Commit 4b2629d8 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

recompile/recompute/reinit -> re-compile/re-compute/re-init

parent 193f46dd
......@@ -40,7 +40,7 @@ executable called "lmp" and a library called "liblammps.a" in the
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
LAMMPS or need to recompile LAMMPS repeatedly, installation of the
LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
After compilation, you can optionally copy the LAMMPS executable and
......
......@@ -35,16 +35,16 @@ This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
do development on LAMMPS or need to recompile LAMMPS repeatedly, the
do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
uninstalling packages), you must recompile and relink the LAMMPS
uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
recompiled.
re-compiled.
NOTE: When you build LAMMPS for the first time, a long list of *.d
files will be printed out rapidly. This is not an error; it is the
......
......@@ -743,7 +743,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt
Single precision cannot be used with MSM. :dd
......@@ -5078,7 +5078,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/point requires atom attribute q} :dt
......@@ -5092,7 +5092,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/shielded requires atom attribute q} :dt
......@@ -5110,7 +5110,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/slater requires atom attribute q} :dt
......@@ -5541,7 +5541,7 @@ See the package gpu command. :dd
{GPUs are requested but Kokkos has not been compiled for CUDA} :dt
Recompile Kokkos with CUDA support to use GPUs. :dd
Re-compile Kokkos with CUDA support to use GPUs. :dd
{Ghost velocity forward comm not yet implemented with Kokkos} :dt
......
......@@ -73,7 +73,7 @@ that package into your current Python installation.
cd $LAMMPS_DIR/python
python install.py :pre
NOTE: Recompiling the shared library requires reinstalling the Python package
NOTE: Recompiling the shared library requires re-installing the Python package
Installation inside of a virtualenv :h5
......
......@@ -1591,7 +1591,7 @@ plugin via the "dump molfile"_dump_molfile.html command. Plugins can
be obtained from a VMD installation which has to match the platform
that you are using to compile LAMMPS for. By adding plugins to VMD,
support for new file formats can be added to LAMMPS (or VMD or other
programs that use them) without having to recompile the application
programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found
at
"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
......
......@@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
......@@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
N = # of extra degrees of freedom to subtract
{extra} syntax is identical to {extra/dof}, will be disabled at some point
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
:ule
......
......@@ -182,7 +182,7 @@ change from zero to one at the location of the spike in g(r).
NOTE: compute rdf can handle dynamic groups and systems where atoms
are added or removed, but this causes that certain normalization
parameters need to be recomputed in every step and include collective
parameters need to be re-computed in every step and include collective
communication operations. This will reduce performance and limit
parallel efficiency and scaling. For systems, where only the type
of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html),
......
......@@ -25,7 +25,7 @@ Define a computation that outputs the CFL-stable time increment per
particle. This time increment is essentially given by the speed of
sound, divided by the SPH smoothing length. Because both the speed of
sound and the smoothing length typically change during the course of a
simulation, the stable time increment needs to be recomputed every
simulation, the stable time increment needs to be re-computed every
time step. This calculation is performed automatically in the
relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
......
......@@ -140,7 +140,7 @@ enough for a processor to acquire the ghost atoms its needs to compute
bond, angle, etc interactions.
If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
weighting list is not recomputed, this can cause a later "fix
weighting list is not re-computed, this can cause a later "fix
shake"_fix_shake.html command to fail due to an atom's bonds being
inconsistent with the weighting list. This should only happen if the
group used in the fix command includes both atoms in the bond, in
......
......@@ -99,7 +99,7 @@ USER-MOLFILE package only provides the interface code, not the plugins.
These can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD
or other programs that use them) without having to recompile the
or other programs that use them) without having to re-compile the
application itself. The plugins are installed in the directory:
<VMDHOME>/plugins/<VMDARCH>/molfile
......
......@@ -14,7 +14,7 @@ fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command
dt/reset = style name of this fix command
N = recompute dt every N timesteps
N = re-compute dt every N timesteps
Tmin = minimum dt allowed which can be NULL (time units)
Tmax = maximum dt allowed which can be NULL (time units)
Xmax = maximum distance for an atom to move in one timestep (distance units)
......
......@@ -63,7 +63,7 @@ electrostatics, or that contain parameters that depend on box size:
all of these options will be initialized based on the cell size in the
LAMMPS-side initial configuration and kept constant during the run.
This is required to e.g. obtain reproducible and conserved forces.
If the cell varies too wildly, it may be advisable to reinitialize
If the cell varies too wildly, it may be advisable to re-initialize
these interactions at each call. This behavior can be requested by
setting the {reset} switch.
......
......@@ -21,7 +21,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{bodyforces} value = {early} or {late}
early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
......
......@@ -442,11 +442,11 @@ couple none :pre
The keyword/value option pairs are used in the following ways.
The {reinit} keyword determines, whether the rigid body properties
are reinitialized between run commands. With the option {yes} (the
are re-initialized between run commands. With the option {yes} (the
default) this is done, with the option {no} this is not done. Turning
off the reinitialization can be helpful to protect rigid bodies against
off the re-initialization can be helpful to protect rigid bodies against
unphysical manipulations between runs or when properties cannot be
easily recomputed (e.g. when read from a file). When using the {infile}
easily re-computed (e.g. when read from a file). When using the {infile}
keyword, the {reinit} option is automatically set to {no}.
The {langevin} and {temp} and {tparam} keywords perform thermostatting
......
......@@ -77,7 +77,7 @@ normalized. But since it represents the {absolute} displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the {auto} parameter. In this case the direction is
recomputed in every step, which can be useful for steering a local
re-computed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
......
......@@ -16,7 +16,7 @@ max_cell_size = global maximum cell size for DSMC interactions (distance units)
seed = random # seed (positive integer)
weighting = macroparticle weighting
Tref = reference temperature (temperature units)
Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps)
Nsample = sample this many times in recomputing v*sigma_max :ul
[Examples:]
......
......@@ -29,7 +29,7 @@ The {python} pair style provides a way to define pairwise additive
potential functions as python script code that is loaded into LAMMPS
from a python file which must contain specific python class definitions.
This allows to rapidly evaluate different potential functions without
having to modify and recompile LAMMPS. Due to python being an
having to modify and re-compile LAMMPS. Due to python being an
interpreted language, however, the performance of this pair style is
going to be significantly slower (often between 20x and 100x) than
corresponding compiled code. This penalty can be significantly reduced
......
......@@ -110,7 +110,7 @@ simulation.
The two exceptions to this rule are (a) if the {angle} or {dihedral}
keywords are set to {yes} (see below), or (b) if the
"delete_bonds"_delete_bonds.html command is used with the {special}
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
option that re-computes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the "delete_bonds"_delete_bonds.html command for more
details.
......
......@@ -177,7 +177,7 @@ void MSM::init()
if (sizeof(FFT_SCALAR) != 8)
error->all(FLERR,"Cannot (yet) use single precision with MSM "
"(remove -DFFT_SINGLE from Makefile and recompile)");
"(remove -DFFT_SINGLE from Makefile and re-compile)");
// extract short-range Coulombic cutoff from pair style
......@@ -419,7 +419,7 @@ void MSM::setup()
boxlo = domain->boxlo_lamda;
// ghost grid points depend on direct sum interaction limits,
// so need to recompute local grid
// so need to re-compute local grid
set_grid_local();
......
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