diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 90f6e9c8bd..3c431b0325 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -791,6 +791,13 @@ foreach(PKG ${DEFAULT_PACKAGES}) endif() endforeach() +# packages that need defines set +foreach(PKG MPIIO) + if(PKG_${PKG}) + add_definitions(-DLMP_${PKG}) + endif() +endforeach() + # dedicated check for entire contents of accelerator packages foreach(PKG ${ACCEL_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md index a11ee28aab..8b3dc4687c 100644 --- a/doc/github-development-workflow.md +++ b/doc/github-development-workflow.md @@ -107,7 +107,9 @@ Here are some items to check: * new style docs should be added to the "overview" files in `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt` and `doc/src/lammps.book` - * new files in packages should be added to `src/.gitignore` + * check whether manual cleanly translates with `make html` and `make pdf` + * check spelling of manual with `make spelling` in doc folder + * new source files in packages should be added to `src/.gitignore` * removed or renamed files in packages should be added to `src/Purge.list` * C++ source files should use C++ style include files for accessing C-library APIs, e.g. `#include ` instead of `#include `. diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index b3ff0a55c5..47801890c4 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that you can browse them locally on your system. Type "make" from the lammps/doc dir to see other options. -NOTE: You can also download a tarball of the documention for the +NOTE: You can also download a tarball of the documentation for the current LAMMPS version (HTML and PDF files), from the website "download page"_http://lammps.sandia.gov/download.html. diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 8881ee44c1..4377981662 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -732,7 +732,7 @@ can be shared across multiple MD packages and can be updated, for as long as the shared PLUMED library is ABI-compatible. The third linkage mode is "runtime" which allows to switch the PLUMED kernel at runtime between different variants through setting the PLUMED_KERNEL environment -varible, which has to point to the location of the libplumedKernel.so +variable, which has to point to the location of the libplumedKernel.so dynamical shared object, which is then loaded at runtime. This is particularly convenient for doing PLUMED development and comparing multiple PLUMED versions without having to recompile the hosting MD @@ -750,7 +750,7 @@ a global PLUMED installation or downloading it during building LAMMPS. -D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be -downloaded (the version of that is hardcoded to a vetted version of +downloaded (the version of that is hard-coded to a vetted version of PLUMED, usually a recent stable release version) and built inside the CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default), CMake will try to detect an installed version of PLUMED and link to @@ -788,7 +788,7 @@ Note that 2 symbolic (soft) links, "includelink" and "liblink" are created in lib/plumed to point into the location of the PLUMED build to use and also a new file lib/plumed/Makefile.lammps is created with settings suitable for LAMMPS to compile and link PLUMED in the desired -linkage mode. After this step is compleded, you can install the +linkage mode. After this step is completed, you can install the USER-PLUMED package and compile LAMMPS in the usual manner: make yes-user-plumed @@ -804,7 +804,7 @@ operating systems, using the static linkage is expected to be the most portable, and thus set to be the default. If you want to change the linkage mode, you have to re-run "make -lib-plumed" with the desired settings [and] do a reinstall if the +lib-plumed" with the desired settings [and] do a re-install if the USER-PLUMED package with "make yes-user-plumed" to update the required makefile settings with the changes in the lib/plumed folder. diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index 500130ecee..c871d4ab42 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -139,7 +139,7 @@ adequate. [Makefile.machine setting]: LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre - # default is LAMMMPS_SMALLBIG if not specified + # default is LAMMPS_SMALLBIG if not specified [CMake and make info]: The default "smallbig" setting allows for simulations with: diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index 0caad589fb..6ac6f52d54 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -66,7 +66,7 @@ In case of problems, you are recommended to contact somebody with experience in using cygwin. If you do come across portability problems requiring changes to the LAMMPS source code, or figure out corrections yourself, please report them on the lammps-users mailing list, or file -them as an issue or pull request on the LAMMPS github project. +them as an issue or pull request on the LAMMPS GitHub project. Using a cross-compiler :h4,link(cross) diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt index a1a94c6d29..bb3fab3683 100644 --- a/doc/src/Commands.txt +++ b/doc/src/Commands.txt @@ -42,10 +42,10 @@ END_RST --> "Input script structure"_Commands_structure.html "Commands by category"_Commands_category.html :all(b) -"All commands"_Commands_all.html -"Fix commands"_Commands_fix.html -"Compute commands"_Commands_compute.html -"Pair commands"_Commands_pair.html +"General commands"_Commands_all.html +"Fix commands"_Commands_fix.html +"Compute commands"_Commands_compute.html +"Pair commands"_Commands_pair.html "Bond, angle, dihedral, improper commands"_Commands_bond.html "KSpace solvers"_Commands_kspace.html :all(b) diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index c0b8c4516d..f137ccffd9 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c "Improper styles"_Commands_bond.html#improper, "KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) -All commands :h3 +General commands :h3 -An alphabetic list of all LAMMPS commands. +An alphabetic list of all general LAMMPS commands. "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index d4d48924a7..fbf292aab2 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(ld,Manual.html) :link(lc,Commands_all.html) -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt index 5d047c6727..134dae82bb 100644 --- a/doc/src/Commands_category.txt +++ b/doc/src/Commands_category.txt @@ -10,10 +10,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Commands by category :h3 This page lists most of the LAMMPS commands, grouped by category. The -"Commands all"_Commands_all.html doc page lists all commands -alphabetically. It also includes long lists of style options for -entries that appear in the following categories as a single command -(fix, compute, pair, etc). +"General commands"_Commands_all.html doc page lists all general commands +alphabetically. Style options for entries like fix, compute, pair etc. +have their own pages where they are listed alphabetically. Initialization: diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index eb802030e2..f566702609 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 6d8f67b503..fb4515b486 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -235,4 +235,4 @@ OPT. "wall/reflect (k)"_fix_wall_reflect.html, "wall/region"_fix_wall_region.html, "wall/region/ees"_fix_wall_ees.html, -"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) +"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt index d56b7fa767..02b41b9d67 100644 --- a/doc/src/Commands_kspace.txt +++ b/doc/src/Commands_kspace.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 7af2cc9bae..bf2b2b4f39 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt index 1d7c754fa7..13a4c2699d 100644 --- a/doc/src/Commands_parse.txt +++ b/doc/src/Commands_parse.txt @@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how strings are assigned to variables and evaluated, and how they can be used in input script commands. -(4) The line is broken into "words" separated by whitespace (tabs, +(4) The line is broken into "words" separated by white-space (tabs, spaces). Note that words can thus contain letters, digits, underscores, or punctuation characters. diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 695b949f7e..de6d974dde 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -421,9 +421,9 @@ This is an internal error. It should normally not occur. :dd This is an internal error. It should normally not occur. :dd -{Bad real space Coulomb cutoff in fix tune/kspace} :dt +{Bad real space Coulombic cutoff in fix tune/kspace} :dt -Fix tune/kspace tried to find the optimal real space Coulomb cutoff using +Fix tune/kspace tried to find the optimal real space Coulombic cutoff using the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd {Balance command before simulation box is defined} :dt @@ -460,7 +460,7 @@ compute. :dd {Big particle in fix srd cannot be point particle} :dt -Big particles must be extended spheriods or ellipsoids. :dd +Big particles must be extended spheroids or ellipsoids. :dd {Bigint setting in lmptype.h is invalid} :dt @@ -780,7 +780,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd Self-explanatory. :dd -{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt +{Cannot change box z boundary to non-periodic for a 2d simulation} :dt Self-explanatory. :dd @@ -1288,7 +1288,7 @@ are defined. :dd You cannot reset the timestep when a fix that keeps track of elapsed time is in place. :dd -{Cannot run 2d simulation with nonperiodic Z dimension} :dt +{Cannot run 2d simulation with non-periodic Z dimension} :dt Use the boundary command to make the z dimension periodic in order to run a 2d simulation. :dd @@ -2116,29 +2116,29 @@ Self-explanatory. :dd Fix setforce cannot be used in this manner. Use fix addforce instead. :dd -{Cannot use nonperiodic boundares with fix ttm} :dt +{Cannot use non-periodic boundares with fix ttm} :dt This fix requires a fully periodic simulation box. :dd -{Cannot use nonperiodic boundaries with Ewald} :dt +{Cannot use non-periodic boundaries with Ewald} :dt For kspace style ewald, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with EwaldDisp} :dt +{Cannot use non-periodic boundaries with EwaldDisp} :dt For kspace style ewald/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPM} :dt +{Cannot use non-periodic boundaries with PPPM} :dt For kspace style pppm, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPMDisp} :dt +{Cannot use non-periodic boundaries with PPPMDisp} :dt For kspace style pppm/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d @@ -3351,21 +3351,21 @@ probably due to errors in the Python code. :dd The default minimum order is 2. This can be reset by the kspace_modify minorder command. :dd -{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt +{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/coul/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt +{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt -If using a Kspace solver, all Coulomb cutoffs of long pair styles must +If using a Kspace solver, all Coulombic cutoffs of long pair styles must be the same. :dd {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt @@ -5938,9 +5938,9 @@ map command will force an atom map to be created. :dd Self-explanatory. :dd -{Input line quote not followed by whitespace} :dt +{Input line quote not followed by white-space} :dt -An end quote must be followed by whitespace. :dd +An end quote must be followed by white-space. :dd {Insertion region extends outside simulation box} :dt @@ -7014,7 +7014,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd {KSpace accuracy too large to estimate G vector} :dt -Reduce the accuracy request or specify gwald explicitly +Reduce the accuracy request or specify gewald explicitly via the kspace_modify command. :dd {KSpace accuracy too low} :dt @@ -8014,7 +8014,7 @@ Self-explanatory. :dd {Package command after simulation box is defined} :dt -The package command cannot be used afer a read_data, read_restart, or +The package command cannot be used after a read_data, read_restart, or create_box command. :dd {Package gpu command without GPU package installed} :dt @@ -9198,7 +9198,7 @@ creates one large file for all processors. :dd {Restart file byte ordering is not recognized} :dt The file does not appear to be a LAMMPS restart file since it doesn't -contain a recognized byte-orderomg flag at the beginning. :dd +contain a recognized byte-ordering flag at the beginning. :dd {Restart file byte ordering is swapped} :dt @@ -9410,7 +9410,7 @@ You may also want to boost the page size. :dd {Small to big integers are not sized correctly} :dt -This error occurs whenthe sizes of smallint, imageint, tagint, bigint, +This error occurs when the sizes of smallint, imageint, tagint, bigint, as defined in src/lmptype.h are not what is expected. Contact the developers if this occurs. :dd diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 0980120a10..079688c639 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -757,7 +757,7 @@ Self-explanatory. :dd This may indicate the shell command did not operate as expected. :dd -{Should not allow rigid bodies to bounce off relecting walls} :dt +{Should not allow rigid bodies to bounce off reflecting walls} :dt LAMMPS allows this, but their dynamics are not computed correctly. :dd @@ -850,10 +850,10 @@ Most FENE models need this setting for the special_bonds command. :dd Most FENE models need this setting for the special_bonds command. :dd -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt +{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential +eliminate neighbors in the neighbor list, which the many-body potential needs to calculated its terms correctly. :dd {Using compute temp/deform with inconsistent fix deform remap option} :dt diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index 4b6db8a047..e26e6abd99 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -78,7 +78,7 @@ micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics -nb3b: use of nonbonded 3-body harmonic pair style +nb3b: use of non-bonded 3-body harmonic pair style neb: nudged elastic band (NEB) calculation for barrier finding nemd: non-equilibrium MD of 2d sheared system obstacle: flow around two voids in a 2d channel diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt index 730b492699..36f6be7194 100644 --- a/doc/src/Howto.txt +++ b/doc/src/Howto.txt @@ -45,7 +45,7 @@ General howto :h3