +191,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 3aca8c3cd3ee1b85a57a90400e67d0e50cbff110..ec84a2d57a13d7066fb49624cba932a425447656 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -103,7 +103,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index 9641e294fad4781f4a73719cf06a12adfcb36db5..d3cf90ec14c2172faf4eec91a5247724acc3428a 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -178,7 +178,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 5166fe1f849799a242ed251dff9179c99af8dd17..fc1824cf62736fcc4612953721c7cd6230069dd4 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -330,7 +330,7 @@ LAMMPS was built with those packages. See the
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index 5c8e31ac42e749f2b28f883985f824044a58e18a..058d54fb5950aec706e4de4b4561cb23f924b5e9 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -253,7 +253,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 6e7c3cbaec68a8b06bdd883ef5139abab1c1648c..83f6ec063d4dd6476555a068a7eac6374544a3be 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -61,7 +61,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index d33e3ec09b8ed21daf8b834d6ea033a59fee962f..4ca8c3c141c39c9c874902f96f5178a1b1941d7a 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -75,7 +75,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index c5f0c88a758c262aa32f49bd795b908e0a192f77..e0838426f637da3e3669fc4c35a17afaa6d6083b 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index da9f37b9c324207c0ea62027c7ef8198b04943ce..6be4562d18849130536383878ac5acc084b20f20 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -168,7 +168,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 133773abd086c0db43f4f49ef942fca4af1a7449..b1678cad5862cf4670a80a68e7c2074337250ba9 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -74,7 +74,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index a48c441f54381cd3bd6630bdb7c3012e77a33d9b..5f7c226cee3ccc7b83c6139bf2a6c25dd2c13468 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -61,7 +61,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index e372092cf0630944ff6397b3e16a0214ce368a62..2ef133da554adf3d141e337e3c1b9f4139f72f35 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -219,7 +219,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index 501a0438013dda39f5b0f73d186bb05f715006dc..b39c7545c7e2bdbc90f72631eaadeca06cfe40c5 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -154,7 +154,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 2295a6640bebedee098ce34f2f5efcc3145cf956..6653b397a0cd04e7dfb56aa1f4c8df9159a9e4a9 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -118,7 +118,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 5fbb6d5c0aeddd647be1030d9899de8980d3182c..3eb5ac5afe5b8cb089d5dea24ed02cdea1ec0eec 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -113,7 +113,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 3f7066c82663bc128198f2bdeea0d6b8ea279bfd..2395707fb45b63425456a1ca612895b90bc289c8 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -104,7 +104,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 9096bdc5234f9768bc565ae445185d021646baa4..81cea1a38d4a255b6fdd01d080cecc67602c3a89 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -145,7 +145,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 6ffd8122aa49f794dac275409c3fb75cc6258893..6fef44559504792a64689a344b34a4f39018d0c8 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -151,7 +151,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index cfa88673d7a4b4b129775748013b89dced4fbc50..b9dc6e0ed861dccef018578664c70ba510927222 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -311,7 +311,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 2e0034ed3b486ef006def0fa2127d80a6b5a2d7d..9ad95eb5fc4e9ddc0bb3f9eda4a1751b0afba726 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -157,7 +157,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 1c348eaaf701668f030133314d213f8bbde83524..360136a4eaef3df735b65cfc0f8e7ce5ca78dc16 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -97,7 +97,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index ec1c06729a9cf18cf5ffeccecb30359de0124b20..08fa88c477961677b4aafd786e13ad1b89befed9 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -94,7 +94,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index 6025b9b11b03556a1f3af14af7f19ae17d198754..6ed8f00236e2e4a4f441401c39823586802818a3 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -156,7 +156,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
When using the USER-INTEL package with this style, there is an
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 01c577cd98fefb15542d3f0049f54491fb3abef7..b99491b477224e621da4429d10c0b20b84c66c0d 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -229,7 +229,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 23a20ad0fd33692cfa85ce503c83d73a4db2b0bb..918e88992440045bda099cb2ad9849ab4faeff14 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -191,7 +191,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index ff703063b3df10854d7ff8ce26e754365dfdeb1f..e0c2b5a5cbb07b7c525d58d48eab97cb763971ca 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -143,7 +143,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index 18e54749aa1752453185ca75bd05897177d1f02c..21d57e4e8841570f44f114961af653ad9dde93b4 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -201,7 +201,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 61ca0b5c359a039c16c0ff47c927130e9ea0e1f1..41a4059cee8d4de828d136343a282310f493403d 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -142,7 +142,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index 9c275a61d39bbc4756e15bd8124a49c89e9f54fe..d9c66d45c0cae201fa12b3799bdf562dc9f55a91 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -183,7 +183,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 26acdb2ccbcc706e60c375d217ed1093896b3816..61d6bde6a92ab34ea2a42527f59a3227ab27b163 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index ecdc1496ab734dcc8f59009de35a8990a6f09905..2037a9451f9e77079971382afde16709657c88e7 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -92,7 +92,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 154fdc1c1352780357de5592eeed38ad32ed1f68..5ab672171b7bd041330965199ebc862119088692 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index 9c1d560c83069077dbb99d3ea572b8d794dcd158..610eee99b300bd96486991c1841cfde1a2b1d8e5 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
This command invokes the specified command on a subset of the
partitions of processors you have defined via the -partition
-command-line switch. See "Section 2.6"_Section_start.html#start_7
+command-line switch. See "Section 2.6"_Section_start.html#start_6
for an explanation of the switch.
Normally, every input script command in your script is invoked by
@@ -49,7 +49,7 @@ argument.
Partitions are numbered from 1 to Np, where Np is the number of
partitions specified by the "-partition command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
{N} can be specified in one of two ways. An explicit numeric value
can be used, as in the 1st example above. Or a wild-card asterisk can
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index 247d422b1c43f732c6202e638c2e73ff223e83cb..3c0305e316d4e5c8a321e27ad4662a5dc1807d40 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -63,7 +63,7 @@ event to occur.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
+switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index 781049af9cce84d928dc5385e577f7d27dc38a49..e54b2cede3b94e8bb13324c22f3352601b8b79d8 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -82,7 +82,7 @@ sub-domain.
Also note that if multiple partitions are being used then P is the
number of processors in this partition; see "this
-section"_Section_start.html#start_7 for an explanation of the
+section"_Section_start.html#start_6 for an explanation of the
-partition command-line switch. Also note that you can prefix the
processors command with the "partition"_partition.html command to
easily specify different Px,Py,Pz values for different partitions.
@@ -249,7 +249,7 @@ partition {Precv} which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of {Psend}
and {Precv} must be integers from 1 to Np, where Np is the number of
partitions you have defined via the "-partition command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
A "dependency" means that the sending partition will create its
regular 3d grid as Px by Py by Pz and after it has done this, it will
@@ -286,7 +286,7 @@ processors and their mapping to the 3d grid to the specified file
processors in the manner you desired, which can be tricky to figure
out, especially when running on multiple partitions or on, a multicore
machine or when the processor ranks were reordered by use of the
-"-reorder command-line switch"_Section_start.html#start_7 or due to
+"-reorder command-line switch"_Section_start.html#start_6 or due to
use of MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes
@@ -300,9 +300,9 @@ The IDs are the processor's rank in this simulation (the world), the
universe (of multiple simulations), and the original MPI communicator
used to instantiate LAMMPS, respectively. The world and universe IDs
will only be different if you are running on more than one partition;
-see the "-partition command-line switch"_Section_start.html#start_7.
+see the "-partition command-line switch"_Section_start.html#start_6.
The universe and original IDs will only be different if you used the
-"-reorder command-line switch"_Section_start.html#start_7 to reorder
+"-reorder command-line switch"_Section_start.html#start_6 to reorder
the processors differently than their rank in the original
communicator LAMMPS was instantiated with.
@@ -332,7 +332,7 @@ The {part} keyword (for the receiving partition) only works with the
[Related commands:]
-"partition"_partition.html, "-reorder command-line switch"_Section_start.html#start_7
+"partition"_partition.html, "-reorder command-line switch"_Section_start.html#start_6
[Default:]
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index 6785eb10660861626bf0e65e82eb09ade46a9a0b..a8aca5369306915b7ad280797bbb72d7e64e9141 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -62,7 +62,7 @@ simulation. The file can be ASCII text or a gzipped text file
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
Also see the explanation of the "-restart command-line
-switch"_Section_start.html#start_7 which can convert a restart file to
+switch"_Section_start.html#start_6 which can convert a restart file to
a data file.
This command can be used multiple times to add new atoms and their
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index d0f4b16175c7863a306475dcb950196d8af438c1..d1091542b8306e45def41e1143711164603849d1 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -81,7 +81,7 @@ wrong.
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the "-restart command-line
-switch"_Section_start.html#start_7 to convert a restart file to a data
+switch"_Section_start.html#start_6 to convert a restart file to a data
file.
Similar to how restart files are written (see the
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 885e5e45f8c647031742c372bc6df9797d84b5cc..5039e4a51615164a410bd85ff6572ac41d3a8bf6 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -375,7 +375,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 5e0c2a9ea54e4d4d7b1837ac55575d9a847f21f2..7c39ae1404eebb9c70d1c7a99730d00200a25af2 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -125,7 +125,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_7 to convert a restart file to a data
+switch"_Section_start.html#start_6 to convert a restart file to a data
file.
NOTE: Although the purpose of restart files is to enable restarting a
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index a67899420bdb1569a3250314ab0ef93600dbde22..ba836a07dd1510b48e48ad5c8f2714bd5c6252b9 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -69,7 +69,7 @@ The {verlet} style is a standard velocity-Verlet integrator.
The {verlet/split} style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
-processors. See "Section 2.7"_Section_start.html#start_7 for an
+processors. See "Section 2.6"_Section_start.html#start_6 for an
explanation of the -partition command-line switch.
Specifically, this style performs all computation except the
@@ -115,7 +115,7 @@ When you run in 2-partition mode with the {verlet/split} style, the
thermodynamic data for the entire simulation will be output to the log
and screen file of the 1st partition, which are log.lammps.0 and
screen.0 by default; see the "-plog and -pscreen command-line
-switches"_Section_start.html#start_7 to change this. The log and
+switches"_Section_start.html#start_6 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyond the 1st timestep of the run.
@@ -259,7 +259,7 @@ Accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
You can specify {respa/omp} explicitly in your input script, or
-you can use the "-suffix command-line switch"_Section_start.html#start_7
+you can use the "-suffix command-line switch"_Section_start.html#start_6
when you invoke LAMMPS, or you can use the "suffix"_suffix.html
command in your input script.
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 127719cdb5f678eef1bb30d62ea2caa15f488b7c..7a4adb50b6c5d642a01e490383bb27fae139b211 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -28,7 +28,7 @@ suffix kk :pre
This command allows you to use variants of various styles if they
exist. In that respect it operates the same as the "-suffix
-command-line switch"_Section_start.html#start_7. It also has options
+command-line switch"_Section_start.html#start_6. It also has options
to turn off or back on any suffix setting made via the command line.
The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or
@@ -105,6 +105,6 @@ input script.
[Related commands:]
-"Command-line switch -suffix"_Section_start.html#start_7
+"Command-line switch -suffix"_Section_start.html#start_6
[Default:] none
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index be7edfba43ba54c3fb1ce4592a1bf69df4428a6b..b1c47c8076e1affde9b4c4ecc45c89148ddbd412 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -32,7 +32,7 @@ replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.7"_Section_start.html#start_7 of the
+switch; see "Section 2.6"_Section_start.html#start_6 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
@@ -70,7 +70,7 @@ As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the "section on command-line
-switches"_Section_start.html#start_7 for info on how to change these
+switches"_Section_start.html#start_6 for info on how to change these
names.
The main screen and log file (log.lammps) will list information about
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 36ec7bf12e06586b3fdd284f399dc3250628a2f4..6102169ee363ca2bdb9dc41d1663f9c1dcb442aa 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -255,7 +255,7 @@ The {part} keyword is useful for multi-replica or multi-partition
simulations to indicate which partition this output and this file
corresponds to, or for use in a "variable"_variable.html to append to
a filename for output specific to this partition. See "Section
-2.7"_Section_start.html#start_7 of the manual for details on running
+2.6"_Section_start.html#start_6 of the manual for details on running
in multi-partition mode.
The {timeremain} keyword returns the remaining seconds when a
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 39a6c542b77a17229b286ac2adf3c725d880a440..768c3e1353fb3e6495f63f2d84830c060b4bf74a 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -40,7 +40,7 @@ time is spent in different sections of the code and thus can provide
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
information about the timing output, see this "discussion of screen
-output in Section 2.8"_Section_start.html#start_8.
+output in Section 2.7"_Section_start.html#start_7.
The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time for a run and not collect any
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index e32e82ef4d38bed75e0dd67f9b619109c01174b3..e3b7c5de0d6a50ac158d167365e976cacb396e58 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -178,7 +178,7 @@ This means variables can NOT be re-defined in an input script (with
two exceptions, read further). This is to allow an input script to be
processed multiple times without resetting the variables; see the
"jump"_jump.html or "include"_include.html commands. It also means
-that using the "command-line switch"_Section_start.html#start_7 -var
+that using the "command-line switch"_Section_start.html#start_6 -var
will override a corresponding index variable setting in the input
script.
@@ -248,7 +248,7 @@ variable.
{Index} style variables with a single string value can also be set by
using the command-line switch -var; see "this
-section"_Section_start.html#start_7 for details.
+section"_Section_start.html#start_6 for details.
The {loop} style is identical to the {index} style except that the
strings are the integers from 1 to N inclusive, if only one argument N
@@ -264,7 +264,7 @@ N1 <= N2 and N2 >= 0 is required.
For the {world} style, one or more strings are specified. There must
be one string for each processor partition or "world". See "this
-section"_Section_start.html#start_7 of the manual for information on
+section"_Section_start.html#start_6 of the manual for information on
running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command assigns one string to each
world. All processors in the world are assigned the same string. The
@@ -277,7 +277,7 @@ different partitions.
For the {universe} style, one or more strings are specified. There
must be at least as many strings as there are processor partitions or
-"worlds". See "this page"_Section_start.html#start_7 for information
+"worlds". See "this page"_Section_start.html#start_6 for information
on running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command initially assigns one
string to each world. When a "next"_next.html command is encountered
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index 033199e98b044431ee980a8ebfbaf9fefa03cfbd..39e5a7f8114627a358350f4b7bb4c799fddb27cc 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -59,7 +59,7 @@ If you want to do more exact restarts, using binary files, see the
"restart"_restart.html, "write_restart"_write_restart.html, and
"read_restart"_read_restart.html commands. You can also convert
binary restart files to text data files, after a simulation has run,
-using the "-r command-line switch"_Section_start.html#start_7.
+using the "-r command-line switch"_Section_start.html#start_6.
NOTE: Only limited information about a simulation is stored in a data
file. For example, no information about atom "groups"_group.html and
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index 8160eec3dfda9ceb8634d648dc0ee38df52f2517..ff3b652dba75feefdb3841bf764f885cc0b3a9d1 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -66,7 +66,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_7 to convert a restart file to a data
+switch"_Section_start.html#start_6 to convert a restart file to a data
file.
NOTE: Although the purpose of restart files is to enable restarting a
diff --git a/src/Make.py b/src/Make.py
deleted file mode 100755
index 3030183e1abf16365e12f595b8ae9f1f4a2224cb..0000000000000000000000000000000000000000
--- a/src/Make.py
+++ /dev/null
@@ -1,2378 +0,0 @@
-#!/usr/bin/env python2
-
-# Make.py tool for managing packages and their auxiliary libs,
-# auto-editing machine Makefiles, and building LAMMPS
-# Syntax: Make.py -h (for help)
-# Notes: should be compatible with python 2.7 and 3.x thanks to 'futurize'
-
-from __future__ import print_function
-import sys,os,re,copy,subprocess,platform
-
-# switch abbrevs
-# switch classes = created class for each switch
-# lib classes = auxiliary package libs
-# build classes = build options with defaults
-# make classes = makefile options with no defaults
-# setargs = makefile settings
-# actionargs = allowed actions (also lib-dir and machine)
-# lib build flags are set if lib is built, for use with zoutput
-
-abbrevs = "adhjmoprsvz"
-
-switchclasses = ("actions","dir","help","jmake","makefile",
- "output","packages","redo","settings","verbose","zoutput")
-libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
- "meam","poems","python","qmmm","reax","voronoi")
-buildclasses = ("intel","kokkos")
-makeclasses = ("cc","flags","mpi","fft","jpg","png")
-
-setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig",
- "smallsmall","exceptions","#exceptions")
-actionargs = ("lib-all","file","clean","exe")
-
-gpubuildflag = 0
-
-# ----------------------------------------------------------------
-# functions
-# ----------------------------------------------------------------
-
-# if flag = 1, print txt and exit
-# if flag = 0, print txt as warning and do not exit
-
-def error(txt,flag=1):
- if flag:
- print("ERROR:",txt)
- sys.exit()
- else:
- print("WARNING:",txt)
-
-# store command-line args as sw = dict of key/value
-# key = switch word, value = list of following args
-# order = list of switches in order specified
-# enforce no switch more than once
-
-def parse_args(args):
- narg = len(args)
- sw = {}
- order = []
- iarg = 0
- while iarg < narg:
- if args[iarg][0] != '-': error("Arg %s is not a switch" % args[iarg])
- switch = args[iarg][1:]
- if switch in sw: error("Duplicate switch %s" % args[iarg])
- order.append(switch)
- first = iarg+1
- last = first
- while last < narg and args[last][0] != '-': last += 1
- sw[switch] = args[first:last]
- iarg = last
- return sw,order
-
-# convert info in switches dict back to a string, in switch_order
-
-def switch2str(switches,switch_order):
- txt = ""
- for switch in switch_order:
- if txt: txt += ' '
- txt += "-%s" % switch
- txt += ' ' + ' '.join(switches[switch])
- return txt
-
-# check if compiler works with ccflags on dummy one-line tmpauto.cpp file
-# return 1 if successful, else 0
-# warn = 1 = print warning if not successful, warn = 0 = no warning
-# NOTE: unrecognized -override-limits can leave verride-limits file
-
-def compile_check(compiler,ccflags,warn):
- open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
- tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
- try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
- shell=True).decode()
- except subprocess.CalledProcessError as e: txt = e.output
- flag = 1
- if txt or not os.path.isfile("tmpauto.o"):
- flag = 0
- if warn:
- print(tmp)
- if txt: print(txt)
- else: print("compile produced no output")
- os.remove("tmpauto.cpp")
- if os.path.isfile("tmpauto.o"): os.remove("tmpauto.o")
- return flag
-
-# check if linker works with linkflags and libs on tmpauto.o file
-# return 1 if successful, else 0
-# warn = 1 = print warning if not successful, warn = 0 = no warning
-
-def link_check(linker,linkflags,libs,warn):
- open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
- tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
- try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
- shell=True).decode()
- except subprocess.CalledProcessError as e: txt = e.output
- flag = 1
- if txt or not os.path.isfile("tmpauto"):
- flag = 0
- if warn:
- print(tmp)
- if txt: print(txt)
- else: print("link produced no output")
- os.remove("tmpauto.cpp")
- if os.path.isfile("tmpauto"): os.remove("tmpauto")
- return flag
-
-# ----------------------------------------------------------------
-# switch classes, one per single-letter switch
-# ----------------------------------------------------------------
-
-# actions
-
-class Actions(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--a action1 action2 ...
- possible actions = lib-all, lib-dir, file, clean, exe or machine
- machine is a Makefile.machine suffix
- actions can be specified in any order
- each action can appear only once
- lib-dir can appear multiple times for different dirs
- some actions depend on installed packages
- installed packages = currently installed + result of -p switch
- actions are invoked in this order, independent of specified order
- (1) lib-all or lib-dir = build auxiliary libraries
- lib-all builds all auxiliary libs needed by installed packages
- lib-dir builds a specific lib whether package installed or not
- dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
- (2) file = create a new src/MAKE/MINE/Makefile.auto
- if file not specified, existing Makefile.auto is NOT changed
- except by -m switch, which will copy Makefile.machine to Makefile.auto
- note that exe action can add an -m switch, as described below
- if file is specified, new Makefile.auto is created
- if "-m machine" specified (or added by exe),
- start with existing Makefile.machine, else existing Makefile.auto
- if "-m none" specified, start Makefile.auto from scratch
- must use -cc and -mpi switches to specify compiler and MPI
- settings for these switches will alter Makefile.auto
- -s, -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
- if these accelerator packages are installed, they induce settings
- that will alter Makefile.auto: opt, user-omp, user-intel, kokkos
- use -z switch to copy final Makefile.auto to new filename
- (3) clean = invoke "make clean-auto" to insure clean build on current files
- useful if compiler flags have changed
- (4) exe or machine = build LAMMPS
- machine can be any existing Makefile.machine suffix
- machine is converted to "exe" action, and additionally:
- "-m machine" is added if -m switch is not specified
- "-o machine" is added if -o switch is not specified
- if either "-m" or "-o" are specified, they are not overridden
- does not invoke any lib builds, since libs could be previously built
- exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
- if file action also specified, it creates a new Makefile.auto
- else if -m switch specified,
- existing Makefile.machine is copied to create Makefile.auto
- else Makefile.auto must already exist and is not changed
- build produces src/lmp_auto, or error message if unsuccessful
- use -o switch to copy src/lmp_auto to new filename
- use -z switch to copy src/MAKE/MINE/Makefile.auto to new filename
-"""
-
- def check(self):
- if not self.inlist: error("-a args are invalid")
- libs = []
- cleans = []
- files = []
- exes = []
- for one in self.inlist:
- if one.startswith("lib-"):
- lib = one[4:]
- if lib != "all" and lib not in libclasses: error("Actions are invalid")
- libs.append(one)
- elif one == "file":
- files.append(one)
- elif one == "clean":
- cleans.append(one)
- elif one == "exe":
- exes.append(one)
- # one action can be unknown, must be a machine (checked in setup)
- else:
- exes.append(one)
- if len(set(libs)) != len(libs) or \
- len(cleans) > 1 or len(files) > 1 or len(exes) > 1:
- error("Actions are invalid")
- self.alist = [action for actions in [libs,cleans,files,exes] \
- for action in actions]
-
- # dedup list of actions concatenated from two lists
- # current self.inlist = specified -a switch + redo command -a switch
- # specified exe/machine action replaces redo exe/machine action
- # operates on and replaces self.inlist
-
- def dedup(self):
- alist = []
- exemachine = 0
- for one in self.inlist:
- if one == "exe" or (one not in actionargs and not one.startswith("lib-")):
- if exemachine: continue
- exemachine = 1
- if one not in alist: alist.append(one)
- self.inlist = alist
-
- # if last action is unknown, assume machine and convert to exe
- # only done if action is a suffix for an existing Makefile.machine
- # return machine if conversion done, else None
-
- def setup(self):
- machine = self.alist[-1]
- if machine in actionargs or machine.startswith("lib-"): return None
- make = MakeReader(machine,2)
- self.alist[-1] = "exe"
- return machine
-
- # build one or more auxiliary package libraries
-
- def lib(self,suffix):
- if suffix != "all":
- print("building",suffix,"library ...")
- txt = "%s.build()" % suffix
- exec(txt)
- else:
- final = packages.final
- for one in packages.lib:
- if final[one]:
- if "user" in one: pkg = one[5:]
- else: pkg = one
- print("building",pkg,"library ...")
- txt = "%s.build()" % pkg
- exec(txt)
-
- # read Makefile.machine
- # if caller = "file", edit via switches
- # if caller = "exe", just read
- # write out new Makefile.auto
-
- def file(self,caller):
-
- # if caller="file", create from mpi or read from Makefile.machine or auto
- # if caller="exe" and "file" action already invoked, read from auto
- # if caller="exe" and no "file" action, read from Makefile.machine or auto
-
- if caller == "file":
- if makefile and makefile.machine == "none":
- if cc and mpi: machine = "mpi"
- else: error("Cannot create makefile unless -cc and -mpi are used")
- elif makefile: machine = makefile.machine
- else: machine = "auto"
- elif caller == "exe" and "file" in self.alist:
- machine = "auto"
- elif caller == "exe" and "file" not in self.alist:
- if makefile and makefile.machine == "none":
- error("Cannot build with makefile = none")
- elif makefile: machine = makefile.machine
- else: machine = "auto"
-
- make = MakeReader(machine,1)
-
- # change makefile settings to user specifications
-
- precompiler = ""
- if caller == "file":
-
- # add compiler/linker and default CCFLAGS,LINKFLAGS
- # if cc.wrap, add wrapper setting for mpi = ompi/mpich
- # precompiler = env variable setting for OpenMPI wrapper compiler
-
- if cc:
- make.setvar("CC",cc.compiler)
- make.setvar("LINK",cc.compiler)
- if cc.wrap:
- if cc.wrap == "nvcc":
- wrapper = os.path.abspath("../lib/kokkos/config/nvcc_wrapper")
- else: wrapper = cc.wrap
- abbrev = cc.abbrev
- if abbrev == "mpi":
- if cc.parent == "mpich":
- make.addvar("CC","-cxx=%s" % wrapper)
- make.addvar("LINK","-cxx=%s" % wrapper)
- elif cc.parent == "openmpi":
- make.addvar("export OMPI_CXX",wrapper,"cc")
- precompiler = "env OMPI_CXX=%s " % wrapper
- else: error("Could not add MPI wrapper compiler, " +
- "did not recognize OpenMPI or MPICH")
- make.setvar("CCFLAGS","-g")
- make.addvar("CCFLAGS","-O3")
- make.setvar("LINKFLAGS","-g")
- make.addvar("LINKFLAGS","-O")
-
- # add MPI settings
-
- if mpi:
- make.delvar("MPI_INC","*")
- make.delvar("MPI_PATH","*")
- make.delvar("MPI_LIB","*")
- if mpi.style == "mpi":
- make.addvar("MPI_INC","-DMPICH_SKIP_MPICXX")
- make.addvar("MPI_INC","-DOMPI_SKIP_MPICXX=1")
- elif mpi.style == "mpich":
- make.addvar("MPI_INC","-DMPICH_SKIP_MPICXX")
- make.addvar("MPI_INC","-DOMPI_SKIP_MPICXX=1")
- if mpi.dir: make.addvar("MPI_INC","-I%s/include" % mpi.dir)
- if mpi.dir: make.addvar("MPI_PATH","-L%s/lib" % mpi.dir)
- make.addvar("MPI_LIB","-lmpich")
- make.addvar("MPI_LIB","-lmpl")
- make.addvar("MPI_LIB","-lpthread")
- elif mpi.style == "ompi":
- make.addvar("MPI_INC","-DMPICH_SKIP_MPICXX")
- make.addvar("MPI_INC","-DOMPI_SKIP_MPICXX=1")
- if mpi.dir: make.addvar("MPI_INC","-I%s/include" % mpi.dir)
- if mpi.dir: make.addvar("MPI_PATH","-L%s/lib" % mpi.dir)
- make.addvar("MPI_LIB","-lmpi")
- make.addvar("MPI_LIB","-lmpi_cxx")
- elif mpi.style == "serial":
- make.addvar("MPI_INC","-I../STUBS")
- make.addvar("MPI_PATH","-L../STUBS")
- make.addvar("MPI_LIB","-lmpi_stubs")
-
- # add accelerator package CCFLAGS and LINKFLAGS and variables
-
- compiler = precompiler + ' '.join(make.getvar("CC"))
- linker = precompiler + ' '.join(make.getvar("LINK"))
-
- final = packages.final
- if final["opt"]:
- if compile_check(compiler,"-restrict",0):
- make.addvar("CCFLAGS","-restrict")
-
- if final["user-omp"]:
- if compile_check(compiler,"-fopenmp",1):
- make.addvar("CCFLAGS","-fopenmp")
- make.addvar("LINKFLAGS","-fopenmp")
- if compile_check(compiler,"-restrict",0):
- make.addvar("CCFLAGS","-restrict")
-
- if final["user-intel"]:
- if intel.mode == "cpu":
- make.delvar("CCFLAGS","-O*")
- make.addvar("CCFLAGS","-O2")
- if compile_check(compiler,"-openmp",1):
- make.addvar("CCFLAGS","-openmp")
- if compile_check(compiler,"-restrict",1):
- make.addvar("CCFLAGS","-restrict")
- if compile_check(compiler,"-no-offload",1):
- make.addvar("CCFLAGS","-no-offload")
- if compile_check(compiler,"-fno-alias",1):
- make.addvar("CCFLAGS","-fno-alias")
- if compile_check(compiler,"-ansi-alias",1):
- make.addvar("CCFLAGS","-ansi-alias")
- if compile_check(compiler,"-xAVX",1):
- make.addvar("CCFLAGS","-xAVX")
- if compile_check(compiler,"-fp-model fast=2",1):
- make.addvar("CCFLAGS","-fp-model fast=2")
- if compile_check(compiler,"-no-prec-div",1):
- make.addvar("CCFLAGS","-no-prec-div")
- if compile_check(compiler,"-override-limits",1):
- make.addvar("CCFLAGS","-override-limits")
- make.addvar("CCFLAGS","-DLAMMPS_MEMALIGN=64")
- make.delvar("CCFLAGS","-DLMP_INTEL_OFFLOAD")
-
- make.delvar("LINKFLAGS","-O*")
- make.addvar("LINKFLAGS","-O2")
- if link_check(linker,"-openmp","",1):
- make.addvar("LINKFLAGS","-openmp")
- if link_check(linker,"-xAVX","",1):
- make.addvar("LINKFLAGS","-xAVX")
- if link_check(linker,"-fpmodel fast=2","",1):
- make.addvar("LINKFLAGS","-fpmodel fast=2")
- if link_check(linker,"-no-prec-div","",1):
- make.addvar("LINKFLAGS","-no-prec-div")
- if link_check(linker,"-override-limits","",1):
- make.addvar("LINKFLAGS","-override-limits")
- make.delvar("LINKFLAGS","-offload")
-
- if link_check(linker,"","-ltbbmalloc",1):
- make.addvar("LIB","-ltbbmalloc")
- if link_check(linker,"","-ltbbmalloc_proxy",1):
- make.addvar("LIB","-ltbbmalloc_proxy")
-
- elif intel.mode == "phi":
- if compile_check(compiler,"-fopenmp",1):
- make.addvar("CCFLAGS","-fopenmp")
- make.addvar("LINKFLAGS","-fopenmp")
- make.addvar("CCFLAGS","-DLAMMPS_MEMALIGN=64")
- if compile_check(compiler,"-restrict",1):
- make.addvar("CCFLAGS","-restrict")
- if compile_check(compiler,"-xHost",1):
- make.addvar("CCFLAGS","-xHost")
- make.addvar("CCFLAGS","-DLMP_INTEL_OFFLOAD")
- if compile_check(compiler,"-fno-alias",1):
- make.addvar("CCFLAGS","-fno-alias")
- if compile_check(compiler,"-ansi-alias",1):
- make.addvar("CCFLAGS","-ansi-alias")
- if compile_check(compiler,"-override-limits",1):
- make.addvar("CCFLAGS","-override-limits")
- if compile_check(compiler,'-offload-option,mic,compiler,' +
- '"-fp-model fast=2 -mGLOB_default_function_attrs=' +
- '\\"gather_scatter_loop_unroll=4\\""',1):
- make.addvar("CCFLAGS",'-offload-option,mic,compiler,' +
- '"-fp-model fast=2 -mGLOB_default_function_attrs=' +
- '\\"gather_scatter_loop_unroll=4\\""')
- if link_check(linker,"-offload","",1):
- make.addvar("LINKFLAGS","-offload")
-
- if final["kokkos"]:
- if kokkos.mode == "omp":
- make.delvar("KOKKOS_DEVICES","*")
- make.delvar("KOKKOS_ARCH","*")
- make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
- if kokkos.archcpu:
- make.addvar("KOKKOS_ARCH",kokkos.archcpu,"lmp")
- elif kokkos.mode == "cuda":
- make.delvar("KOKKOS_DEVICES","*")
- make.delvar("KOKKOS_ARCH","*")
- make.addvar("KOKKOS_DEVICES","Cuda, OpenMP","lmp")
- if kokkos.archgpu:
- if kokkos.archgpu[0] == "3": value = "Kepler" + kokkos.archgpu
- elif kokkos.archgpu[0] == "2": value = "Fermi" + kokkos.archgpu
- else: error("Unrecognized Kokkos archgpu setting")
- if kokkos.archcpu: value += ", %s" % kokkos.archcpu
- make.addvar("KOKKOS_ARCH",value,"lmp")
- elif kokkos.mode == "phi":
- make.delvar("KOKKOS_DEVICES","*")
- make.delvar("KOKKOS_ARCH","*")
- make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
- make.addvar("KOKKOS_ARCH","KNC","lmp")
-
- # add LMP_INC ifdef settings
-
- if settings:
- list = settings.inlist
- for one in list:
- if one == "gzip": make.addvar("LMP_INC","-DLAMMPS_GZIP")
- elif one == "#gzip": make.delvar("LMP_INC","-DLAMMPS_GZIP")
- elif one == "ffmpeg": make.addvar("LMP_INC","-DLAMMPS_FFMPEG")
- elif one == "#ffmpeg": make.delvar("LMP_INC","-DLAMMPS_FFMPEG")
- elif one == "smallbig":
- make.delvar("LMP_INC","-DLAMMPS_BIGBIG")
- make.delvar("LMP_INC","-DLAMMPS_SMALLSMALL")
- elif one == "bigbig":
- make.delvar("LMP_INC","-DLAMMPS_SMALLBIG")
- make.delvar("LMP_INC","-DLAMMPS_SMALLSMALL")
- make.addvar("LMP_INC","-DLAMMPS_BIGBIG")
- elif one == "smallsmall":
- make.delvar("LMP_INC","-DLAMMPS_SMALLBIG")
- make.delvar("LMP_INC","-DLAMMPS_BIGBIG")
- make.addvar("LMP_INC","-DLAMMPS_SMALLSMALL")
- elif one == "exceptions": make.addvar("LMP_INC","-DLAMMPS_EXCEPTIONS")
- elif one == "#exception": make.delvar("LMP_INC","-DLAMMPS_EXCEPTIONS")
-
- # add FFT, JPG, PNG settings
-
- if fft:
- make.delvar("FFT_INC","*")
- make.delvar("FFT_PATH","*")
- make.delvar("FFT_LIB","*")
- if fft.mode == "none": make.addvar("FFT_INC","-DFFT_NONE")
- else:
- make.addvar("FFT_INC","-DFFT_%s" % fft.mode.upper())
- make.addvar("FFT_LIB",fft.lib)
- if fft.dir:
- make.addvar("FFT_INC","-I%s/include" % fft.dir)
- make.addvar("FFT_PATH","-L%s/lib" % fft.dir)
- else:
- if fft.incdir: make.addvar("FFT_INC","-I%s" % fft.incdir)
- if fft.libdir: make.addvar("FFT_PATH","-L%s" % fft.libdir)
-
- if jpg:
- if jpg.on == 0:
- make.delvar("LMP_INC","-DLAMMPS_JPEG")
- make.delvar("JPG_LIB","-ljpeg")
- else:
- make.addvar("LMP_INC","-DLAMMPS_JPEG")
- make.addvar("JPG_LIB","-ljpeg")
- if jpg.dir:
- make.addvar("JPG_INC","-I%s/include" % jpg.dir)
- make.addvar("JPG_PATH","-L%s/lib" % jpg.dir)
- else:
- if jpg.incdir: make.addvar("JPG_INC","-I%s" % jpg.incdir)
- if jpg.libdir: make.addvar("JPG_PATH","-L%s" % jpg.libdir)
-
- if png:
- if png.on == 0:
- make.delvar("LMP_INC","-DLAMMPS_PNG")
- make.delvar("JPG_LIB","-lpng")
- else:
- make.addvar("LMP_INC","-DLAMMPS_PNG")
- make.addvar("JPG_LIB","-lpng")
- if png.dir:
- make.addvar("JPG_INC","-I%s/include" % png.dir)
- make.addvar("JPG_PATH","-L%s/lib" % png.dir)
- else:
- if png.incdir: make.addvar("JPG_INC","-I%s" % png.incdir)
- if png.libdir: make.addvar("JPG_PATH","-L%s" % png.libdir)
-
- # finally after all other settings, add explicit flags
-
- if flags:
- for var,action,flist in flags.flags:
- values = make.getvar(var)
- if values == None:
- error("Flags for a non-existent Makefile.auto variable")
- for flag in flist:
- flag = "-" + flag
- if action == "add": make.addvar(var,flag)
- elif action == "del": make.delvar(var,flag)
-
- # set self.stubs if Makefile.auto uses STUBS lib in MPI settings
-
- if make.getvar("MPI_LIB") and "-lmpi_stubs" in make.getvar("MPI_LIB"):
- self.stubs = 1
- else: self.stubs = 0
-
- # write out Makefile.auto
- # unless caller = "exe" and "file" action already invoked
-
- if caller == "file" or "file" not in self.alist:
- # make certain that 'MAKE/MINE' folder exists.
- subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,
- stderr=subprocess.STDOUT,shell=True)
- make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
- print("Created src/MAKE/MINE/Makefile.auto")
-
- # test full compile and link
- # unless caller = "file" and "exe" action will be invoked later
-
- if caller == "file" and "exe" in self.alist: return
- compiler = precompiler + ' '.join(make.getvar("CC"))
- ccflags = ' '.join(make.getvar("CCFLAGS"))
- linker = precompiler + ' '.join(make.getvar("LINK"))
- linkflags = ' '.join(make.getvar("LINKFLAGS"))
- libs = ' '.join(make.getvar("LIB"))
- if not compile_check(compiler,ccflags,1):
- error("Test of compilation failed")
- if not link_check(linker,linkflags,libs,1): error("Test of link failed")
-
- # invoke "make clean-auto" to force clean before build
-
- def clean(self):
- txt = "cd %s; make clean-auto" % dir.src
- subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- print("Performed make clean-auto")
-
- # build LAMMPS using Makefile.auto and -j setting
- # invoke self.file() first, to test makefile compile/link
- # delete existing lmp_auto, so can detect if build fails
- # build STUBS lib (if unbuilt) if Makefile.auto MPI settings need it
-
- def exe(self):
- self.file("exe")
- subprocess.check_output("cd %s; rm -f lmp_auto" % dir.src,stderr=subprocess.STDOUT,shell=True)
- if self.stubs and not os.path.isfile("%s/STUBS/libmpi_stubs.a" % dir.src):
- print("building serial STUBS library ...")
- tmp = "cd %s/STUBS; make clean; make" % dir.src
- txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
- if not os.path.isfile("%s/STUBS/libmpi_stubs.a" % dir.src):
- print(txt)
- error('Unsuccessful "make stubs"')
- print("Created src/STUBS/libmpi_stubs.a")
-
- # special hack for shannon GPU cluster
- # must use "srun make" if on it and building w/ GPU package, else just make
- # this is b/c Cuda libs are not all available on host
-
- make = "make"
- if "shannon" == platform.node() and packages.final["gpu"]:
- make = "srun make"
-
- if jmake: tmp = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
- else: tmp = "cd %s; %s auto" % (dir.src,make)
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(tmp,shell=True)
- else:
- print(tmp)
- try: subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/lmp_auto" % dir.src):
- error('Unsuccessful "make auto"')
- elif not output: print("Created src/lmp_auto")
-
-# dir switch
-
-class Dir(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--d dir
- dir = LAMMPS home dir
- if -d not specified, working dir must be lammps/src
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) != 1:
- error("-d args are invalid")
-
- # if inlist = None, check that cwd = lammps/src
- # store cwd and lammps dir
- # derive src,make,lib dirs from lammps dir
- # check that they all exist
-
- def setup(self):
- self.cwd = os.getcwd()
- if self.inlist == None: self.lammps = ".."
- else: self.lammps = self.inlist[0]
- self.lammps = os.path.realpath(self.lammps)
- self.src = self.lammps + "/src"
- self.make = self.lammps + "/src/MAKE"
- self.lib = self.lammps + "/lib"
- if not os.path.isdir(self.lammps): error("LAMMPS home dir is invalid")
- if not os.path.isdir(self.src): error("LAMMPS src dir is invalid")
- if not os.path.isdir(self.lib): error("LAMMPS lib dir is invalid")
-
-# help switch
-
-class Help(object):
- def __init__(self,list): pass
-
- def help(self):
- return """
-Syntax: Make.py switch args ...
- switches can be listed in any order
- help switch:
- -h prints help and syntax for all other specified switches
- switch for actions:
- -a lib-all, lib-dir, clean, file, exe or machine
- list one or more actions, in any order
- machine is a Makefile.machine suffix
- one-letter switches:
- -d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
- -r (redo), -s (settings), -v (verbose), -z (makefile output)
- switches for libs:
- -atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
- -meam, -poems, -python, -qmmm, -reax, -voronoi
- switches for build and makefile options:
- -intel, -kokkos, -cc, -flags, -mpi, -fft, -jpg, -png
-"""
-
-# jmake switch
-
-class Jmake(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--j N
- use N procs for performing parallel make commands
- used when building a lib or LAMMPS itself
- if -j not specified, serial make commands run on single core
-"""
-
- def check(self):
- if len(self.inlist) != 1: error("-j args are invalid")
- if not self.inlist[0].isdigit(): error("-j args are invalid")
- n = int(self.inlist[0])
- if n <= 0: error("-j args are invalid")
- self.n = n
-
-# makefile switch
-
-class Makefile(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--m machine
- use Makefile.machine under src/MAKE as starting point to create Makefile.auto
- if machine = "none", file action will create Makefile.auto from scratch
- must use -cc and -mpi switches to specify compiler and MPI
- if -m not specified, file/exe actions alter existing Makefile.auto
-"""
-
- def check(self):
- if len(self.inlist) != 1: error("-m args are invalid")
- self.machine = self.inlist[0]
-
-# output switch
-
-class Output(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--o machine
- copy final src/lmp_auto to lmp_machine in working dir
- if -o not specified, exe action only produces src/lmp_auto
-"""
-
- def check(self):
- if len(self.inlist) != 1: error("-o args are invalid")
- self.machine = self.inlist[0]
-
-# packages switch
-
-class Packages(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--p = package1 package2 ...
- list of packages to install or uninstall in order specified
- operates on set of packages currently installed
- valid package names:
- any LAMMPS standard or user package (type "make package" to see list)
- prefix by yes/no to install/uninstall (see abbrevs)
- yes-molecule, yes-user-atc, no-molecule, no-user-atc
- can use LAMMPS categories (type "make package" to see list)
- all = all standard and user packages (also none = no-all)
- std (or standard) = all standard packages
- user = all user packages
- lib = all standard and user packages with auxiliary libs
- can abbreviate package names and yes/no
- omp = user-omp = yes-user-omp
- ^omp = ^user-omp = no-user-omp
- user = yes-user, ^user = no-user
- all = yes-all, ^all = none = no-all
- when action performed, list is processed in order,
- as if typed "make yes/no" for each
- if "orig" or "original" is last package in list,
- set of installed packages will be restored to original (current) list
- after "build" action is performed
- if -p not specified, currently installed packages are not changed
-"""
-
- def check(self):
- if self.inlist != None and not self.inlist: error("-p args are invalid")
-
- def setup(self):
-
- # extract package lists from src/Makefile
- # remove names from lib that there are not Make.py lib-classes for
- # most don't actually have libs, so nothing to control from Make.py
-
- make = MakeReader("%s/Makefile" % dir.src)
- std = make.getvar("PACKAGE")
- user = make.getvar("PACKUSER")
- lib = make.getvar("PACKLIB")
- lib.remove("kim")
- lib.remove("kokkos")
- lib.remove("user-molfile")
- lib.remove("python")
- lib.remove("user-quip")
- all = std + user
-
- # plist = command line args expanded to yes-package or no-package
-
- plist = []
- if self.inlist:
- for one in self.inlist:
- if one in std:
- plist.append("yes-%s" % one)
- elif one in user:
- plist.append("yes-%s" % one)
- elif "user-"+one in user:
- plist.append("yes-user-%s" % one)
- elif one == "std" or one == "standard" or one == "user" or \
- one == "lib" or one == "all": plist.append("yes-%s" % one)
- elif one.startswith("yes-"):
- if one[4:] in std: plist.append("yes-%s" % one[4:])
- elif one[4:] in user: plist.append("yes-%s" % one[4:])
- elif "user-"+one[4:] in user: plist.append("yes-user-%s" % one[4:])
- elif one == "yes-std" or one == "yes-standard" or \
- one == "yes-user" or one == "yes-lib" or one == "yes-all":
- plist.append("yes-%s" % one[4:])
- else: error("Invalid package name %s" % one)
- elif one.startswith("no-"):
- if one[3:] in std: plist.append("no-%s" % one[3:])
- elif one[3:] in user: plist.append("no-%s" % one[3:])
- elif "user-"+one[3:] in user: plist.append("no-user-%s" % one[3:])
- elif one == "no-std" or one == "no-standard" or one == "no-user" or \
- one == "no-lib" or one == "no-all":
- plist.append("no-%s" % one[3:])
- else: error("Invalid package name %s" % one)
- elif one.startswith('^'):
- if one[1:] in std: plist.append("no-%s" % one[1:])
- elif one[1:] in user: plist.append("no-%s" % one[1:])
- elif "user-"+one[1:] in user: plist.append("no-user-%s" % one[1:])
- elif one == "^std" or one == "^standard" or one == "^user" or \
- one == "^lib" or one == "^all": plist.append("no-%s" % one[1:])
- else: error("Invalid package name %s" % one)
- elif one == "none": plist.append("no-all")
- elif one == "orig": plist.append(one)
- else: error("Invalid package name %s" % one)
- if "orig" in plist and plist.index("orig") != len(plist)-1:
- error('-p orig arg must be last')
- if plist.count("orig") > 1: error('-p orig arg must be last')
-
- # original = dict of all packages
- # key = package name, value = 1 if currently installed, else 0
-
- original = {}
- tmp = "cd %s; make ps" % dir.src
- output = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode().split('\n')
- pattern = "Installed\s+(\w+): package (\S+)"
- for line in output:
- m = re.search(pattern,line)
- if not m: continue
- pkg = m.group(2).lower()
- if pkg not in all: error('Package list does not match "make ps" results')
- if m.group(1) == "NO": original[pkg] = 0
- elif m.group(1) == "YES": original[pkg] = 1
-
- # final = dict of all packages after plist applied to original
- # key = package name, value = 1 if installed, else 0
-
- final = copy.deepcopy(original)
- for i,one in enumerate(plist):
- if "yes" in one:
- pkg = one[4:]
- yes = 1
- else:
- pkg = one[3:]
- yes = 0
- if pkg in all:
- final[pkg] = yes
- elif pkg == "std" or pkg == "standard":
- for pkg in std: final[pkg] = yes
- elif pkg == "user":
- for pkg in user: final[pkg] = yes
- elif pkg == "lib":
- for pkg in lib: final[pkg] = yes
- elif pkg == "all":
- for pkg in all: final[pkg] = yes
-
- self.std = std
- self.user = user
- self.lib = lib
- self.all = all
- self.plist = plist
- self.original = original
- self.final = final
-
- # install packages in plist
-
- def install(self):
- if self.plist: print("Installing packages ...")
- for one in self.plist:
- if one == "orig": continue
- subprocess.check_output("cd %s; make %s" % (dir.src,one),
- stderr=subprocess.STDOUT,shell=True)
- if self.plist and verbose:
- txt = subprocess.check_output("cd %s; make ps" % dir.src,
- stderr=subprocess.STDOUT,
- shell=True).decode()
- print("Package status after installation:")
- print(txt)
-
- # restore packages to original list if requested
- # order of re-install should not matter matter b/c of Depend.sh
-
- def uninstall(self):
- if not self.plist or self.plist[-1] != "orig": return
- print("Restoring packages to original state ...")
- subprocess.check_output("cd %s; make no-all" % dir.src,
- stderr=subprocess.STDOUT,shell=True)
- for one in self.all:
- if self.original[one]:
- subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),
- stderr=subprocess.STDOUT,shell=True)
- if verbose:
- txt = subprocess.check_output("cd %s; make ps" % dir.src,
- stderr=subprocess.STDOUT,
- shell=True).decode()
- print("Restored package status:")
- print(txt)
-
-# redo switch
-
-class Redo(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--r file label1 label2 ...
- all args are optional
- invoke Make.py commands from a file
- other specified switches are merged with file commands (see below)
- redo file format:
- blank lines and lines starting with "#" are skipped
- other lines are treated as commands
- each command is a list of Make.py args, as if typed at command-line
- commands can have leading label, followed by ":"
- commands cannot contain a "-r" switch
- if no args, execute previous command, which is stored in src/Make.py.last
- if one arg, execute all commands from specified file
- unlabeled or labeled commands are all executed
- if multiple args, execute only matching labeled commands from file
- if other switches are specified,
- if file command does not have the switch, it is added
- if file command has the switch, the specified switch replaces it
- except if -a (action) switch is both specified and in the file command,
- two sets of actions are merged and duplicates removed
- if both switches have "exe or machine" action,
- the specified exe/machine overrides the file exe/machine
-"""
-
- def check(self):
- if len(self.inlist) == 0:
- self.dir = 1
- self.file = "Make.py.last"
- self.labels = []
- else:
- self.dir = 0
- self.file = self.inlist[0]
- self.labels = self.inlist[1:]
-
- # read redo file
- # self.commands = list of commands to execute
-
- def setup(self):
- file = self.file
- if not os.path.isfile(file): error("Redo file %s does not exist" % file)
- lines = open(file,'r').readlines()
-
- cmdlines = []
- for line in lines:
- line = line.strip()
- if not line or line[0] == '#' : continue
- cmdlines.append(line)
-
- # if no labels, add all file commands to command list
- # if labels, make a dict with key = label, value = command
- # and discard unlabeled commands
-
- dict = {}
- commands = []
- for line in cmdlines:
- words = line.split()
- if "-r" in words: error("Redo command cannot contain -r switch")
- if words[0][-1] == ':': label = words[0][:-1]
- else: label = None
- if not self.labels:
- if label: subprocess.append(' '.join(words[1:]))
- else: subprocess.append(line)
- else:
- if not label: continue
- dict[label] = ' '.join(words[1:])
-
- # extract labeled commands from dict and add to command list
-
- for label in self.labels:
- if label not in dict: error("Redo label not in redo file")
- subprocess.append(dict[label])
-
- self.commands = commands
-
-# settings switch
-
-class Settings(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--s set1 set2 ...
- possible settings = gzip #gzip ffmpeg #ffmpeg
- smallbig bigbig smallsmall exceptions #exceptions
- alter LAMMPS ifdef settings in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- gzip and #gzip turn on/off LAMMPS_GZIP setting
- ffmpeg and #ffmpeg turn on/off LAMMPS_FFMPEG setting
- smallbig, bigbig, smallsmall turn on LAMMPS_SMALLBIG, etc
- and turn off other two
- exceptions and #exceptions turn on/off LAMMPS_EXCEPTIONS setting
-"""
-
- def check(self):
- if not self.inlist: error("-s args are invalid")
- for one in self.inlist:
- if one not in setargs: error("-s args are invalid")
-
-# verbose switch
-
-class Verbose(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--v (no arguments)
- produce verbose output as Make.py executes
- if -v not specified, minimal output is produced
-"""
-
- def check(self):
- if len(self.inlist): error("-v args are invalid")
-
-# zoutput switch for making copy of final Makefile.auto
-
-class Zoutput(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
-
- def help(self):
- return """
--z machine
- copy created/used src/MAKE/MINE/Makefile.auto to Makefile.machine in same dir
- copy created/used lib/*/Makefile.auto and lib/*/Makefile.lammps to
- Makefile_lib.machine and Makefile_lib_lammps.machine in same dir
- this can be used to preserve the machine Makefile and lib Makefiles
-"""
-
- def check(self):
- if len(self.inlist) != 1: error("-z args are invalid")
- self.machine = self.inlist[0]
-
-# ----------------------------------------------------------------
-# lib classes, one per LAMMPS auxiliary lib
-# ----------------------------------------------------------------
-
-# ATC lib
-
-class ATC(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "g++"
- self.lammpsflag = 0
-
- def help(self):
- return """
--atc make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = g++)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-atc args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-atc args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-atc args are invalid")
-
- def build(self):
- libdir = dir.lib + "/atc"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" %
- libdir,stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libatc.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/atc library")
- else: print("Created lib/atc library")
-
-# AWPMD lib
-
-class AWPMD(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "mpicc"
- self.lammpsflag = 0
-
- def help(self):
- return """
--awpmd make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = mpicc)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-awpmd args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-awpmd args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-awpmd args are invalid")
-
- def build(self):
- libdir = dir.lib + "/awpmd"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" %
- libdir,stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libawpmd.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/awpmd library")
- else: print("Created lib/awpmd library")
-
-# COLVARS lib
-
-class COLVARS(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "g++"
- self.lammpsflag = 0
-
- def help(self):
- return """
--colvars make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = g++)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-colvars args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-colvars args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-colvars args are invalid")
-
- def build(self):
- libdir = dir.lib + "/colvars"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" %
- libdir,stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libcolvars.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/colvars library")
- else: print("Created lib/colvars library")
-
-# CUDA lib
-
-class CUDA(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.mode = "double"
- self.arch = "35"
-
- def help(self):
- return """
--cuda mode=double arch=35
- all args are optional and can be in any order
- mode = double or mixed or single (def = double)
- arch = M (def = 35)
- M = 31,35,37,etc for Kepler
- M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470)
- M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
- M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-cuda args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-cuda args are invalid")
- if words[0] == "mode": self.mode = words[1]
- elif words[0] == "arch": self.arch = words[1]
- else: error("-cuda args are invalid")
- if self.mode != "double" and self.mode != "mixed" and \
- self.mode != "single":
- error("-cuda args are invalid")
- if not self.arch.isdigit(): error("-cuda args are invalid")
-
- def build(self):
- libdir = dir.lib + "/cuda"
- subprocess.check_output("cd %s; make clean" % libdir,
- stderr=subprocess.STDOUT,shell=True)
- if self.mode == "double": n = 2
- elif self.mode == "mixed": n = 3
- elif self.mode == "single": n = 1
- if jmake: txt = "cd %s; make -j %d precision=%d arch=%s" % \
- (libdir,jmake.n,n,self.arch)
- else: txt = "cd %s; make precision=%d arch=%s" % \
- (libdir,n,self.arch)
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/liblammpscuda.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/cuda library")
- else: print("Created lib/cuda library")
-
-# GPU lib
-
-class GPU(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "linux.double"
- self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
-
- def help(self):
- return """
--gpu make=suffix lammps=suffix2 mode=double arch=N home=path
- all args are optional and can be in any order
- make = use Makefile.suffix (def = linux.double)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
- mode = double or mixed or single (def = CUDA_PREC in makefile)
- arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
- (def = CUDA_ARCH in makefile)
- home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-gpu args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-gpu args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- elif words[0] == "mode":
- self.mode = words[1]
- self.modeflag = 1
- elif words[0] == "arch":
- self.arch = words[1]
- self.archflag = 1
- elif words[0] == "home":
- self.home = words[1]
- self.homeflag = 1
- else: error("-gpu args are invalid")
- if self.modeflag and (self.mode != "double" and
- self.mode != "mixed" and
- self.mode != "single"):
- error("-gpu args are invalid")
- if self.archflag and not self.arch.isdigit():
- error("-gpu args are invalid")
-
- def build(self):
- global gpubuildflag
- gpubuildflag = 1
- libdir = dir.lib + "/gpu"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.modeflag:
- if self.mode == "double":
- make.setvar("CUDA_PRECISION","-D_DOUBLE_DOUBLE")
- elif self.mode == "mixed":
- make.setvar("CUDA_PRECISION","-D_SINGLE_DOUBLE")
- elif self.mode == "single":
- make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
- if self.archflag:
- make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
- if self.homeflag:
- make.setvar("CUDA_HOME",self.home)
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- # special hack for shannon GPU cluster
- # must use "srun make" if on it, else just make
- # this is b/c Cuda libs are not all available on host
-
- make = "make"
- if "shannon" == platform.node(): make = "srun make"
-
- subprocess.check_output("cd %s; %s -f Makefile.auto clean" %
- (libdir,make),stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
- else: txt = "cd %s; %s -f Makefile.auto" % (libdir,make)
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libgpu.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/gpu library")
- else: print("Created lib/gpu library")
-
-# H5MD lib
-
-class H5MD(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "h5cc"
- self.lammpsflag = 0
-
- def help(self):
- return """
--h5md make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = h5cc)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-h5md args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-h5md args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-h5md args are invalid")
-
- def build(self):
- libdir = dir.lib + "/h5md"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make clean" % libdir,
- stderr=subprocess.STDOUT,shell=True)
- txt = "cd %s; make" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libch5md.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/h5md library")
- else: print("Created lib/h5md library")
-
-# MEAM lib
-
-class MEAM(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "gfortran"
- self.lammpsflag = 0
-
- def help(self):
- return """
--meam make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = gfortran)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-meam args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-meam args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-meam args are invalid")
-
- def build(self):
- libdir = dir.lib + "/meam"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" %
- libdir,stderr=subprocess.STDOUT,shell=True)
- # do not use -j for MEAM build, parallel build does not work
- txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libmeam.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/meam library")
- else: print("Created lib/meam library")
-
-# POEMS lib
-
-class POEMS(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "g++"
- self.lammpsflag = 0
-
- def help(self):
- return """
--poems make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = g++)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-poems args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-poems args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-poems args are invalid")
-
- def build(self):
- libdir = dir.lib + "/poems"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,
- stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libpoems.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/poems library")
- else: print("Created lib/poems library")
-
-# PYTHON lib
-
-class PYTHON(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "g++"
- self.lammpsflag = 0
-
- def help(self):
- return """
--python lammps=suffix
- arg is optional, use Makefile.lammps if not specified
- lammps = use Makefile.lammps.suffix
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-python args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-python args are invalid")
- if words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-python args are invalid")
-
- def build(self):
- libdir = dir.lib + "/python"
- if self.lammpsflag:
- subprocess.check_output("cd %s; cp Makefile.lammps.%s Makefile.lammps" %
- (libdir,self.lammps))
- if not os.path.isfile("%s/Makefile.lammps.%s" % (libdir,self.lammps)):
- error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" %
- self.lammps)
- else: print("Created lib/python/Makefile.lammps file")
-
-# QMMM lib
-
-class QMMM(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "gfortran"
- self.lammpsflag = 0
-
- def help(self):
- return """
--qmmm make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = gfortran)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-qmmm args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-qmmm args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-qmmm args are invalid")
-
- def build(self):
- libdir = dir.lib + "/qmmm"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- subprocess.check_output("cd %s; make -f Makefile.auto clean" %
- libdir,stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libqmmm.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/qmmm library")
- else: print("Created lib/qmmm library")
-
-# REAX lib
-
-class REAX(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.make = "gfortran"
- self.lammpsflag = 0
-
- def help(self):
- return """
--reax make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = gfortran)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-reax args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-reax args are invalid")
- if words[0] == "make": self.make = words[1]
- elif words[0] == "lammps":
- self.lammps = words[1]
- self.lammpsflag = 1
- else: error("-reax args are invalid")
-
- def build(self):
- libdir = dir.lib + "/reax"
- make = MakeReader("%s/Makefile.%s" % (libdir,self.make))
- if self.lammpsflag:
- make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
- make.write("%s/Makefile.auto" % libdir)
-
- cmd = "cd %s; make -f Makefile.auto clean" % libdir
- subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
- if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: txt = "cd %s; make -f Makefile.auto" % libdir
-
- # if verbose, print output as build proceeds, else only print if fails
-
- if verbose: subprocess.call(txt,shell=True)
- else:
- try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- except subprocess.CalledProcessError as e: print(e.output)
-
- if not os.path.isfile("%s/libreax.a" % libdir) or \
- not os.path.isfile("%s/Makefile.lammps" % libdir):
- error("Unsuccessful build of lib/reax library")
- else: print("Created lib/reax library")
-
-# VORONOI lib
-
-class VORONOI(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.install = ""
-
- def help(self):
- return """
--voronoi install="-d dir -v version -g -b -i installdir -l incdir libdir"
- arg is optional, only needed if want to run install.py script
- install = args to use with lib/voronoi/install.py script
- must enclose in quotes since install.py args have switches
- install.py can download, build, install, setup links to the Voro++ library
- see lib/voronoi/README for details on Voro++ and using install.py
-"""
-
- def check(self):
- if self.inlist != None and len(self.inlist) == 0:
- error("-voronoi args are invalid")
- for one in self.inlist:
- words = one.split('=')
- if len(words) != 2: error("-voronoi args are invalid")
- if words[0] == "install": self.install = words[1]
- else: error("-voronoi args are invalid")
-
- def build(self):
- if not self.install: return
- libdir = dir.lib + "/voronoi"
- cmd = "cd %s; python install.py %s" % (libdir,self.install)
- txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,
- shell=True).decode()
- if verbose: print(txt)
- print("Created lib/voronoi library")
-
-# ----------------------------------------------------------------
-# build classes for intel, kokkos build options
-# ----------------------------------------------------------------
-
-# Intel class
-
-class Intel(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.mode = "cpu"
-
- def help(self):
- return """
--intel mode
- mode = cpu or phi (def = cpu)
- build Intel package for CPU or Xeon Phi
-"""
-
- def check(self):
- if self.inlist == None: return
- if len(self.inlist) != 1: error("-intel args are invalid")
- self.mode = self.inlist[0]
- if self.mode != "cpu" and self.mode != "phi":
- error("-intel args are invalid")
-
-# Kokkos class
-
-class Kokkos(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.mode = ""
- self.archgpu = None
- self.archcpu = None
-
- def help(self):
- return """
--kokkos mode archgpu=N archcpu=SNB
- mode is not optional, arch is optional
- mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
- build Kokkos package for omp or cuda or phi
- sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
- archgpu = number like 35 (Kepler) or 21 (Fermi) (def = none)
- sets KOKKOS_ARCH for GPU to appropriate value
- archcpu = SNB or HSW or BGQ or Power7 or Power8 (def = none)
- for CPU = SandyBridge, Haswell, BGQ, Power7, Power8
- sets KOKKOS_ARCH for GPU to appropriate value
-"""
-
- def check(self):
- print(self.inlist)
- if self.inlist != None and len(self.inlist) == 0:
- error("-kokkos args are invalid")
-
- if self.inlist == None: return
- if len(self.inlist) < 1: error("-kokkos args are invalid")
- self.mode = self.inlist[0]
- if self.mode != "omp" and self.mode != "cuda" and self.mode != "phi":
- error("-kokkos args are invalid")
- for one in self.inlist[1:]:
- words = one.split('=')
- if len(words) != 2: error("-kokkos args are invalid")
- if words[0] == "archgpu": self.archgpu = words[1]
- elif words[0] == "archcpu": self.archcpu = words[1]
- else: error("-kokkos args are invalid")
-
-# ----------------------------------------------------------------
-# makefile classes for CC, FLAGS, MPI, JPG, PNG, FFT settings
-# ----------------------------------------------------------------
-
-# Cc class
-
-class Cc(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.compiler = self.abbrev = ""
- self.wrap = ""
- self.parent = ""
-
- def help(self):
- return """
--cc compiler wrap=wcompiler,parent
- alter CC setting in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- compiler is required, all other args are optional
- compiler = any string with g++ or icc or icpc
- or mpi (or mpicxx, mpiCC, mpiicpc, etc)
- can be compiler name or full path to compiler
- mpi by itself is changed to mpicxx
- wcompiler = compiler for mpi wrapper to use
- use nvcc for building for Kokkos/cuda with provided nvcc_wrapper
- parent = openmpi or mpich
- parent style determines syntax for setting low-level compiler
-"""
-
- def check(self):
- if len(self.inlist) < 1: error("-cc args are invalid")
- self.compiler = self.inlist[0]
- if self.compiler == "mpi":
- self.compiler = "mpicxx"
- self.abbrev = "mpi"
- elif self.compiler.startswith("mpi"):
- self.abbrev = "mpi"
- elif self.compiler == "g++" or self.compiler == "icc" or \
- self.compiler == "icpc":
- self.abbrev = self.compiler
- elif "mpi" in self.compiler: self.abbrev = "mpi"
- elif "g++" in self.compiler: self.abbrev = "g++"
- elif "icc" in self.compiler: self.abbrev = "icc"
- elif "icpc" in self.compiler: self.abbrev = "icpc"
- else: error("-cc args are invalid")
- for one in self.inlist[1:]:
- words = one.split('=')
- if len(words) != 2: error("-cc args are invalid")
- args = words[1].split(',')
- if len(args) != 2: error("-cc args are invalid")
- if words[0] == "wrap":
- if self.abbrev != "mpi": error("-cc compiler is not a wrapper")
- self.wrap = args[0]
- self.parent = args[1]
- else: error("-cc args are invalid")
-
-# Flags class
-
-class Flags(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.flags = []
-
- def help(self):
- return """
--flags var action N f1 f2 ... var action N f1 f2 ...
- alter variable settings (flags) in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- var = CCFLAGS, LINKFLAGS, LIB, etc
- any variable in Makefile.auto, must already exist
- action = add or del
- N = # of flags to follow
- f1,f2,etc = flag to add or delete
- "-" char will be prepended to each flag
- for example: add 4 g O3 xHost "fp-model fast=2"
- will add: -g -O3 -xHost -fp-model fast=2
- for add: if flag already exists, no change is made
- for delete: flag of form "-O*", will delete any wildcard match
- for -O,-O2,-O3,etc: existing -O* will first be removed
-"""
-
- def check(self):
- if len(self.inlist) < 1: error("-flags args are invalid")
- narg = len(self.inlist)
- i = 0
- while i < narg:
- if i+3 > narg: error("-flags args are invalid")
- var = self.inlist[i]
- action = self.inlist[i+1]
- if action != "add" and action != "del": error("-flags args are invalid")
- nflag = int(self.inlist[i+2])
- i += 3
- if i+nflag > narg: error("-flags args are invalid")
- flags = self.inlist[i:i+nflag]
- self.flags.append([var,action,flags])
- i += nflag
-
-# Mpi class
-
-class Mpi(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.style = self.dir = ""
-
- def help(self):
- return """
--mpi style dir=path
- alter MPI settings in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- style is required, all other args are optional
- style = mpi or mpich or ompi or serial
- mpi = no MPI settings (assume compiler is MPI wrapper)
- mpich = use explicit settings for MPICH
- ompi = use explicit settings for OpenMPI
- serial = use settings for src/STUBS library
- dir = path for MPICH or OpenMPI directory
- add -I and -L settings for include and lib sub-dirs
-"""
-
- def check(self):
- if len(self.inlist) < 1: error("-mpi args are invalid")
- self.style = self.inlist[0]
- if self.style != "mpi" and self.style != "mpich" and \
- self.style != "ompi" and self.style != "serial":
- error("-mpi args are invalid")
- for one in self.inlist[1:]:
- words = one.split('=')
- if len(words) != 2: error("-mpi args are invalid")
- if words[0] == "dir": self.dir = words[1]
- else: error("-mpi args are invalid")
-
-# Fft class
-
-class Fft(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.dir = self.incdir = self.libdir = ""
-
- def help(self):
- return """
--fft mode lib=libname dir=homedir idir=incdir ldir=libdir
- alter FFT settings in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- mode is required, all other args are optional
- first removes all current FFT variable settings
- mode = none or fftw or fftw3 or ...
- adds -DFFT_MODE setting
- lib = name of FFT library to link with (def is libname = mode)
- adds -llib{libname} setting, e.g. -llibfftw3
- dir = home dir for include and library files (def = none)
- adds -Idir/include and -Ldir/lib settings
- if set, overrides idir and ldir args
- idir = dir for include file (def = none)
- adds -Iidir setting
- ldir = dir for library file (def = none)
- adds -Lldir setting
-"""
-
- def check(self):
- if not len(self.inlist): error("-fft args are invalid")
- self.mode = self.inlist[0]
- self.lib = "-l%s" % self.mode
- for one in self.inlist[1:]:
- words = one.split('=')
- if len(words) != 2: error("-fft args are invalid")
- if words[0] == "lib": self.lib = "-l%s" % words[1]
- elif words[0] == "dir": self.dir = words[1]
- elif words[0] == "idir": self.incdir = words[1]
- elif words[0] == "ldir": self.libdir = words[1]
- else: error("-fft args are invalid")
-
-# Jpg class
-
-class Jpg(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.on = 1
- self.dir = self.incdir = self.libdir = ""
-
- def help(self):
- return """
--jpg flag dir=homedir idir=incdir ldir=libdir
- alter JPG settings in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- change JPG settings in makefile
- all args are optional, flag must come first if specified
- flag = yes or no (def = yes)
- include or exclude JPEG support
- adds/removes -DLAMMPS_JPEG and -ljpeg settings
- dir = home dir for include and library files (def = none)
- adds -Idir/include and -Ldir/lib settings
- if set, overrides idir and ldir args
- idir = dir for include file (def = none)
- adds -Iidir setting
- ldir = dir for library file (def = none)
- adds -Lldir setting
-"""
-
- def check(self):
- for i,one in enumerate(self.inlist):
- if one == "no" and i == 0: self.on = 0
- elif one == "yes" and i == 0: self.on = 1
- else:
- words = one.split('=')
- if len(words) != 2: error("-jpeg args are invalid")
- if words[0] == "dir": self.dir = words[1]
- elif words[0] == "idir": self.incdir = words[1]
- elif words[0] == "ldir": self.libdir = words[1]
- else: error("-jpeg args are invalid")
-
-# Png class
-
-class Png(object):
- def __init__(self,list):
- self.inlist = copy.copy(list)
- self.on = 1
- self.dir = self.incdir = self.libdir = ""
-
- def help(self):
- return """
--png flag dir=homedir idir=incdir ldir=libdir
- alter PNG settings in Makefile.auto
- only happens if new Makefile.auto is created by use of "file" action
- all args are optional, flag must come first if specified
- flag = yes or no (def = yes)
- include or exclude PNG support
- adds/removes -DLAMMPS_PNG and -lpng settings
- dir = home dir for include and library files (def = none)
- adds -Idir/include and -Ldir/lib settings
- if set, overrides idir and ldir args
- idir = dir for include file (def = none)
- adds -Iidir setting
- ldir = dir for library file (def = none)
- adds -Lldir setting
-"""
-
- def check(self):
- for i,one in enumerate(self.inlist):
- if one == "no" and i == 0: self.on = 0
- elif one == "yes" and i == 0: self.on = 1
- else:
- words = one.split('=')
- if len(words) != 2: error("-png args are invalid")
- if words[0] == "dir": self.dir = words[1]
- elif words[0] == "idir": self.incdir = words[1]
- elif words[0] == "ldir": self.libdir = words[1]
- else: error("-png args are invalid")
-
-# ----------------------------------------------------------------
-# auxiliary classes
-# ----------------------------------------------------------------
-
-# read, tweak, and write a Makefile
-
-class MakeReader(object):
-
- # read a makefile
- # flag = 0 if file is full path name
- # flag = 1,2 if file is suffix for any Makefile.machine under src/MAKE
- # look for this file in same order that src/Makefile does
- # if flag = 1, read the file
- # if flag = 2, just check if file exists
-
- def __init__(self,file,flag=0):
- if flag == 0:
- if not os.path.isfile(file): error("Makefile %s does not exist" % file)
- lines = open(file,'r').readlines()
- else:
- mfile = "%s/MAKE/MINE/Makefile.%s" % (dir.src,file)
- if not os.path.isfile(mfile):
- mfile = "%s/MAKE/Makefile.%s" % (dir.src,file)
- if not os.path.isfile(mfile):
- mfile = "%s/MAKE/OPTIONS/Makefile.%s" % (dir.src,file)
- if not os.path.isfile(mfile):
- mfile = "%s/MAKE/MACHINES/Makefile.%s" % (dir.src,file)
- if not os.path.isfile(mfile):
- error("Makefile.%s does not exist" % file)
- if flag == 1: lines = open(mfile,'r').readlines()
- else: return
-
- # scan lines of makefile
- # if not a variable line, just copy to newlines
- # if a variable line, concatenate any continuation lines
- # convert variable to var dict entry: key = name, value = list of words
- # discard any portion of value string with a comment char
- # varinfo = list of variable info: (name, name with whitespace for print)
- # add index into varinfo to newlines
- # ccindex = index of "CC =" line, to add OMPI var before it
- # lmpindex = index of "LAMMPS-specific settings"
- # line to add KOKKOS vars before it
-
- var = {}
- varinfo = []
- newlines = []
- pattern = "(\S+\s+=\s+)(.*)"
- conditional = 0
- multiline = 0
- self.ccindex = self.lmpindex = 0
-
- for line in lines:
- line = line[:-1]
- if "CC =" in line: self.ccindex = len(newlines)
- if "LAMMPS-specific settings" in line: self.lmpindex = len(newlines)
- if "ifeq" in line:
- conditional = 1
- continue
- if conditional:
- if "endif" in line:
- conditional = 0
- continue
- if multiline:
- if '#' in line: line = line[:line.find('#')]
- morevalues = line.split()
- values = values[:-1] + morevalues
- if values[-1] != '\\':
- var[name] = values
- multiline = 0
- newlines.append(str(len(varinfo)))
- varinfo.append((name,namewhite))
- continue
- varflag = 1
- if len(line.strip()) == 0: varflag = 0
- elif line.lstrip()[0] == '#': varflag = 0
- else:
- m = re.match(pattern,line)
- if not m: varflag = 0
- if varflag:
- namewhite = m.group(1)
- name = namewhite.split()[0]
- if name in var:
- error("Makefile variable %s appears more than once" % name)
- remainder = m.group(2)
- if '#' in remainder: remainder = remainder[:remainder.find('#')]
- values = remainder.split()
- if values and values[-1] == '\\': multiline = 1
- else:
- var[name] = values
- newlines.append(str(len(varinfo)))
- varinfo.append((name,namewhite))
- else:
- newlines.append(line)
-
- self.var = var
- self.varinfo = varinfo
- self.lines = newlines
-
- # return list of values associated with var
- # return None if var not defined
-
- def getvar(self,var):
- if var in self.var: return self.var[var]
- else: return None
-
- # set var to single value
- # if var not defined, error
-
- def setvar(self,var,value):
- if var not in self.var: error("Variable %s not in makefile" % var)
- self.var[var] = [value]
-
- # add value to var
- # do not add if value already defined by var
- # if var not defined,
- # create new variable using "where"
- # where="cc", line before "CC =" line, use ":="
- # where="lmp", 2 lines before "LAMMPS-specific settings" line, use "="
-
- def addvar(self,var,value,where=""):
- if var in self.var:
- if value not in self.var[var]: self.var[var].append(value)
- else:
- if not where:
- error("Variable %s with value %s is not in makefile" % (var,value))
- if where == "cc":
- if not self.ccindex: error("No 'CC =' line in makefile to add variable")
- index = self.ccindex
- varwhite = "%s :=\t\t" % var
- elif where == "lmp":
- if not self.lmpindex: error("No 'LAMMPS-specific settings line' " +
- "in makefile to add variable")
- index = self.lmpindex - 2
- varwhite = "%s =\t\t" % var
- self.var[var] = [value]
- varwhite = "%s =\t\t" % var
- self.lines.insert(index,str(len(self.varinfo)))
- self.varinfo.append((var,varwhite))
-
- # if value = None, remove entire var
- # no need to update lines or varinfo, write() will ignore deleted vars
- # else remove value from var
- # value can have trailing '*' to remove wildcard match
- # if var or value not defined, ignore it
-
- def delvar(self,var,value=None):
- #if var == "KOKKOS_DEVICES":
- # print self.var,value
- if var not in self.var: return
- if not value:
- del self.var[var]
- #print "AGAIN",self.var
- elif value and value[-1] != '*':
- if value not in self.var[var]: return
- self.var[var].remove(value)
- else:
- value = value[:-1]
- values = self.var[var]
- dellist = []
- for i,one in enumerate(values):
- if one.startswith(value): dellist.append(i)
- while dellist: values.pop(dellist.pop())
- self.var[var] = values
-
- # write stored makefile lines to file, using vars that may have been updated
- # do not write var if not in dict, since has been deleted
- # wrap var values into multiple lines if needed
- # file = 1 if this is Makefile.auto, change 1st line to use "auto"
-
- def write(self,file,flag=0):
- fp = open(file,'w')
- for i,line in enumerate(self.lines):
- if not line.isdigit():
- if flag and i == 0:
- line = "# auto = makefile auto-generated by Make.py"
- print(line, file=fp)
- else:
- index = int(line)
- name = self.varinfo[index][0]
- txt = self.varinfo[index][1]
- if name not in self.var: continue
- values = self.var[name]
- print("%s%s" % (txt,' '.join(values)), file=fp)
-
-# ----------------------------------------------------------------
-# main program
-# ----------------------------------------------------------------
-
-# parse command-line args
-# switches dict: key = switch letter, value = list of args
-# switch_order = list of switches in order
-# will possibly be merged with redo file args below
-
-cmd_switches,cmd_switch_order = parse_args(sys.argv[1:])
-
-if "v" in cmd_switches:
- # debug
- #print "Command-line parsing:"
- #for switch in cmd_switch_order:
- # print " %s: %s" % (switch,' '.join(cmd_switches[switch]))
- pass
-
-# check for redo switch, process redo file
-# redolist = list of commands to execute
-
-redoflag = 0
-redolist = []
-
-if 'r' in cmd_switches and 'h' not in cmd_switches:
- redoflag = 1
- redo = Redo(cmd_switches['r'])
- redo.check()
- redo.setup()
- redolist = redo.commands
- redoindex = 0
- del redo
- if not redolist: error("No commands to execute from redo file")
-
-# loop over Make.py commands
-# if no redo switch, loop once for command-line command
-# if redo, loop over one or more commands from redo file
-
-while 1:
-
- # if redo:
- # parse next command from redo file
- # use command-line switches to add/replace file command switches
- # do not add -r, since already processed
- # and don't want -r swtich to appear in Make.py.last file
- # if -a in both: concatenate, de-dup,
- # specified exe/machine action replaces file exe/machine action
- # print resulting new command
- # else just use command-line switches
-
- if redoflag:
- if redoindex == len(redolist): break
- args = redolist[redoindex].split()
- switches,switch_order = parse_args(args)
- redoindex += 1
-
- for switch in cmd_switches:
- if switch == 'r': continue
- if switch == 'a' and switch in switches:
- tmp = Actions(cmd_switches[switch] + switches[switch])
- tmp.dedup()
- switches[switch] = tmp.inlist
- continue
- if switch not in switches: switch_order.append(switch)
- switches[switch] = cmd_switches[switch]
-
- argstr = switch2str(switches,switch_order)
- print("Redo command: Make.py",argstr)
- else:
- switches = cmd_switches
- switch_order = cmd_switch_order
-
- # initialize all class variables to None
-
- for one in switchclasses: exec("%s = None" % one)
- for one in libclasses: exec("%s = None" % one)
- for one in buildclasses: exec("%s = None" % one)
- for one in makeclasses: exec("%s = None" % one)
-
- # classes = dictionary of created classes
- # key = switch, value = class instance
-
- classes = {}
- for switch in switches:
- if len(switch) == 1 and switch in abbrevs:
- i = abbrevs.index(switch)
- txt = '%s = classes["%s"] = %s(switches["%s"])' % \
- (switchclasses[i],switch,switchclasses[i].capitalize(),switch)
- exec(txt)
- elif switch in libclasses:
- i = libclasses.index(switch)
- txt = '%s = classes["%s"] = %s(switches["%s"])' % \
- (libclasses[i],switch,libclasses[i].upper(),switch)
- exec(txt)
- elif switch in buildclasses:
- i = buildclasses.index(switch)
- txt = '%s = classes["%s"] = %s(switches["%s"])' % \
- (buildclasses[i],switch,buildclasses[i].capitalize(),switch)
- exec(txt)
- elif switch in makeclasses:
- i = makeclasses.index(switch)
- txt = '%s = classes["%s"] = %s(switches["%s"])' % \
- (makeclasses[i],switch,makeclasses[i].capitalize(),switch)
- exec(txt)
- else: error("Unknown command-line switch -%s" % switch)
-
- # print help messages and exit
-
- if help or (actions and "-h" in actions.inlist) or not switches:
- if not help: help = Help(None)
- print(help.help())
- for switch in switch_order:
- if switch == "h": continue
- print(classes[switch].help()[1:])
- sys.exit()
-
- # create needed default classes if not specified with switch
- # dir and packages plus lib and build classes so defaults are set
-
- if not dir: dir = Dir(None)
- if not packages: packages = Packages(None)
-
- for one in libclasses:
- txt = "if not %s: %s = %s(None)" % (one,one,one.upper())
- exec(txt)
-
- for one in buildclasses:
- txt = "if not %s: %s = %s(None)" % (one,one,one.capitalize())
- exec(txt)
-
- # error check on args for all classes
-
- for switch in classes: classes[switch].check()
-
- # prep for action
- # actions.setup() detects if last action = machine
- # if yes, induce addition of "-m" and "-o" switches
-
- dir.setup()
- packages.setup()
-
- if actions:
- machine = actions.setup()
- if machine:
- switches['a'][-1] = "exe"
- if 'm' not in switches:
- switches['m'] = [machine]
- switch_order.insert(-1,'m')
- makefile = classes['m'] = Makefile(switches['m'])
- makefile.check()
- if 'o' not in switches:
- switches['o'] = [machine]
- switch_order.insert(-1,'o')
- output = classes['o'] = Output(switches['o'])
- output.check()
-
- # perform actions
-
- packages.install()
-
- if actions:
- for action in actions.alist:
- print("Action %s ..." % action)
- if action.startswith("lib-"): actions.lib(action[4:])
- elif action == "file": actions.file("file")
- elif action == "clean": actions.clean()
- elif action == "exe": actions.exe()
-
- packages.uninstall()
-
- # create copy of executable if requested, and exe action performed
-
- if output and actions and "exe" in actions.alist:
- txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
- subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- print("Created lmp_%s in %s" % (output.machine,dir.cwd))
-
- # create copy of Makefile.auto if requested, and file or exe action performed
- # ditto for library Makefile.auto and Makefile.lammps files
-
- if zoutput and actions and \
- ("file" in actions.alist or "exe" in actions.alist):
- txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
- (dir.src,dir.src,zoutput.machine)
- subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- print("Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src))
- if gpubuildflag:
- txt = "cp %s/gpu/Makefile.auto %s/MAKE/MINE/Makefile_gpu.%s" % \
- (dir.lib,dir.src,zoutput.machine)
- subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- print("Created Makefile_gpu.%s in %s/MAKE/MINE" % \
- (zoutput.machine,dir.src))
- txt = "cp %s/gpu/Makefile.lammps %s/MAKE/MINE/Makefile_gpu_lammps.%s" % \
- (dir.lib,dir.src,zoutput.machine)
- subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
- print("Created Makefile_gpu_lammps.%s in %s/MAKE/MINE" % \
- (zoutput.machine,dir.src))
-
- # write current Make.py command to src/Make.py.last
-
- fp = open("%s/Make.py.last" % dir.src,'w')
- print("# last invoked Make.py command", file=fp)
- print(switch2str(switches,switch_order), file=fp)
- fp.close()
-
- # if not redoflag, done
-
- if not redoflag: break