diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 31f2cb549e..f8b52056fc 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -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 diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt index a18d812b59..ad18695e46 100644 --- a/doc/src/Build_make.txt +++ b/doc/src/Build_make.txt @@ -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 diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index d279b5e975..a74182967c 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -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 diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt index 8be4b66e78..a12bf13f2e 100644 --- a/doc/src/Howto_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -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 diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 188081c8dd..3519720911 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -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. diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt index 647ff71e36..dd12685dc5 100644 --- a/doc/src/Speed_measure.txt +++ b/doc/src/Speed_measure.txt @@ -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. diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index 192ea0bc9e..5ba2100fba 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -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 diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index 04b38682cc..d11ae9e3bf 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -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), diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt index 92f5923de0..e9ff2e739b 100644 --- a/doc/src/compute_smd_tlsph_dt.txt +++ b/doc/src/compute_smd_tlsph_dt.txt @@ -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. diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt index b29fa82f2d..4e33604696 100644 --- a/doc/src/delete_bonds.txt +++ b/doc/src/delete_bonds.txt @@ -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 diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index dd2b212f0b..b5f157cf29 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -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: /plugins//molfile diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index be4fbd255b..0c5a4493ae 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -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) diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index b115aba7df..64486a9cc7 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -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. diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index ddb5f9a4cd..f50747948a 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -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 diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index d489762e80..5d65856735 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -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 diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index 644c04eadb..774842c7cf 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -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 diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt index adaeeb8390..8b1ceab858 100644 --- a/doc/src/pair_dsmc.txt +++ b/doc/src/pair_dsmc.txt @@ -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:] diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index b7130c8a10..e8baf14d2e 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -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 diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 07b4986673..283aad6c2d 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -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. diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 9f3221449b..efa2c87296 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -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(); diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 11bf2ae01e..785146a0d6 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -394,7 +394,7 @@ void PairAGNI::read_file(char *file) if (nwords == 0) continue; if (nwords > MAXWORD) - error->all(FLERR,"Increase MAXWORD and recompile"); + error->all(FLERR,"Increase MAXWORD and re-compile"); // words = ptrs to all words in line