diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0f99cc6274..eaa699106c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -497,10 +497,44 @@ if(BUILD_LIB) if(LAMMPS_DEPS) add_dependencies(lammps ${LAMMPS_DEPS}) endif() + set(LAMMPS_CXX_HEADERS + angle.h + atom.h + bond.h + citeme.h + comm.h + compute.h + dihedral.h + domain.h + error.h + fix.h + force.h + group.h + improper.h + input.h + kspace.h + lammps.h + lattice.h + lmppython.h + memory.h + modify.h + neighbor.h + neigh_list.h + output.h + pair.h + pointers.h + region.h + timer.h + universe.h + update.h + variable.h) + list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/) + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) @@ -551,11 +585,11 @@ include(Documentation) ############################################################################### # Install potential and force field files in data directory ############################################################################### -set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) -install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR}) - -set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files) -install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR}) +set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps) +install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR}) +if(BUILD_TOOLS) + install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) +endif() configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in index 42f222d67c..1c13583914 100644 --- a/cmake/etc/profile.d/lammps.csh.in +++ b/cmake/etc/profile.d/lammps.csh.in @@ -1,4 +1,4 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ -if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@ +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials +if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in index c1967cb5b2..1542a8982f 100644 --- a/cmake/etc/profile.d/lammps.sh.in +++ b/cmake/etc/profile.d/lammps.sh.in @@ -1,5 +1,5 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} -MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@} +LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials} +MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files} export LAMMPS_POTENTIALS MSI2LMP_LIBRARY diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md new file mode 100644 index 0000000000..c9f8bd5cb1 --- /dev/null +++ b/doc/include-file-conventions.md @@ -0,0 +1,133 @@ +# Outline of include file conventions in LAMMPS + +This purpose of this document is to provide a point of reference +for LAMMPS developers and contributors as to what include files +and definitions to put where into LAMMPS source. +Last change 2019-07-05 + +## Table of Contents + + * [Motivation](#motivation) + * [Rules](#rules) + * [Tools](#tools) + * [Legacy Code](#legacy-code) + +## Motivation + +The conventions outlined in this document are supposed to help make +maintenance of the LAMMPS software easier. By trying to achieve +consistency across files contributed by different developers, it will +become easier for the code maintainers to modify and adjust files and, +overall, the chance for errors or portability issues will be reduced. +The rules employed are supposed to minimize naming conflicts and +simplify dependencies between files and thus speed up compilation. They +may, as well, make otherwise hidden dependencies visible. + +## Rules + +Below are the various rules that are applied. Not all are enforced +strictly and automatically. If there are no significant side effects, +exceptions may be possible for cases where a full compliance to the +rules may require a large effort compared to the benefit. + +### Core Files Versus Package Files + +All rules listed below are most strictly observed for core LAMMPS files, +which are the files that are not part of a package, and the files of the +packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of +the spectrum are USER packages and legacy packages that predate these +rules and thus may not be fully compliant. Also, new contributions +will be checked more closely, while existing code will be incrementally +adapted to the rules as time and required effort permits. + +### System Versus Local Header Files + +All system- or library-provided include files are included with angular +brackets (examples: `#include ` or `#include `) while +include files provided with LAMMPS are included with double quotes +(examples: `#include "pointers.h"` or `#include "compute_temp.h"`). + +For headers declaring functions of the C-library, the corresponding +C++ versions should be included (examples: `#include ` or +`#include `). However, these includes are limited to those defined +in the C++98 standard. Some files thus must use the older style until +the minimum C++ standard requirement of LAMMPS is lifted to C++11 or +even beyond (examples: `#include ` versus `#include ` +or `#include ` versus `#include `). + +### C++ Standard Compliance + +LAMMPS core files currently correspond to the C++98 standard. Files +requiring C++11 or later are only permitted in (optional) packages +and particularly packages that are not part of the list of commonly +used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID. + +Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams. +Since using both at the same time can cause problems, iostreams should +be avoided where possible. + +### Lean Header Files + +Header files will typically contain the definition of a (single) class. +These header files should have as few include statements as possible. +This is particularly important for classes that implement a "style" and +thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will +all be included in the auto-generated `"some_style.h"` files which +results in a high potential for direct or indirect symbol name clashes. + +In the ideal case, the header would only include one file defining the +parent class. That would typically be either `#include "pointers.h"` for +the `Pointers` class, or a header of a class derived from it like +`#include "pair.h"` for the `Pair` class and so on. References to other +classes inside the class should be make through pointers, for which forward +declarations (inside the `LAMMPS_NS` or the new class' namespace) can +be employed. The full definition will then be included into the corresponding +implementation file. In the given example from above, the header file +would be called `some_name.h` and the implementation `some_name.cpp` (all +lower case with underscores, while the class itself would be in camel case +and no underscores `SomeName`, and the style name with lower case names separated by +a forward slash). + +### Implementation Files + +In the implementation files (typically, those would have the same base name +as the corresponding header with a .cpp extension instead of .h) include +statements should follow the "include what you use" principle. + +### Order of Include Statements + +Include files should be included in this order: +* the header matching the implementation (`some_class.h` for file `some_class.cpp`) +* mpi.h +* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* LAMMPS local headers (preferably in alphabetical order) + +### Special Cases and Exceptions + +#### pointers.h + +The `pointer.h` header file also includes `cstdio` and `lmptype.h` +(and through it `stdint.h`, `intttypes.h`, and `climits`). +This means any header including `pointers.h` can assume that `FILE`, +`NULL`, `INT_MAX` are defined. + +## Tools + +The [Include What You Use tool](https://include-what-you-use.org/) +can be used to provide supporting information about compliance with +the rules listed here. There are some limitations and the IWYU tool +may give incorrect advice. The tools is activated by setting the +CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the +path of the `include-what-you-use` command. When activated, the +tool will be run after each compilation and provide suggestions for +which include files should be added or removed. + +## Legacy Code + +A lot of code predates the application of the rules in this document +and the rules themselves are a moving target. So there are going to be +significant chunks of code that do not fully comply. This applies +for example to the USER-REAXC, or the USER-ATC package. The LAMMPS +developers are dedicated to make an effort to improve the compliance +and welcome volunteers wanting to help with the process. + diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index a16ba995a8..6eb23b2bb5 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up repeated compilation even more. -After compilation, you can optionally copy the LAMMPS executable and -library into your system folders (by default under $HOME/.local) with: +After compilation, you may optionally install the LAMMPS executable into +your system with: make install # optional, copy LAMMPS executable & library elsewhere :pre +This will install the lammps executable and library (if requested), some +tools (if configured) and additional files like library API headers, +manpages, potential and force field files. The location of the installation +tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults +to $\{HOME\}/.local + :line There are 3 variants of CMake: a command-line version (cmake), a text mode diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 1507d6b22c..9f346ba8c1 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -129,6 +129,16 @@ Self-explanatory. :dd Self-explanatory. :dd +{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt + +The communication cutoff defaults to the maximum of what is inferred from +pair and bond styles (will be zero, if none are defined) and what is specified +via "comm_modify cutoff"_comm_modify.html (defaults to 0.0). If this results +to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use +incorrect periodic images of atoms in interaction lists. To avoid, either use +"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify +cutoff"_comm_modify.html. :dd + {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt Self-explanatory. :dd diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index fd33491253..99d29864dc 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -46,16 +46,15 @@ software version 7.5 or later must be installed on your system. See the discussion for the "GPU package"_Speed_gpu.html for details of how to check and do this. -NOTE: Kokkos with CUDA currently implicitly assumes that the MPI -library is CUDA-aware and has support for GPU-direct. This is not -always the case, especially when using pre-compiled MPI libraries -provided by a Linux distribution. This is not a problem when using -only a single GPU and a single MPI rank on a desktop. When running -with multiple MPI ranks, you may see segmentation faults without -GPU-direct support. These can be avoided by adding the flags "-pk -kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or -by using the command "package kokkos gpu/direct off"_package.html in -the input file. +NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library +is CUDA-aware. This is not always the case, especially when using +pre-compiled MPI libraries provided by a Linux distribution. This is not +a problem when using only a single GPU with a single MPI rank. When +running with multiple MPI ranks, you may see segmentation faults without +CUDA-aware MPI support. These can be avoided by adding the flags "-pk +kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by +using the command "package kokkos cuda/aware off"_package.html in the +input file. [Building LAMMPS with the KOKKOS package:] @@ -217,9 +216,8 @@ case, also packing/unpacking communication buffers on the host may give speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS is recommended in this scenario. -Using a CUDA-aware MPI library with -support for GPU-direct is highly recommended. GPU-direct use can be -avoided by using "-pk kokkos gpu/direct no"_package.html. As above for +Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be +avoided by using "-pk kokkos cuda/aware no"_package.html. 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 should not exceed N. diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index 6b9187e512..61c987f587 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively. :line +[Restart info:] + +This angle style writes the settings for the "angle_style table" +command to "binary restart files"_restart.html, so a angle_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +angle_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This angle style can only be used if LAMMPS was built with the diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index fbf6eb5815..7235214af0 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively. :line +[Restart info:] + +This bond style writes the settings for the "bond_style table" +command to "binary restart files"_restart.html, so a bond_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +bond_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This bond style can only be used if LAMMPS was built with the MOLECULE diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 482259142b..5f03636c1d 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -69,9 +69,15 @@ processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the "neighbor"_neighbor.html command for more information about the skin distance. If the specified Rcut is greater than the neighbor cutoff, then extra ghost atoms will be acquired. -If the provided cutoff is smaller, the provided value will be ignored -and the ghost cutoff is set to the neighbor cutoff. Specifying a -cutoff value of 0.0 will reset any previous value to the default. +If the provided cutoff is smaller, the provided value will be ignored, +the ghost cutoff is set to the neighbor cutoff and a warning will be +printed. Specifying a cutoff value of 0.0 will reset any previous value +to the default. If bonded interactions exist and equilibrium bond length +information is available, then also a heuristic based on that bond length +is computed. It is used as communication cutoff, if there is no pair +style present and no {comm_modify cutoff} command used. Otherwise a +warning is printed, if this bond based estimate is larger than the +communication cutoff used. A The {cutoff/multi} option is equivalent to {cutoff}, but applies to communication mode {multi} instead. Since in this case the communication diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 3f679f5709..b3cfd37570 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -191,6 +191,16 @@ switch"_Run_options.html when you invoke LAMMPS, or you can use the See the "Speed packages"_Speed_packages.html doc page for more instructions on how to use the accelerated styles effectively. +[Restart info:] + +This dihedral style writes the settings for the "dihedral_style table" +command to "binary restart files"_restart.html, so a dihedral_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +dihedral_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This dihedral style can only be used if LAMMPS was built with the diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index b72f34e36e..560f5375a7 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -189,6 +189,16 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. +[Restart info:] + +This dihedral style writes the settings for the "dihedral_style table/cut" +command to "binary restart files"_restart.html, so a dihedral_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +dihedral_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This dihedral style can only be used if LAMMPS was built with the diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 34f0e6daf7..3f428e2103 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -24,7 +24,7 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization - {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms + {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l @@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l [Examples:] +For unabridged example scripts and files, see examples/USER/misc/bond_react. + molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre @@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation. +Fix bond/react creates and maintains two important dynamic groups of +atoms when using the {stabilization} keyword. The first group contains +all atoms currently involved in a reaction; this group is +automatically thermostatted by an internally-created +"nve/limit"_fix_nve_limit.html integrator. The second group contains +all atoms currently not involved in a reaction. This group should be +used by a thermostat in order to time integrate the system. The name +of this group of non-reacting atoms is created by appending '_REACT' +to the group-ID argument of the {stabilization} keyword, as shown in +the second example above. + +NOTE: When using reaction stabilization, you should generally not have +a separate thermostat which acts on the 'all' group. + The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, the fix bond/react @@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group -contains only non-reacting atoms at a given timestep, and therefore -should be used by a subsequent system-wide time integrator such as -nvt, npt, or nve, as shown in the second example above. The time -integration command should be placed after the fix bond/react command -due to the internal dynamic grouping performed by fix bond/react. +contains only atoms not involved in a reaction at a given timestep, +and therefore should be used by a subsequent system-wide time +integrator such as nvt, npt, or nve, as shown in the second example +above (full examples can be found at examples/USER/misc/bond_react). +The time integration command should be placed after the fix bond/react +command due to the internal dynamic grouping performed by fix +bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. -NOTE: If the group-ID is previously unused, the internally-created -group applies to all atoms in the system, i.e. you should generally -not have a separate thermostat which acts on the 'all' group, or any -other group. - The following comments pertain to each {react} argument (in other words, can be customized for each reaction, or reaction step): @@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction by-products, this feature can be used to remove specific topologies, such as small rings, that may be otherwise indistinguishable. -Also, it may be beneficial to ensure reacting atoms are at a certain -temperature before being released to the overall thermostat. For this, -you can use the internally-created dynamic group named -"bond_react_MASTER_group." For example, adding the following command -would thermostat the group of all atoms currently involved in a -reaction: +Optionally, you can enforce additional behaviors on reacting atoms. +For example, it may be beneficial to force reacting atoms to remain at +a certain temperature. For this, you can use the internally-created +dynamic group named "bond_react_MASTER_group", which consists of all +atoms currently involved in a reaction. For example, adding the +following command would add an additional thermostat to the group of +all currently-reacting atoms: fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre diff --git a/doc/src/package.txt b/doc/src/package.txt index 6a6d17bcbc..edd409a842 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -64,7 +64,7 @@ args = arguments specific to the style :l {no_affinity} values = none {kokkos} args = keyword value ... zero or more keyword/value pairs may be appended - keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct} + keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware} {neigh} value = {full} or {half} full = full neighbor list half = half neighbor list built in thread-safe manner @@ -87,9 +87,9 @@ args = arguments specific to the style :l no = perform communication pack/unpack in non-KOKKOS mode host = perform pack/unpack on host (e.g. with OpenMP threading) device = perform pack/unpack on device (e.g. on GPU) - {gpu/direct} = {off} or {on} - off = do not use GPU-direct - on = use GPU-direct (default) + {cuda/aware} = {off} or {on} + off = do not use CUDA-aware MPI + on = use CUDA-aware MPI (default) {omp} args = Nthreads keyword value ... Nthread = # of OpenMP threads to associate with each MPI process zero or more keyword/value pairs may be appended @@ -520,19 +520,21 @@ pack/unpack communicated data. When running small systems on a GPU, performing the exchange pack/unpack on the host CPU can give speedup since it reduces the number of CUDA kernel launches. -The {gpu/direct} keyword chooses whether GPU-direct will be used. When +The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When this keyword is set to {on}, buffers in GPU memory are passed directly through MPI send/receive calls. This reduces overhead of first copying -the data to the host CPU. However GPU-direct is not supported on all +the data to the host CPU. However CUDA-aware MPI is not supported on all systems, which can lead to segmentation faults and would require using a -value of {off}. If LAMMPS can safely detect that GPU-direct is not +value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not available (currently only possible with OpenMPI v2.0.0 or later), then -the {gpu/direct} keyword is automatically set to {off} by default. When -the {gpu/direct} keyword is set to {off} while any of the {comm} +the {cuda/aware} keyword is automatically set to {off} by default. When +the {cuda/aware} keyword is set to {off} while any of the {comm} keywords are set to {device}, the value for these {comm} keywords will be automatically changed to {host}. This setting has no effect if not -running on GPUs. GPU-direct is available for OpenMPI 1.8 (or later -versions), Mvapich2 1.9 (or later), and CrayMPI. +running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later +versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment +variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu" +flag is used. :line @@ -641,8 +643,8 @@ switch"_Run_options.html. For the KOKKOS package, the option defaults for GPUs are neigh = full, neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default -value, comm = device, gpu/direct = on. When LAMMPS can safely detect -that GPU-direct is not available, the default value of gpu/direct +value, comm = device, cuda/aware = on. When LAMMPS can safely detect +that CUDA-aware MPI is not available, the default value of cuda/aware becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The option neigh/thread = on when there are 16K atoms or less on an MPI diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index cf9b823ba3..aa29c061fb 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1544,6 +1544,7 @@ Mandelli Manh manifoldforce Manolopoulos +manpages manybody MANYBODY Maras diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized similarity index 88% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized index 73cb2eb270..b152dec00a 100644 --- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized @@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 & fix 1 statted_grp_REACT nvt temp 300 300 100 +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized new file mode 100644 index 0000000000..1e5a493821 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized @@ -0,0 +1,48 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 deleted file mode 100644 index 344439f94c..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299879 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225228 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.80615652 0.0034851739 1 1 - 3750 297.55588 -0.49626039 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37593 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779678 0.0034851739 1 1 - 4200 241.30632 -33.371788 0.0034851739 1 1 - 4250 242.17258 -9.986197 0.0034851739 1 1 - 4300 300.85311 -7.9244294 0.0034851739 1 1 - 4350 273.15684 -21.257283 0.0034851739 1 1 - 4400 305.77463 -5.8720722 0.0034851739 1 1 - 4450 314.97697 45.0373 0.0034851739 1 1 - 4500 310.77723 16.958773 0.0034851739 1 1 - 4550 302.1742 12.156862 0.0034851739 1 1 - 4600 319.74799 6.84889 0.0034851739 1 1 - 4650 270.86805 -13.767905 0.0034851739 1 1 - 4700 249.81731 -31.197487 0.0034851739 1 1 - 4750 285.86481 -9.8916364 0.0034851739 1 1 - 4800 233.98321 7.1338571 0.0034851739 1 1 - 4850 302.60551 49.262889 0.0034851739 1 1 - 4900 316.55056 34.663247 0.0034851739 1 1 - 4950 357.32741 11.583006 0.0034851739 1 1 - 5000 400.21045 -8.1781061 0.0034851739 1 1 - 5050 390.01845 -20.490275 0.0034851739 1 1 - 5100 378.84247 -41.328757 0.0034851739 1 1 - 5150 324.02038 -15.023862 0.0034851739 1 1 - 5200 262.08429 10.937354 0.0034851739 1 1 - 5250 255.75508 16.381455 0.0034851739 1 1 - 5300 277.84989 40.68232 0.0034851739 1 1 - 5350 302.92832 9.1989494 0.0034851739 1 1 - 5400 283.7196 -1.6584671 0.0034851739 1 1 - 5450 300.71266 -4.7030295 0.0034851739 1 1 - 5500 343.5499 -0.30550044 0.0034851739 1 1 - 5550 369.51271 21.691649 0.0034851739 1 1 - 5600 372.69789 -38.67994 0.0034851739 1 1 - 5650 327.41266 11.352137 0.0034851739 1 1 - 5700 278.98614 -23.827304 0.0034851739 1 1 - 5750 308.30054 -20.756187 0.0034851739 1 1 - 5800 341.45594 28.058441 0.0034851739 1 1 - 5850 322.97844 -10.731921 0.0034851739 1 1 - 5900 304.53591 32.825279 0.0034851739 1 1 - 5950 287.1752 -36.780091 0.0034851739 1 1 - 6000 296.52681 18.781896 0.0034851739 1 1 - 6050 314.25442 15.992829 0.0034851739 1 1 - 6100 313.86576 3.4342714 0.0034851739 1 1 - 6150 325.64196 32.392039 0.0034851739 1 1 - 6200 367.42931 -27.160706 0.0034851739 1 1 - 6250 369.30798 39.020934 0.0034851739 1 1 - 6300 328.92285 -23.175157 0.0034851739 1 1 - 6350 305.63077 4.9024453 0.0034851739 1 1 - 6400 241.70341 -13.676629 0.0034851739 1 1 - 6450 265.66717 2.40612 0.0034851739 1 1 - 6500 249.36037 13.420255 0.0034851739 1 1 - 6550 294.53814 10.853462 0.0034851739 1 1 - 6600 308.2025 18.995308 0.0034851739 1 1 - 6650 305.43797 -49.56785 0.0034851739 1 1 - 6700 320.27344 11.336281 0.0034851739 1 1 - 6750 321.78666 -23.463899 0.0034851739 1 1 - 6800 303.40388 7.6224553 0.0034851739 1 1 - 6850 297.18966 51.52256 0.0034851739 1 1 - 6900 284.18909 -8.4947203 0.0034851739 1 1 - 6950 331.03663 13.233655 0.0034851739 1 1 - 7000 311.37928 -43.265479 0.0034851739 1 1 - 7050 286.81661 -14.174683 0.0034851739 1 1 - 7100 302.84119 12.048954 0.0034851739 1 1 - 7150 297.19357 -43.111968 0.0034851739 1 1 - 7200 332.47359 26.048249 0.0034851739 1 1 - 7250 262.70677 41.176242 0.0034851739 1 1 - 7300 250.61405 -23.413982 0.0034851739 1 1 - 7350 296.91117 35.88133 0.0034851739 1 1 - 7400 245.09229 -13.447194 0.0034851739 1 1 - 7450 272.28131 -23.322585 0.0034851739 1 1 - 7500 209.04985 13.871239 0.0034851739 1 1 - 7550 255.00955 4.9325621 0.0034851739 1 1 - 7600 312.30937 -37.368274 0.0034851739 1 1 - 7650 305.65903 55.245496 0.0034851739 1 1 - 7700 325.09504 -18.347711 0.0034851739 1 1 - 7750 363.28282 -22.479686 0.0034851739 1 1 - 7800 350.17429 26.849547 0.0034851739 1 1 - 7850 271.70853 -17.764575 0.0034851739 1 1 - 7900 272.66484 -11.701967 0.0034851739 1 1 - 7950 298.60202 -12.765675 0.0034851739 1 1 - 8000 274.58852 49.641532 0.0034851739 1 1 - 8050 304.72347 -0.55414183 0.0034851739 1 1 - 8100 328.30757 -39.861301 0.0034851739 1 1 - 8150 406.67601 2.8999409 0.0034851739 1 1 - 8200 332.20083 -51.217399 0.0034851739 1 1 - 8250 354.50609 53.128769 0.0034851739 1 1 - 8300 337.2758 20.68562 0.0034851739 1 1 - 8350 361.89708 -54.185869 0.0034851739 1 1 - 8400 305.63496 24.058529 0.0034851739 1 1 - 8450 303.27461 4.304683 0.0034851739 1 1 - 8500 253.53694 -10.909021 0.0034851739 1 1 - 8550 277.03017 23.241479 0.0034851739 1 1 - 8600 291.41844 -22.240665 0.0034851739 1 1 - 8650 307.85368 31.919587 0.0034851739 1 1 - 8700 309.19724 0.53529642 0.0034851739 1 1 - 8750 354.6583 11.565515 0.0034851739 1 1 - 8800 329.78598 19.5996 0.0034851739 1 1 - 8850 240.79198 21.803515 0.0034851739 1 1 - 8900 318.40749 -59.816923 0.0034851739 1 1 - 8950 308.47211 -57.808635 0.0034851739 1 1 - 9000 271.51207 50.943482 0.0034851739 1 1 - 9050 249.4005 6.7529187 0.0034851739 1 1 - 9100 221.8772 47.196092 0.0034851739 1 1 - 9150 297.9351 4.0058184 0.0034851739 1 1 - 9200 274.85051 -24.774393 0.0034851739 1 1 - 9250 336.04757 5.3799028 0.0034851739 1 1 - 9300 380.44956 -22.389381 0.0034851739 1 1 - 9350 336.9824 23.050616 0.0034851739 1 1 - 9400 304.46425 32.530218 0.0034851739 1 1 - 9450 317.55591 -22.265425 0.0034851739 1 1 - 9500 323.70901 -7.0159787 0.0034851739 1 1 - 9550 316.07308 28.062131 0.0034851739 1 1 - 9600 262.74608 -0.78519192 0.0034851739 1 1 - 9650 271.55045 -21.430123 0.0034851739 1 1 - 9700 239.6022 14.483637 0.0034851739 1 1 - 9750 338.1437 -0.72765302 0.0034851739 1 1 - 9800 334.50189 19.495144 0.0034851739 1 1 - 9850 354.87554 19.272719 0.0034851739 1 1 - 9900 334.02141 -22.393457 0.0034851739 1 1 - 9950 293.63651 19.178873 0.0034851739 1 1 - 10000 319.81736 21.904414 0.0034851739 1 1 -Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms - -Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14 -Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04 -Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49 -Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62 -Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22 -Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19 -Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40 -Other | | 0.01666 | | | 0.90 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 823 ave 823 max 823 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 deleted file mode 100644 index 377781f48f..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299878 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225229 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.8061567 0.0034851739 1 1 - 3750 297.55588 -0.49626022 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37594 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779683 0.0034851739 1 1 - 4200 241.30632 -33.371789 0.0034851739 1 1 - 4250 242.17258 -9.9861962 0.0034851739 1 1 - 4300 300.85311 -7.924429 0.0034851739 1 1 - 4350 273.15684 -21.257282 0.0034851739 1 1 - 4400 305.77464 -5.8720712 0.0034851739 1 1 - 4450 314.97697 45.037299 0.0034851739 1 1 - 4500 310.77723 16.958771 0.0034851739 1 1 - 4550 302.17421 12.156862 0.0034851739 1 1 - 4600 319.74799 6.8488914 0.0034851739 1 1 - 4650 270.86805 -13.767907 0.0034851739 1 1 - 4700 249.81731 -31.197484 0.0034851739 1 1 - 4750 285.86481 -9.8916332 0.0034851739 1 1 - 4800 233.98321 7.1338518 0.0034851739 1 1 - 4850 302.60551 49.262886 0.0034851739 1 1 - 4900 316.55055 34.663238 0.0034851739 1 1 - 4950 357.32741 11.583013 0.0034851739 1 1 - 5000 400.21044 -8.1780861 0.0034851739 1 1 - 5050 390.01845 -20.490268 0.0034851739 1 1 - 5100 378.84249 -41.328772 0.0034851739 1 1 - 5150 324.02039 -15.023852 0.0034851739 1 1 - 5200 262.08427 10.937367 0.0034851739 1 1 - 5250 255.75506 16.381495 0.0034851739 1 1 - 5300 277.84991 40.682283 0.0034851739 1 1 - 5350 302.92834 9.1989644 0.0034851739 1 1 - 5400 283.71964 -1.6583895 0.0034851739 1 1 - 5450 300.71261 -4.703054 0.0034851739 1 1 - 5500 343.54987 -0.30546396 0.0034851739 1 1 - 5550 369.51272 21.691639 0.0034851739 1 1 - 5600 372.69786 -38.679919 0.0034851739 1 1 - 5650 327.41256 11.352201 0.0034851739 1 1 - 5700 278.9861 -23.82728 0.0034851739 1 1 - 5750 308.30037 -20.756238 0.0034851739 1 1 - 5800 341.4559 28.058314 0.0034851739 1 1 - 5850 322.9786 -10.731862 0.0034851739 1 1 - 5900 304.53598 32.825105 0.0034851739 1 1 - 5950 287.17515 -36.780057 0.0034851739 1 1 - 6000 296.52688 18.782156 0.0034851739 1 1 - 6050 314.25411 15.99272 0.0034851739 1 1 - 6100 313.86572 3.4344108 0.0034851739 1 1 - 6150 325.64197 32.39212 0.0034851739 1 1 - 6200 367.4298 -27.161154 0.0034851739 1 1 - 6250 369.30937 39.020881 0.0034851739 1 1 - 6300 328.92245 -23.175612 0.0034851739 1 1 - 6350 305.6293 4.9011587 0.0034851739 1 1 - 6400 241.70456 -13.675247 0.0034851739 1 1 - 6450 265.66574 2.4049735 0.0034851739 1 1 - 6500 249.3592 13.420453 0.0034851739 1 1 - 6550 294.5367 10.856753 0.0034851739 1 1 - 6600 308.20246 18.992923 0.0034851739 1 1 - 6650 305.43756 -49.57151 0.0034851739 1 1 - 6700 320.27395 11.339101 0.0034851739 1 1 - 6750 321.7875 -23.463361 0.0034851739 1 1 - 6800 303.40316 7.6256997 0.0034851739 1 1 - 6850 297.18652 51.52186 0.0034851739 1 1 - 6900 284.19084 -8.496294 0.0034851739 1 1 - 6950 331.04173 13.227745 0.0034851739 1 1 - 7000 311.38027 -43.26105 0.0034851739 1 1 - 7050 286.82046 -14.171194 0.0034851739 1 1 - 7100 302.81691 12.058085 0.0034851739 1 1 - 7150 297.18018 -43.110658 0.0034851739 1 1 - 7200 332.46131 26.051496 0.0034851739 1 1 - 7250 262.72288 41.161451 0.0034851739 1 1 - 7300 250.62739 -23.440907 0.0034851739 1 1 - 7350 296.92141 35.869216 0.0034851739 1 1 - 7400 245.06807 -13.467896 0.0034851739 1 1 - 7450 272.2659 -23.292836 0.0034851739 1 1 - 7500 209.05776 13.888665 0.0034851739 1 1 - 7550 255.03716 4.9662624 0.0034851739 1 1 - 7600 312.26011 -37.350427 0.0034851739 1 1 - 7650 305.5823 55.208039 0.0034851739 1 1 - 7700 325.13382 -18.370791 0.0034851739 1 1 - 7750 363.24898 -22.473126 0.0034851739 1 1 - 7800 350.19254 26.792307 0.0034851739 1 1 - 7850 271.76418 -17.843445 0.0034851739 1 1 - 7900 272.70301 -11.709349 0.0034851739 1 1 - 7950 298.5993 -12.736235 0.0034851739 1 1 - 8000 274.52611 49.657345 0.0034851739 1 1 - 8050 304.73711 -0.52485689 0.0034851739 1 1 - 8100 328.29239 -39.901891 0.0034851739 1 1 - 8150 406.52096 2.8669076 0.0034851739 1 1 - 8200 332.17309 -51.168754 0.0034851739 1 1 - 8250 354.68419 53.003157 0.0034851739 1 1 - 8300 337.28934 20.766408 0.0034851739 1 1 - 8350 361.81133 -54.159227 0.0034851739 1 1 - 8400 305.59597 24.011667 0.0034851739 1 1 - 8450 303.25823 4.423341 0.0034851739 1 1 - 8500 253.50747 -11.026949 0.0034851739 1 1 - 8550 277.13504 23.204625 0.0034851739 1 1 - 8600 291.40211 -22.253861 0.0034851739 1 1 - 8650 307.93765 32.14162 0.0034851739 1 1 - 8700 309.1529 0.36279434 0.0034851739 1 1 - 8750 355.10326 11.677219 0.0034851739 1 1 - 8800 330.21328 19.235269 0.0034851739 1 1 - 8850 241.29109 21.707386 0.0034851739 1 1 - 8900 319.15363 -60.010115 0.0034851739 1 1 - 8950 308.88552 -57.637014 0.0034851739 1 1 - 9000 272.22373 51.15837 0.0034851739 1 1 - 9050 248.84947 7.3390565 0.0034851739 1 1 - 9100 221.91564 48.387079 0.0034851739 1 1 - 9150 298.03506 2.9058639 0.0034851739 1 1 - 9200 274.25114 -24.597819 0.0034851739 1 1 - 9250 334.08373 5.1079577 0.0034851739 1 1 - 9300 383.07285 -23.274763 0.0034851739 1 1 - 9350 335.00581 20.94212 0.0034851739 1 1 - 9400 309.23862 34.074744 0.0034851739 1 1 - 9450 312.62262 -28.468057 0.0034851739 1 1 - 9500 324.54274 2.851136 0.0034851739 1 1 - 9550 313.32781 22.468182 0.0034851739 1 1 - 9600 269.04372 4.064934 0.0034851739 1 1 - 9650 270.98476 -21.520127 0.0034851739 1 1 - 9700 236.8736 16.250728 0.0034851739 1 1 - 9750 333.94686 1.6864148 0.0034851739 1 1 - 9800 330.91875 12.150018 0.0034851739 1 1 - 9850 343.8603 25.338853 0.0034851739 1 1 - 9900 330.93364 -28.292992 0.0034851739 1 1 - 9950 291.25518 25.795948 0.0034851739 1 1 - 10000 319.25565 25.323846 0.0034851739 1 1 -Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms - -Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s -93.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94 -Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22 -Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39 -Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51 -Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91 -Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33 -Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03 -Other | | 0.02359 | | | 0.66 - -Nlocal: 11 ave 44 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33 ave 44 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 205.75 ave 823 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 new file mode 100644 index 0000000000..de1167c652 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000181113 secs + read_data CPU = 0.0251833 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms + +Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s +87.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13 +Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01 +Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70 +Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60 +Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74 +Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80 +Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64 +Other | | 0.001306 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 740 ave 740 max 740 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 new file mode 100644 index 0000000000..b9c7a3ba15 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000178751 secs + read_data CPU = 0.0385782 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms + +Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s +98.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85 +Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84 +Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16 +Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78 +Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03 +Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93 +Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10 +Other | | 0.0008281 | | | 0.31 + +Nlocal: 11 ave 21 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 32.5 ave 43 max 23 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 185 ave 376 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 new file mode 100644 index 0000000000..14cac1dfad --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000217102 secs + read_data CPU = 0.00630778 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms + +Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s +91.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17 +Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42 +Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78 +Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61 +Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74 +Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98 +Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91 +Other | | 0.001336 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 818 ave 818 max 818 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 new file mode 100644 index 0000000000..6b13dd60d3 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000163256 secs + read_data CPU = 0.0244579 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms + +Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56 +Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62 +Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04 +Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16 +Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31 +Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13 +Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91 +Other | | 0.0007123 | | | 0.28 + +Nlocal: 11 ave 29 max 0 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 25 ave 31 max 12 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 204.5 ave 443 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/lib/poems/system.h b/lib/poems/system.h index 1b59395de7..573044ce33 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -15,7 +15,6 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - #ifndef SYSTEM_H #define SYSTEM_H @@ -31,7 +30,6 @@ #include "workspace.h" #include "matrixfun.h" #include "onsolver.h" -#include "system.h" #include "inertialframe.h" #include "rigidbody.h" #include "revolutejoint.h" diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index afec2a9b28..3cf23b87eb 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_asphere.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -20,7 +20,6 @@ #include "atom_vec_tri.h" #include "update.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 651c228e41..4350678bbd 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_asphere.h" #include #include -#include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -26,7 +26,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 828c064a52..2f8f11978e 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -15,15 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include "math_extra.h" #include "fix_nh_asphere.h" +#include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 5f201a8463..70880701ca 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 5d52891169..26d4fff81d 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 61e3c35293..93ccf008f4 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -15,16 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 9cc430592a..3a7d7e86e9 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere_noforce.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 51a502df89..5e17cb355f 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -11,9 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_line.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index fb9bf64c58..797fea1c5b 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -11,9 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 5ef91923eb..597fb03514 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_asphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 3d4ed3f183..93b164c503 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -15,11 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gayberne.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "citeme.h" #include "memory.h" #include "error.h" diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 4873b44dc4..fdeb09aac4 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_line_lj.h" +#include #include "atom.h" #include "atom_vec_line.h" #include "force.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index b100a5f184..f139564320 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -15,11 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_resquared.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index cefd73f976..0984b0a30c 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tri_lj.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 10529ad3af..353ce5550c 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "body_nparticle.h" +#include +#include +#include "my_pool_chunk.h" #include "math_extra.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index d352c789d7..caf7e4bb8c 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -15,8 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "body_rounded_polygon.h" +#include +#include +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 99a380a932..98f7913859 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -15,12 +15,14 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "body_rounded_polyhedron.h" +#include +#include +#include +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" -#include "domain.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 20f7d76708..c12502df42 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_body_local.h" +#include +#include #include "atom.h" #include "atom_vec_body.h" #include "body.h" #include "update.h" -#include "domain.h" #include "force.h" -#include "bond.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index b560bdd11d..4cf9ac5009 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -16,9 +16,9 @@ based on ComputeTempAsphere ------------------------------------------------------------------------- */ +#include "compute_temp_body.h" #include #include -#include "compute_temp_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" @@ -27,7 +27,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index 9739842419..b9a0c81e15 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -16,15 +16,10 @@ based on FixNHAsphere ------------------------------------------------------------------------- */ -#include -#include -#include -#include "math_extra.h" #include "fix_nh_body.h" +#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index e647488bce..a65c951c96 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nph_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 3c30e9e4e9..7e8097486e 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_npt_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index 0c74facf34..185e397540 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 273b5e7fff..efb05143a1 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nvt_body.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 221937461b..e51476de60 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -15,19 +15,15 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_body_polygon.h" +#include +#include #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 24a9e51dad..42c62de436 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -15,19 +15,15 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_body_polyhedron.h" +#include +#include #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index f2eb2aa520..bd7aba5455 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_body_nparticle.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 69495ea57f..f5e18e9d89 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -18,11 +18,10 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_body_rounded_polygon.h" +#include +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 60f6df3582..2df58d45cd 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -20,12 +20,10 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_body_rounded_polyhedron.h" -#include "math_extra.h" +#include +#include +#include #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" @@ -41,7 +39,6 @@ #include "math_const.h" using namespace LAMMPS_NS; -using namespace MathExtra; using namespace MathConst; #define DELTA 10000 diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index d550767e5e..99e1b39c9d 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -15,10 +15,10 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "angle_class2.h" +#include #include #include -#include -#include "angle_class2.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 8444ada057..cc155747ac 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2) #ifndef LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 26c4e63a4d..cfc1a93bde 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -15,12 +15,11 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include #include "bond_class2.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 89d930b548..f0fcc6825e 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -20,7 +20,6 @@ BondStyle(class2,BondClass2) #ifndef LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index c471b1f353..725228666e 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -15,14 +15,13 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "dihedral_class2.h" +#include #include #include -#include -#include "dihedral_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index a4ea9e4bd9..32cd289137 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2) #ifndef LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index ccb81aebd9..ca7ac95239 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -15,14 +15,13 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "improper_class2.h" +#include #include #include -#include -#include "improper_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index 1cc3417731..cac805046a 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -20,7 +20,6 @@ ImproperStyle(class2,ImproperClass2) #ifndef LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 60b988926a..a0088e52b7 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -9,11 +9,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -21,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 8dc038b8fc..e999a3682e 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index c92c7b78f1..b56c076996 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -11,17 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 095d01eef3..58593a99b1 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -15,13 +15,11 @@ Contributing authors: Jeremy Lechman (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_colloid.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index aefa96b1fb..71a5f8c056 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -15,23 +15,19 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_brownian.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 389ae084b7..c3eb4f28a5 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -16,14 +16,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_brownian_poly.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -32,14 +29,12 @@ #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 04c35a7c00..ad25184181 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -15,15 +15,12 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_colloid.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" #include "memory.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4e629bd442..4492de3cbb 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -16,18 +16,15 @@ Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lubricate.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "modify.h" #include "fix.h" @@ -35,7 +32,6 @@ #include "fix_wall.h" #include "input.h" #include "variable.h" -#include "random_mars.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 3ea3d4fe4a..4f7e3917e8 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -15,25 +15,20 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_lubricateU.h" #include #include -#include -#include #include -#include "pair_lubricateU.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "math_const.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 4fec95dcd8..0f16d94300 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -17,24 +17,19 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_lubricateU_poly.h" #include #include -#include -#include #include -#include "pair_lubricateU_poly.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index ffbe7fce3c..e347441cf4 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -17,13 +17,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lubricate_poly.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" @@ -33,8 +31,6 @@ #include "modify.h" #include "fix.h" #include "fix_deform.h" -#include "memory.h" -#include "random_mars.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index ab7d088508..1866fa60b5 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -15,16 +15,13 @@ Contributing authors: Randy Schunk (Sandia) ------------------------------------------------------------------------- */ -#include -#include #include "pair_yukawa_colloid.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 7be1a10fe2..c76b7afa17 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "dump_xyz_gz.h" -#include "domain.h" #include "error.h" #include "update.h" diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index dac0d60fce..0dc03e47f2 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -16,11 +16,9 @@ (hendrik.heenen at mytum.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "compute_temp_cs.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -28,7 +26,6 @@ #include "force.h" #include "group.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "comm.h" #include "memory.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index f4d7447ade..9440bca109 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -16,19 +16,13 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_dsf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index a19f8c34a8..b56389e180 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -15,23 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 7b52c28664..398c2ba1ee 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -12,24 +12,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_wolf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 8df91f39a3..1392ec1880 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -15,23 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index c8c8387d6d..8280799389 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -15,22 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 36e037bfc8..20b7339480 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -11,25 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -#include -#include -#include -#include #include "pair_coul_wolf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 56c75f0f5d..7ad544051a 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -15,27 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index a6f454dc98..0b6a27888f 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_dipole.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 18b78c55e0..14c511c100 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_cut_dipole_cut.h" +#include +#include +#include #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 42446a3777..fe020ed2e6 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_dipole_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index fbdc47a15b..5e7819c2f4 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -15,23 +15,19 @@ Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_lj_long_dipole_long.h" +#include #include -#include -#include #include #include "math_const.h" #include "math_vector.h" -#include "pair_lj_long_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index f0558e6a02..d4397503dc 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_gpu.h" #include #include -#include "fix_gpu.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 9f76975ef1..d4d36a5837 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_beck_gpu.h" #include #include #include #include -#include "pair_beck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 291ad8ad1f..7314024d71 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index eb204691c7..79c0d5f147 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_gpu.h" #include #include #include #include -#include "pair_born_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4877a442b5..5f74d3fc7c 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 851174988b..693c2abffb 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 253d2d7282..e9edc4f1c2 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_gpu.h" #include #include #include #include -#include "pair_born_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index ed602f9cab..182673fb0d 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut_gpu.h" #include #include #include #include -#include "pair_buck_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index d6b9e53282..75e784fafa 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_gpu.h" #include #include #include #include -#include "pair_buck_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 8c85407e6e..1559c45b88 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_gpu.h" #include #include #include #include -#include "pair_buck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index 0ee8708b5b..4db18dbc52 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_colloid_gpu.h" #include #include #include #include -#include "pair_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index fb50c446b1..8a3eb12f8d 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen ------------------------------------------------------------------------- */ +#include "pair_coul_cut_gpu.h" #include #include #include #include -#include "pair_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index ec771a9935..1fc07f8dac 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) ------------------------------------------------------------------------- */ +#include "pair_coul_debye_gpu.h" #include #include #include #include -#include "pair_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 1753b8a91c..408be036dd 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf_gpu.h" #include #include #include #include -#include "pair_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index 6ca00d6361..c70424e472 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index f75d10b6dd..9623c25f2f 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pair_coul_long_gpu.h" #include #include #include #include -#include "pair_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index b1e45fbecd..5fcad6a350 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_gpu.h" #include #include #include #include -#include "pair_dpd_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 0693a27344..2d6798a12d 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_tstat_gpu.h" #include #include #include #include -#include "pair_dpd_tstat_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 9b3412d3d1..bc55c66676 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_gpu.h" #include #include #include -#include "pair_eam_alloy_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 11ef28af3e..ac379a9ce6 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_gpu.h" #include #include #include -#include "pair_eam_fs_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 4788a72417..57106f48a4 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_gpu.h" #include #include #include #include -#include "pair_eam_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 099529f3df..e4742a3bef 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -20,7 +20,6 @@ PairStyle(eam/gpu,PairEAMGPU) #ifndef LMP_PAIR_EAM_GPU_H #define LMP_PAIR_EAM_GPU_H -#include #include "pair_eam.h" namespace LAMMPS_NS { diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index c596a9d644..842b84acf2 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_gauss_gpu.h" #include #include #include #include -#include "pair_gauss_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 4ed2750e57..f00accda15 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_gayberne_gpu.h" #include #include #include #include -#include "pair_gayberne_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 5bc30c809d..16b6b835c0 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj96_cut_gpu.h" #include #include #include #include -#include "pair_lj96_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 134295c69f..bacbb400b1 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_charmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index fdffb06a8d..e34dbb0f99 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_class2_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index bbb9168169..68f27598f3 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_gpu.h" #include #include #include #include -#include "pair_lj_class2_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 95eee6ae8f..542de37840 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_lj_cubic_gpu.h" #include #include #include #include -#include "pair_lj_cubic_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 69fefbcdea..cf3dd711dc 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index de86c58647..20354e732c 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 87eac52749..ccaf86efa6 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index c854dab83d..36c72f1143 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index f87dc0ec91..79ca90698a 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_msm_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index d2c925d950..e2c8b8d686 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 774ff2fae4..fb76376d34 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 6dde9689f7..809e5cf05e 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 31f4fd651c..a530f7ff9a 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_expand_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index a2e1cf54e3..86f8a76b52 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com ------------------------------------------------------------------------- */ +#include "pair_lj_expand_gpu.h" #include #include #include #include -#include "pair_lj_expand_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index e03f4b2e50..78f8b8b461 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_gpu.h" #include #include #include #include -#include "pair_lj_gromacs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index f5029df5dc..24ff8a4f28 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_sdk_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 4797a34408..2621f49aeb 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_gpu.h" #include #include #include #include -#include "pair_lj_sdk_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index dd25a70eee..cf26cdf3b4 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sf_dipole_sf_gpu.h" #include #include #include #include -#include "pair_lj_sf_dipole_sf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 838d28033f..f3a384113f 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_mie_cut_gpu.h" #include #include #include #include -#include "pair_mie_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 1f94643e3a..dcad227045 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_morse_gpu.h" #include #include #include #include -#include "pair_morse_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 5e90f788bf..b12a790c81 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_resquared_gpu.h" #include #include #include #include -#include "pair_resquared_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 42adb02553..0efcb20c8d 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_soft_gpu.h" #include #include #include #include -#include "pair_soft_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 0cc858e57d..8999cb6c47 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_sw_gpu.h" #include #include #include #include -#include "pair_sw_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index a0b6562e5e..4432265874 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_table_gpu.h" #include #include #include #include -#include "pair_table_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index cd0c5e6693..e0dc021b57 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_gpu.h" #include #include #include #include -#include "pair_tersoff_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index fd55ddc6e6..a17efb55e8 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_gpu.h" #include #include #include #include -#include "pair_tersoff_mod_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index d3828962e2..765d25f8e6 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl_gpu.h" #include #include #include #include -#include "pair_tersoff_zbl_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 31422b0f4d..97c2eebf24 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -17,11 +17,11 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_gpu.h" #include #include #include #include -#include "pair_ufm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index b496359b8a..3b74e5685e 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -14,12 +14,12 @@ /* ---------------------------------------------------------------------- Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ -#include + +#include "pair_vashishta_gpu.h" #include #include #include #include -#include "pair_vashishta_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 3645f392a2..51c7e683db 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_colloid_gpu.h" #include #include #include #include -#include "pair_yukawa_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index 90317fea34..5dc13c7750 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_gpu.h" #include #include #include #include -#include "pair_yukawa_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index 99471cbe90..5e24281145 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -15,12 +15,12 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_zbl_gpu.h" #include "lmptype.h" #include #include #include #include -#include "pair_zbl_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 1bb1a39703..bbb270ff8e 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -15,12 +15,12 @@ Contributing authors: Mike Brown (ORNL), Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pppm_gpu.h" #include #include #include #include #include -#include "pppm_gpu.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 73c1c9fc11..1df5c9d0a8 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_freeze.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" -#include "comm.h" #include "respa.h" #include "error.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 3ffca8db9d..3b1bbcef35 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_pour.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 8513fc702b..e7464a78a9 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -16,15 +16,13 @@ Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_gran.h" +#include +#include #include "atom.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" #include "modify.h" #include "respa.h" #include "math_const.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 72798bf7b7..95553b83b7 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -15,19 +15,12 @@ Contributing authors: Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_gran_region.h" +#include #include "region.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "comm.h" @@ -35,7 +28,6 @@ using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; // same as FixWallGran diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 728491c17a..4a362c0928 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -15,11 +15,9 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gran_hertz_history.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index cfcc2743ba..d4be320554 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -15,10 +15,8 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_gran_hooke.h" +#include #include "atom.h" #include "force.h" #include "fix.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 5a78b9d79a..771a5566df 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -15,14 +15,11 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gran_hooke_history.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 77b1981786..b87e64a456 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -16,14 +16,11 @@ See the README file in the top-level LAMMPS directory. Leo Silbert (SNL), Gary Grest (SNL) ----------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_granular.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index e35afa9a8b..cddc81c333 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -157,8 +157,7 @@ void KimQuery::command(int narg, char **arg) input->variable->set(3,varcmd); echo_var_assign(splitname.str(), varcmd[2]); } - } - else { + } else { varcmd[0] = varname; varcmd[1] = (char *) "string"; varcmd[2] = value; diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 74b92a3e2b..d935d994bd 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -54,17 +54,12 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ #include "pair_kim.h" - #include #include #include - -// includes from LAMMPS #include "atom.h" #include "comm.h" -#include "universe.h" #include "force.h" -#include "input.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -72,7 +67,6 @@ #include "memory.h" #include "domain.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 0f46c958d6..fd9757aab3 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_charmm_kokkos.h" #include #include -#include "angle_charmm_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 836714764d..809ce7e7dd 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "angle_class2_kokkos.h" #include #include -#include "angle_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 4a4866948f..da0ff398f1 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_cosine_kokkos.h" #include #include -#include "angle_cosine_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index dbe705800c..fc274bb894 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_harmonic_kokkos.h" #include #include -#include "angle_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index 813c5ddbf2..4637a9a21c 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_kokkos.h" +#include #include "atom_vec.h" #include "atom_vec_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 06358289b6..736e1c1fca 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 6e530bdbe9..4fec5740d6 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 3195ea0876..74c05a506c 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 77d0c1dae3..3f26b1e9ea 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 317914e4f8..144ef26f19 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 19443b231f..1fdbcbec8c 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index c4dd90ce05..40303051b2 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_hybrid_kokkos.h" +#include #include "atom_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 1bbbd26319..4cfb186b17 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -20,7 +20,6 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos) #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H #define LMP_ATOM_VEC_HYBRID_KOKKOS_H -#include #include "atom_vec_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 9871b1247a..f3b4ae98ca 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 3b64ceeb42..7e217df2a6 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_sphere_kokkos.h" +#include +#include #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 798fb41c92..04281bfdd2 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "bond_class2_kokkos.h" #include #include -#include "bond_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index b5cdc1a05a..361bb61f7e 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_fene_kokkos.h" #include #include -#include "bond_fene_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 51a9fa4389..792d98fe88 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_harmonic_kokkos.h" #include #include -#include "bond_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 87986a9ca9..d0bd978ae7 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -418,7 +418,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) if (sendproc[iswap] != me) { double* buf_send_pair; double* buf_recv_pair; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf_send_pair = k_buf_send_pair.view().data(); buf_recv_pair = k_buf_recv_pair.view().data(); } else { @@ -436,7 +436,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) MPI_Send(buf_send_pair,n,MPI_DOUBLE,sendproc[iswap],0,world); if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf_recv_pair.modify(); k_buf_recv_pair.sync(); } diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 81cf1f0563..fc6de0a0d7 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "comm_tiled_kokkos.h" +#include #include "comm_brick.h" #include "atom_kokkos.h" #include "atom_vec.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 7b76f54f57..a2fcf63125 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_kokkos.h" #include #include -#include "compute_temp_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "force.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 61ddcc425a..94fd0b9bb7 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm_kokkos.h" #include #include -#include "dihedral_charmm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 98436bc696..4b8d171f61 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "dihedral_class2_kokkos.h" #include #include -#include "dihedral_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index f50dea2c36..825d106e04 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_opls_kokkos.h" #include #include -#include "dihedral_opls_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 7b9336ed3b..05eb1c22f6 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_deform_kokkos.h" #include #include #include -#include "fix_deform_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "comm.h" diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index d092cb4802..20579a6dc5 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -11,15 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_dpd_energy_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" -#include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index 346e440f55..bf2a882539 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -15,11 +15,11 @@ Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University) ------------------------------------------------------------------------- */ +#include "fix_enforce2d_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "error.h" -#include "fix_enforce2d_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 2f730d1193..89561c9a92 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -15,8 +15,6 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include #include "fix_eos_table_rx_kokkos.h" #include "atom_kokkos.h" #include "error.h" @@ -24,7 +22,6 @@ #include "memory_kokkos.h" #include "comm.h" #include -#include "modify.h" #include "atom_masks.h" #define MAXLINE 1024 diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 0947fee693..651f790a25 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -11,23 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_langevin_kokkos.h" +#include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" +#include "group.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory_kokkos.h" -#include "group.h" -#include "random_mars.h" #include "compute.h" #include "comm.h" #include "modify.h" #include "input.h" +#include "region.h" #include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 38500531ca..2d4911bfda 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_momentum_kokkos.h" #include #include -#include "fix_momentum_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "domain.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index fae9ef8f30..578f2f5c70 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh_kokkos.h" #include #include #include -#include "fix_nh_kokkos.h" #include "math_extra.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index c5072e6ae9..3830860fd7 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index c488c8e4f3..5b751c9e4d 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 6db8ff8c0f..f94b68dbce 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_kokkos.h" #include #include -#include "fix_nve_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" @@ -98,7 +98,7 @@ KOKKOS_INLINE_FUNCTION void FixNVEKokkos::initial_integrate_rmass_item(int i) const { if (mask[i] & groupbit) { - const double dtfm = dtf / rmass[type[i]]; + const double dtfm = dtf / rmass[i]; v(i,0) += dtfm * f(i,0); v(i,1) += dtfm * f(i,1); v(i,2) += dtfm * f(i,2); @@ -154,7 +154,7 @@ KOKKOS_INLINE_FUNCTION void FixNVEKokkos::final_integrate_rmass_item(int i) const { if (mask[i] & groupbit) { - const double dtfm = dtf / rmass[type[i]]; + const double dtfm = dtf / rmass[i]; v(i,0) += dtfm * f(i,0); v(i,1) += dtfm * f(i,1); v(i,2) += dtfm * f(i,2); diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 4db42a62fb..66165dd7bc 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_kokkos.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index 6860676911..ff374b885f 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom_kokkos.h" #include #include -#include "fix_property_atom_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 12369261b3..e51fbacaaf 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -16,26 +16,19 @@ Kamesh Arumugam (NVIDIA) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax_kokkos.h" +#include #include "kokkos.h" #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" -#include "group.h" -#include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "update.h" #include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "pair_reaxc_kokkos.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 9aed0b9ae4..51702bc603 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,26 +15,13 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" -#include "update.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" #include "compute.h" -#include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" -#include "reaxc_types.h" #include "reaxc_defs.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index bd92251960..f3bce2f9c0 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -15,27 +15,18 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include "atom.h" -#include -#include "fix_ave_atom.h" #include "fix_reaxc_species_kokkos.h" -#include "domain.h" -#include "update.h" +#include "atom.h" +#include "fix_ave_atom.h" +#include "reaxc_defs.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" #include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" #include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 80333e1e9b..e06fc14585 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_rx_kokkos.h" +#include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "memory_kokkos.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 634bc05ac3..6f14a71382 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -11,22 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce_kokkos.h" +#include #include "atom_kokkos.h" #include "update.h" #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "force.h" #include "atom_masks.h" #include "kokkos_base.h" +#include "region.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h index 3cbf3d3720..ecbfd71e36 100644 --- a/src/KOKKOS/fix_setforce_kokkos.h +++ b/src/KOKKOS/fix_setforce_kokkos.h @@ -23,7 +23,6 @@ FixStyle(setforce/kk/host,FixSetForceKokkos) #define LMP_FIX_SET_FORCE_KOKKOS_H #include "fix_setforce.h" -#include "region.h" #include "kokkos_type.h" namespace LAMMPS_NS { @@ -82,7 +81,7 @@ class FixSetForceKokkos : public FixSetForce { typename AT::t_f_array f; typename AT::t_int_1d_randomread mask; - Region* region; + class Region* region; }; } diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 968f877abd..9bd8594341 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -33,31 +33,23 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_shardlow_kokkos.h" +#include +#include #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" #include "domain.h" -#include "modify.h" -// #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy_kokkos.h" -#include "pair.h" #include "npair_ssa_kokkos.h" -#include "citeme.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 5dbb054175..61346144c8 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93_kokkos.h" +#include #include "atom_kokkos.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 75a5c1a81e..ba104d19a9 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_reflect_kokkos.h" #include #include -#include "fix_wall_reflect_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "update.h" diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 14b84a5733..ac33b15d73 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm_kokkos.h" +#include #include "comm.h" #include "kspace.h" #include "memory_kokkos.h" @@ -529,7 +529,7 @@ void GridCommKokkos::forward_comm(KSpace *kspace, int which) if (swap[m].sendproc != me) { FFT_SCALAR* buf1; FFT_SCALAR* buf2; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); } else { @@ -545,7 +545,7 @@ void GridCommKokkos::forward_comm(KSpace *kspace, int which) swap[m].sendproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf2.modify(); k_buf2.sync(); } @@ -579,7 +579,7 @@ void GridCommKokkos::reverse_comm(KSpace *kspace, int which) if (swap[m].recvproc != me) { FFT_SCALAR* buf1; FFT_SCALAR* buf2; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); } else { @@ -595,7 +595,7 @@ void GridCommKokkos::reverse_comm(KSpace *kspace, int which) swap[m].recvproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf2.modify(); k_buf2.sync(); } diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index ad32e6da4e..defd5e16f5 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -15,23 +15,16 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_class2_kokkos.h" +#include #include "atom_kokkos.h" -#include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index bb397a2c2f..7d6437dbf5 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -15,23 +15,17 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_harmonic_kokkos.h" +#include #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 3fa84d98b2..a353c3dd18 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kokkos.h" #include #include #include @@ -18,7 +19,6 @@ #include #include #include -#include "kokkos.h" #include "lammps.h" #include "force.h" #include "neighbor_kokkos.h" @@ -28,32 +28,36 @@ #ifdef KOKKOS_ENABLE_CUDA -// for detecting GPU-direct support: -// the function int have_gpu_direct() -// - returns -1 if GPU-direct support is unknown -// - returns 0 if no GPU-direct support available -// - returns 1 if GPU-direct support is available +// for detecting CUDA-aware MPI support: +// the variable int have_cuda_aware +// - is 1 if CUDA-aware MPI support is available +// - is 0 if CUDA-aware MPI support is unavailable +// - is -1 if CUDA-aware MPI support is unknown -#define GPU_DIRECT_UNKNOWN static int have_gpu_direct() {return -1;} +#define CUDA_AWARE_UNKNOWN static int have_cuda_aware = -1; -// OpenMPI supports detecting GPU-direct as of version 2.0.0 -#if OPEN_MPI +// OpenMPI supports detecting CUDA-aware MPI as of version 2.0.0 +#if (OPEN_MPI) #if (OMPI_MAJOR_VERSION >= 2) + #include -#if defined(MPIX_CUDA_AWARE_SUPPORT) -static int have_gpu_direct() { return MPIX_Query_cuda_support(); } + +#if defined(MPIX_CUDA_AWARE_SUPPORT) && MPIX_CUDA_AWARE_SUPPORT +static int have_cuda_aware = 1; +#elif defined(MPIX_CUDA_AWARE_SUPPORT) && !MPIX_CUDA_AWARE_SUPPORT +static int have_cuda_aware = 0; #else -GPU_DIRECT_UNKNOWN -#endif +CUDA_AWARE_UNKNOWN +#endif // defined(MPIX_CUDA_AWARE_SUPPORT) #else // old OpenMPI -GPU_DIRECT_UNKNOWN -#endif +CUDA_AWARE_UNKNOWN +#endif // (OMPI_MAJOR_VERSION >=2) #else // unknown MPI library -GPU_DIRECT_UNKNOWN -#endif +CUDA_AWARE_UNKNOWN +#endif // OPEN_MPI #endif // KOKKOS_ENABLE_CUDA @@ -66,6 +70,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) kokkos_exists = 1; lmp->kokkos = this; + exchange_comm_changed = 0; + forward_comm_changed = 0; + reverse_comm_changed = 0; + delete memory; memory = new MemoryKokkos(lmp); memoryKK = (MemoryKokkos*) memory; @@ -145,29 +153,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) #ifdef KOKKOS_ENABLE_CUDA if (ngpus <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested"); - - // check and warn about GPU-direct availability when using multiple MPI tasks - - int nmpi = 0; - MPI_Comm_size(world,&nmpi); - if ((nmpi > 1) && (me == 0)) { - if ( 1 == have_gpu_direct() ) { - ; // all good, nothing to warn about - } else if (-1 == have_gpu_direct() ) { - error->warning(FLERR,"Kokkos with CUDA assumes GPU-direct is available," - " but cannot determine if this is the case\n try" - " '-pk kokkos gpu/direct off' when getting segmentation faults"); - } else if ( 0 == have_gpu_direct() ) { - error->warning(FLERR,"GPU-direct is NOT available, " - "using '-pk kokkos gpu/direct off' by default"); - } else { - ; // should never get here - } - } #endif #ifndef KOKKOS_ENABLE_SERIAL - if (nthreads == 1) + if (nthreads == 1 && me == 0) error->warning(FLERR,"When using a single thread, the Kokkos Serial backend " "(i.e. Makefile.kokkos_mpi_only) gives better performance " "than the OpenMP backend"); @@ -183,7 +172,11 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // default settings for package kokkos command binsize = 0.0; - gpu_direct_flag = 1; +#ifdef KOKKOS_ENABLE_CUDA + cuda_aware_flag = 1; +#else + cuda_aware_flag = 0; +#endif neigh_thread = 0; neigh_thread_set = 0; neighflag_qeq_set = 0; @@ -206,10 +199,66 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } -#if KOKKOS_USE_CUDA - // only if we can safely detect, that GPU-direct is not available, change default - if (0 == have_gpu_direct()) gpu_direct_flag = 0; +#ifdef KOKKOS_ENABLE_CUDA + + // check and warn about CUDA-aware MPI availability when using multiple MPI tasks + // change default only if we can safely detect that CUDA-aware MPI is not available + + int nmpi = 0; + MPI_Comm_size(world,&nmpi); + if (nmpi > 0) { + + // Check for IBM Spectrum MPI + + int len; + char mpi_version[MPI_MAX_LIBRARY_VERSION_STRING]; + MPI_Get_library_version(mpi_version, &len); + if (strstr(&mpi_version[0], "Spectrum") != NULL) { + cuda_aware_flag = 0; + char* str; + if (str = getenv("OMPI_MCA_pml_pami_enable_cuda")) + if((strcmp(str,"1") == 0)) { + have_cuda_aware = 1; + cuda_aware_flag = 1; + } + + if (!cuda_aware_flag) + if (me == 0) + error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI"); + } + + if (cuda_aware_flag == 1 && have_cuda_aware == 0) { + if (me == 0) + error->warning(FLERR,"Turning off CUDA-aware MPI since it is not detected, " + "use '-pk kokkos cuda/aware on' to override"); + cuda_aware_flag = 0; + } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative? + // MVAPICH2 +#if (defined MPICH) && (defined MVAPICH2_VERSION) + char* str; + cuda_aware_flag = 0; + if (str = getenv("MV2_ENABLE_CUDA") + if ((strcmp(str,"1") == 0)) + cuda_aware_flag = 1; + + if (!cuda_aware_flag) + if (me == 0) + error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI"); + // pure MPICH or some unsupported MPICH derivative +#elif (defined MPICH) && !(defined MVAPICH2_VERSION) + if (me == 0) + error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI"); + cuda_aware_flag = 0; +#else + if (me == 0) + error->warning(FLERR,"Kokkos with CUDA assumes CUDA-aware MPI is available," + " but cannot determine if this is the case\n try" + " '-pk kokkos cuda/aware off' if getting segmentation faults"); + #endif + } // if (-1 == have_cuda_aware) + } // nmpi > 0 +#endif // KOKKOS_ENABLE_CUDA #ifdef KILL_KOKKOS_ON_SIGSEGV signal(SIGSEGV, my_signal_handler); @@ -290,6 +339,7 @@ void KokkosLMP::accelerator(int narg, char **arg) exchange_comm_classic = 0; exchange_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + exchange_comm_changed = 0; iarg += 2; } else if (strcmp(arg[iarg],"comm/forward") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -301,6 +351,7 @@ void KokkosLMP::accelerator(int narg, char **arg) forward_comm_classic = 0; forward_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + forward_comm_changed = 0; iarg += 2; } else if (strcmp(arg[iarg],"comm/reverse") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -312,11 +363,12 @@ void KokkosLMP::accelerator(int narg, char **arg) reverse_comm_classic = 0; reverse_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + reverse_comm_changed = 0; iarg += 2; - } else if (strcmp(arg[iarg],"gpu/direct") == 0) { + } else if (strcmp(arg[iarg],"cuda/aware") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); - if (strcmp(arg[iarg+1],"off") == 0) gpu_direct_flag = 0; - else if (strcmp(arg[iarg+1],"on") == 0) gpu_direct_flag = 1; + if (strcmp(arg[iarg+1],"off") == 0) cuda_aware_flag = 0; + else if (strcmp(arg[iarg+1],"on") == 0) cuda_aware_flag = 1; else error->all(FLERR,"Illegal package kokkos command"); iarg += 2; } else if (strcmp(arg[iarg],"neigh/thread") == 0) { @@ -329,15 +381,38 @@ void KokkosLMP::accelerator(int narg, char **arg) } else error->all(FLERR,"Illegal package kokkos command"); } - // if "gpu/direct off" and "comm device", change to "comm host" + // if "cuda/aware off" and "comm device", change to "comm host" - if (!gpu_direct_flag) { - if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) - exchange_comm_on_host = 1; - if (forward_comm_classic == 0 && forward_comm_on_host == 0) - forward_comm_on_host = 1; - if (reverse_comm_classic == 0 && reverse_comm_on_host == 0) - reverse_comm_on_host = 1; + if (!cuda_aware_flag) { + if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) { + exchange_comm_on_host = 1; + exchange_comm_changed = 1; + } + if (forward_comm_classic == 0 && forward_comm_on_host == 0) { + forward_comm_on_host = 1; + forward_comm_changed = 1; + } + if (reverse_comm_classic == 0 && reverse_comm_on_host == 0) { + reverse_comm_on_host = 1; + reverse_comm_changed = 1; + } + } + + // if "cuda/aware on" and comm flags were changed previously, change them back + + if (cuda_aware_flag) { + if (exchange_comm_changed) { + exchange_comm_on_host = 0; + exchange_comm_changed = 0; + } + if (forward_comm_changed) { + forward_comm_on_host = 0; + forward_comm_changed = 0; + } + if (reverse_comm_changed) { + reverse_comm_on_host = 0; + reverse_comm_changed = 0; + } } // set newton flags diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 46044799c4..b9f1e66c68 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -32,10 +32,13 @@ class KokkosLMP : protected Pointers { int exchange_comm_on_host; int forward_comm_on_host; int reverse_comm_on_host; + int exchange_comm_changed; + int forward_comm_changed; + int reverse_comm_changed; int nthreads,ngpus; int numa; int auto_sync; - int gpu_direct_flag; + int cuda_aware_flag; int neigh_thread; int neigh_thread_set; int newtonflag; diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 942c2af241..e900bbd6d1 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -14,7 +14,7 @@ #ifndef LMP_LMPTYPE_KOKKOS_H #define LMP_LMPTYPE_KOKKOS_H -#include "lmptype.h" +#include "pointers.h" #include #include diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index 127168ef8b..f5fc725347 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -1,7 +1,7 @@ +#include "math_special_kokkos.h" #include #include -#include "math_special_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp index ecf0e08535..0e46f7fc61 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.cpp +++ b/src/KOKKOS/nbin_ssa_kokkos.cpp @@ -19,11 +19,8 @@ #include "nbin_ssa_kokkos.h" #include "neighbor.h" #include "atom_kokkos.h" -#include "group.h" #include "domain.h" -#include "comm.h" #include "update.h" -#include "error.h" #include "atom_masks.h" // #include "memory_kokkos.h" diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp index 7dde05745c..0ce0f4d3ff 100644 --- a/src/KOKKOS/npair_copy_kokkos.cpp +++ b/src/KOKKOS/npair_copy_kokkos.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index e614e624c9..bb393c9b95 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,13 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" #include "atom_kokkos.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 57ac3a9c57..2a72617525 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -15,20 +15,16 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_cut_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 349c4c0601..fdf395684a 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_long_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 02c02c986e..375d0dc1ea 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index 54ba0b63ce..5a1a6eefac 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -11,28 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_cut_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 8966e30394..8dd7e4f3d2 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_debye_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index 748fed71a7..836b12ba39 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -15,22 +15,15 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_dsf_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index a21cb050ff..84b89c6373 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_long_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 20391d9530..3ca8f16a79 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -15,21 +15,14 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_wolf_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index a44ef1790e..21fd32a2c8 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -15,22 +15,16 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy_kokkos.h" #include -#include -#include -#include #include "atom_kokkos.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" -#include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "modify.h" -#include "pair_dpd_fdt_energy_kokkos.h" #include "error.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index b5442c0d29..48bf63386a 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -15,13 +15,11 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_alloy_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 6593ccae73..e1dd9ab47d 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos) #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H #define LMP_PAIR_EAM_ALLOY_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 16701febd6..6536dd745a 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -15,13 +15,11 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_fs_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index f75605ff6d..e93977869e 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos) #ifndef LMP_PAIR_EAM_FS_KOKKOS_H #define LMP_PAIR_EAM_FS_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index d423f2c927..f6eef5b53c 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -15,13 +15,10 @@ Contributing authors: Stan Moore (SNL), Christian Trott (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 4040eba858..3bf89c549a 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/kk/host,PairEAMKokkos) #ifndef LMP_PAIR_EAM_KOKKOS_H #define LMP_PAIR_EAM_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 3a857a6485..8698687377 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -15,20 +15,17 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_exp6_rx_kokkos.h" #include -#include #include #include -#include "pair_exp6_rx_kokkos.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special_kokkos.h" #include "memory_kokkos.h" #include "error.h" -#include "modify.h" #include "fix.h" #include #include "atom_masks.h" @@ -41,7 +38,6 @@ #endif using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecialKokkos; #define MAXLINE 1024 diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 00df4a8f3c..b5b0a9d02b 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -11,20 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_hybrid_kokkos.h" +#include #include "atom_kokkos.h" #include "force.h" #include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "update.h" -#include "comm.h" #include "memory_kokkos.h" -#include "error.h" #include "respa.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 94e034f875..799354cf01 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -20,7 +20,6 @@ PairStyle(hybrid/kk,PairHybridKokkos) #ifndef LMP_PAIR_HYBRID_KOKKOS_H #define LMP_PAIR_HYBRID_KOKKOS_H -#include #include "pair_hybrid.h" #include "pair_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index a2c3edab65..0cebd79c88 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "pair_hybrid_overlay_kokkos.h" #include #include -#include "pair_hybrid_overlay_kokkos.h" #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index 510740112a..ae6cb61b60 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -15,28 +15,21 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 51c96354f9..9cdef267e2 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_charmm_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 22faa98935..441070248d 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_long_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 60d480188b..1f7642e965 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_cut_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -24,15 +22,12 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 4c8aea8e92..c88ff9378e 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -11,28 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_long_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index dd42baa4e0..9900e7361f 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index cb5ab96871..1601e4a4b2 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -11,28 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_cut_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 800092a09b..6e7d1eeb8b 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_debye_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index f793485b47..b7dc7cc26d 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -15,20 +15,16 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_dsf_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 02150586f4..122d59af82 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -11,20 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_long_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 4ba8c00f88..df750b7524 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -11,28 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 5ea6c9e438..38bebc364f 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_expand_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 2421d059da..a46a5c0441 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs_coul_gromacs_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 09a0261ae1..23ed5e5595 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index c2375fa7a8..25f081d255 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -11,22 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_kokkos.h" #include #include -#include #include -#include "pair_lj_sdk_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -34,7 +30,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define KOKKOS_CUDA_MAX_THREADS 256 diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index b308330ead..d3e3042a34 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -15,20 +15,16 @@ Contributing authors: Stefan Paquay (Eindhoven University of Technology) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_morse_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 7d17ac3f43..75247859ed 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -21,21 +21,16 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include -#include -#include "math_const.h" -#include -#include #include "pair_multi_lucy_rx_kokkos.h" +#include +#include +#include "math_const.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory_kokkos.h" #include "error.h" -#include "citeme.h" -#include "modify.h" -#include "fix.h" #include "atom_masks.h" #include "neigh_request.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 64651be270..d0ad1f1b09 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -15,11 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_reaxc_kokkos.h" #include -#include #include #include -#include "pair_reaxc_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +26,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "math_special.h" #include "memory_kokkos.h" @@ -38,7 +34,6 @@ #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" -#include "modify.h" #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 89dfc4d884..783ea33c4e 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -23,7 +23,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #ifndef LMP_PAIR_REAXC_KOKKOS_H #define LMP_PAIR_REAXC_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index da4737a2c1..e85afa362f 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_sw_kokkos.h" +#include #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" @@ -30,7 +27,6 @@ #include "memory_kokkos.h" #include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 737d600d1e..5ee24ad479 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -15,15 +15,11 @@ Contributing author: Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_table_kokkos.h" +#include #include "kokkos.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index ec7a2ffb94..daebeda8db 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -15,11 +15,10 @@ Contributing author: Dan Ibanez (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx_kokkos.h" #include #include -#include #include -#include "pair_table_rx_kokkos.h" #include "kokkos.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 9252e3de52..b360b20ef3 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Ray Shan (SNL) and Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index f73d4fe2d8..7d41fe2346 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos) #ifndef LMP_PAIR_TERSOFF_KOKKOS_H #define LMP_PAIR_TERSOFF_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 585074b128..81ef486999 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_mod_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index d7c94ffc93..889e1eadfa 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos) #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_mod.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index e1e2211ab5..4593f32e36 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -15,11 +15,9 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_zbl_kokkos.h" +#include +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -28,8 +26,6 @@ #include "neigh_request.h" #include "neigh_list_kokkos.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 3af4e0d8eb..0c7fa2e963 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos) #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_zbl.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 4a1f291b17..614d3334d5 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -15,11 +15,9 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_vashishta_kokkos.h" +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" @@ -28,9 +26,7 @@ #include "force.h" #include "comm.h" #include "memory_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 27e18533a2..6dfffd4a54 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -14,26 +14,22 @@ /* ---------------------------------------------------------------------- Contributing authors: Stefan Paquay (Brandeis University) ------------------------------------------------------------------------- */ -#include -#include + #include "pair_yukawa_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 06c84e5189..5697dd5b00 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -15,21 +15,16 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_zbl_kokkos.h" +#include +#include #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -39,7 +34,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index c9c0d6d1d4..b5539ef6e4 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -15,20 +15,15 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "pppm_kokkos.h" +#include +#include #include "atom_kokkos.h" #include "comm.h" #include "gridcomm_kokkos.h" #include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp index 51ebcb154e..2d8865feb0 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp +++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "comm.h" #include "rand_pool_wrap_kokkos.h" +#include "comm.h" #include "lammps.h" #include "kokkos.h" #include "random_mars.h" diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index 730ef81466..b28230290e 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -11,11 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_block_kokkos.h" -#include "domain.h" -#include "force.h" #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index b80d5e0646..2d2f0a9815 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet_kokkos.h" #include "neighbor.h" #include "domain.h" #include "comm.h" -#include "atom.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "force.h" @@ -29,15 +27,10 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" #include "memory_kokkos.h" -#include "error.h" #include "kokkos.h" -#include - using namespace LAMMPS_NS; template diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index ccbb3ed708..d74d90b0d6 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -18,12 +18,9 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "ewald.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 89ef7e39a8..c3442beef5 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -15,12 +15,10 @@ Contributing authors: Julien Tranchida (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole.h" #include -#include -#include #include #include -#include "ewald_dipole.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -32,9 +30,6 @@ #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index 698203c85c..e7d67680a1 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -15,29 +15,22 @@ Contributing authors: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole_spin.h" #include -#include -#include #include #include -#include "ewald_dipole_spin.h" #include "atom.h" #include "comm.h" #include "force.h" #include "pair.h" #include "domain.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.00001 diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 0603d68eb2..a7ac66fdd3 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -15,12 +15,10 @@ Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_disp.h" #include #include -#include -#include #include -#include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" #include "math_special.h" diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 7d3c8c83f2..e4c38a57f5 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -19,11 +19,11 @@ Paul Coffman (IBM) added MPI collectives remap ------------------------------------------------------------------------- */ +#include "fft3d.h" #include #include #include #include -#include "fft3d.h" #include "remap.h" #ifdef FFT_KISS diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index a51818d986..8c3d2f27ad 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include + // User-settable FFT precision // FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag) diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index b9a6f0ae46..507b23d27d 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fft3d_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 0c726985dc..cfd88609b3 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,13 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_tune_kspace.h" +#include +#include +#include #include "update.h" -#include "domain.h" -#include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" #include "pair.h" @@ -31,9 +29,6 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" -#include -#include -#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) #define GOLD 1.618034 @@ -101,7 +96,7 @@ void FixTuneKspace::init() double old_acc = force->kspace->accuracy/force->kspace->two_charge_force; char old_acc_str[16]; snprintf(old_acc_str,16,"%g",old_acc); - strcpy(new_acc_str,old_acc_str); + strncpy(new_acc_str,old_acc_str,16); int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); @@ -131,36 +126,37 @@ void FixTuneKspace::pre_exchange() // test Ewald store_old_kspace_settings(); strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 2) { // test PPPM store_old_kspace_settings(); strcpy(new_kspace_style,"pppm"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 3) { // test MSM store_old_kspace_settings(); strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 4) { store_old_kspace_settings(); - cout << "ewald_time = " << ewald_time << endl; - cout << "pppm_time = " << pppm_time << endl; - cout << "msm_time = " << msm_time << endl; + if (screen) fprintf(screen,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); + if (logfile) fprintf(logfile,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); // switch to fastest one strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); if (pppm_time < ewald_time && pppm_time < msm_time) strcpy(new_kspace_style,"pppm"); else if (msm_time < pppm_time && msm_time < ewald_time) { strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); } update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); @@ -243,8 +239,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, p_pair_settings_file = tmpfile(); force->pair->write_restart(p_pair_settings_file); rewind(p_pair_settings_file); - - cout << "Creating new pair style: " << new_pair_style << endl; + if (screen) fprintf(screen,"Creating new pair style: %s\n",new_pair_style); + if (logfile) fprintf(logfile,"Creating new pair style: %s\n",new_pair_style); // delete old pair style and create new one force->create_pair(new_pair_style,1); @@ -253,7 +249,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, double *pcutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *pcutoff; - cout << "Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Coulomb cutoff for real space: %g\n", current_cutoff); // close temporary file fclose(p_pair_settings_file); @@ -321,7 +318,8 @@ void FixTuneKspace::adjust_rcut(double time) int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *p_cutoff; - cout << "Old Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Old Coulomb cutoff for real space: %g\n",current_cutoff); + if (logfile) fprintf(logfile,"Old Coulomb cutoff for real space: %g\n",current_cutoff); // use Brent's method from Numerical Recipes to find optimal real space cutoff @@ -391,7 +389,8 @@ void FixTuneKspace::adjust_rcut(double time) // report the new cutoff double *new_cutoff = (double *) force->pair->extract("cut_coul",itmp); current_cutoff = *new_cutoff; - cout << "Adjusted Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); store_old_kspace_settings(); update_pair_style(new_pair_style,pair_cut_coul); diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 6f40fc8711..1ccd735317 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -20,7 +20,6 @@ FixStyle(tune/kspace,FixTuneKspace) #ifndef LMP_FIX_TUNE_KSPACE_H #define LMP_FIX_TUNE_KSPACE_H -#include #include "fix.h" namespace LAMMPS_NS { @@ -52,10 +51,10 @@ class FixTuneKspace : public Fix { double ewald_time,pppm_time,msm_time; double pair_cut_coul; - char new_acc_str[12]; - char new_kspace_style[20]; - char new_pair_style[20]; - char base_pair_style[20]; + char new_acc_str[16]; + char new_kspace_style[64]; + char new_pair_style[64]; + char base_pair_style[64]; int old_differentiation_flag; int old_slabflag; diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index ba08c9be26..368e7370fe 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm.h" -#include "comm.h" +#include #include "kspace.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index d7cc3f6876..81dbabdbbd 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -15,12 +15,10 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm.h" #include #include -#include -#include #include -#include "msm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index 0f81eb9c3f..bf393473e7 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -20,9 +20,6 @@ KSpaceStyle(msm,MSM) #ifndef LMP_MSM_H #define LMP_MSM_H -#include "lmptype.h" -#include - #include "kspace.h" namespace LAMMPS_NS { diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index c7896db50c..9119d51878 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -15,10 +15,9 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg.h" #include #include -#include -#include #include #include "atom.h" #include "gridcomm.h" @@ -27,12 +26,8 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg.h" - -#include "math_const.h" using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index f12f5779d9..e248a24ef7 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -15,11 +15,9 @@ Contributing author: Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_long.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index eaa1c116c1..7300cd92e0 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -15,23 +15,17 @@ Contributing author: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 0a1ec88da5..c97856fa3c 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index 257d1b661f..1355a2f13a 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -11,23 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index c7a4a4b2f6..8127cbc127 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,12 +15,11 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_long_coul_long.h" +#include #include -#include -#include #include #include "math_vector.h" -#include "pair_buck_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" @@ -29,7 +28,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index ae268b9857..7cedf3d003 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -15,20 +15,16 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 960505142c..5d42e1f046 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -15,21 +15,13 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index b40eab244b..751ee77388 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -15,17 +15,14 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_long.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 72a8e340bc..a93a1275f4 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -15,21 +15,13 @@ Contributing authors: Paul Crozier (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index cdde211157..494a349768 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -19,18 +19,14 @@ additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmmfsw_coul_long.h" +#include +#include #include "atom.h" -#include "update.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index fde7fa8e35..fb79451b37 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -15,17 +15,15 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index c2e566a117..4ebbcb9a3f 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -15,27 +15,17 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index f5889fd520..c98092f19b 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -16,23 +16,18 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_tip4p_long.h" +#include +#include +#include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 493866a895..610fc4e89b 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -17,12 +17,11 @@ University New Orleans) ------------------------------------------------------------------------- */ +#include "pair_lj_long_coul_long.h" +#include #include -#include -#include #include #include "math_vector.h" -#include "pair_lj_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" @@ -31,7 +30,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 3137b9d79a..08409dce72 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -16,23 +16,18 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_long_tip4p_long.h" +#include +#include +#include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 9419fdf196..2c47f42beb 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -16,23 +16,18 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tip4p_long.h" +#include +#include +#include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 1abb19e947..75470c962f 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -18,12 +18,10 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pppm.h" #include #include -#include -#include #include -#include "pppm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 6426b9c22d..11b98076d9 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm,PPPM) #ifndef LMP_PPPM_H #define LMP_PPPM_H -#include "lmptype.h" -#include +#include "kspace.h" #if defined(FFT_FFTW3) #define LMP_FFT_LIB "FFTW3" @@ -42,8 +41,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { class PPPM : public KSpace { diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 3285dba21c..bd23dedef1 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -15,11 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg.h" #include #include -#include #include - #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -27,9 +26,8 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "pppm_cg.h" - #include "math_const.h" +#include "remap.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 21a777dd75..0eb761d9be 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -15,20 +15,15 @@ Contributing authors: Stan Moore (SNL), Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole.h" #include #include -#include -#include #include -#include "pppm_dipole.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 878d40c82e..9e9f07322c 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -15,33 +15,23 @@ Contributing author: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole_spin.h" #include #include -#include -#include -#include -#include "pppm_dipole_spin.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" #include "memory.h" #include "error.h" #include "update.h" #include "math_const.h" -#include "math_special.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define MAXORDER 7 #define OFFSET 16384 diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index ba0e85bbba..c30d55dd68 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -16,12 +16,10 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pppm_disp.h" #include #include -#include -#include #include -#include "pppm_disp.h" #include "math_const.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index 8674669274..130671fa28 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm/disp,PPPMDisp) #ifndef LMP_PPPM_DISP_H #define LMP_PPPM_DISP_H -#include "lmptype.h" -#include +#include "kspace.h" #if defined(FFT_FFTW3) #define LMP_FFT_LIB "FFTW3" @@ -41,8 +40,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 2bc63a84bb..bc46152e2b 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -16,13 +16,12 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include #include "pppm_disp_tip4p.h" +#include #include "pppm_disp.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index a5ed6de626..7b708d0355 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -15,15 +15,12 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pppm_stagger.h" #include #include -#include -#include #include -#include "pppm_stagger.h" #include "atom.h" #include "gridcomm.h" -#include "force.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index b9fe3e6488..f664a0dca3 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -15,12 +15,12 @@ Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include #include "pppm_tip4p.h" +#include +#include #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 26541f121e..d4cfdea2b0 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "remap.h" +#include #include #include -#include "remap.h" #define PACK_DATA FFT_SCALAR diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 8ea2918d7f..7929cd053c 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "remap_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 645b298e09..7d4e89272d 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -15,9 +15,9 @@ Contributing author: Christian Negre (LANL) ------------------------------------------------------------------------- */ +#include "fix_latte.h" #include #include -#include "fix_latte.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/MAKE/MACHINES/Makefile.lassen_kokkos b/src/MAKE/MACHINES/Makefile.lassen_kokkos new file mode 100644 index 0000000000..23697bfea2 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.lassen_kokkos @@ -0,0 +1,125 @@ +# lassen_kokkos = KOKKOS/CUDA, V100 GPU and Power9, IBM Spectrum MPI, nvcc compiler with gcc 7.3.1 + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) +export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +CC = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +CCFLAGS = -g -O3 +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +LINKFLAGS = -g -O3 +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared +KOKKOS_DEVICES = Cuda +KOKKOS_ARCH = Power9,Volta70 + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/include +MPI_PATH = +MPI_LIB = -L/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/lib -lmpi_ibm + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = +FFT_PATH = +FFT_LIB = + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 5019e7711a..2f324bf097 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -15,16 +15,13 @@ Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb.h" #include #include -#include #include #include "pair_comb.h" #include "pair_comb3.h" -#include "fix_qeq_comb.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index dd4c9f7290..c3a0ac08f3 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -20,7 +20,6 @@ FixStyle(qeq/comb,FixQEQComb) #ifndef LMP_FIX_QEQ_COMB_H #define LMP_FIX_QEQ_COMB_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 68511b8709..64c778659c 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -16,11 +16,11 @@ Chandra Veer Singh (Cornell) ------------------------------------------------------------------------- */ +#include "pair_adp.h" +#include #include -#include #include #include -#include "pair_adp.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index e3c5a1627b..fcc3a3efd2 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -20,28 +20,23 @@ Thomas C. O'Connor (JHU) 2014 ------------------------------------------------------------------------- */ +#include "pair_airebo.h" #include -#include -#include #include #include -#include "pair_airebo.h" #include "atom.h" #include "neighbor.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 @@ -3198,6 +3193,7 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj, dN3[0]=0.0; dN3[1]=0.0; dN3[2]=0.0; + piRC=0.0; if (typei==0 && typej==0) { @@ -4348,70 +4344,70 @@ void PairAIREBO::Sptricubic_patch_coeffs( ) { const double C_inv[64][32] = { // output_matrix(2, 8*4, get_matrix(3)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 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0}, + { 4, -4, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, -2, 2, -2, 0, 0, 0, 0, 2, 2, -2, -2, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 9, -9, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 4, -4, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + {-3, 0, 0, 0, 3, 0, 0, 0, -2, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 3, 0, 0, 0}, + { 9, -9, 0, 0, -9, 9, 0, 0, 6, -6, 0, 0, 3, -3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 3, 0, 0, -6, -3, 0, 0}, + {-6, 6, 0, 0, 6, -6, 0, 0, -4, 4, 0, 0, -2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, -3, 0, 0, 3, 3, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -9, 0, 0, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 0, 0, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 9, 0, -9, 0, -9, 0, 9, 0, 6, 0, -6, 0, 3, 0, -3, 0, 6, 0, 3, 0, -6, 0, -3, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, -9, 0, -9, 0, 9, 0}, + {-27,27, 27,-27, 27,-27,-27, 27,-18, 18, 18,-18, -9, 9, 9, -9,-18, 18, -9, 9, 18,-18, 9, -9,-18, -9, 18, 9, 18, 9,-18, -9}, + {18,-18,-18, 18,-18, 18, 18,-18, 12,-12,-12, 12, 6, -6, -6, 6, 12,-12, 6, -6,-12, 12, -6, 6, 9, 9, -9, -9, -9, -9, 9, 9}, + {-6, 0, 6, 0, 6, 0, -6, 0, -4, 0, 4, 0, -2, 0, 2, 0, -3, 0, -3, 0, 3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 0, 6, 0, 6, 0, -6, 0}, + {18,-18,-18, 18,-18, 18, 18,-18, 12,-12,-12, 12, 6, -6, -6, 6, 9, -9, 9, -9, -9, 9, -9, 9, 12, 6,-12, -6,-12, -6, 12, 6}, + {-12,12, 12,-12, 12,-12,-12, 12, -8, 8, 8, -8, -4, 4, 4, -4, -6, 6, -6, 6, 6, -6, 6, -6, -6, -6, 6, 6, 6, 6, -6, -6}, + { 2, 0, 0, 0, -2, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, -2, 0, 0, 0}, + {-6, 6, 0, 0, 6, -6, 0, 0, -3, 3, 0, 0, -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -4, -2, 0, 0, 4, 2, 0, 0}, + { 4, -4, 0, 0, -4, 4, 0, 0, 2, -2, 0, 0, 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 0, -2, -2, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 0, 0, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, -4, 0, 0, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + {-6, 0, 6, 0, 6, 0, -6, 0, -3, 0, 3, 0, -3, 0, 3, 0, -4, 0, -2, 0, 4, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 0, 6, 0, 6, 0, -6, 0}, + {18,-18,-18, 18,-18, 18, 18,-18, 9, -9, -9, 9, 9, -9, -9, 9, 12,-12, 6, -6,-12, 12, -6, 6, 12, 6,-12, -6,-12, -6, 12, 6}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -8, 8, -4, 4, 8, -8, 4, -4, -6, -6, 6, 6, 6, 6, -6, -6}, + { 4, 0, -4, 0, -4, 0, 4, 0, 2, 0, -2, 0, 2, 0, -2, 0, 2, 0, 2, 0, -2, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, -4, 0, -4, 0, 4, 0}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -6, 6, -6, 6, 6, -6, 6, -6, -8, -4, 8, 4, 8, 4, -8, -4}, + { 8, -8, -8, 8, -8, 8, 8, -8, 4, -4, -4, 4, 4, -4, -4, 4, 4, -4, 4, -4, -4, 4, -4, 4, 4, 4, -4, -4, -4, -4, 4, 4} }; double dx = xmax - xmin; double dy = ymax - ymin; @@ -4461,22 +4457,22 @@ void PairAIREBO::Spbicubic_patch_coeffs( ) { const double C_inv[16][12] = { // output_matrix(1, 4*3, get_matrix(2)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, - -3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, - 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, - 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, - -3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, - 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3, - -6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3, - 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, - -6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2, - 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2, + { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0}, + {-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0}, + { 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0}, + { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0}, + {-3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0}, + { 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3}, + {-6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3}, + { 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0}, + {-6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2}, + { 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2} }; double dx = xmax - xmin; double dy = ymax - ymin; diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 8e92807afb..04d3fc399f 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -21,7 +21,6 @@ PairStyle(airebo,PairAIREBO) #define LMP_PAIR_AIREBO_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp index a39f7df82e..121f9557fd 100644 --- a/src/MANYBODY/pair_airebo_morse.cpp +++ b/src/MANYBODY/pair_airebo_morse.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse.h" -#include "force.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index c157e0763c..e604f44003 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -15,8 +15,9 @@ Contributing author: Sergey Lishchuk ------------------------------------------------------------------------- */ -#include #include "pair_atm.h" +#include +#include #include "atom.h" #include "citeme.h" #include "comm.h" diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 39f48cd05e..6b7468558e 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -32,24 +32,19 @@ Rules"_http://lammps.sandia.gov/open_source.html ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "pair_bop.h" +#include +#include +#include +#include #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index 3bd9b8cea9..eca0ec52b8 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -26,8 +26,6 @@ PairStyle(bop,PairBOP) #define LMP_PAIR_BOP_H #include "pair.h" -#include -#include "update.h" namespace LAMMPS_NS { @@ -44,20 +42,20 @@ class PairBOP : public Pair { private: int me; - int maxneigh; // maximum size of neighbor list on this processor - int maxneigh3; // maximum size of neighbor list on this processor - int update_list; // check for changing maximum size of neighbor list - int maxbopn; // maximum size of bop neighbor list for allocation - int maxnall; // maximum size of bop neighbor list for allocation - int *map; // mapping from atom types to elements - int nelements; // # of unique elments - int nr; // increments for the BOP pair potential - int ntheta; // increments for the angle function - int npower; // power of the angular function - int nBOt; // second BO increments - int bop_types; // number of elments in potential - int npairs; // number of element pairs - char **elements; // names of unique elements + int maxneigh; // maximum size of neighbor list on this processor + int maxneigh3; // maximum size of neighbor list on this processor + int update_list; // check for changing maximum size of neighbor list + int maxbopn; // maximum size of bop neighbor list for allocation + int maxnall; // maximum size of bop neighbor list for allocation + int *map; // mapping from atom types to elements + int nelements; // # of unique elments + int nr; // increments for the BOP pair potential + int ntheta; // increments for the angle function + int npower; // power of the angular function + int nBOt; // second BO increments + int bop_types; // number of elments in potential + int npairs; // number of element pairs + char **elements; // names of unique elements int ***elem2param; int nparams; int bop_step; @@ -66,23 +64,22 @@ class PairBOP : public Pair { int allocate_neigh; int nb_pi,nb_sg; int ago1; -// int cnt1; - int *BOP_index; // index for neighbor list position - int *BOP_total; // index for neighbor list position - int *BOP_index3; // index for neighbor list position - int *BOP_total3; // index for neighbor list position - int *neigh_index; // index for neighbor list position - int *neigh_index3; // index for neighbor list position - int neigh_total; // total number of neighbors stored - int neigh_total3; // total number of neighbors stored - int *cos_index; // index for neighbor cosine if not using on the fly - int *neigh_flag; // index for neighbor cosine if not using on the fly - int *neigh_flag3; // index for neighbor cosine if not using on the fly - int cos_total; // number of cosines stored if not using on the fly - int neigh_ct; // limit for large arrays + int *BOP_index; // index for neighbor list position + int *BOP_total; // index for neighbor list position + int *BOP_index3; // index for neighbor list position + int *BOP_total3; // index for neighbor list position + int *neigh_index; // index for neighbor list position + int *neigh_index3; // index for neighbor list position + int neigh_total; // total number of neighbors stored + int neigh_total3; // total number of neighbors stored + int *cos_index; // index for neighbor cosine if not using on the fly + int *neigh_flag; // index for neighbor cosine if not using on the fly + int *neigh_flag3; // index for neighbor cosine if not using on the fly + int cos_total; // number of cosines stored if not using on the fly + int neigh_ct; // limit for large arrays -/*Parameters variables*/ + // Parameters variables int ncutoff,nfunc; int a_flag; @@ -98,51 +95,50 @@ class PairBOP : public Pair { double beta3,rsmall,rbig,rcore; char **words; - double cutmax; //max cutoff for all elements - int otfly; //Defines whether to do on the fly - //calculations of angles and distances - //on the fly will slow down calculations - //but requires less memory on = 1, off=0 + double cutmax; // max cutoff for all elements + int otfly; // Defines whether to do on the fly + // calculations of angles and distances + // on the fly will slow down calculations + // but requires less memory on = 1, off=0 -/* Neigh variables */ + // Neigh variables double *rcut,*rcut3,*dr,*rdr,*dr3,*rdr3; double *rcutsq,*rcutsq3; double **disij,*rij; double rcutall,rctroot; -/*Triple variables */ + // Triple variables double *cosAng,***dcosAng,***dcAng; -/*Double variables */ + // Double variables double *betaS,*dBetaS,*betaP; double *dBetaP,*repul,*dRepul; -/*Sigma variables */ + // Sigma variables int *itypeSigBk,nSigBk; double sigB,sigB_0; double sigB1; - -/*Pi variables */ + // Pi variables int *itypePiBk,nPiBk; double piB,piB_0; -/*Grids1 variables */ + // Grids1 variables double **pBetaS,**pBetaS1,**pBetaS2,**pBetaS3; double **pBetaS4,**pBetaS5,**pBetaS6; -/*Grids2 variables */ + // Grids2 variables double **pBetaP,**pBetaP1,**pBetaP2,**pBetaP3; double **pBetaP4,**pBetaP5,**pBetaP6; -/*Grids3 variables */ + // Grids3 variables double **pRepul,**pRepul1,**pRepul2,**pRepul3; double **pRepul4,**pRepul5,**pRepul6; @@ -155,13 +151,13 @@ class PairBOP : public Pair { double ****gfunc4,****gfunc5,****gfunc6; double dtheta,rdtheta; -/*Grids4 variables */ + // Grids4 variables double **FsigBO,**FsigBO1,**FsigBO2,**FsigBO3; double **FsigBO4,**FsigBO5,**FsigBO6; double dBO,rdBO; -/* End of BOP variables */ + // End of BOP variables double **rcmin,**rcmax,**rcmaxp; struct B_PI{ @@ -211,14 +207,6 @@ class PairBOP : public Pair { void memory_theta_destroy(); void memory_theta_grow(); double cutoff(double, double, int, double); -/* - double betaSfunc(int, double); - double dBetaSfunc(int, double, double, double); - double betaPfunc(int, double); - double dBetaPfunc(int, double, double, double); - double repulfunc(int, double); - double dRepulfunc(int, double, double, double); -*/ void read_table(char *); void allocate(); @@ -229,9 +217,7 @@ class PairBOP : public Pair { void grow_pi(int,int); void grow_sigma(int,int); }; - } - #endif #endif diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 980aa84b2a..2fc4caec7b 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -18,11 +18,11 @@ and Aidan Thompson's Tersoff code in LAMMPS ------------------------------------------------------------------------- */ +#include "pair_comb.h" +#include #include -#include #include #include -#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "my_page.h" #include "math_const.h" #include "memory.h" diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index c798d5f347..19788dfab1 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -21,7 +21,6 @@ PairStyle(comb,PairComb) #define LMP_PAIR_COMB_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 097f235ff2..6f1732dbb7 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -17,19 +17,19 @@ Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr) ------------------------------------------------------------------------- */ +#include "pair_comb3.h" +#include #include -#include #include #include -#include "pair_comb3.h" #include "atom.h" #include "comm.h" #include "force.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index 5d7e5d6beb..210f843139 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -21,7 +21,6 @@ PairStyle(comb3,PairComb3) #define LMP_PAIR_COMB3_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index b7957349b6..acb0e654d8 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -15,11 +15,11 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam.h" +#include #include -#include #include #include -#include "pair_eam.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 234552157b..8bcb44c347 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -20,7 +20,6 @@ PairStyle(eam,PairEAM) #ifndef LMP_PAIR_EAM_H #define LMP_PAIR_EAM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index c004030240..5b7f9877d7 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -15,10 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_alloy.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index c111c6d950..28004eae7f 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -17,15 +17,14 @@ Germany Department of Materials Science ------------------------------------------------------------------------- */ +#include "pair_eam_cd.h" +#include #include -#include #include #include -#include "pair_eam_cd.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index bbda84fdf1..7e00783922 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -15,10 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_fs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index f1c028ef38..dd65d92cdd 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -15,11 +15,10 @@ Contributing author: Xiaowang Zhou (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_eim.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 50f9934c44..f9fb2d5a77 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -20,7 +20,6 @@ PairStyle(eim,PairEIM) #ifndef LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index e4b74f7a29..667311812b 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -16,11 +16,11 @@ based on PairTersoff by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_gw.h" +#include #include -#include #include #include -#include "pair_gw.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index f3dd1bc04b..d39bf53b99 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -16,16 +16,13 @@ Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU) ------------------------------------------------------------------------- */ +#include "pair_gw_zbl.h" +#include #include -#include #include #include -#include "pair_gw_zbl.h" #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 05cdea8055..873a675cd9 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -16,27 +16,21 @@ based on pair_airebo by Ase Henry (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "pair_lcbop.h" +#include +#include +#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define TOL 1.0e-9 @@ -1099,19 +1093,6 @@ void PairLCBOP::read_file(char *filename) init coefficients for TF_conj ------------------------------------------------------------------------- */ -#include -#include -#include -template< class function > void print_function( double x_0, double x_1, size_t n, function f, std::ostream &stream ) { - double dx = (x_1-x_0)/n; - for( double x=x_0; x<=x_1+0.0001; x+=dx ) { - double f_val, df; - f_val = f(x, &df); - stream << x << " " << f_val << " " << df << std::endl; - } - stream << std::endl; -} - void PairLCBOP::spline_init() { for( size_t N_conj_ij=0; N_conj_ij<2; N_conj_ij++ ) // N_conj_ij for( size_t N_ij=0; N_ij<4-1; N_ij++ ) diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index 0d7c7a51b1..c7a7fab46d 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -21,7 +21,6 @@ PairStyle(lcbop,PairLCBOP) #define LMP_PAIR_LCBOP_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index a61b403459..92456790cc 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -16,18 +16,16 @@ (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ +#include "pair_nb3b_harmonic.h" +#include #include -#include #include #include -#include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index d3aca4e889..d3964b292c 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -16,11 +16,11 @@ This modifies from pair_tersoff.cpp by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_polymorphic.h" +#include #include -#include #include #include -#include "pair_polymorphic.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" @@ -30,10 +30,7 @@ #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 32f1c5414a..e7c3cd0d26 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,6 +22,7 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index e07a1b3495..06357d8368 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -26,7 +26,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) { global settings ------------------------------------------------------------------------- */ -void PairREBO::settings(int narg, char **/*arg*/) +void PairREBO::settings(int narg, char ** /* arg */) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 5a148fb152..f1d1a6fa9f 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -15,21 +15,19 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_sw.h" +#include #include -#include #include #include -#include "pair_sw.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 213b1037bb..62c74576e0 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -15,11 +15,11 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff.h" +#include #include -#include #include #include -#include "pair_tersoff.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index e8fdecfe01..698dd8fa03 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -16,22 +16,18 @@ Vitaly Dozhdikov (JIHT of RAS) - MOD addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod.h" +#include #include -#include #include #include -#include "pair_tersoff_mod.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" +#include "math_const.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 4a5904c106..6c2c4f4e7a 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -15,24 +15,18 @@ Contributing author: Ganga P Purja Pun (George Mason University, Fairfax) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_c.h" +#include #include -#include #include #include -#include "pair_tersoff_mod_c.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 353e3d2264..ab06e6ec31 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -16,22 +16,19 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl.h" +#include #include -#include #include #include -#include "pair_tersoff_zbl.h" #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" - #include "math_const.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 3d4b1d900e..13b44c58a4 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -16,21 +16,19 @@ Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_vashishta.h" +#include #include -#include #include #include -#include "pair_vashishta.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index d4eaa59f1a..bf39183b9d 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -15,21 +15,14 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_vashishta_table.h" +#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "error.h" #include "force.h" #include "comm.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 7d817ffbb1..9a4a0b6a7f 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -16,14 +16,13 @@ Alexander Stukowski ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_atom_swap.h" +#include +#include +#include +#include +#include #include "atom.h" -#include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "update.h" #include "modify.h" #include "fix.h" @@ -40,18 +39,12 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include -using namespace std; using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 19895704f1..a5ce89b16b 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -20,7 +20,6 @@ FixStyle(atom/swap,FixAtomSwap) #ifndef LMP_FIX_MCSWAP_H #define LMP_FIX_MCSWAP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 05edc0509e..2ff0e4126f 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -11,19 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_bond_break.h" #include #include -#include -#include "fix_bond_break.h" #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index e1dd18cb5b..3f63a22d60 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_bond_create.h" #include #include -#include -#include "fix_bond_create.h" #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "pair.h" #include "comm.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 9a72667907..187c552416 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_bond_swap.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "pair.h" @@ -23,7 +23,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index 0443144c23..d24159d807 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -21,7 +21,6 @@ FixStyle(bond/swap,FixBondSwap) #define LMP_FIX_BONDSWAP_H #include "fix.h" -#include "pair.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 7ab0879335..1050fd4712 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,13 +15,12 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_gcmc.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "molecule.h" #include "update.h" #include "modify.h" @@ -43,10 +42,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -371,7 +367,7 @@ void FixGCMC::options(int narg, char **arg) ngrouptypesmax*sizeof(char *), "fix_gcmc:grouptypestrings"); } - grouptypes[ngrouptypes] = atoi(arg[iarg+1]); + grouptypes[ngrouptypes] = force->inumeric(FLERR,arg[iarg+1]); int n = strlen(arg[iarg+2]) + 1; grouptypestrings[ngrouptypes] = new char[n]; strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]); diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index 5d0b7aab8f..da4232d19b 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -20,7 +20,6 @@ FixStyle(gcmc,FixGCMC) #ifndef LMP_FIX_GCMC_H #define LMP_FIX_GCMC_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 46c5e592ae..e57f1cdf4a 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -22,7 +22,6 @@ #include #include "atom.h" #include "force.h" -#include "update.h" #include "group.h" #include "random_mars.h" #include "comm.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index c71eaa2295..43bffa7e8d 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -15,12 +15,10 @@ Contributing authors: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "pair_dsmc.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index 727481dcc0..7d4ae13f0f 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_client_md.h" #include #include -#include "fix_client_md.h" #include "update.h" #include "atom.h" #include "comm.h" diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index 61221ca26e..f8fc349746 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "message.h" +#include #include "error.h" // CSlib interface diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp index f587fb76df..dbcec08488 100644 --- a/src/MESSAGE/server.cpp +++ b/src/MESSAGE/server.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "server.h" +#include #include "error.h" // customize by adding a new server protocol include and enum diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index bef327616e..e16095ad4c 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "server_md.h" #include #include -#include "server_md.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index f6291f4204..6123bf49af 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -15,14 +15,13 @@ Contributing authors: Rob Hoy ------------------------------------------------------------------------- */ -#include #include "compute_msd_nongauss.h" +#include #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "fix_store.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index d2e43a9f69..06188de238 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -15,12 +15,11 @@ Contributing author: Sai Jayaraman (University of Notre Dame) ------------------------------------------------------------------------- */ -#include -#include "atom.h" -#include #include "compute_ti.h" +#include +#include +#include "atom.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "force.h" #include "pair.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index a82cba20bd..1a2b71ab6d 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -22,12 +22,11 @@ support for groups ------------------------------------------------------------------------- */ +#include "dump_xtc.h" #include -#include #include #include #include -#include "dump_xtc.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 66aed34846..c9d4958594 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_deposit.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 38958b80e7..e3104c890d 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -20,7 +20,6 @@ FixStyle(deposit,FixDeposit) #ifndef LMP_FIX_DEPOSIT_H #define LMP_FIX_DEPOSIT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 004c8ad7bc..5a13b93b91 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -16,10 +16,9 @@ Stan Moore (Sandia) for dipole terms ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_efield.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 1bf7a15f1f..d868254c50 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_evaporate.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -25,7 +24,6 @@ #include "force.h" #include "group.h" #include "random_park.h" -#include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 2bf02889a5..380c038e4a 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -16,18 +16,15 @@ Andrew Baczewski (Michigan State/SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_gld.h" -#include "math_extra.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index 73853775a3..68a27b68be 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -15,14 +15,13 @@ Contributing author: Axel Kohlmeyer (ICTP, Italy) ------------------------------------------------------------------------- */ -#include #include "fix_oneway.h" +#include #include "atom.h" #include "domain.h" #include "error.h" #include "force.h" #include "region.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 02cce5a014..1453ceb317 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -18,11 +18,11 @@ (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ +#include "fix_orient_bcc.h" #include #include #include #include -#include "fix_orient_bcc.h" #include "atom.h" #include "update.h" #include "respa.h" @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index fc827ceb8f..082ecaf459 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -15,11 +15,11 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) ------------------------------------------------------------------------- */ +#include "fix_orient_fcc.h" #include #include #include #include -#include "fix_orient_fcc.h" #include "atom.h" #include "update.h" #include "respa.h" @@ -27,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index f1aec3ff69..d0add6fecb 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -16,11 +16,9 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include "fix_thermal_conductivity.h" #include #include -#include -#include "fix_thermal_conductivity.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 170103b0d0..eb9eb2620d 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -16,16 +16,14 @@ Carolyn Phillips (University of Michigan) ------------------------------------------------------------------------- */ +#include "fix_ttm.h" #include #include #include -#include -#include "fix_ttm.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 8e33c1c614..d5a97cd4b0 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -16,11 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_viscosity.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index 124832b63e..a084491a78 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -15,11 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_nm_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index a8428ab980..df8a34062a 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -15,11 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_nm_cut_coul_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index af21f02881..4109fb0d9e 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -15,20 +15,16 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_nm_cut_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 2d8d0ce7e5..9806b0bbd2 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,7 +1,6 @@ -#include -#include -#include #include "xdr_compat.h" +#include +#include /* This file is needed for systems, that do not provide XDR support * in their system libraries. It was written for windows, but will diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h index 3062235080..5dfa01e0e8 100644 --- a/src/MISC/xdr_compat.h +++ b/src/MISC/xdr_compat.h @@ -3,7 +3,6 @@ #include #include -#include #ifdef __cplusplus extern "C" { diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index efd1c682f7..8a45f29368 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "angle_charmm.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index 2228ad8732..444c833d37 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -20,7 +20,6 @@ AngleStyle(charmm,AngleCharmm) #ifndef LMP_ANGLE_CHARMM_H #define LMP_ANGLE_CHARMM_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 6e1b9fa2fb..645cf66ff2 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index f2406bc5dd..ca1f4178f8 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -20,7 +20,6 @@ AngleStyle(cosine,AngleCosine) #ifndef LMP_ANGLE_COSINE_H #define LMP_ANGLE_COSINE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index eca10970f2..679a8deb0e 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -15,16 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_delta.h" +#include #include "atom.h" #include "neighbor.h" #include "domain.h" -#include "comm.h" #include "force.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index 1e19ecaf79..70b574b234 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -20,7 +20,6 @@ AngleStyle(cosine/delta,AngleCosineDelta) #ifndef LMP_ANGLE_COSINE_DELTA_H #define LMP_ANGLE_COSINE_DELTA_H -#include #include "angle_cosine_squared.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index cb0a26871a..22c2f7ce8b 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -15,9 +15,9 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_periodic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index e131e85101..f0188b6c17 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -20,7 +20,6 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic) #ifndef LMP_ANGLE_PERIODIC_H #define LMP_ANGLE_PERIODIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 28d63344a4..56b3ee58cf 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_squared.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index 8e8c84c0f9..a19a923850 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -20,7 +20,6 @@ AngleStyle(cosine/squared,AngleCosineSquared) #ifndef LMP_ANGLE_COSINE_SQUARED_H #define LMP_ANGLE_COSINE_SQUARED_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 48b493d9b2..2e96884c9d 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "angle_harmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index e0c067653b..f371178d58 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -20,7 +20,6 @@ AngleStyle(harmonic,AngleHarmonic) #ifndef LMP_ANGLE_HARMONIC_H #define LMP_ANGLE_HARMONIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index c18b4c43b0..54046c2ba8 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -15,10 +15,11 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "angle_table.h" +#include #include #include #include -#include "angle_table.h" #include "atom.h" #include "neighbor.h" #include "domain.h" @@ -278,8 +279,7 @@ double AngleTable::equilibrium_angle(int i) void AngleTable::write_restart(FILE *fp) { - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); + write_restart_settings(fp); } /* ---------------------------------------------------------------------- @@ -287,6 +287,26 @@ void AngleTable::write_restart(FILE *fp) ------------------------------------------------------------------------- */ void AngleTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void AngleTable::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void AngleTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -294,8 +314,6 @@ void AngleTable::read_restart(FILE *fp) } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 0088ace39b..8c854dc2e6 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -20,7 +20,6 @@ AngleStyle(table,AngleTable) #ifndef LMP_ANGLE_TABLE_H #define LMP_ANGLE_TABLE_H -#include #include "angle.h" namespace LAMMPS_NS { @@ -35,6 +34,8 @@ class AngleTable : public Angle { double equilibrium_angle(int); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int, int, int, int); protected: diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index bdafdae148..4eba471b8f 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 275c424941..0bcd614f94 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index 036324cb2c..76c60ba121 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 49606f0a69..73cec70456 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 14e7736b50..c9ccfc6d2b 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -11,12 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_template.h" #include "atom.h" #include "molecule.h" -#include "force.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index c023a7e81e..776291701b 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_fene.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 58cd6ce289..1963e3ca22 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -20,7 +20,6 @@ BondStyle(fene,BondFENE) #ifndef LMP_BOND_FENE_H #define LMP_BOND_FENE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index b1bfdc6a1b..d03dfd9125 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_fene_expand.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index cb316ac5f2..8cfc17dc68 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -20,7 +20,6 @@ BondStyle(fene/expand,BondFENEExpand) #ifndef LMP_BOND_FENE_EXPAND_H #define LMP_BOND_FENE_EXPAND_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index f65adeb2cb..284c9202fd 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -15,13 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_gromos.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index c26ad64b3d..966b914437 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -20,7 +20,6 @@ BondStyle(gromos,BondGromos) #ifndef LMP_BOND_GROMOS_H #define LMP_BOND_GROMOS_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index cb8434ce6e..7b19034629 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_harmonic.h" +#include +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index 5c692b2a8e..576e63629b 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -20,7 +20,6 @@ BondStyle(harmonic,BondHarmonic) #ifndef LMP_BOND_HARMONIC_H #define LMP_BOND_HARMONIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 91dd2dbc49..6e16070cae 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -15,12 +15,11 @@ Contributing author: Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "bond_morse.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index c4d60bc217..030a94a8da 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -20,7 +20,6 @@ BondStyle(morse,BondMorse) #ifndef LMP_BOND_MORSE_H #define LMP_BOND_MORSE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 9999ead47f..e06b1b9aac 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_nonlinear.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 175421264b..7782b93778 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -20,7 +20,6 @@ BondStyle(nonlinear,BondNonlinear) #ifndef LMP_BOND_NONLINEAR_H #define LMP_BOND_NONLINEAR_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 895202ff00..352b642bbe 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -15,14 +15,12 @@ Contributing authors: Chris Lorenz and Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "bond_quartic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" -#include "update.h" #include "force.h" #include "pair.h" #include "memory.h" diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 2aaa76e2c3..60ccf307b9 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -20,7 +20,6 @@ BondStyle(quartic,BondQuartic) #ifndef LMP_BOND_QUARTIC_H #define LMP_BOND_QUARTIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 10851774d7..ce41303a7d 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -15,13 +15,13 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "bond_table.h" +#include #include #include #include -#include "bond_table.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" @@ -222,8 +222,7 @@ double BondTable::equilibrium_distance(int i) void BondTable::write_restart(FILE *fp) { - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); + write_restart_settings(fp); } /* ---------------------------------------------------------------------- @@ -231,6 +230,26 @@ void BondTable::write_restart(FILE *fp) ------------------------------------------------------------------------- */ void BondTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void BondTable::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void BondTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -238,8 +257,6 @@ void BondTable::read_restart(FILE *fp) } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index 5766239167..b08059415b 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -20,7 +20,6 @@ BondStyle(table,BondTable) #ifndef LMP_BOND_TABLE_H #define LMP_BOND_TABLE_H -#include #include "bond.h" namespace LAMMPS_NS { @@ -35,6 +34,8 @@ class BondTable : public Bond { double equilibrium_distance(int); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int, double, int, int, double &); protected: diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 68c62eb4fd..8cc0713024 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -15,15 +15,13 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm.h" #include #include -#include #include -#include "dihedral_charmm.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 8f51b398db..4be3925dad 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -20,7 +20,6 @@ DihedralStyle(charmm,DihedralCharmm) #ifndef LMP_DIHEDRAL_CHARMM_H #define LMP_DIHEDRAL_CHARMM_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index f65d01e9ed..f384c4cd36 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -18,15 +18,13 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "dihedral_charmmfsw.h" #include #include -#include #include -#include "dihedral_charmmfsw.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index dd31067a8d..b33250004b 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -20,7 +20,6 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw) #ifndef LMP_DIHEDRAL_CHARMMFSW_H #define LMP_DIHEDRAL_CHARMMFSW_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index ddb94dc571..f1e5811a84 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_harmonic.h" #include #include -#include -#include "dihedral_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 2031261256..938e59918b 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(harmonic,DihedralHarmonic) #ifndef LMP_DIHEDRAL_HARMONIC_H #define LMP_DIHEDRAL_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index d19731c097..56f7a3b5e8 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -16,13 +16,11 @@ Mark Stevens (Sandia) ------------------------------------------------------------------------- */ +#include "dihedral_helix.h" #include #include -#include -#include "dihedral_helix.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 745ab84115..0213c59e8a 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -20,7 +20,6 @@ DihedralStyle(helix,DihedralHelix) #ifndef LMP_DIHEDRAL_HELIX_H #define LMP_DIHEDRAL_HELIX_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 04e7bbb627..eda7cede3e 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -15,12 +15,11 @@ Contributing author: Mathias Puetz (SNL) and friends ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_multi_harmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 32f17e75ae..bb3d7183f7 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic) #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H #define LMP_DIHEDRAL_MULTI_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 293245e411..556efd850a 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -15,13 +15,12 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_opls.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index c1e64ada1e..01878173cd 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -20,7 +20,6 @@ DihedralStyle(opls,DihedralOPLS) #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 3395c7ef14..fb0a550898 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -27,20 +27,16 @@ - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415. ------------------------------------------------------------------------- */ +#include "fix_cmap.h" #include #include #include #include -#include -#include "fix_cmap.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "respa.h" -#include "modify.h" #include "domain.h" #include "force.h" -#include "group.h" #include "comm.h" #include "math_const.h" #include "memory.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 01e9729e80..abd2d4e11e 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_cvff.h" #include #include -#include -#include "improper_cvff.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index d4c30cc2ee..055d2ca9b8 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -20,7 +20,6 @@ ImproperStyle(cvff,ImproperCvff) #ifndef LMP_IMPROPER_CVFF_H #define LMP_IMPROPER_CVFF_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index c5421fffdb..778fe646e1 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_harmonic.h" #include #include -#include -#include "improper_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index fbbb8d33d6..5949c6911e 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(harmonic,ImproperHarmonic) #ifndef LMP_IMPROPER_HARMONIC_H #define LMP_IMPROPER_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 3de46df0f3..d3adf19993 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -15,14 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "improper_umbrella.h" #include #include -#include -#include "improper_umbrella.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index dc2262d01c..da9d6c8f4b 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -20,7 +20,6 @@ ImproperStyle(umbrella,ImproperUmbrella) #ifndef LMP_IMPROPER_UMBRELLA_H #define LMP_IMPROPER_UMBRELLA_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index ddc1110081..53c3101708 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -15,15 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_hbond_dreiding_lj.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 055f0ed46b..3039a662e6 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -15,15 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_hbond_dreiding_morse.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index af4611e014..5ebfe0a110 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -15,11 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_charmm.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index d68d5e8f6d..ff7dbb290b 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_lj_charmm_coul_charmm_implicit.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 0e1cbd85a5..4fb7cc5229 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -19,11 +19,10 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmmfsw_coul_charmmfsh.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index 2b3d2c60f5..e5f25a511b 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_cut_tip4p_cut.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "neighbor.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index e6fb9aab99..3a6702c9b2 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include #include "pair_tip4p_cut.h" +#include +#include #include "atom.h" #include "force.h" #include "neighbor.h" @@ -26,12 +26,10 @@ #include "angle.h" #include "bond.h" #include "comm.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index f2f2991442..2b663554cc 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -15,12 +15,12 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include #include "dump_atom_mpiio.h" +#include +#include +#include #include "domain.h" -#include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index ad49fa1182..36b43e3f08 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -21,7 +21,6 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO) #define LMP_DUMP_ATOM_MPIIO_H #include "dump_atom.h" -#include namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index c580d2e7af..31848b550c 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -15,18 +15,12 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_cfg_mpiio.h" #include #include #include -#include "dump_cfg_mpiio.h" #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "update.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3650ca994e..dca5833c5b 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -15,20 +15,15 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_custom_mpiio.h" #include #include #include -#include "dump_custom_mpiio.h" -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" #include "input.h" #include "variable.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index f15d340cd1..f5caab3a9c 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -15,21 +15,13 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_xyz_mpiio.h" #include #include #include -#include "dump_xyz_mpiio.h" -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "update.h" -#include "modify.h" #include "compute.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 804df211dc..e8ef5c6c4e 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "restart_mpiio.h" #include #include -#include "restart_mpiio.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index b282595240..caa9a528a7 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -15,10 +15,10 @@ Contributing authors: Lauren Abbott (Sandia) ------------------------------------------------------------------------- */ +#include "fix_mscg.h" #include #include #include -#include "fix_mscg.h" #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index fc2b6731ee..ad24aaee63 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -19,9 +19,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_eam_opt.h" #include #include -#include "pair_eam_opt.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index d80d3d1ec4..3dc6bdb6b4 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_opt.h" #include #include -#include "pair_lj_charmm_coul_long_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index a25010cf1f..a1f97aaae9 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index c6684461be..3b3a19a9e8 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index 92facca43e..f8181d69a6 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -15,8 +15,8 @@ OPT version: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_opt.h" +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 243b64391f..c323d078c4 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -15,8 +15,9 @@ OPT version: Wayne Mitchell (Loyola University New Orleans) ------------------------------------------------------------------------- */ -#include #include "pair_lj_long_coul_long_opt.h" +#include +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index c9c6bba355..1d2e226777 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_morse_opt.h" #include #include -#include "pair_morse_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index f463dac3f1..eabb093b18 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -17,9 +17,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_opt.h" #include #include -#include "pair_ufm_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index c4fa0bd43b..3e3312bf01 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -15,14 +15,12 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_peri.h" +#include +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "citeme.h" diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index 4bf8fa17a5..230b766725 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -15,14 +15,12 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include #include "compute_damage_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 990731a227..095f619838 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -15,19 +15,17 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_dilatation_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" +#include "fix.h" #include "force.h" -#include "pair.h" #include "pair_peri_lps.h" -#include "pair_peri_pmb.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" -#include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index d08fb98e07..e312630b62 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -15,15 +15,14 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_plasticity_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" +#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 66137e6a01..70f46dcdc1 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -15,9 +15,9 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "fix_peri_neigh.h" -#include "pair_peri_pmb.h" +#include +#include #include "pair_peri_lps.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" @@ -25,7 +25,6 @@ #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index c00495ba4d..2579a9b75a 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -15,15 +15,14 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_peri_eps.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" using namespace LAMMPS_NS; @@ -451,12 +449,12 @@ void PairPeriEPS::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double myieldstress_one = atof(arg[7]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double myieldstress_one = force->numeric(FLERR,arg[7]); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index f0418c8c8d..f32ce5fb1c 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -15,15 +15,14 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_peri_lps.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index ad2f3fb7c7..ceab40d88d 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -15,23 +15,21 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_peri_pmb.h" +#include #include #include -#include #include -#include "pair_peri_pmb.h" #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 24a9f92a97..bd1eaa5fd2 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -15,15 +15,14 @@ Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_peri_ves.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -428,13 +427,13 @@ void PairPeriVES::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double mlambdai_one = atof(arg[7]); - double mtaui_one = atof(arg[8]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double mlambdai_one = force->numeric(FLERR,arg[7]); + double mtaui_one = force->numeric(FLERR,arg[8]); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 41cfcede34..c8646f5b14 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -17,20 +17,18 @@ Kurt Anderson (anderk5@rpi.edu) ------------------------------------------------------------------------- */ +#include "fix_poems.h" #include #include -#include #include #include #include "workspace.h" -#include "fix_poems.h" #include "atom.h" #include "domain.h" #include "update.h" #include "respa.h" #include "modify.h" #include "force.h" -#include "output.h" #include "group.h" #include "comm.h" #include "citeme.h" diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 7b2c77a1bd..6892c51d7e 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -22,6 +22,8 @@ FixStyle(poems,FixPOEMS) #include "fix.h" +class Workspace; + namespace LAMMPS_NS { class FixPOEMS : public Fix { @@ -94,7 +96,7 @@ class FixPOEMS : public Fix { // POEMS object - class Workspace *poems; + Workspace *poems; // internal class functions diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 280c2d91e2..57ea2e9148 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -15,14 +15,11 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_python_invoke.h" -#include "atom.h" +#include // IWYU pragma: keep +#include #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "lmppython.h" #include "python_compat.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index ec21dbeadd..be63b851a2 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -15,16 +15,9 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_python_move.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "memory.h" -#include "neigh_list.h" +#include // IWYU pragma: keep +#include #include "lmppython.h" #include "error.h" #include "python_compat.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 2148fc67b8..0d79a31946 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -15,13 +15,11 @@ Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_python.h" +#include // IWYU pragma: keep #include #include -#include "pair_python.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "memory.h" #include "update.h" diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index aaa4f74c69..1188942e75 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -15,8 +15,10 @@ Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include "lmppython.h" +#include "python_impl.h" +#include +#include +#include // IWYU pragma: keep #include "force.h" #include "input.h" #include "variable.h" diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index 2ccdda95c9..f890f54f3b 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -15,6 +15,7 @@ #define LMP_PYTHON_IMPL_H #include "pointers.h" +#include "lmppython.h" namespace LAMMPS_NS { diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 0ab010b7bb..7768c01a41 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -16,29 +16,19 @@ Based on fix qeq/reax by H. Metin Aktulga ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq.h" +#include +#include +#include #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" #include "force.h" -#include "kspace.h" -#include "group.h" -#include "pair.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace FixConst; #define MAXLINE 1024 diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index ba88f4f1c3..a2cc683b56 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -15,24 +15,21 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_dynamic.h" +#include #include -#include #include #include -#include "fix_qeq_dynamic.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 1e3686f99c..265528a089 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -15,26 +15,23 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_fire.h" +#include #include -#include #include #include -#include "fix_qeq_fire.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "pair_comb.h" #include "pair_comb3.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 9517343974..8fb9fd3273 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -15,14 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_point.h" +#include +#include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 6367feacc5..37951adb1a 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -15,14 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_shielded.h" +#include +#include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 3443a519a2..4f5369eb87 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -15,14 +15,12 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_slater.h" #include -#include #include #include -#include "fix_qeq_slater.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -33,7 +31,6 @@ #include "kspace.h" #include "respa.h" #include "math_const.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index df14221586..a6abcce85d 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -15,16 +15,13 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "compute_event_displace.h" +#include +#include #include "atom.h" #include "domain.h" #include "modify.h" #include "fix_event.h" -#include "memory.h" #include "error.h" #include "force.h" #include "update.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 8fc5de6b16..41f91332cb 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -15,17 +15,11 @@ Contributing author: Mike Brown (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event.h" #include "atom.h" -#include "update.h" #include "domain.h" -#include "neighbor.h" -#include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index eae1ad021d..0d32516dee 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_hyper.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index a311a6444a..19a89e988c 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -15,17 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_prd.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index 0916fdf493..d0b94a216b 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -15,17 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_tad.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp index c86c00ad45..21a4fde04d 100644 --- a/src/REPLICA/fix_hyper.cpp +++ b/src/REPLICA/fix_hyper.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_hyper.h" +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 0c76b29911..5e9da02768 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_global.h" #include #include -#include #include -#include "fix_hyper_global.h" #include "atom.h" #include "update.h" #include "force.h" @@ -24,7 +23,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index a6db4419f0..e8773095d1 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -11,21 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_local.h" #include #include -#include #include -#include "fix_hyper_local.h" #include "atom.h" #include "update.h" #include "force.h" #include "pair.h" #include "domain.h" #include "comm.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h index 6f13acb606..8fb3a445c2 100644 --- a/src/REPLICA/fix_hyper_local.h +++ b/src/REPLICA/fix_hyper_local.h @@ -21,7 +21,6 @@ FixStyle(hyper/local,FixHyperLocal) #define LMP_FIX_HYPER_LOCAL_H #include "fix_hyper.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index e1b1e46a53..7b377ae9ec 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -16,11 +16,10 @@ new options for inter-replica forces, first/last replica treatment ------------------------------------------------------------------------- */ +#include "fix_neb.h" #include #include -#include #include -#include "fix_neb.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 00b91684e9..af2a963616 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "hyper.h" +#include +#include #include "update.h" -#include "atom.h" #include "domain.h" #include "region.h" #include "integrate.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 4061ec6541..dafc0c0875 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -11,16 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "neb.h" #include #include #include #include -#include "neb.h" #include "universe.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index f585a0c8a7..b53992711c 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,7 +20,6 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 6d450f48e3..f631cc6a0a 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -15,16 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" -#include -#include -#include -#include #include "prd.h" +#include +#include #include "universe.h" #include "update.h" #include "atom.h" @@ -40,11 +33,9 @@ #include "fix.h" #include "fix_event_prd.h" #include "force.h" -#include "pair.h" #include "random_park.h" #include "random_mars.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index da42ba6fae..8a51f6d00e 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -15,36 +15,24 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "tad.h" #include #include -#include #include -#include "tad.h" #include "universe.h" #include "update.h" #include "atom.h" #include "domain.h" -#include "region.h" -#include "comm.h" -#include "velocity.h" #include "integrate.h" #include "min.h" #include "neighbor.h" #include "modify.h" #include "neb.h" #include "compute.h" -#include "fix.h" #include "fix_event_tad.h" #include "fix_store.h" #include "force.h" -#include "pair.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index fe3e3fb993..46fc3af649 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -15,10 +15,9 @@ Contributing author: Mark Sears (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "temper.h" +#include +#include #include "universe.h" #include "domain.h" #include "atom.h" @@ -27,13 +26,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 7042fc6993..a5ed1a671d 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -15,7 +15,6 @@ Contributing authors: Yuxing Peng and Chris Knight (U Chicago) ------------------------------------------------------------------------- */ -#include #include "verlet_split.h" #include "universe.h" #include "neighbor.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index a3ddffd9ab..e15c0deb82 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_erotate_rigid.h" +#include #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 4de13532b2..031919b7a9 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_ke_rigid.h" +#include #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index ec2799b6bc..57f69a64e2 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_rigid_local.h" +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 1476c71d3f..a5efc22d11 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,10 +22,10 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_ehex.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "region.h" @@ -33,14 +33,9 @@ #include "force.h" #include "update.h" #include "modify.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "fix_shake.h" -#include "neighbor.h" -#include "comm.h" -#include "timer.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index e29ddac135..860ed3d1f3 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -22,8 +22,6 @@ FixStyle(ehex,FixEHEX) #define LMP_FIX_EHEX_H #include "fix.h" -#include "fix_shake.h" -#include "region.h" #define EHEX_DEBUG 0 namespace LAMMPS_NS { @@ -41,9 +39,9 @@ class FixEHEX : public Fix { double memory_usage(); void update_scalingmask(); void com_properties(double *, double *, double *, double*, double *, double*); - bool rescale_atom(int i, Region*region); + bool rescale_atom(int i, class Region *region); virtual void grow_arrays(int nmax); - bool check_cluster(tagint *shake_atom, int n, Region * region); + bool check_cluster(tagint *shake_atom, int n, class Region *region); private: int iregion; @@ -53,14 +51,14 @@ class FixEHEX : public Fix { char *idregion; int me; - double **x; // coordinates - double **f; // forces - double **v; // velocities - double *mass; // masses - double *rmass; // reduced masses - int *type; // atom types + double **x; // coordinates + double **f; // forces + double **v; // velocities + double *mass; // masses + double *rmass; // reduced masses + int *type; // atom types int nlocal; // number of local atoms - FixShake * fshake; // pointer to fix_shake/fix_rattle + class FixShake * fshake; // pointer to fix_shake/fix_rattle int constraints; // constraints (0/1) int cluster; // rescaling entire clusters (0/1) int hex; // HEX mode (0/1) diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 403f3091c6..93bf610e94 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -15,33 +15,22 @@ Contributing author: Peter Wirnsberger (University of Cambridge) ------------------------------------------------------------------------- */ +#include "fix_rattle.h" #include #include -#include #include -#include -#include "fix_rattle.h" #include "atom.h" -#include "atom_vec.h" -#include "molecule.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "domain.h" #include "force.h" -#include "bond.h" -#include "angle.h" #include "comm.h" -#include "group.h" -#include "fix_respa.h" -#include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; using namespace MathExtra; // set RATTLE_DEBUG 1 to check constraints at end of timestep diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index 48edaef379..cab148f10c 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -20,7 +20,6 @@ FixStyle(rattle,FixRattle) #ifndef LMP_FIX_RATTLE_H #define LMP_FIX_RATTLE_H -#include "fix.h" #include "fix_shake.h" namespace LAMMPS_NS { diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index abb669bc02..912f529403 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid.h" +#include #include -#include #include #include -#include "fix_rigid.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -31,7 +31,6 @@ #include "force.h" #include "input.h" #include "variable.h" -#include "output.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4dceb1b8b4..4738e253f6 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,10 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_rigid_nh.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "compute.h" @@ -32,7 +31,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5016d3f168..1545e913c0 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,10 +17,10 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_rigid_nh_small.h" +#include +#include +#include #include "math_extra.h" #include "atom.h" #include "compute.h" @@ -32,7 +32,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 45a4a8d09c..706e08ec12 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index d32e3043f4..32ac58220d 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_small.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index da5d5ffaa5..1f19fb4ec7 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index f1fd5470da..e8924be79f 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_small.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index dedd71c98d..14e230ab9c 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,11 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid_small.h" +#include #include -#include #include #include -#include "fix_rigid_small.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -31,7 +32,6 @@ #include "neighbor.h" #include "force.h" #include "input.h" -#include "output.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 23ced2d0e7..48a08118c5 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_shake.h" #include #include -#include +#include #include -#include -#include "fix_shake.h" -#include "fix_rattle.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 2e515839c5..5e85b39076 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_append_atoms.h" +#include #include #include -#include -#include "fix_append_atoms.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index c800e8a85d..2e9f751824 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,22 +17,19 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_msst.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "comm.h" -#include "output.h" #include "modify.h" #include "fix_external.h" #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" -#include "thermo.h" #include "memory.h" #include "error.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index c6df6646cf..8ad787d759 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nphug.h" +#include +#include #include "modify.h" #include "error.h" #include "update.h" @@ -22,8 +21,6 @@ #include "force.h" #include "domain.h" #include "group.h" -#include "memory.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index eb89e19517..5a359d9f6f 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_piston.h" #include #include -#include -#include "fix_wall_piston.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "lattice.h" #include "update.h" diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index cc7a84281e..7ca9d52467 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_sna_atom.h" #include #include -#include "compute_sna_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 0a82cdeb00..7744a23612 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_snad_atom.h" #include #include -#include "compute_snad_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 374bf32298..c26edf36e0 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_snav_atom.h" #include #include -#include "compute_snav_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -21,7 +22,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 4dce39361f..59b333fa31 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,24 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_snap.h" +#include #include #include #include -#include "pair_snap.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "sna.h" -#include "domain.h" #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 985110bdee..01d2d12b8f 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -18,14 +18,8 @@ #include "sna.h" #include #include "math_const.h" -#include "math_extra.h" -#include -#include - #include "memory.h" #include "error.h" -#include "comm.h" -#include "atom.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 8cc38dbc15..ad1384ffd2 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -23,16 +23,14 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "atom_vec_spin.h" #include -#include #include #include "atom.h" -#include "atom_vec_spin.h" #include "comm.h" #include "domain.h" #include "error.h" #include "fix.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "utils.h" diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 501b708c88..1f808eb1bd 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -21,21 +21,17 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include -#include "atom.h" #include "compute_spin.h" -#include "domain.h" +#include +#include +#include "atom.h" #include "error.h" #include "force.h" -#include "math_special.h" #include "math_const.h" #include "memory.h" -#include "modify.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathSpecial; using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index ec6f719a77..ec9c98c4f8 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -21,31 +21,19 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include +#include "fix_langevin_spin.h" #include #include -#include - -#include "atom.h" -#include "atom_vec_ellipsoid.h" #include "comm.h" -#include "compute.h" -#include "domain.h" #include "error.h" -#include "fix_langevin_spin.h" #include "force.h" -#include "group.h" -#include "input.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "modify.h" -#include "random_mars.h" #include "random_park.h" -#include "region.h" #include "respa.h" #include "update.h" -#include "variable.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -142,13 +130,11 @@ void FixLangevinSpin::init() void FixLangevinSpin::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) - post_force(vflag); - else { + if (utils::strmatch(update->integrate_style,"^respa")) { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); - } + } else post_force(vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index a8cb0cd2ca..5acbbf59e8 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -21,15 +21,13 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ +#include "fix_neb_spin.h" #include #include -#include #include -#include "fix_neb_spin.h" #include "universe.h" #include "update.h" #include "atom.h" -#include "domain.h" #include "comm.h" #include "modify.h" #include "compute.h" @@ -37,11 +35,9 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index b992f17cc3..b1b466b5a4 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -21,38 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nve_spin.h" #include - #include "atom.h" -#include "atom_vec.h" #include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_nve_spin.h" #include "fix_precession_spin.h" #include "fix_langevin_spin.h" #include "fix_setforce_spin.h" #include "force.h" -#include "math_vector.h" -#include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "pair.h" -#include "pair_hybrid.h" #include "pair_spin.h" -#include "respa.h" #include "update.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; -using namespace MathExtra; static const char cite_fix_nve_spin[] = "fix nve/spin command:\n\n" diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 4800575c06..1e3b87c1fb 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -21,8 +21,6 @@ FixStyle(nve/spin,FixNVESpin) #define LMP_FIX_NVE_SPIN_H #include "fix.h" -#include "pair.h" -#include "pair_spin.h" namespace LAMMPS_NS { diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 1ea134d367..3296b28228 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -21,21 +21,16 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "fix_precession_spin.h" +#include #include -#include -#include #include #include "atom.h" #include "error.h" -#include "domain.h" -#include "error.h" -#include "fix_precession_spin.h" #include "force.h" #include "input.h" #include "math_const.h" -#include "memory.h" #include "modify.h" -#include "neigh_list.h" #include "respa.h" #include "update.h" #include "variable.h" diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index c2807418ec..e36a9d260d 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -21,20 +21,15 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce_spin.h" #include "atom.h" #include "update.h" #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index dda414ff97..553526ea8e 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -17,11 +17,10 @@ Please cite the related publication: ------------------------------------------------------------------------- */ +#include "min_spin.h" #include #include -#include #include -#include "min_spin.h" #include "universe.h" #include "atom.h" #include "force.h" @@ -29,8 +28,6 @@ #include "output.h" #include "timer.h" #include "error.h" -#include "modify.h" -#include "math_special.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 46a0541488..2bcfe6573a 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -21,18 +21,12 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "neb_spin.h" #include #include #include #include -#include "neb_spin.h" #include "citeme.h" -#include "compute.h" #include "force.h" #include "universe.h" #include "atom.h" @@ -49,10 +43,8 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "math_const.h" using namespace LAMMPS_NS; -using namespace MathConst; static const char cite_neb_spin[] = "neb/spin command:\n\n" diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index c128eaffa4..568eca0957 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -20,7 +20,6 @@ CommandStyle(neb/spin,NEBSpin) #ifndef LMP_NEB_SPIN_H #define LMP_NEB_SPIN_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 929b79bef3..fef247c09b 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -21,26 +21,15 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include +#include "pair_spin.h" #include - #include "atom.h" -#include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "memory.h" #include "modify.h" #include "pair.h" -#include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "pair_spin.h" #include "update.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 1be8550c65..3a909e1d13 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_SPIN_H #define LMP_PAIR_SPIN_H -#include "pair.h" +#include "pair.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4ff198488a..fb0ec8bb20 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -21,16 +21,16 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_spin_dipole_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "math_const.h" diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index e3575a6a07..670fccfce2 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -13,20 +13,19 @@ /* ------------------------------------------------------------------------ Contributing authors: Julien Tranchida (SNL) - Stan Moore (SNL) + Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include - #include "pair_spin_dipole_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "kspace.h" @@ -59,12 +58,12 @@ lockfixnvespin(NULL) no_virial_fdotr_compute = 1; lattice_flag = 0; - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) mub = 9.274e-4; // in A.Ang^2 mu_0 = 785.15; // in eV/Ang/A^2 mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } @@ -243,7 +242,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; int *type = atom->type; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; @@ -314,36 +313,36 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) bij[2] = (3.0*bij[1] + pre2*expm2) * r2inv; bij[3] = (5.0*bij[2] + pre3*expm2) * r2inv; - compute_long(i,j,eij,bij,fmi,spi,spj); - compute_long_mech(i,j,eij,bij,fmi,spi,spj); + compute_long(i,j,eij,bij,fmi,spi,spj); + compute_long_mech(i,j,eij,bij,fmi,spi,spj); } // force accumulation - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - if (rsq <= local_cut2) { - evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + - spi[2]*fmi[2]; - evdwl *= hbar; - } + if (rsq <= local_cut2) { + evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + + spi[2]*fmi[2]; + evdwl *= hbar; + } } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); } } @@ -365,7 +364,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; double **fm_long = atom->fm_long; ilist = list->ilist; @@ -550,7 +549,7 @@ void PairSpinDipoleLong::write_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]) { - fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); + fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); } } } @@ -573,10 +572,10 @@ void PairSpinDipoleLong::read_restart(FILE *fp) if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) { - fread(&cut_spin_long[i][j],sizeof(int),1,fp); - } - MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); + if (me == 0) { + fread(&cut_spin_long[i][j],sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } } } diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 41430d230f..afd2deaa6a 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_dmi.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "fix.h" #include "fix_nve_spin.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_dmi.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index 93b6d9501e..cc28018ad0 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_exchange.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_exchange.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 1f1488b93c..6756ebc3cc 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_magelec.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_magelec.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 03041da17f..355ba20f39 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -21,29 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_neel.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_neel.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index d87d2b5e56..d5eec91f50 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -15,10 +15,10 @@ Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF) ------------------------------------------------------------------------- */ +#include "fix_srd.h" +#include #include #include -#include -#include "fix_srd.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +27,6 @@ #include "group.h" #include "update.h" #include "force.h" -#include "pair.h" #include "domain.h" #include "neighbor.h" #include "comm.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 24b0c3cec5..ab113df28a 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_srd.h" -#include "atom.h" -#include "modify.h" +#include +#include #include "fix.h" #include "domain.h" #include "lattice.h" diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index af7a489bb1..cd92750b9a 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -76,6 +76,23 @@ int MPI_Finalized(int *flag) /* ---------------------------------------------------------------------- */ +/* return "LAMMPS MPI STUBS" as name of the library */ + +int MPI_Get_library_version(char *version, int *resultlen) +{ + const char string[] = "LAMMPS MPI STUBS"; + int len; + + if (!version || !resultlen) return MPI_ERR_ARG; + + len = strlen(string); + memcpy(version,string,len+1); + *resultlen = len; + return MPI_SUCCESS; +} + +/* ---------------------------------------------------------------------- */ + /* return "localhost" as name of the processor */ int MPI_Get_processor_name(char *name, int *resultlen) diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h index 1eca1ec527..063dc542be 100644 --- a/src/STUBS/mpi.h +++ b/src/STUBS/mpi.h @@ -63,6 +63,7 @@ extern "C" { #define MPI_IN_PLACE NULL #define MPI_MAX_PROCESSOR_NAME 128 +#define MPI_MAX_LIBRARY_VERSION_STRING 128 typedef void MPI_User_function(void *invec, void *inoutvec, int *len, MPI_Datatype *datatype); @@ -79,6 +80,7 @@ typedef struct _MPI_Status MPI_Status; int MPI_Init(int *argc, char ***argv); int MPI_Initialized(int *flag); int MPI_Finalized(int *flag); +int MPI_Get_library_version(char *version, int *resultlen); int MPI_Get_processor_name(char *name, int *resultlen); int MPI_Get_version(int *major, int *minor); diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/USER-ADIOS/dump_atom_adios.cpp index 55d6c5fbf9..e711b8a583 100644 --- a/src/USER-ADIOS/dump_atom_adios.cpp +++ b/src/USER-ADIOS/dump_atom_adios.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_atom_adios.h" +#include #include "atom.h" #include "domain.h" #include "error.h" @@ -23,7 +24,6 @@ #include "memory.h" #include "universe.h" #include "update.h" -#include #include "adios2.h" diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/USER-ADIOS/dump_custom_adios.cpp index 67f3deeb64..ee6d7d7e49 100644 --- a/src/USER-ADIOS/dump_custom_adios.cpp +++ b/src/USER-ADIOS/dump_custom_adios.cpp @@ -16,6 +16,8 @@ ------------------------------------------------------------------------- */ #include "dump_custom_adios.h" +#include +#include #include "atom.h" #include "compute.h" #include "domain.h" @@ -30,8 +32,6 @@ #include "universe.h" #include "update.h" #include "variable.h" -#include -#include #include "adios2.h" diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index f53343ced1..e2a1768f55 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// LAMMPS #include "fix_atc.h" +#include +#include +#include #include "fix_nve.h" #include "atom.h" #include "force.h" @@ -24,7 +26,7 @@ #include "pointers.h" #include "comm.h" #include "group.h" -// ATC + #include "ATC_Method.h" #include "ATC_Transfer.h" #include "ATC_TransferKernel.h" @@ -34,10 +36,6 @@ #include "ATC_CouplingMass.h" #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" -// other -#include -#include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index bffe49e6c5..bce334a7b3 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -15,15 +15,12 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_wavepacket.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 7722c93121..a147a11081 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -15,15 +15,14 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_awpmd.h" +#include "pair_awpmd_cut.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" +#include "utils.h" #include "TCP/wpmd_split.h" @@ -62,7 +61,7 @@ void FixNVEAwpmd::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; awpmd_pair=(PairAWPMDCut *)force->pair; diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h index 140d234308..832f5821a3 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.h +++ b/src/USER-AWPMD/fix_nve_awpmd.h @@ -25,7 +25,6 @@ FixStyle(nve/awpmd,FixNVEAwpmd) #define LMP_FIX_NVE_awpmd_H #include "fix.h" -#include "pair_awpmd_cut.h" namespace LAMMPS_NS { @@ -45,7 +44,7 @@ class FixNVEAwpmd : public Fix { double *step_respa; int mass_require; - PairAWPMDCut *awpmd_pair; + class PairAWPMDCut *awpmd_pair; }; } diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 1b7bf35c28..75ebb0e251 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -15,11 +15,12 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_awpmd_cut.h" +#include +#include +#include +#include +#include #include "atom.h" #include "update.h" #include "min.h" @@ -32,6 +33,9 @@ #include "memory.h" #include "error.h" +#include "logexc.h" +#include "vector_3.h" +#include "TCP/wpmd.h" #include "TCP/wpmd_split.h" using namespace LAMMPS_NS; diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index c43910ec6d..d0a24b99a3 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -14,10 +14,11 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "compute_pressure_bocs.h" #include +#include #include #include -#include "compute_pressure_bocs.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 7bdb8933e3..936e5ff58e 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -14,11 +14,10 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "fix_bocs.h" #include #include #include -#include "fix_bocs.h" -#include "math_extra.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index 557d62aac6..682f325345 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -14,8 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include #include "bond_oxdna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 9d6453f5a8..f549fc423d 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -14,12 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include #include "bond_oxdna_fene.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 72b3388793..ff8e1c0ee2 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -14,16 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_dot.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" #include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index c73801c97a..59def4c812 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -15,10 +15,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_dotc_langevin.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -26,7 +25,6 @@ #include "update.h" #include "comm.h" #include "random_mars.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index c63a37cde2..e4ed1bbd03 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -14,7 +14,6 @@ #ifndef MF_OXDNA_H #define MF_OXDNA_H -#include #include "math_extra.h" namespace MFOxdna { diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 4fde5e37b4..609b63e27f 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna2_coaxstk.h" +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index ca5f44b815..630dd7a559 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -14,29 +14,21 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna2_dh.h" -#include "mf_oxdna.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; -using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index f2fb77b3b2..d8a263676f 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -14,10 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6b10117f91..d71acc2029 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna_coaxstk.h" +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index ddfe32946c..f187fc7403 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna_excv.h" +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 03e83e1324..e9852d0e38 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna_hbond.h" +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific base-pairing strength diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 3c7a3f05bc..3d0c4e9136 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna_stk.h" +#include +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific stacking strength diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index d5248937ca..95f5694818 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna_xstk.h" +#include +#include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 823c725e07..862c165bbd 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -18,9 +18,9 @@ lj/sdk potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ -#include -#include #include "angle_sdk.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "pair.h" diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index 293004ad4d..2e94b44470 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -20,7 +20,6 @@ AngleStyle(sdk,AngleSDK) #ifndef LMP_ANGLE_SDK_H #define LMP_ANGLE_SDK_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 7dd6c04436..1301dc4155 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -16,20 +16,14 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_sdk.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -37,7 +31,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 33a1659df9..62acf00d27 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -16,21 +16,16 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_sdk_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -38,7 +33,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define EWALD_F 1.12837917 diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index d26f8efcdc..f168089fae 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -16,28 +16,18 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_sdk_coul_msm.h" +#include +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" #include "error.h" #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index 651999f79c..2c43a3fb26 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -8,33 +8,22 @@ // Colvars repository at GitHub. +#include "colvarproxy_lammps.h" #include +#include +#include +#include +#include +#include +#include + #include "lammps.h" -#include "atom.h" #include "error.h" #include "output.h" #include "random_park.h" -#include "fix_colvars.h" - #include "colvarmodule.h" -#include "colvar.h" -#include "colvarbias.h" -#include "colvaratoms.h" #include "colvarproxy.h" -#include "colvarproxy_lammps.h" - -#include -#include -#include - -#include -#include -#include - -#include -#include -#include #define HASH_FAIL -1 diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index c3d9dbb35f..8ed03309a3 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -10,33 +10,22 @@ #ifndef COLVARPROXY_LAMMPS_H #define COLVARPROXY_LAMMPS_H -#include "colvarproxy_lammps_version.h" +#include "colvarproxy_lammps_version.h" // IWYU pragma: export + +#include +#include +#include +#include #include "colvarmodule.h" #include "colvarproxy.h" -#include "colvarvalue.h" +#include "colvartypes.h" -#include "lammps.h" -#include "domain.h" -#include "force.h" -#include "update.h" - -#include -#include -#include - -/* struct for packed data communication of coordinates and forces. */ -struct commdata { - int tag,type; - double x,y,z,m,q; -}; - -inline std::ostream & operator<< (std::ostream &out, const commdata &cd) -{ - out << " (" << cd.tag << "/" << cd.type << ": " - << cd.x << ", " << cd.y << ", " << cd.z << ") "; - return out; -} +#include "random_park.h" +#include "lammps.h" // IWYU pragma: keep +#include "domain.h" // IWYU pragma: keep +#include "force.h" // IWYU pragma: keep +#include "update.h" // IWYU pragma: keep /// \brief Communication between colvars and LAMMPS /// (implementation of \link colvarproxy \endlink) @@ -46,8 +35,8 @@ class colvarproxy_lammps : public colvarproxy { protected: // pointers to LAMMPS class instances - class LAMMPS_NS::LAMMPS *_lmp; - class LAMMPS_NS::RanPark *_random; + LAMMPS_NS::LAMMPS *_lmp; + LAMMPS_NS::RanPark *_random; // state of LAMMPS properties double t_target, my_timestep, my_boltzmann, my_angstrom; diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index ff0e8fb334..4a57e59fbd 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -24,27 +24,29 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include "fix_colvars.h" +#include #include #include -#include +#include +#include +#include +#include -#include "fix_colvars.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "group.h" +#include "force.h" #include "memory.h" #include "modify.h" -#include "random_park.h" #include "respa.h" #include "universe.h" #include "update.h" #include "citeme.h" #include "colvarproxy_lammps.h" +#include "colvarmodule.h" static const char colvars_pub[] = "fix colvars command:\n\n" @@ -57,6 +59,19 @@ static const char colvars_pub[] = " note = {doi: 10.1080/00268976.2013.813594}\n" "}\n\n"; +/* struct for packed data communication of coordinates and forces. */ +struct LAMMPS_NS::commdata { + int tag,type; + double x,y,z,m,q; +}; + +inline std::ostream & operator<< (std::ostream &out, const LAMMPS_NS::commdata &cd) +{ + out << " (" << cd.tag << "/" << cd.type << ": " + << cd.x << ", " << cd.y << ", " << cd.z << ") "; + return out; +} + /* re-usable integer hash table code with static linkage. */ /** hash table top level data structure */ diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index a0c197fca4..985457e746 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,10 +34,9 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" +#include -// forward declaration class colvarproxy_lammps; -struct commdata; namespace LAMMPS_NS { @@ -64,7 +63,7 @@ class FixColvars : public Fix { virtual void restart(char *); protected: - class colvarproxy_lammps *proxy; // pointer to the colvars proxy class + colvarproxy_lammps *proxy; // pointer to the colvars proxy class char *conf_file; // name of colvars config file char *inp_name; // name/prefix of colvars restart file char *out_name; // prefix string for all output files diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 858336c9d5..1e37e2de9c 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,15 +17,13 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" +#include +#include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 7b46364f18..a1369df2fb 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,17 +17,14 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" -#include "force.h" #include "error.h" -#include -#include -#include - using namespace LAMMPS_NS; #define BUFLEN 4096 #define DELTA 16384 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index dcafe57ba8..971d9bd380 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,13 +15,12 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ +#include "compute_saed.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_saed.h" #include "compute_saed_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index d6b7549272..f48951f1ff 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,13 +16,12 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ +#include "compute_xrd.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_xrd.h" #include "compute_xrd_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 4d9af66818..c3a72e494b 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -16,17 +16,14 @@ Incorporating SAED: Shawn Coleman (Arkansas) ------------------------------------------------------------------------- */ +#include "fix_saed_vtk.h" #include #include #include -#include "fix_saed_vtk.h" #include "update.h" #include "modify.h" #include "compute.h" #include "compute_saed.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index 2fc09c781c..94abbf0194 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -20,7 +20,6 @@ FixStyle(saed/vtk,FixSAEDVTK) #ifndef LMP_FIX_SAED_VTK_H #define LMP_FIX_SAED_VTK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index de673caec0..d1768d473e 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 08aa19bcdf..0ef7868164 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -15,13 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "compute_dpd.h" +#include #include "atom.h" #include "update.h" -#include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index 78f842a68f..0fd732f669 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -15,21 +15,15 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_dpd_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "group.h" #include "memory.h" #include "error.h" #include "comm.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index 5759a164f5..6ee88ea88a 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -11,14 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_dpd_energy.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" #include "pair_dpd_fdt_energy.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index 919e6829f3..5b25519a40 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -15,8 +15,6 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include #include "fix_eos_cv.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 7d701f5fb8..ff9a186c47 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -15,9 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table.h" +#include #include #include -#include "fix_eos_table.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 779cee0e8b..9f1bd6a3bb 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -15,10 +15,11 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table_rx.h" +#include #include #include #include -#include "fix_eos_table_rx.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index cb8349786f..03e8ae49a4 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_rx.h" +#include #include #include #include #include // DBL_EPSILON -#include "fix_rx.h" #include "atom.h" #include "error.h" #include "group.h" diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 4e133480ad..b0efeb634d 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -33,27 +33,25 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include +#include "fix_shardlow.h" #include #include #include -#include "fix_shardlow.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "npair.h" #include "memory.h" #include "domain.h" #include "modify.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "pair.h" #include "npair_half_bin_newton_ssa.h" #include "citeme.h" diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp index dcd434cb4a..e3fa71aedf 100644 --- a/src/USER-DPD/nbin_ssa.cpp +++ b/src/USER-DPD/nbin_ssa.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "group.h" #include "domain.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp index ba90ebc465..2139173d47 100644 --- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp +++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp @@ -17,7 +17,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_ssa.h" -#include "neighbor.h" #include "nstencil_ssa.h" #include "nbin_ssa.h" #include "neigh_list.h" @@ -25,7 +24,6 @@ #include "atom_vec.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "memory.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp index 451381c104..9953fca62c 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp index cdd3b8856f..4dd3c4a5fe 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 07ef8190f0..1cb9d68d06 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 12e6989c00..22741a055d 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt_energy.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 13521b52b1..5cf2859ae3 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_exp6_rx.h" +#include #include -#include #include #include #include -#include "pair_exp6_rx.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" @@ -29,7 +28,6 @@ #include "fix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index f2d0d7b1fb..e767f93367 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx.h" #include #include -#include #include -#include "pair_table_rx.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 4830e950d0..a12c248680 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -11,19 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_drude.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" -#include "group.h" #include "modify.h" -#include "fix.h" +#include "fix_drude.h" #include "domain.h" -#include "lattice.h" -#include "memory.h" #include "error.h" #include "comm.h" diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/USER-DRUDE/compute_temp_drude.h index 88d767f8b7..530c84ce3d 100644 --- a/src/USER-DRUDE/compute_temp_drude.h +++ b/src/USER-DRUDE/compute_temp_drude.h @@ -21,7 +21,6 @@ ComputeStyle(temp/drude,ComputeTempDrude) #define LMP_COMPUTE_TEMP_DRUDE_H #include "compute.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -37,7 +36,7 @@ class ComputeTempDrude : public Compute { private: int fix_dof; - FixDrude * fix_drude; + class FixDrude * fix_drude; char *id_temp; class Compute *temperature; bigint dof_core, dof_drude; diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 7800efe7ff..080408459c 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_drude.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "modify.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 34742a0683..4128c508d6 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ /** Fix Drude Transform ******************************************************/ +#include "fix_drude_transform.h" +#include #include #include -#include "fix_drude_transform.h" +#include "fix_drude.h" #include "atom.h" #include "domain.h" #include "comm.h" #include "error.h" #include "modify.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/USER-DRUDE/fix_drude_transform.h index 41f4e147ed..b74a500c95 100644 --- a/src/USER-DRUDE/fix_drude_transform.h +++ b/src/USER-DRUDE/fix_drude_transform.h @@ -22,7 +22,6 @@ FixStyle(drude/transform/inverse,FixDrudeTransform) #define LMP_FIX_DRUDE_TRANSFORM_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -42,7 +41,7 @@ class FixDrudeTransform : public Fix { void unpack_forward_comm(int n, int first, double *buf); protected: double * mcoeff; - FixDrude * fix_drude; + class FixDrude * fix_drude; }; } diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index b9d1139f83..d413c31bd7 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -11,17 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_langevin_drude.h" +#include +#include +#include +#include "fix_drude.h" #include "atom.h" #include "force.h" #include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" -#include "group.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/USER-DRUDE/fix_langevin_drude.h index d65440582c..9437883ba3 100644 --- a/src/USER-DRUDE/fix_langevin_drude.h +++ b/src/USER-DRUDE/fix_langevin_drude.h @@ -21,7 +21,6 @@ FixStyle(langevin/drude,FixLangevinDrude) #define LMP_FIX_LANGEVIN_DRUDE_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -51,7 +50,7 @@ class FixLangevinDrude : public Fix { class RanMars *random_core, *random_drude; int zero; bigint ncore; - FixDrude * fix_drude; + class FixDrude * fix_drude; class Compute *temperature; char *id_temp; }; diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 1ebe4a4c2d..851effd89c 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -15,20 +15,17 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_thole_long.h" +#include +#include +#include +#include "fix_drude.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/USER-DRUDE/pair_lj_cut_thole_long.h index 27a917c737..4c3a883064 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.h +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.h @@ -21,7 +21,6 @@ PairStyle(lj/cut/thole/long,PairLJCutTholeLong) #define LMP_PAIR_LJ_CUT_THOLE_LONG_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -58,7 +57,7 @@ class PairLJCutTholeLong : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude *fix_drude; + class FixDrude *fix_drude; virtual void allocate(); }; diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 1bb75af825..1f81263e95 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_thole.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -24,7 +23,7 @@ #include "memory.h" #include "error.h" #include "fix.h" -#include "fix_store.h" +#include "fix_drude.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-DRUDE/pair_thole.h b/src/USER-DRUDE/pair_thole.h index 2c462b431a..88c00b6d20 100644 --- a/src/USER-DRUDE/pair_thole.h +++ b/src/USER-DRUDE/pair_thole.h @@ -21,7 +21,6 @@ PairStyle(thole,PairThole) #define LMP_PAIR_THOLE_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -46,7 +45,7 @@ class PairThole : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude * fix_drude; + class FixDrude * fix_drude; virtual void allocate(); }; diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index cf4555f02e..552a89c04a 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,15 +15,12 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_electron.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "citeme.h" #include "memory.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index b1b87cd3df..c943366f1b 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -15,7 +15,6 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include #include #include #include "compute_ke_atom_eff.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index b4f571cb63..3e277fc66c 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "compute_ke_eff.h" #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 621eff210f..dcf7e86234 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_deform_eff.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 956461adf1..e9295ea680 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -15,11 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "compute_temp_eff.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 8cab690367..b27699cde9 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" #include "force.h" -#include "modify.h" #include "domain.h" #include "region.h" #include "group.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index d362113997..5158d7c681 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -17,19 +17,13 @@ #include #include -#include #include #include "fix_langevin_eff.h" -#include "math_extra.h" #include "atom.h" -#include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 3e0a59612c..034233732e 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,12 +15,10 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include #include #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "domain.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 699dd9f949..ea719c91c0 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,8 +15,6 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include #include #include "fix_nve_eff.h" diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 9e23ee023b..8516accd31 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "fix_nvt_eff.h" #include "group.h" #include "modify.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index ed2274dcf9..0ebbf04d64 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include "fix_nvt_sllod_eff.h" #include "math_extra.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 37f45b3c28..4a8f4b0372 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -23,8 +23,6 @@ #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index f566922ef7..a4c0557620 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ +#include #include -#include #include #include #include "pair_eff_cut.h" @@ -31,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "atom_vec_electron.h" using namespace LAMMPS_NS; diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index dc0b71e71b..1853828db3 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -15,7 +15,7 @@ Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include +#include "compute_fep.h" #include #include #include @@ -34,7 +34,6 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "compute_fep.h" using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 7304bc4ef6..46cf32cf0b 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -15,10 +15,8 @@ Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_adapt_fep.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index 86a6d02819..a4ff3ca846 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_cut_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 9d3ffc0da1..c0030f8935 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -16,19 +16,16 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_long_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index ac6f1e6384..4c3be6addb 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_long_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index ae79515488..bbe67e4ff3 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_cut_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 275486d1e2..a3e0f732a2 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_coul_long_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index d22cd53883..d98a5db5f3 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_class2_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 35c9162dbc..38fcb6fc07 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_cut_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 79253d2b9c..740daabf62 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_long_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 4192d6546b..5e9a77877e 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -16,11 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -28,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 8ac28f9fa9..d4f6dcb910 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_tip4p_long_soft.h" +#include +#include +#include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 21f616a082..2803e7df49 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_morse_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 9b6a6841fe..9cea5b54c5 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tip4p_long_soft.h" +#include +#include +#include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 5d173ee6a9..155ecfaff9 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -24,7 +24,6 @@ AngleStyle(charmm/intel,AngleCharmmIntel) #ifndef LMP_ANGLE_CHARMM_INTEL_H #define LMP_ANGLE_CHARMM_INTEL_H -#include #include "angle_charmm.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index e7768542a1..c00292f7ce 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -24,7 +24,6 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel) #ifndef LMP_ANGLE_HARMONIC_INTEL_H #define LMP_ANGLE_HARMONIC_INTEL_H -#include #include "angle_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index afe3b85470..58fcdb8669 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -24,7 +24,6 @@ BondStyle(fene/intel,BondFENEIntel) #ifndef LMP_BOND_FENE_INTEL_H #define LMP_BOND_FENE_INTEL_H -#include #include "bond_fene.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index b86a560d6e..3c1d050a3b 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -24,7 +24,6 @@ BondStyle(harmonic/intel,BondHarmonicIntel) #ifndef LMP_BOND_HARMONIC_INTEL_H #define LMP_BOND_HARMONIC_INTEL_H -#include #include "bond_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index e815fa75c9..812b49d50c 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -24,7 +24,6 @@ ImproperStyle(cvff/intel,ImproperCvffIntel) #ifndef LMP_IMPROPER_CVFF_INTEL_H #define LMP_IMPROPER_CVFF_INTEL_H -#include #include "improper_cvff.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index ce38e8fc31..6d7c829961 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -24,7 +24,6 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel) #ifndef LMP_IMPROPER_HARMONIC_INTEL_H #define LMP_IMPROPER_HARMONIC_INTEL_H -#include #include "improper_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 75fc9828b9..9022f439c4 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -29,7 +29,6 @@ authors for more details. #ifndef INTEL_SIMD_H #define INTEL_SIMD_H -#include #include "intel_preprocess.h" #include "immintrin.h" diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index 83b1fbf6a1..a9590f6b3d 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -20,7 +20,6 @@ PairStyle(eam/intel,PairEAMIntel) #ifndef LMP_PAIR_EAM_INTEL_H #define LMP_PAIR_EAM_INTEL_H -#include #include "pair_eam.h" #include "fix_intel.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 31c54aee76..8ad3dbe33e 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -20,15 +20,14 @@ #include #include #include -#include #include +#include +#include #include "comm.h" #include "memory.h" #include "error.h" #include "domain.h" #include "atom.h" -#include -#include #include "group.h" #include "random_mars.h" #include "update.h" diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index df17561380..10fffed018 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -18,16 +18,15 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ +#include "fix_lb_momentum.h" +#include #include #include -#include "fix_lb_momentum.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "error.h" #include "fix_lb_fluid.h" #include "modify.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index ce6ca0c9a1..d61692419a 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -15,17 +15,14 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_lb_pc.h" +#include +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory.h" -#include "comm.h" #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 83dc751631..af1b01043d 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -16,21 +16,18 @@ Based on fix_rigid (version from 2008). ------------------------------------------------------------------------- */ +#include "fix_lb_rigid_pc_sphere.h" +#include #include -#include #include #include -#include "fix_lb_rigid_pc_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "group.h" #include "comm.h" #include "force.h" -#include "output.h" #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index afe23477be..59fddebd67 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -15,10 +15,8 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_lb_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 00293bfec7..74a9a1833f 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_manifoldforce.h" // For stuff +#include #include -#include #include "atom.h" #include "update.h" #include "respa.h" @@ -21,7 +21,6 @@ #include "force.h" #include "manifold.h" -#include "fix_manifoldforce.h" // For stuff #include "manifold_factory.h" // For constructing manifold diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 527bee3f86..1d5afc7afc 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -43,9 +43,9 @@ FixStyle(manifoldforce,FixManifoldForce) #define LMP_FIX_MANIFOLDFORCE_H #include "fix.h" -#include "manifold.h" namespace LAMMPS_NS { +namespace user_manifold { class manifold; } class FixManifoldForce : public Fix { public: diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index de134e32ed..7f8d9d5675 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -32,24 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nve_manifold_rattle.h" +#include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include "group.h" -#include #include "input.h" #include "variable.h" #include "citeme.h" -#include "memory.h" #include "comm.h" - -#include "fix_nve_manifold_rattle.h" #include "manifold_factory.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 2bc821ab04..581ecf36d3 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -42,12 +42,10 @@ FixStyle(nve/manifold/rattle,FixNVEManifoldRattle) #define LMP_FIX_NVE_MANIFOLD_RATTLE_H #include "fix.h" -#include "manifold.h" - namespace LAMMPS_NS { -// namespace user_manifold { +namespace user_manifold { class manifold; } class FixNVEManifoldRattle : public Fix { public: @@ -98,9 +96,7 @@ namespace LAMMPS_NS { user_manifold::manifold *ptr_m; - void print_stats( const char * ); - int was_var( const char * ); virtual void update_var_params(); diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index a4eed66336..2789f8738a 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -32,25 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nvt_manifold_rattle.h" #include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "group.h" -#include "input.h" -#include "variable.h" #include "citeme.h" -#include "memory.h" -#include "comm.h" #include "modify.h" #include "compute.h" -#include "fix_nvt_manifold_rattle.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index cc3e1245bf..ac2aee8a26 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -35,8 +35,7 @@ #ifndef LMP_MANIFOLD_FACTORY_H #define LMP_MANIFOLD_FACTORY_H - -#include "manifold.h" +#include #include /* @@ -79,14 +78,16 @@ static FILE *screen = fopen("/dev/stdout","w"); #define FLERR __FILE__,__LINE__ // Equivalent to definition in pointers.h #endif // USE_PHONY_LAMMPS - - /* Here the actual implementation of LAMMPS-related functions begins. */ namespace LAMMPS_NS { +class LAMMPS; namespace user_manifold { +// forward declaration +class manifold; + // Templated, so needs to be in header. template void make_manifold_if( manifold **man_ptr, const char *name, @@ -103,8 +104,6 @@ namespace user_manifold { int , char ** ); } // namespace user_manifold - } // namespace LAMMPS_NS - #endif // LMP_MANIFOLD_FACTORY_H diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 530e0a876d..e4ef039832 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,6 +1,6 @@ #include "manifold_thylakoid.h" #include - +#include "manifold_thylakoid_shared.h" #include "comm.h" #include "domain.h" // For some checks regarding the simulation box. #include "error.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 5e5d3b9c41..35ad4dfd9c 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -3,14 +3,11 @@ #include "manifold.h" #include -#include - -#include "manifold_thylakoid_shared.h" namespace LAMMPS_NS { namespace user_manifold { - + struct thyla_part; class manifold_thylakoid : public manifold { public: diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index ff9027dfb3..da55805790 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,13 +1,12 @@ #ifndef LMP_MEAM_H #define LMP_MEAM_H -#include "memory.h" #include -#include #define maxelt 5 namespace LAMMPS_NS { +class Memory; typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t; diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index c55b1b45c4..867106df88 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,5 +1,4 @@ #include "meam.h" -#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 3bb9328142..155941422c 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,4 +1,6 @@ #include "meam.h" +#include +#include "memory.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 06fbb57adb..09aad90111 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,6 +1,7 @@ #include "meam.h" -#include "math_special.h" +#include #include +#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index b099ead8d5..74e8af1cde 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "meam.h" +#include #include "memory.h" using namespace LAMMPS_NS; @@ -43,7 +44,7 @@ MEAM::MEAM(Memory* mem) rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0; for (int j = 0; j < maxelt; j++) { lattce_meam[i][j] = FCC; - Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; + Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0; } } diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 2a762d1204..7000eac6ae 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,6 +1,10 @@ #include "meam.h" -#include "math_special.h" +#include +#include #include +#include "math_special.h" +#include "memory.h" + using namespace LAMMPS_NS; void diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 7c96fadb44..a9034a1af3 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -15,16 +15,14 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_meamc.h" +#include #include #include #include "meam.h" -#include "pair_meamc.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index a006e70bdb..31dd8ba022 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -24,7 +24,6 @@ PairStyle(meam,PairMEAMC) #include "pair.h" namespace LAMMPS_NS { -class MEAM; class PairMEAMC : public Pair { public: diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index eee8ae25b0..edc7a34331 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -10,13 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_edpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index fd3c01f0c6..4c9db36645 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_mdpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index f91731f8ac..74ac47066b 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -11,19 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_tdpd.h" +#include #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "update.h" #include "memory.h" #include "error.h" -#include "input.h" #include "utils.h" using namespace LAMMPS_NS; @@ -66,7 +63,7 @@ void AtomVecTDPD::process_args(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command"); - atom->cc_species = force->inumeric(FLERR,arg[0]); + atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp); cc_species = atom->cc_species; // reset sizes that depend on cc_species @@ -802,7 +799,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) x[nlocal][2] = coord[2]; for(int k = 0; k < cc_species; k++) - cc[nlocal][k] = atof( values[5+k] ); + cc[nlocal][k] = utils::numeric(FLERR,values[5+k],true,lmp); image[nlocal] = imagetmp; diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp index 119e0079d1..9eb6e9752b 100644 --- a/src/USER-MESO/compute_edpd_temp_atom.cpp +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_edpd_temp_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index 24bef2b1f7..e62d9a8a79 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_edpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index f663165f78..116bbf506a 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -20,13 +20,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_dpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 8719d0d262..bd9cd9cc2a 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -29,13 +29,11 @@ Communications, 2015, 51: 11038-11040. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_edpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index 24b1bbcf48..b7fe37d7ee 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -25,13 +25,11 @@ -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_tdpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index 89e8005b43..990f6a5b78 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_tdpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index e428b02822..f72b6d6b93 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -16,14 +16,12 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_edpd.h" +#include #include -#include -#include #include #include -#include "pair_edpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 4102499d46..56adad26ce 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -16,13 +16,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_mdpd.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index 2fd238088c..05cb123f61 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -19,9 +19,8 @@ Contributing author: Zhen Li (Brown University) ------------------------------------------------------------------------- */ -#include -#include #include "pair_mdpd_rhosum.h" +#include #include "atom.h" #include "force.h" #include "comm.h" @@ -30,8 +29,6 @@ #include "memory.h" #include "error.h" #include "neighbor.h" -#include "update.h" -#include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 7df9d6d163..346401b1ba 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -16,13 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tdpd.h" +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp index 68701037f4..bc15873739 100644 --- a/src/USER-MGPT/mgpt_linalg.cpp +++ b/src/USER-MGPT/mgpt_linalg.cpp @@ -20,8 +20,6 @@ #include #include -#include -#include #define restrict __restrict__ diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h index c19ea40774..8f46592e8a 100644 --- a/src/USER-MGPT/mgpt_readpot.h +++ b/src/USER-MGPT/mgpt_readpot.h @@ -20,7 +20,8 @@ #define READPOT__ #include - +#include +#include #include "mgpt_splinetab.h" struct potdata { diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index 91c624eec5..0634872c70 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -21,17 +21,16 @@ (2011). See LLNL copyright notice at bottom of this file. ------------------------------------------------------------------------- */ +#include "pair_mgpt.h" +#include #include -#include #include #include #include -#include "pair_mgpt.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index 94c66fb603..ff71edc9f3 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -30,9 +30,7 @@ PairStyle(mgpt,PairMGPT) #ifndef LMP_PAIR_MGPT_H #define LMP_PAIR_MGPT_H -#include -#include -#include +#include #include #include "pair.h" @@ -78,29 +76,29 @@ public: Link(const K &k,Link *n) : next(n),key(k),hits(1) {} static void *operator new(std::size_t sz) { - const size_t align = 32; - size_t x = (size_t) (void *) ::operator new(sz+align); - size_t y = (x + align) - ((x+align)&(align-1)); - assert(sizeof(void *) <= align); - assert((x & (sizeof(void *)-1)) == 0); - ((void **) y)[-1] = (void *) x; - return (void *) y; + const size_t align = 32; + size_t x = (size_t) (void *) ::operator new(sz+align); + size_t y = (x + align) - ((x+align)&(align-1)); + assert(sizeof(void *) <= align); + assert((x & (sizeof(void *)-1)) == 0); + ((void **) y)[-1] = (void *) x; + return (void *) y; } static void operator delete(void *ptr) { - ::operator delete(((void **) ptr)[-1]); + ::operator delete(((void **) ptr)[-1]); } }; int isprime(int x) { if(x%2 == 0) - return 0; + return 0; else { - int k = 3; - while(k*k <= x) { - if(x%k == 0) return 0; - k = k+2; - } - return 1; + int k = 3; + while(k*k <= x) { + if(x%k == 0) return 0; + k = k+2; + } + return 1; } } @@ -118,25 +116,25 @@ public: Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); } Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {} void next() { - if(idx >= H.Size()) return; - if(p != 0) p = p->next; - if(p == 0) { - do { - idx = idx+1; - if(idx >= H.Size()) return; - p = H.table[idx]; - } while(p == 0); - } + if(idx >= H.Size()) return; + if(p != 0) p = p->next; + if(p == 0) { + do { + idx = idx+1; + if(idx >= H.Size()) return; + p = H.table[idx]; + } while(p == 0); + } } K *key() { return &p->key; } T *data() { return &p->data; } Link *link() { return p; } int operator==(const Iterator &a) { - return idx==a.idx && p==a.p; + return idx==a.idx && p==a.p; } int operator!=(const Iterator &a) { - return !(*this == a); + return !(*this == a); } }; @@ -148,7 +146,7 @@ public: table = new Link *[size]; for(int i = 0; inext; - delete p; - p = q; - } + Link *p = table[i]; + while(p != 0) { + Link *q = p->next; + delete p; + p = q; + } } delete[] table; } @@ -180,24 +178,24 @@ public: int idx = key.hash() % size; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } used = used + 1; if(1) { - table[idx] = new Link(key,table[idx]); - return &table[idx]->data; + table[idx] = new Link(key,table[idx]); + return &table[idx]->data; } else { /* This is for threading... and incomplete */ - typedef Link *LinkPtr; - LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); + typedef Link *LinkPtr; + LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); - while(ptr != 0) { - last = ptr; - ptr = ptr->next; - } - *((volatile LinkPtr *) &(last->next)) = dataptr; - return &(dataptr->data); + while(ptr != 0) { + last = ptr; + ptr = ptr->next; + } + *((volatile LinkPtr *) &(last->next)) = dataptr; + return &(dataptr->data); } } void Remove(const K &key) { @@ -206,28 +204,28 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - last = p; - p = p->next; - count = count + 1; + last = p; + p = p->next; + count = count + 1; } if(p != 0) { - used = used - 1; - if(last == 0) - table[idx] = p->next; - else - last->next = p->next; - delete p; + used = used - 1; + if(last == 0) + table[idx] = p->next; + else + last->next = p->next; + delete p; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; } @@ -237,19 +235,19 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - p = p->next; - count = count + 1; + p = p->next; + count = count + 1; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; @@ -284,46 +282,46 @@ public: } void zero() { for(int i = 0; i<8; i++) - for(int j = 0; j<8; j++) - m[i][j] = 0.0; + for(int j = 0; j<8; j++) + m[i][j] = 0.0; } void operator=(const Matrix &A) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = A.m[i][j]; + for(int j = 1; j<=sz; j++) + m[i][j] = A.m[i][j]; } void operator=(double x) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = x; + for(int j = 1; j<=sz; j++) + m[i][j] = x; } Matrix operator+(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] + B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] + B.m[i][j]; return s; } Matrix operator-(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] - B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] - B.m[i][j]; return s; } Matrix operator-() const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = -m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = -m[i][j]; return s; } Matrix operator*(double x) const { Matrix P; for(int i = 1; i<=sz; i++) - for(int j = 0; j<=sz; j++) - P.m[i][j] = m[i][j] * x; + for(int j = 0; j<=sz; j++) + P.m[i][j] = m[i][j] * x; return P; } Matrix operator/(double x) const { @@ -332,8 +330,8 @@ public: Matrix transpose() const { Matrix T; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - T.m[j][i] = m[i][j]; + for(int j = 1; j<=sz; j++) + T.m[j][i] = m[i][j]; return T; } }; @@ -375,13 +373,13 @@ public: int align_check() { return - (H1H2.align_check() << 0) | - (H1xH2.align_check() << 1) | - (H1yH2.align_check() << 2) | - (H1zH2.align_check() << 3) | - (H1H2x.align_check() << 4) | - (H1H2y.align_check() << 5) | - (H1H2z.align_check() << 6) ; + (H1H2.align_check() << 0) | + (H1xH2.align_check() << 1) | + (H1yH2.align_check() << 2) | + (H1zH2.align_check() << 3) | + (H1H2x.align_check() << 4) | + (H1H2y.align_check() << 5) | + (H1H2z.align_check() << 6) ; } void zero() { @@ -397,18 +395,18 @@ public: void make_bond(const double xx[][3],int i,int j,bond_data *bptr); void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr); triplet_data *get_triplet(const double xx[][3],int i,int j,int k, - Hash *bhash,triplet_data *twork, - double *dvir_ij_p,double *dvir_ik_p); + Hash *bhash,triplet_data *twork, + double *dvir_ij_p,double *dvir_ik_p); int c1_outside(const double a[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; + double cog = a[p]; + if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; } } else { @@ -416,63 +414,63 @@ public: for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; - if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; + double cog = a[p]; + if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; + if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rmax*rmax) - return 1; + return 1; } return 0; } int c2_outside(const double a[3],const double b[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; } } else { double rout = 0.0; for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; - if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; + if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rcrit*rcrit) - return 1; + return 1; } return 0; } double get_weight(const int triclinic, - const double a[3] = 0,const double b[3] = 0, - const double c[3] = 0,const double d[3] = 0) { + const double a[3] = 0,const double b[3] = 0, + const double c[3] = 0,const double d[3] = 0) { const double *s0 = triclinic ? domain->sublo_lamda : domain->sublo, *s1 = triclinic ? domain->subhi_lamda : domain->subhi; @@ -499,46 +497,46 @@ public: } void force_debug_3t(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_3v(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_4(double xx[][3], - int i0,int j0,int k0,int m0, - int i ,int j ,int k ,int m , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz, - double dfmx,double dfmy,double dfmz); + int i0,int j0,int k0,int m0, + int i ,int j ,int k ,int m , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz, + double dfmx,double dfmy,double dfmz); double numderiv3t(double xx[][3],int i,int j,int k,int p); double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert); double numderiv4(double xx[][3],int i,int j,int k,int m,int p); void compute_x(const int *nnei,const int * const *nlist, - double *e_s,double *e_p,double *e_t,double *e_q, - int evflag,int newton_pair); + double *e_s,double *e_p,double *e_t,double *e_q, + int evflag,int newton_pair); /* Reimplementation of bond matrix computation */ void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat, - double &fl_0,double &fl_x,double &fl_y,double &fl_z, - double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); + double &fl_0,double &fl_x,double &fl_y,double &fl_z, + double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); void hamltn_5_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); void hamltn_7_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); /* * */ // Old matrix routines, only used in force debug routines. @@ -547,9 +545,9 @@ public: Matrix h; for(int l = 1; l <= lmax; l++) { for(int n = 1; n <= lmax; n++) { - h.m[l][n] = 0.0; - for(int m = 1; m <= lmax; m++) - h.m[l][n] += ha.m[l][m] * hb.m[m][n]; + h.m[l][n] = 0.0; + for(int m = 1; m <= lmax; m++) + h.m[l][n] += ha.m[l][m] * hb.m[m][n]; } } return h; @@ -561,7 +559,7 @@ public: for(int n = 1; n <= lmax; n++) { double cquan = 0.0; for(int m = 1; m <= lmax; m++) - cquan += ha.m[n][m] * hb.m[m][n]; + cquan += ha.m[n][m] * hb.m[m][n]; zquan += cquan; } return zquan; @@ -573,32 +571,32 @@ public: int i,j,k; if(lmax == 5) { - const int n = 5; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 5; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else if(lmax == 7) { - const int n = 7; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 7; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else { - const int n = lmax; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = lmax; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } } @@ -609,7 +607,7 @@ public: for(i = 0; i -#include #include "angle_cosine_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index 030709a0e2..febabcc090 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -20,7 +20,6 @@ AngleStyle(cosine/shift,AngleCosineShift) #ifndef LMP_ANGLE_COSINE_SHIFT_H #define LMP_ANGLE_COSINE_SHIFT_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 8c6282de20..79cb0fea7c 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_shift_exp.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 8b8e389380..9614ddcc19 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -18,7 +18,6 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp) #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H #define LMP_ANGLE_COSINE_SHIFT_EXP_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 781da46869..0956ba3b8f 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -15,9 +15,9 @@ Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk ------------------------------------------------------------------------- */ -#include -#include #include "angle_dipole.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 6c5dccb803..187822d0d4 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -20,7 +20,6 @@ AngleStyle(dipole,AngleDipole) #ifndef LMP_ANGLE_DIPOLE_H #define LMP_ANGLE_DIPOLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 8f5074ff5d..dcf5080431 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index 14b4eedf57..53eeea98da 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -20,7 +20,6 @@ AngleStyle(fourier,AngleFourier) #ifndef ANGLE_FOURIER_H #define ANGLE_FOURIER_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index 615556bbe7..bbe3f8520b 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier_simple.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index 3a7bd37750..df2253317f 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -20,7 +20,6 @@ AngleStyle(fourier/simple,AngleFourierSimple) #ifndef ANGLE_FOURIER_SIMPLE_H #define ANGLE_FOURIER_SIMPLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 21a96100aa..5c5f3411e4 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -16,9 +16,9 @@ [ based on angle_harmonic.cpp] ------------------------------------------------------------------------- */ -#include -#include #include "angle_quartic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index 7043cab064..b916a5f89f 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -20,7 +20,6 @@ AngleStyle(quartic,AngleQuartic) #ifndef LMP_ANGLE_QUARTIC_H #define LMP_ANGLE_QUARTIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index c7e4444cce..fdd3111783 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index ff0d358243..b77cefb4af 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift,BondHarmonicShift) #ifndef LMP_BOND_HARMONIC_SHIFT_H #define LMP_BOND_HARMONIC_SHIFT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 5b396f5d72..0688cb428a 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift_cut.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index 5db76d51aa..ad2bcd61ad 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut) #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H #define LMP_BOND_HARMONIC_SHIFT_CUT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index 6fa16f1a9a..ba97be25d4 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -21,11 +21,10 @@ branicio@usc.edu ------------------------------------------------------------------------- */ -#include -#include -#include - #include "compute_cnp_atom.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp index 0367d7fe6d..00f7e6dc8b 100644 --- a/src/USER-MISC/compute_entropy_atom.cpp +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -15,10 +15,9 @@ Contributing author: Pablo Piaggi (EPFL Lausanne) ------------------------------------------------------------------------- */ +#include "compute_entropy_atom.h" #include #include -#include -#include "compute_entropy_atom.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -28,13 +27,11 @@ #include "force.h" #include "pair.h" #include "comm.h" -#include "math_extra.h" #include "math_const.h" #include "memory.h" #include "error.h" #include "domain.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index c250eaf677..6d2509d685 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_cylinder.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -22,7 +21,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" #include "citeme.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index 087c01bd8e..ba949727b0 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_grem.h" -#include "atom.h" +#include #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index cb2a0b9713..2f932321e1 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop.h" #include #include #include -#include -#include "compute_stress_mop.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 5499a37a46..5f6d0a36b2 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop_profile.h" #include #include #include -#include -#include "compute_stress_mop_profile.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 36093bd1e1..94c6115186 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -15,16 +15,13 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_rotate.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index c411ea8150..820dfabdeb 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -15,14 +15,12 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ +#include "dihedral_cosine_shift_exp.h" #include #include -#include -#include "dihedral_cosine_shift_exp.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index fc4be5049b..4d180f42de 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -20,7 +20,6 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp) #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index af86259c01..7cc250b1a8 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -16,16 +16,13 @@ [ based on dihedral_charmm.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_fourier.h" #include #include -#include -#include "dihedral_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "pair.h" #include "update.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index c1ed843c34..8b6291fc4c 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -20,7 +20,6 @@ DihedralStyle(fourier,DihedralFourier) #ifndef LMP_DIHEDRAL_FOURIER_H #define LMP_DIHEDRAL_FOURIER_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index ea2b76f415..f1e0018689 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_nharmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 7c6a35b200..6fd1da3b8b 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -20,7 +20,6 @@ DihedralStyle(nharmonic,DihedralNHarmonic) #ifndef DIHEDRAL_NHARMONIC_H #define DIHEDRAL_NHARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 8436e73c5c..02effc2f4f 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_helix.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_quadratic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index edc29c3cf8..0b99cbc4f7 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -20,7 +20,6 @@ DihedralStyle(quadratic,DihedralQuadratic) #ifndef LMP_DIHEDRAL_QUADRATIC_H #define LMP_DIHEDRAL_QUADRATIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 3b30121551..78d45f923d 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -17,22 +17,19 @@ and Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_spherical.h" #include #include -#include #include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "pair.h" -#include "update.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" -#include "dihedral_spherical.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index ae0ece189a..472db36f33 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -20,7 +20,6 @@ DihedralStyle(spherical,DihedralSpherical) #ifndef LMP_DIHEDRAL_SPHERICAL_H #define LMP_DIHEDRAL_SPHERICAL_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index a97ae3649f..59a16f376f 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,21 +17,20 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" #include "dihedral_table.h" @@ -1012,8 +1011,7 @@ void DihedralTable::coeff(int narg, char **arg) void DihedralTable::write_restart(FILE *fp) { - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); + write_restart_settings(fp); } /* ---------------------------------------------------------------------- @@ -1021,6 +1019,27 @@ void DihedralTable::write_restart(FILE *fp) ------------------------------------------------------------------------- */ void DihedralTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void DihedralTable::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void DihedralTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -1029,8 +1048,6 @@ void DihedralTable::read_restart(FILE *fp) MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 08bd21ba83..a7b8417b48 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -36,6 +36,8 @@ class DihedralTable : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int type, int i1, int i2, int i3, int i4); protected: diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 18a645cd75..87f0c9bf66 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -16,25 +16,23 @@ Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett ------------------------------------------------------------------------- */ +#include "dihedral_table_cut.h" +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep -#include "dihedral_table_cut.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "citeme.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "error.h" #include "utils.h" @@ -42,8 +40,6 @@ using namespace LAMMPS_NS; using namespace MathConst; using namespace std; -using namespace MathExtra; - static const char cite_dihedral_tablecut[] = "dihedral_style table/cut command:\n\n" @@ -1003,8 +999,7 @@ void DihedralTableCut::coeff(int narg, char **arg) void DihedralTableCut::write_restart(FILE *fp) { - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); + write_restart_settings(fp); } /* ---------------------------------------------------------------------- @@ -1013,8 +1008,26 @@ void DihedralTableCut::write_restart(FILE *fp) void DihedralTableCut::read_restart(FILE *fp) { + read_restart_settings(fp); allocate(); +} +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralTableCut::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralTableCut::read_restart_settings(FILE *fp) +{ if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); fread(&tablength,sizeof(int),1,fp); diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h index dd645bedda..b07e925f08 100644 --- a/src/USER-MISC/dihedral_table_cut.h +++ b/src/USER-MISC/dihedral_table_cut.h @@ -33,6 +33,8 @@ class DihedralTableCut : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); protected: double *aat_k,*aat_theta0_1,*aat_theta0_2; diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 2cd1ac7527..665f1d4a60 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -15,9 +15,9 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include #include "fix_addtorque.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,6 @@ #include "respa.h" #include "input.h" #include "variable.h" -#include "memory.h" #include "error.h" #include "group.h" #include "force.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index dc52d94b14..b1bcc07fa7 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -21,11 +21,12 @@ see J. Chem. Phys. 133, 154103 (2010) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate_long.h" +#include #include #include #include #include -#include "fix_ave_correlate_long.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 548a0e7183..a0c5863e99 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong) #ifndef LMP_FIX_AVE_CORRELATE_LONG_H #define LMP_FIX_AVE_CORRELATE_LONG_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index c641912db6..05dc54c57e 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -15,11 +15,10 @@ See the README file in the top-level LAMMPS directory. Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ +#include "fix_bond_react.h" #include #include #include -#include -#include "fix_bond_react.h" #include "update.h" #include "modify.h" #include "respa.h" @@ -1286,7 +1285,7 @@ void FixBondReact::make_a_guess() for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues. + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues. } if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) { status = GUESSFAIL; @@ -1397,7 +1396,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) { @@ -1449,7 +1448,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) { @@ -1560,7 +1559,7 @@ void FixBondReact::inner_crosscheck_loop() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } if (guess_branch[avail_guesses-1] == 0) avail_guesses--; diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index 0831ebcf89..2130f07420 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -16,16 +16,14 @@ Information: k.avchachov@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_electron_stopping.h" +#include +#include #include "mpi.h" #include "atom.h" #include "update.h" #include "domain.h" #include "region.h" -#include "group.h" #include "force.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 9ab113aeaa..a245b6b4e5 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -18,31 +18,21 @@ /* ---------------------------------------------------------------------- Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), - Michele Ceriotti (EPFL) + Michele Ceriotti (EPFL) ------------------------------------------------------------------------- */ +#include "fix_ffl.h" #include #include #include -#include -#include "fix_ffl.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index f6cc1c435f..bfc5f58f93 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -16,30 +16,25 @@ some subroutines are from fix_shake.cpp ------------------------------------------------------------------------- */ +#include "fix_filter_corotate.h" #include +#include +#include #include #include -#include "fix_filter_corotate.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "bond.h" +#include "comm.h" +#include "domain.h" #include "angle.h" +#include "bond.h" #include "math_const.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "region.h" #include "memory.h" #include "error.h" #include "force.h" -#include "comm.h" -#include "error.h" -#include "memory.h" -#include "domain.h" -#include "integrate.h" #include "respa.h" -#include "neighbor.h" #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index b6366ec509..70be1f1e45 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -16,13 +16,12 @@ Joel.Eaves@Colorado.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_flow_gauss.h" +#include +#include #include "atom.h" #include "force.h" #include "group.h" -#include "comm.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 01da7f87cf..b8bdc66d08 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -16,28 +16,19 @@ Axel Kohylmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_gle.h" #include #include #include #include -#include "fix_gle.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 635acf705c..4272740068 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -22,19 +22,14 @@ Tom Keyes (Boston University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include "comm.h" #include "fix_grem.h" +#include #include "atom.h" #include "force.h" #include "update.h" #include "modify.h" #include "domain.h" -#include "input.h" #include "compute.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 1c3eafdc46..10aaa285a5 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,8 +58,6 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include -#include #include #include diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index 32892d87a8..08b39ee89b 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -15,15 +15,12 @@ Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_ipi.h" +#include +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "kspace.h" #include "modify.h" @@ -32,8 +29,6 @@ #include "neighbor.h" #include "irregular.h" #include "domain.h" -#include "compute_pressure.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 2ac2a7c9fc..410a269f8c 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -15,18 +15,16 @@ Contributing author: Efrem Braun (UC Berkeley) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nvk.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include "compute.h" #include "math_extra.h" -#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 3929d47d6b..8f790f0a59 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -21,10 +21,11 @@ Version 1.0 ------------------------------------------------------------------------- */ +#include "fix_pimd.h" +#include #include #include #include -#include "fix_pimd.h" #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 6a6e71ebaa..c638adf6a4 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -13,12 +13,11 @@ Contributing author: Ulf R. Pedersen, ulf@urp.dk ------------------------------------------------------------------------- */ -#include -#include +#include "fix_rhok.h" +#include #include #include -#include "fix_rhok.h" #include "atom.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index cbebdebdbf..32c040c2b4 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -16,10 +16,10 @@ based on fix spring by: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_smd.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index ebc161ff99..c0db252db4 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -15,9 +15,10 @@ Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include #include "fix_srp.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "domain.h" @@ -635,11 +636,11 @@ void FixSRP::restart(char *buf) int FixSRP::modify_param(int /*narg*/, char **arg) { if (strcmp(arg[0],"btype") == 0) { - btype = atoi(arg[1]); + btype = force->inumeric(FLERR,arg[1]); return 2; } if (strcmp(arg[0],"bptype") == 0) { - bptype = atoi(arg[1]); + bptype = force->inumeric(FLERR,arg[1]); return 2; } return 0; diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index 7dbf044bda..f8343df8a6 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -20,7 +20,6 @@ FixStyle(SRP,FixSRP) #ifndef LMP_FIX_SRP_H #define LMP_FIX_SRP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 305e29e033..8481b34a6b 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -18,9 +18,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include #include "fix_ti_spring.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index a34c2eb42f..55526a9149 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -17,17 +17,14 @@ Vasily Pisarev (Joint Institute for High Temperatures of RAS) ------------------------------------------------------------------------- */ -#include "lmptype.h" +#include "fix_ttm_mod.h" #include #include #include -#include -#include "fix_ttm_mod.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index 5ca16ebdad..bd7e230472 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -15,21 +15,13 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ +#include "fix_wall_ees.h" #include #include "math_extra.h" -#include "fix_wall_ees.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" -#include "domain.h" -#include "region.h" -#include "force.h" -#include "lattice.h" -#include "update.h" -#include "output.h" -#include "respa.h" #include "error.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 33bf636e64..5c6bb1874b 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -15,19 +15,16 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_region_ees.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_extra.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index c8eb0808fb..2ea804b95d 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -16,14 +16,12 @@ gvog@chemeng.ntua.gr ------------------------------------------------------------------------- */ +#include "improper_cossq.h" #include #include -#include -#include "improper_cossq.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index ea880adfaf..9e430bfa1a 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -20,7 +20,6 @@ ImproperStyle(cossq,ImproperCossq) #ifndef LMP_IMPROPER_COSSQ_H #define LMP_IMPROPER_COSSQ_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 50babcc84e..2efab8b5f8 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -15,16 +15,14 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "improper_distance.h" #include #include -#include -#include "improper_distance.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index 57e4d671e9..d7575c3585 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -20,7 +20,6 @@ ImproperStyle(distance,ImproperDistance) #ifndef LMP_IMPROPER_DISTANCE_H #define LMP_IMPROPER_DISTANCE_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 288d888d12..a0ef3a2058 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -16,15 +16,12 @@ [ based on improper_umbrella.cpp Tod A Pascal (Caltech) ] ------------------------------------------------------------------------- */ +#include "improper_fourier.h" #include #include -#include -#include -#include "improper_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 0525c45494..91dfacfd8e 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -20,7 +20,6 @@ ImproperStyle(fourier,ImproperFourier) #ifndef LMP_IMPROPER_FOURIER_H #define LMP_IMPROPER_FOURIER_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 36ba73af0f..48db5a41e9 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -36,16 +36,13 @@ of j. ------------------------------------------------------------------------- */ +#include "improper_ring.h" #include #include -#include -#include "improper_ring.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index c31329816f..7c53c6f59f 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -20,7 +20,6 @@ ImproperStyle(ring,ImproperRing) #ifndef LMP_IMPROPER_RING_H #define LMP_IMPROPER_RING_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 21a6f1deee..b3abc647ef 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -15,18 +15,16 @@ Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ +#include "pair_agni.h" +#include #include -#include #include #include -#include "pair_agni.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index afd15d7fdb..e977197522 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -15,21 +15,18 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_mdf.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index a86921d296..a375901ecd 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -14,11 +14,9 @@ Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_diel.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index f74dcfe7d8..9264e51287 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -18,11 +18,8 @@ [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_shield.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index 118c033b5c..20ec3abcf9 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -20,19 +20,17 @@ Phys. Rev. B, 98, 235404 (2018). ------------------------------------------------------------------------- */ +#include "pair_drip.h" +#include #include -#include #include #include -#include -#include "pair_drip.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "my_page.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h index 0a8f90dfc2..3ea6c735a6 100644 --- a/src/USER-MISC/pair_drip.h +++ b/src/USER-MISC/pair_drip.h @@ -31,8 +31,6 @@ PairStyle(drip, PairDRIP) #define LMP_PAIR_DRIP_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 43b472594a..aa19849baa 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -14,16 +14,14 @@ contact: stevene.strong at gmail dot com ------------------------------------------------------------------------- */ -#include -#include -#include -#include - #include "pair_e3b.h" +#include +#include +#include +#include #include "atom.h" #include "neighbor.h" -#include "neigh_request.h" #include "neigh_list.h" #include "force.h" #include "comm.h" diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 0b5220fdfd..8dee4a606b 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -21,12 +21,12 @@ Phys. Rev. B 58, 2539 (1998) ------------------------------------------------------------------------- */ +#include "pair_edip.h" +#include #include #include -#include #include #include -#include "pair_edip.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index ab48fbaa73..9f953610de 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -17,12 +17,11 @@ Contributing author: Chao Jiang ------------------------------------------------------------------------- */ +#include "pair_edip_multi.h" +#include #include -#include -#include #include #include -#include "pair_edip_multi.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index bd5da71f4a..8507fd49f6 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -15,12 +15,12 @@ Contributing author: Jan Los ------------------------------------------------------------------------- */ +#include "pair_extep.h" +#include #include -#include #include #include #include -#include "pair_extep.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h index 535e7261e3..1f127b71e0 100644 --- a/src/USER-MISC/pair_extep.h +++ b/src/USER-MISC/pair_extep.h @@ -21,7 +21,6 @@ PairStyle(extep,PairExTeP) #define LMP_PAIR_EXTEP_H #include "pair.h" -#include "my_page.h" #define MAXTYPES 8 #define NSPLINE 5 diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 24d0b191d8..e6cfc02f63 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -15,18 +15,13 @@ Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gauss_cut.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index a41c660b7b..b94db6a871 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_ilp_graphene_hbn.h" #include #include -#include #include #include -#include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 07c3b2e97b..ae4662cdc5 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #define LMP_PAIR_ILP_GRAPHENE_HBN_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index e73278968d..0009531ca8 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_full.h" #include -#include #include #include #include -#include "pair_kolmogorov_crespi_full.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 9923b409a7..68dede0dd5 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #define LMP_PAIR_KolmogorovCrespi_FULL_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index 79d6aa3daf..61c326ac87 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -21,11 +21,11 @@ The simplification is that all normals are taken along the z-direction ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_z.h" +#include #include -#include #include #include -#include "pair_kolmogorov_crespi_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index c9d90e2850..8930042cef 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -22,11 +22,11 @@ [Lebedeva et al., Physica E, 44(6), 949-954, 2012.] ------------------------------------------------------------------------- */ +#include "pair_lebedeva_z.h" +#include #include -#include #include #include -#include "pair_lebedeva_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index e2e81e4943..50f59107a0 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lennard_mdf.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index 562a60aa99..2f4e886a61 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,18 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" -#include "atom.h" -#include "comm.h" -#include "domain.h" -#include "force.h" -#include "memory.h" - -#include "error.h" - -#include -#include +#include #include #include +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index fe21538f2d..ffa828826f 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -15,17 +15,15 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_expand_coul_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index cfe125f21f..3fe0fa6bf9 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_mdf.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index af7d23370d..758962ce29 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -16,10 +16,10 @@ Samuel Genheden (University of Southampton) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_sf_dipole_sf.h" +#include +#include +#include #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index f09919ce0f..79e7ac7e09 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -31,15 +31,13 @@ conform with pairing, updated to LAMMPS style ------------------------------------------------------------------------- */ +#include "pair_meam_spline.h" #include -#include #include #include -#include "pair_meam_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index af1e8788bd..eeadacf33a 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -23,15 +23,13 @@ * 01-Aug-12 - RER: First code version. ------------------------------------------------------------------------- */ +#include "pair_meam_sw_spline.h" #include -#include #include #include -#include "pair_meam_sw_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 1716149a98..29d5715302 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -16,10 +16,9 @@ Ya Zhou (Penn State University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_momb.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 7c7973f830..c3cbe39db7 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_morse_smooth_linear.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 01deaf0fbe..416ace8132 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -25,9 +25,11 @@ There is an example script for this package in examples/USER/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ +#include "pair_srp.h" +#include +#include #include #include -#include "pair_srp.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index e0985d1dce..5c4f60f354 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -20,11 +20,11 @@ 1) Tersoff, Phys. Rev. B 39, 5566 (1988) ------------------------------------------------------------------------- */ +#include "pair_tersoff_table.h" +#include #include -#include #include #include -#include "pair_tersoff_table.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 031a449689..d0e2fa5606 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -15,26 +15,21 @@ Contributing author: David Stelter (BU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "temper_grem.h" +#include +#include #include "fix_grem.h" #include "universe.h" #include "domain.h" -#include "atom.h" #include "update.h" #include "integrate.h" #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 7cf8fbab9b..9fd4bd6d06 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -17,10 +17,9 @@ Contact Email: amulyapervaje@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "temper_npt.h" +#include +#include #include "universe.h" #include "domain.h" #include "atom.h" @@ -29,13 +28,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index e8e6f279de..bb0a01d546 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -16,10 +16,10 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ +#include "angle_class2_p6.h" +#include #include #include -#include -#include "angle_class2_p6.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index b583a45b19..f2f324c0c6 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -20,7 +20,6 @@ AngleStyle(class2/p6,AngleClass2P6) #ifndef LMP_ANGLE_CLASS2_P6_H #define LMP_ANGLE_CLASS2_P6_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 3829d2b8dc..c17b2a1dba 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -16,9 +16,9 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_buck6d.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" @@ -26,13 +26,11 @@ #include "force.h" #include "pair.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index 689b1634e0..1d0df10228 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -20,7 +20,6 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d) #ifndef LMP_ANGLE_COSINE_BUCK6D_H #define LMP_ANGLE_COSINE_BUCK6D_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 3f1e61e54a..12f7062ccc 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -19,17 +19,13 @@ [ abbreviated from and verified via DLPOLY2.0 ] ------------------------------------------------------------------------- */ +#include "improper_inversion_harmonic.h" #include #include -#include -#include -#include "improper_inversion_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 201c9e358d..206b40aebf 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic) #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H #define LMP_IMPROPER_INVERSION_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 282bb0c58f..9c917d1c19 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -18,11 +18,9 @@ Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck6d_coul_gauss_dsf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index d6a4121d21..953507ce21 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -17,11 +17,10 @@ References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck6d_coul_gauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -29,12 +28,10 @@ #include "neighbor.h" #include "neigh_list.h" #include "memory.h" -#include "math_const.h" #include "error.h" #include "math_special.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 732fea74bd..d9d8ec3c97 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -15,15 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "dump_molfile.h" +#include #include #include -#include "dump_molfile.h" #include "domain.h" #include "atom.h" #include "comm.h" #include "update.h" -#include "output.h" #include "group.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index ca1a61850c..5cff56753b 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -15,11 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "reader_molfile.h" #include #include -#include "reader_molfile.h" -#include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 118ba00226..f135446915 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index e072d136e1..0cf5489663 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_class2_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index a6dfb20433..7f4d994c4f 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_delta_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 9097c8569c..0543c94799 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3fcea7ad1d..907315f83b 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" +#include "timer.h" #include "math_special.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 6bd2feb023..6c42319905 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 56486faac1..5c0afcf316 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6dd2a3bb3b..27c47b90d8 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index da2e819ee2..6af5b44a03 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_dipole_omp.h" +#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b2f9b47e05..98527c2028 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 93532a30e5..71d0197b72 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 824b254287..ee08bbd8ad 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index fff08ddb39..5745948222 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_quartic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e8c762092c..e0b1da0baf 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_sdk_omp.h" +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "comm.h" #include "force.h" -#include "math_const.h" - -#include - #include "lj_sdk_common.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index d9d80b744d..4f6edf2073 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_table_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index fdd73c20b0..7d1b693faf 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index a8eec11760..aefae6dcf7 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index be7dcd4b49..2b579114ba 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 8f0926c0e9..ba23217a1f 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -20,9 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index a3bb69c53c..5515284f9a 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 5c16e27a32..a871fa8c04 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 39e957c137..4117da9159 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index c0203de0d6..e6526dc8dc 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 8fa3daf8ab..0d1a648415 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index fd0ccaf79d..60d3a5601c 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 1616988385..8e1e792c73 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index b09863613e..95ad9af6a6 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -15,13 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 03ac9d9bab..6c2bc02ff4 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index c64cad9fc3..d77e9d6b3e 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 94bdae3795..93dbd773ca 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -15,20 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" -#include "math_const.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 10ccbd3d9f..84aa584d9e 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 8c8e29cac0..51b07754e2 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 38961e1746..4cb6919a96 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index e74238265d..203884531b 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 64eaffe6fe..af12bb866e 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 8df622b847..8cea62aaea 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index 792ee90c26..6b10027b9d 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -15,19 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include - #include "dihedral_table_omp.h" +#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "neighbor.h" #include "force.h" -#include "update.h" -#include "error.h" - +#include "timer.h" #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp index 584e56b1f0..a18931c551 100644 --- a/src/USER-OMP/domain_omp.cpp +++ b/src/USER-OMP/domain_omp.cpp @@ -15,7 +15,6 @@ Contributing author : Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "domain.h" #include "accelerator_omp.h" #include "atom.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index b56fc25142..aadf63741d 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,15 +15,14 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include #include "ewald_omp.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" - -#include - +#include "timer.h" #include "math_const.h" #include "suffix.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index eae918ec52..fa6b698821 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -15,19 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "input.h" #include "modify.h" -#include "respa.h" #include "variable.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index efa7f5a3f1..c2bc8af5e0 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -11,18 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_neigh_history_omp.h" +#include +#include "my_page.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "force.h" #include "pair.h" -#include "update.h" #include "memory.h" -#include "modify.h" #include "error.h" #if defined(_OPENMP) diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index 76a47b71fd..2abd739f71 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_nh_omp.h" +#include #include "atom.h" #include "compute.h" #include "domain.h" #include "error.h" #include "modify.h" -#include -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index a32f0f8b51..64bc536bb0 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,12 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere_omp.h" #include "atom.h" -#include "atom_vec.h" #include "compute.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp index c61ad7155c..61ed82b16f 100644 --- a/src/USER-OMP/fix_nve_omp.cpp +++ b/src/USER-OMP/fix_nve_omp.cpp @@ -13,7 +13,6 @@ #include "fix_nve_omp.h" #include "atom.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index 2286120bee..ccdd654874 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_sphere_omp.h" +#include #include "atom.h" -#include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" -#include "error.h" #include "math_vector.h" #include "math_extra.h" diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index e439647c12..208dfb9432 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,18 +15,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_omp.h" +#include #include "math_extra.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "modify.h" #include "fix.h" #include "fix_deform.h" #include "compute.h" #include "error.h" +#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index a4587b1c14..1fca1e739b 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -24,13 +24,10 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "integrate.h" -#include "min.h" #include "timer.h" #include "fix_omp.h" #include "thr_data.h" -#include "thr_omp.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -40,8 +37,11 @@ #include "kspace.h" #include -#include -#include + +#if defined(_OPENMP) +#include +#endif + #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 2f0a90a790..b0573dfa97 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -15,24 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb_omp.h" #include #include #include -#include "fix_qeq_comb_omp.h" -#include "fix_omp.h" +#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" #include "group.h" #include "memory.h" -#include "modify.h" #include "error.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "respa.h" #include "update.h" -#include "pair_comb_omp.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index 45da91305d..f7945b5579 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -31,26 +31,22 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax_omp.h" -#include "pair_reaxc_omp.h" +#include +#include +#include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "force.h" -#include "group.h" -#include "pair.h" -#include "respa.h" #include "memory.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" + +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 53d0134741..74b2a92775 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -16,7 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh_omp.h" - +#include +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -24,12 +25,12 @@ #include "comm.h" #include "compute.h" #include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "modify.h" #include "update.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index 7db45ed9bf..31d53868c8 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index a041706f38..1e7c139d52 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 12c6362ed8..b807ddba7c 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -16,16 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_omp.h" - +#include +#include +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" +#include "error.h" #include "domain.h" -#include - #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index a0495b3b93..41f6c53e40 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_small_omp.h" - +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index c2b493f425..3bff179b44 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 3b328e5b78..0f99f2732f 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index fe1fc45bec..fdc29c74b1 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index b5af428cb9..b49b895c78 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 6e02d0968e..32e837fdfe 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index e198b99337..c8fe685faa 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,15 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_ring_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" -#include "update.h" -#include "error.h" #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index ceaca35074..f3fdf4570f 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 8a920e05d5..3c5439db5d 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,10 +16,10 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg_omp.h" #include #include #include -#include #include #include "atom.h" @@ -29,12 +29,14 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg_omp.h" +#include "thr_omp.h" +#include "timer.h" -#include "math_const.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 74cbb56be7..81f84e8f6f 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -16,15 +16,11 @@ ------------------------------------------------------------------------- */ #include "msm_omp.h" -#include "atom.h" +#include #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "memory.h" -#include "math_const.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index d9e0fb9297..3bda2e4c5a 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -13,16 +13,13 @@ #include "npair_full_bin_atomonly_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp index b915aca002..b0b0070df5 100644 --- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp index e1f75c06e2..d3e30b4932 100644 --- a/src/USER-OMP/npair_full_bin_omp.cpp +++ b/src/USER-OMP/npair_full_bin_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 9bc196e17a..707db2edcf 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_multi_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp index b33f76bb22..527df58fd6 100644 --- a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp index 1d0f26d638..2719f5dc2c 100644 --- a/src/USER-OMP/npair_full_nsq_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +23,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp index 02d98ff6ab..a69779d96d 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_half_bin_atomonly_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp index 24fe75ec55..5f8ffdab29 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp index ff74b54d7d..35807645cf 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp index f7d969ba27..2700d6863b 100644 --- a/src/USER-OMP/npair_half_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp @@ -13,11 +13,9 @@ #include "npair_half_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "molecule.h" #include "domain.h" #include "my_page.h" diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp index c843d623cd..d94845898c 100644 --- a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 705d1b8d9f..c06737dc1c 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index f16dd027a0..50df756be4 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index ce93e85485..8b78b311dd 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp index add4c44d9e..f0eb211425 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp index 01da73cf1e..55b9f9e512 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_nsq_newton_omp.cpp index 3815b1b85b..223da622e8 100644 --- a/src/USER-OMP/npair_half_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp index f094691b71..9bb4d277fe 100644 --- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp index de7ef5f7d5..9ed0ae482d 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_omp.h" -#include "neighbor.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp index f20d101bc9..cd03684940 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp index 0f726cdd7f..b1e7467ec7 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp index 2783e1255e..c22965895d 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp index dff2a762d5..1b437482c4 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp index 3053b81594..8e0581d4ce 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp index b02bfa345e..38a2c0d61f 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_size_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp index 717012b226..d1505e1b2e 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp index 5a55029d30..9027b0728d 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 947e4e1ad2..7d2fe4f109 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -13,12 +13,8 @@ #include "npair_halffull_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6e158d372d..3fcc8c2e98 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_halffull_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index 90c3777932..8d0605fae9 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_beck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index 567eddc9cb..55da972c4e 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index fce2013745..35ad4fcb48 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index cef9fb0955..6367976c7d 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" @@ -26,6 +26,7 @@ #include "random_mars.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "fix_wall.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 239a820242..dcb4124634 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index cc7e81b9c5..8d5c80513a 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_buck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 056daf210a..267beeecbd 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_cut_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index d202e314bf..4d3f92c495 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_debye_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 217fb844c3..bd7f5cfed2 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -12,14 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_dsf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "timer.h" #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index 0913a2b188..92d5bd7b15 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 77db3d9183..b7f3a7f4d4 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -12,15 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_dpd_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "update.h" #include "random_mars.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 85cab4fe7b..87d637e80d 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,13 +15,15 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_thole_long_omp.h" #include #include #include #include -#include "pair_lj_cut_thole_long_omp.h" #include "atom.h" #include "comm.h" +#include "domain.h" +#include "fix_drude.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -29,7 +31,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "domain.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index e2c1da1a89..18fc207015 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_omp.h" +#include #include "atom.h" #include "domain.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 3a5f03364d..04ac59b121 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lubricate_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 2f17515130..aedd438066 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,6 +34,8 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -42,32 +44,27 @@ #include "neigh_list.h" #include "neigh_request.h" #include "modify.h" -#include "fix.h" #include "fix_reaxc.h" #include "citeme.h" #include "memory.h" #include "error.h" #include "timer.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" -#include "reaxc_control.h" -#include "reaxc_ffield.h" #include "reaxc_forces_omp.h" #include "reaxc_init_md_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_traj.h" -#include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" #if defined(_OPENMP) #include #endif +#include "suffix.h" using namespace LAMMPS_NS; #ifdef OMP_TIMING diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h index ad8c368aaf..0cae28f56b 100644 --- a/src/USER-OMP/pair_reaxc_omp.h +++ b/src/USER-OMP/pair_reaxc_omp.h @@ -22,7 +22,6 @@ PairStyle(reax/c/omp,PairReaxCOMP) #include "pair_reaxc.h" #include "thr_omp.h" -#include "suffix.h" namespace LAMMPS_NS { diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 2b4619f685..1117979f1f 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,20 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg_omp.h" +#include #include #include -#include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "neighbor.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" - +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 435341a31c..de902b1a57 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,15 +16,20 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include "pppm_disp_omp.h" +#include #include #include -#include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" -#include "memory.h" #include "math_const.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index a53c5b2ac5..fc9466e395 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,23 +15,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_disp_tip4p_omp.h" +#include #include #include -#include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" -#include "math_special.h" - +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #ifdef FFT_SINGLE #define ZEROF 0.0f diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index 66190b3f51..3ef3de1ab7 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_omp.h" +#include #include #include -#include "pppm_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" + +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 5fe44d2b71..d7c12613d9 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_tip4p_omp.h" +#include #include #include -#include "pppm_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index 33780f5e3f..d581819e00 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -26,9 +26,13 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" #include "pair_reaxc_omp.h" #include "reaxc_types.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp index 5160c6f55d..b6a76b3f3a 100644 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_bonds_omp.cpp @@ -26,13 +26,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_bonds_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" +#include "pair_reaxc_omp.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 0a08bd6a46..971667cc2d 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,19 +26,19 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" -#include "thr_data.h" - #include "reaxc_forces_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" +#include "pair_reaxc_omp.h" + #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" #include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body_omp.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles_omp.h" #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h index d1e2a5c65a..6df0288656 100644 --- a/src/USER-OMP/reaxc_forces_omp.h +++ b/src/USER-OMP/reaxc_forces_omp.h @@ -30,7 +30,6 @@ #define __FORCES_OMP_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" void Init_Force_FunctionsOMP( control_params* ); void Compute_ForcesOMP( reax_system*, control_params*, simulation_data*, diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 7acf26262e..d06966a92d 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,10 +26,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" // To access Calculate_Theta() #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index fe7682d035..9d40479ddf 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -26,18 +26,16 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" #include "reaxc_init_md_omp.h" -#include "reaxc_allocate.h" +#include +#include "reaxc_defs.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" -#include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" +#include "error.h" // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 7552e7a733..5f4b6d4eb0 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -26,13 +26,14 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" -#include "thr_data.h" - #include "reaxc_multi_body_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index ea92e0c210..564088880a 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -29,6 +29,7 @@ #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index d290dc264f..68bacb7202 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -26,14 +26,14 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" -#include "thr_data.h" - -#include "reaxc_types.h" #include "reaxc_torsion_angles_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include "fix_omp.h" +#include "pair_reaxc_omp.h" + +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #if defined(_OPENMP) diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 195f16a75d..104fadbbae 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -26,13 +26,16 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_valence_angles_omp.h" +#include +#include #include "pair_reaxc_omp.h" -#include "thr_data.h" +#include "fix_omp.h" +#include "error.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_valence_angles.h" -#include "reaxc_valence_angles_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index 9c8555c66d..5add419253 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,13 +15,11 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "respa_omp.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "atom.h" +#include "domain.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -32,11 +30,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix_respa.h" -#include "timer.h" -#include "memory.h" #include "error.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 3cea1b0018..edff17cad3 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,10 +18,6 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#if defined(_OPENMP) -#include -#endif - #include "timer.h" namespace LAMMPS_NS { @@ -35,7 +31,7 @@ class ThrData { public: ThrData(int tid, class Timer *t); - ~ThrData() { delete _timer; _timer = NULL; }; + ~ThrData() { delete _timer; _timer = nullptr; }; void check_tid(int); // thread id consistency check int get_tid() const { return _tid; }; // our thread id. @@ -140,7 +136,7 @@ class ThrData { // disabled default methods private: - ThrData() : _tid(-1), _timer(NULL) {}; + ThrData() : _tid(-1), _timer(nullptr) {}; }; //////////////////////////////////////////////////////////////////////// diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 22f751e6c0..51030358d3 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -22,7 +22,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #include "modify.h" #include "neighbor.h" #include "timer.h" @@ -34,7 +33,6 @@ #include "angle.h" #include "dihedral.h" #include "improper.h" -#include "kspace.h" #include "compute.h" #include "math_const.h" diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 87d921290e..062d77bc0e 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -18,10 +18,13 @@ #ifndef LMP_THR_OMP_H #define LMP_THR_OMP_H +#if defined(_OPENMP) +#include +#endif #include "pointers.h" #include "error.h" -#include "fix_omp.h" -#include "thr_data.h" +#include "fix_omp.h" // IWYU pragma: export +#include "thr_data.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -31,8 +34,6 @@ class Bond; class Angle; class Dihedral; class Improper; -class KSpace; -class Fix; class ThrOMP { diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index d94bd11a80..559ef4c36f 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -3,15 +3,15 @@ // #include -#include +#include +#include #include "dynamical_matrix.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "comm.h" +#include "error.h" #include "group.h" #include "force.h" -#include "math_extra.h" #include "memory.h" #include "bond.h" #include "angle.h" @@ -25,7 +25,6 @@ #include "finish.h" #include - using namespace LAMMPS_NS; enum{REGULAR,ESKM}; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index cdbe4068bc..9b663ce383 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,8 +23,8 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_phonon.h" #include "fft3d_wrap.h" @@ -33,7 +33,6 @@ #include "domain.h" #include "force.h" #include "group.h" -#include "lattice.h" #include "modify.h" #include "update.h" #include "citeme.h" diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index 41e6540b97..ad3d3facdb 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -16,15 +16,14 @@ under Contributing author: PM Larsen (MIT) ------------------------------------------------------------------------- */ +#include "compute_ptm_atom.h" #include #include -#include #include #include #include "atom.h" #include "comm.h" -#include "compute_ptm_atom.h" #include "error.h" #include "force.h" #include "memory.h" @@ -32,7 +31,6 @@ under #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "pair.h" #include "update.h" #include "ptm_functions.h" diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp index 45643ec515..8dd06e8168 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.cpp +++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include #include #include -#include #include "ptm_convex_hull_incremental.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp index 3068e7a7f6..cedd35126d 100644 --- a/src/USER-PTM/ptm_index.cpp +++ b/src/USER-PTM/ptm_index.cpp @@ -12,20 +12,17 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_convex_hull_incremental.h" #include "ptm_deformation_gradient.h" #include "ptm_functions.h" -#include "ptm_graph_data.h" #include "ptm_initialize_data.h" #include "ptm_neighbour_ordering.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" #include "ptm_quat.h" #include "ptm_structure_matcher.h" -#include #include -#include #include #include -#include #include +#include static double calculate_interatomic_distance(int type, double scale) { assert(type >= 1 && type <= 8); diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 49dc6f2323..ff8245fe44 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -7,14 +7,12 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include -#include -#include -#include -#include -#include #include "ptm_initialize_data.h" +#include "ptm_canonical_coloured.h" +#include "ptm_convex_hull_incremental.h" +#include "ptm_graph_tools.h" +#include "ptm_neighbour_ordering.h" +#include static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index 20c9921962..4e7f3e8f0a 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -12,12 +12,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_graph_data.h" -#include "ptm_graph_tools.h" #include "ptm_deformation_gradient.h" #include "ptm_fundamental_mappings.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_canonical_coloured.h" -#include "ptm_convex_hull_incremental.h" #include "ptm_alt_templates.h" diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index cb72a43711..1332b8819b 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -9,16 +9,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI //todo: normalize vertices -#include +#include "ptm_neighbour_ordering.h" #include #include #include #include #include +#include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_normalize_vertices.h" namespace ptm { diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index e03963048b..f11dd98ee9 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #define PTM_POLAR_H #include -#include namespace ptm { diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp index 4a93499b3a..527f4d1116 100644 --- a/src/USER-PTM/ptm_quat.cpp +++ b/src/USER-PTM/ptm_quat.cpp @@ -7,9 +7,9 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ +#include "ptm_quat.h" #include #include -#include #include diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index d50676a3c1..b587ad225f 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -7,20 +7,16 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include +#include "ptm_structure_matcher.h" #include #include -#include -#include -#include +#include #include "ptm_convex_hull_incremental.h" #include "ptm_canonical_coloured.h" #include "ptm_graph_data.h" #include "ptm_graph_tools.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" -#include "ptm_structure_matcher.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h index e75892f8cb..63bc5ed1fe 100644 --- a/src/USER-PTM/ptm_structure_matcher.h +++ b/src/USER-PTM/ptm_structure_matcher.h @@ -12,7 +12,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_initialize_data.h" #include "ptm_constants.h" - +#include "ptm_convex_hull_incremental.h" namespace ptm { diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index dfe61eb24f..dc4ce4e747 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -52,7 +52,7 @@ such enhancements or derivative works thereof, in binary and source code form. * \brief Function implementations for the voronoicell and related classes. */ #include -#include +#include #include #include "ptm_voronoi_config.h" #include "ptm_voronoi_cell.h" diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index eb091dd36b..69e3b5bdc4 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -56,9 +56,6 @@ such enhancements or derivative works thereof, in binary and source code form. #define PTM_VOROPP_CELL_HH #include -#include - -#include "ptm_voronoi_config.h" namespace ptm_voro { diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b9b07664d2..abbf1701b8 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -16,31 +16,22 @@ Implementation of the Multi-Scale Shock Method with quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qbmsst.h" #include #include #include #include -#include "fix_qbmsst.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" #include "comm.h" -#include "input.h" -#include "output.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" #include "kspace.h" -#include "thermo.h" #include "utils.h" using namespace LAMMPS_NS; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 015f953b8e..593ca31006 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -16,28 +16,21 @@ Implementation of the colored thermostat for quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qtb.h" #include #include #include #include -#include "fix_qtb.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp index 77b82b3e55..bc5b26b699 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/USER-REAXC/compute_spec_atom.cpp @@ -11,19 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_spec_atom.h" -#include "math_extra.h" +#include #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" #include "memory.h" #include "error.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" #include "pair_reaxc.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h index 4d5cb86d71..cf0aa0215d 100644 --- a/src/USER-REAXC/compute_spec_atom.h +++ b/src/USER-REAXC/compute_spec_atom.h @@ -21,7 +21,6 @@ ComputeStyle(SPEC/ATOM,ComputeSpecAtom) #define LMP_COMPUTE_SPEC_ATOM_H #include "compute.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 6c0da278c2..924b6806de 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -18,15 +18,13 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax.h" +#include +#include +#include #include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -39,6 +37,7 @@ #include "citeme.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp index dc67ad6ffb..c98adf5b45 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/USER-REAXC/fix_reaxc.cpp @@ -23,8 +23,6 @@ #include "fix_reaxc.h" #include "atom.h" -#include "pair.h" -#include "comm.h" #include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 9dc347826f..f7ad7ed6d4 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -15,22 +15,14 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds.h" +#include +#include #include "atom.h" #include "update.h" #include "pair_reaxc.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "reaxc_list.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index d72f5446b5..e83e01f1d5 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -20,9 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #ifndef LMP_FIX_REAXC_BONDS_H #define LMP_FIX_REAXC_BONDS_H -#include #include "fix.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 46426d484a..74692f1c9b 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -16,27 +16,23 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ +#include "fix_reaxc_species.h" +#include #include -#include #include #include "fix_ave_atom.h" -#include "fix_reaxc_species.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "pair_reaxc.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" -#include "reaxc_list.h" +#include "pair_reaxc.h" +#include "reaxc_defs.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h index 23a470fd0a..937af98527 100644 --- a/src/USER-REAXC/fix_reaxc_species.h +++ b/src/USER-REAXC/fix_reaxc_species.h @@ -21,11 +21,6 @@ FixStyle(reax/c/species,FixReaxCSpecies) #define LMP_FIX_REAXC_SPECIES_H #include "fix.h" -#include "pointers.h" - -#include "pair_reaxc.h" -#include "reaxc_types.h" -#include "reaxc_defs.h" #define BUFLEN 1000 diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 8f8dcfb8fc..959405576e 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -21,6 +21,11 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc.h" +#include +#include +#include +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -35,6 +40,7 @@ #include "memory.h" #include "error.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" #include "reaxc_control.h" @@ -45,9 +51,7 @@ #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_traj.h" #include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 460f8aeb6a..6303db5619 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -24,14 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_allocate.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" -#if defined(_OPENMP) +#if defined(LMP_USER_OMP) && defined(_OPENMP) #include #endif diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 1ed58a0bfd..869e796661 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -24,9 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp index 48fb872324..4cfd2a3c3a 100644 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ b/src/USER-REAXC/reaxc_bonds.cpp @@ -24,12 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" void Bonds( reax_system *system, control_params * /*control*/, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 535226fff8..12aa989fa2 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -24,8 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_control.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 9534637645..e3a6645fc2 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -24,12 +24,16 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "error.h" #include "reaxc_ffield.h" +#include +#include +#include +#include +#include +#include "reaxc_defs.h" +#include "error.h" #include "reaxc_tool_box.h" - char Read_Force_Field( FILE *fp, reax_interaction *reax, control_params *control ) { diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h index 7cef730f91..b6fe1c9ea9 100644 --- a/src/USER-REAXC/reaxc_ffield.h +++ b/src/USER-REAXC/reaxc_ffield.h @@ -28,6 +28,7 @@ #define __FFIELD_H_ #include "reaxc_types.h" +#include char Read_Force_Field( FILE*, reax_interaction*, control_params* ); diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 186cde681a..6cd627f05d 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -24,24 +24,22 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_forces.h" +#include +#include +#include #include "reaxc_bond_orders.h" #include "reaxc_bonds.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body.h" #include "reaxc_nonbonded.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" #include "error.h" - interaction_function Interaction_Functions[NUM_INTRS]; void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp index be34df7571..5929703bad 100644 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index df5de49034..966ad78c34 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -24,17 +24,19 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_init_md.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_allocate.h" #include "reaxc_forces.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h index ab519a4c72..5d593f50ea 100644 --- a/src/USER-REAXC/reaxc_init_md.h +++ b/src/USER-REAXC/reaxc_init_md.h @@ -28,7 +28,7 @@ #define __INIT_MD_H_ #include "reaxc_types.h" - +#include void Initialize( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index 51aa8bca0f..f68a2a2abb 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -24,15 +24,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "update.h" #include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_reset_tools.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" #include "reaxc_traj.h" -#include "reaxc_vector.h" int Init_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, @@ -85,7 +82,7 @@ int Init_Output_Files( reax_system *system, control_params *control, /************************ close output files ************************/ -int Close_Output_Files( reax_system *system, control_params *control, +int Close_Output_Files( reax_system *system, control_params * /* control */, output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) { if (out_control->write_steps > 0) diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index cd4f815286..53bd05bc8d 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -24,8 +24,8 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_list.h" +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 8d33a33fba..622483fdc9 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -24,12 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_lookup.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_nonbonded.h" #include "reaxc_tool_box.h" - void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n){ int i; diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h index 3fd0c2581a..3aae7e0b63 100644 --- a/src/USER-REAXC/reaxc_lookup.h +++ b/src/USER-REAXC/reaxc_lookup.h @@ -28,6 +28,7 @@ #define __LOOKUP_H_ #include "reaxc_types.h" +namespace LAMMPS_NS { class Error; } void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n); @@ -35,8 +36,9 @@ void Tridiagonal_Solve( const double *a, const double *b, void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, cubic_spline_coef *coef, unsigned int n ); -void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n ); +void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, + double v0, double vlast, cubic_spline_coef *coef, + unsigned int n ); int Init_Lookup_Tables( reax_system*, control_params*, storage*, mpi_datatypes*, char* ); diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index f7d72a2678..ed1a3d5ac1 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -24,11 +24,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_multi_body.h" -#include "reaxc_bond_orders.h" +#include +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_vector.h" void Atom_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index b0fea8c1b9..497a1a0ebe 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -24,10 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_nonbonded.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index e00656694c..91b1a9e14f 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -24,8 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_reset_tools.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_tool_box.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp index 5024feffcf..166f070be6 100644 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ b/src/USER-REAXC/reaxc_system_props.cpp @@ -24,11 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void Compute_System_Energy( reax_system *system, simulation_data *data, MPI_Comm comm ) diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h index 161060e184..4d80e22966 100644 --- a/src/USER-REAXC/reaxc_system_props.h +++ b/src/USER-REAXC/reaxc_system_props.h @@ -28,6 +28,7 @@ #define __SYSTEM_PROP_H_ #include "reaxc_types.h" +#include void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index ffe42e37bb..811c2ed0ee 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -24,8 +24,15 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_tool_box.h" +#include +#include +#include +#include "reaxc_defs.h" + +#if !defined(_MSC_VER) +#include +#endif #include "error.h" diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 0465376dba..b325819265 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -28,7 +28,7 @@ #define __TOOL_BOX_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" +namespace LAMMPS_NS { class Error; } /* from system_props.h */ double Get_Time( ); diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index ed76368d68..ce944b217f 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -24,11 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_torsion_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #define MIN_SINE 1e-10 diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index 356d7b6eeb..fb493feae5 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -24,10 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_traj.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index 0821c065cc..319c373927 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -27,19 +27,11 @@ #ifndef __REAX_TYPES_H_ #define __REAX_TYPES_H_ -#include #include "lmptype.h" - -#include -#include +#include #include -#include -#include -#include -#include #include "accelerator_kokkos.h" - namespace LAMMPS_NS { class Error;} #if defined LMP_USER_OMP diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index 4ba870b6d9..560955fa9d 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_valence_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp index b54d329ce9..207d745df3 100644 --- a/src/USER-REAXC/reaxc_vector.cpp +++ b/src/USER-REAXC/reaxc_vector.cpp @@ -24,9 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void rvec_Copy( rvec dest, rvec src ) { diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h index 906b200dc9..549c1f927c 100644 --- a/src/USER-REAXC/reaxc_vector.h +++ b/src/USER-REAXC/reaxc_vector.h @@ -27,9 +27,7 @@ #ifndef __VECTOR_H_ #define __VECTOR_H_ -#include "pair.h" #include "reaxc_types.h" -#include "reaxc_defs.h" void rvec_Copy( rvec, rvec ); void rvec_Scale( rvec, double, rvec ); diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp index 85b08a2af7..176cd8b895 100644 --- a/src/USER-SDPD/fix_meso_move.cpp +++ b/src/USER-SDPD/fix_meso_move.cpp @@ -16,11 +16,10 @@ Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com ------------------------------------------------------------------------- */ +#include "fix_meso_move.h" #include #include -#include "fix_meso_move.h" #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp index 49c9ca8614..e93c543e72 100644 --- a/src/USER-SDPD/fix_rigid_meso.cpp +++ b/src/USER-SDPD/fix_rigid_meso.cpp @@ -27,17 +27,10 @@ and all codes relevant to that has been removed ------------------------------------------------------------------------- */ -#include #include "fix_rigid_meso.h" #include "math_extra.h" #include "atom.h" -#include "compute.h" #include "domain.h" -#include "update.h" -#include "modify.h" -#include "group.h" -#include "force.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index db80debe51..d799869db3 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -18,9 +18,8 @@ references: Espanol and Revenga, Phys Rev E 67, 026705 (2003) ------------------------------------------------------------------------- */ -#include -#include #include "pair_sdpd_taitwater_isothermal.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 9c634be091..604504c5a7 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -22,24 +22,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_smd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" -#include "fix_adapt.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; + #define NMAT_FULL 9 #define NMAT_SYMM 6 diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp index 8193ad6ccf..46cbc602f2 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_contact_radius.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp index 9603fd5c64..96a936cd82 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_damage.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp index d937aa98a4..f88da8bc33 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -29,7 +29,6 @@ #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp index 67466ebb72..c1c001a5dd 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp index 20dfa64edd..272a2c59e5 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain_rate.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp index 5c78e604b6..d9c0a99b07 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -22,13 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_rho.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 37ad78dcea..09aeeea74a 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -22,20 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_tlsph_defgrad.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index bbab274b5c..ba1a9306ef 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -22,13 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include -#include #include "compute_smd_tlsph_shape.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index a94a3cd511..f0061bf7a1 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -23,12 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_tlsph_strain.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp index a54b07dd1e..9c78b192ce 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_tlsph_stress.h" +#include #include #include -#include "compute_smd_tlsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp index b24223b8b5..06706a85ad 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_triangle_vertices.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp index 89b85f7bc1..cf1535759c 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_ulsph_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp index 7f1bbc4c29..ea477375ce 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_ulsph_stress.h" +#include #include #include -#include "compute_smd_ulsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index 17a6b556e8..eb1f144275 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -22,13 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_vol.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index f015c6c4df..ab6dd5ef5c 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -22,21 +22,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_smd_adjust_dt.h" -#include "atom.h" +#include +#include #include "update.h" -#include "integrate.h" -#include "domain.h" -#include "lattice.h" #include "force.h" #include "pair.h" #include "modify.h" #include "fix.h" -#include "output.h" -#include "dump.h" #include "comm.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index f931ae94ff..8464bed609 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -22,22 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "fix_smd_integrate_tlsph.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "error.h" #include "pair.h" -#include "neigh_list.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "modify.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index 6c4705eb96..0f0d224f95 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -22,25 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_smd_integrate_ulsph.h" #include -#include #include #include -#include "fix_smd_integrate_ulsph.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" #include "pair.h" -#include "domain.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index fe8695b23e..cbaad9ac4c 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -22,25 +22,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "fix_smd_move_triangulated_surface.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" -#include "domain.h" #include "math_const.h" using namespace Eigen; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 4bc8b5127b..2964ded544 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -23,9 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_smd_setvel.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index a2813cc3ca..6aa23fe3b2 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -24,20 +24,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_smd_tlsph_reference_configuration.h" +#include +#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "lattice.h" #include "force.h" #include "pair.h" #include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" #include "domain.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h index 8549621c2f..5f952bde93 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h @@ -35,7 +35,6 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration) #define LMP_FIX_SMD_TLSPH_REFERENCE_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index a37ba67a80..9183bcd9ea 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -15,21 +15,15 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_smd_wall_surface.h" +#include +#include +#include +#include #include "atom.h" #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "pair.h" -#include "lattice.h" #include "memory.h" #include "error.h" #include "atom_vec.h" diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 541be9f05c..97be94d833 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -26,17 +26,14 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_hertz.h" +#include #include -#include #include #include -#include "pair_smd_hertz.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1d7bbca780..82b7c8ff9d 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -22,15 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include -#include -#include -#include #include "pair_smd_tlsph.h" +#include +#include +#include +#include +#include +#include #include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "domain.h" @@ -41,12 +39,9 @@ #include "fix.h" #include "comm.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "math_special.h" -#include "update.h" #include "smd_material_models.h" #include "smd_kernels.h" #include "smd_math.h" @@ -1781,9 +1776,8 @@ void PairTlsph::init_style() { optional granular history list ------------------------------------------------------------------------- */ -void PairTlsph::init_list(int id, NeighList *ptr) { - if (id == 0) - list = ptr; +void PairTlsph::init_list(int id, class NeighList *ptr) { + if (id == 0) list = ptr; } /* ---------------------------------------------------------------------- @@ -1791,8 +1785,7 @@ void PairTlsph::init_list(int id, NeighList *ptr) { ------------------------------------------------------------------------- */ double PairTlsph::memory_usage() { - - return 118 * nmax * sizeof(double); + return 118.0 * nmax * sizeof(double); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index d3a4983379..f9052be087 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -26,20 +26,15 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_triangulated_surface.h" +#include #include -#include #include #include -#include -#include #include -#include "pair_smd_triangulated_surface.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 2c4a2de989..b53eb779de 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -22,19 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include -#include #include "pair_smd_ulsph.h" +#include +#include +#include +#include +#include #include "atom.h" #include "domain.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 4213428872..5ee67fbb4e 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -21,6 +21,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "smd_material_models.h" +#include +#include +#include #include #include #include "math_special.h" diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index ba7f8eb88c..f61fc1a72e 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -38,25 +38,24 @@ . ------------------------------------------------------------------------- */ +#include "pair_smtbq.h" +#include #include -#include #include #include +#include #include -#include "pair_smtbq.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" -#include "domain.h" #include #include diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index aa3e680c61..cd7c2251ab 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_meso.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp index e39dee2b5f..c56243e5ed 100644 --- a/src/USER-SPH/compute_meso_e_atom.cpp +++ b/src/USER-SPH/compute_meso_e_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_e_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp index eeb3f987bc..b2fbd2d70a 100644 --- a/src/USER-SPH/compute_meso_rho_atom.cpp +++ b/src/USER-SPH/compute_meso_rho_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_rho_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp index dc4f3407f1..bab96468dd 100644 --- a/src/USER-SPH/compute_meso_t_atom.cpp +++ b/src/USER-SPH/compute_meso_t_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_t_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index b688eccfea..4f4e532291 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 29e8a1554c..b7f0675ef8 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso_stationary.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index bafa26be89..cff9009015 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_heatconduction.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" #include "neigh_list.h" diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index db5ec964bc..f206bf68f5 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_idealgas.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 7d315c975c..3173e2a47d 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_lj.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 842dddc744..fa51dc3781 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index cf3c0e914b..f2a34d4edd 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 5cbaa5959f..9ca03e3476 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater_morris.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 3339e0555b..9d15fbc441 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_force_tally.h" +#include +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 2a5f724953..350bc4b4b6 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_heat_flux_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index 5fabd4a77b..ce647a04c3 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_mol_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" #include "update.h" -#include "memory.h" #include "error.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index 8e6703bde1..edfa49b1b1 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 07d685a9c2..1ea096e286 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_stress_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 8b62853042..adb9970c12 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -13,21 +13,14 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_uef.h" +#include #include "fix_nh_uef.h" #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 999296ec7e..698c4452c2 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,11 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_uef.h" +#include #include "fix_nh_uef.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "error.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 58b3ec5a1f..8e6268eee6 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -13,15 +13,10 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ - -#include -#include -#include #include "dump_cfg.h" +#include #include "atom.h" -#include "domain.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "error.h" #include "uef_utils.h" diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index bffcd7849f..8873688eb7 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,19 +13,16 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nh_uef.h" +#include +#include #include "atom.h" #include "force.h" -#include "group.h" #include "comm.h" #include "citeme.h" #include "irregular.h" #include "modify.h" #include "compute.h" -#include "kspace.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 2e6731f494..0f8861cdf5 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -15,10 +15,9 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_cross.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h index 7709c10414..ba958f98ec 100644 --- a/src/USER-YAFF/angle_cross.h +++ b/src/USER-YAFF/angle_cross.h @@ -20,7 +20,6 @@ AngleStyle(cross,AngleCross) #ifndef LMP_ANGLE_CROSS_H #define LMP_ANGLE_CROSS_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 53cb11b5df..b90db37afa 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -15,10 +15,9 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h index 2d19b4d1b4..985c4bb9b4 100644 --- a/src/USER-YAFF/angle_mm3.h +++ b/src/USER-YAFF/angle_mm3.h @@ -20,7 +20,6 @@ AngleStyle(mm3,AngleMM3) #ifndef LMP_ANGLE_MM3_H #define LMP_ANGLE_MM3_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index ee1ebcdd61..2a7d5d1843 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -15,12 +15,11 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include #include "bond_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h index 9711d89529..56f3136ea8 100644 --- a/src/USER-YAFF/bond_mm3.h +++ b/src/USER-YAFF/bond_mm3.h @@ -20,7 +20,6 @@ BondStyle(mm3,BondMM3) #ifndef LMP_BOND_MM3_H #define LMP_BOND_MM3_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index b45087a9ab..2b62f827e7 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_distharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h index b8b9ae780e..0a8d34ac44 100644 --- a/src/USER-YAFF/improper_distharm.h +++ b/src/USER-YAFF/improper_distharm.h @@ -20,7 +20,6 @@ ImproperStyle(distharm,ImproperDistHarm) #ifndef LMP_IMPROPER_DISTHARM_H #define LMP_IMPROPER_DISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index ae702820cb..bcc0549f7e 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_sqdistharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h index 301b5066cb..3aceb01a03 100644 --- a/src/USER-YAFF/improper_sqdistharm.h +++ b/src/USER-YAFF/improper_sqdistharm.h @@ -20,7 +20,6 @@ ImproperStyle(sqdistharm,ImproperSQDistHarm) #ifndef LMP_IMPROPER_SQDISTHARM_H #define LMP_IMPROPER_SQDISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index f37dcc3ed1..ab983a78bc 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 931ed1d116..4175ef915d 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_mm3_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index 860126fa77..d5976f85d3 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -15,16 +15,14 @@ Contributing author: Daniel Schwen ------------------------------------------------------------------------- */ +#include "compute_voronoi_atom.h" #include #include #include -#include -#include "voro++.hh" -#include "compute_voronoi_atom.h" +#include #include "atom.h" #include "group.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 74bd470572..a3fff2fe16 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -19,14 +19,14 @@ #ifdef LMP_KOKKOS -#include "kokkos.h" -#include "atom_kokkos.h" -#include "comm_kokkos.h" -#include "comm_tiled_kokkos.h" -#include "domain_kokkos.h" -#include "neighbor_kokkos.h" -#include "memory_kokkos.h" -#include "modify_kokkos.h" +#include "kokkos.h" // IWYU pragma: export +#include "atom_kokkos.h" // IWYU pragma: export +#include "comm_kokkos.h" // IWYU pragma: export +#include "comm_tiled_kokkos.h" // IWYU pragma: export +#include "domain_kokkos.h" // IWYU pragma: export +#include "neighbor_kokkos.h" // IWYU pragma: export +#include "memory_kokkos.h" // IWYU pragma: export +#include "modify_kokkos.h" // IWYU pragma: export #define LAMMPS_INLINE KOKKOS_INLINE_FUNCTION diff --git a/src/angle.cpp b/src/angle.cpp index 2a297990ac..1b9532ea32 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "angle.h" #include "atom.h" #include "comm.h" diff --git a/src/angle.h b/src/angle.h index 3d8371242e..c0d1199dcd 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,8 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -46,6 +45,8 @@ class Angle : protected Pointers { virtual double equilibrium_angle(int) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double single(int, int, int, int) = 0; virtual double memory_usage(); diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index b5af217b7b..cc29c9978e 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -15,12 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "angle_deprecated.h" +#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -43,7 +44,7 @@ void AngleDeprecated::settings(int, char **) // hybrid substyles are created in AngleHybrid::settings(), so when this is // called, our style was just added at the end of the list of substyles - if (strncmp(my_style,"hybrid",6) == 0) { + if (utils::strmatch(my_style,"^hybrid")) { AngleHybrid *hybrid = (AngleHybrid *)force->angle; my_style = hybrid->keywords[hybrid->nstyles]; } diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 6afa7413b2..6ffbc19d08 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "angle_hybrid.h" +#include #include #include -#include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" @@ -324,6 +323,7 @@ void AngleHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -349,6 +349,7 @@ void AngleHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_angle(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 4fde71e43f..730d55b0e2 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -20,7 +20,6 @@ AngleStyle(hybrid,AngleHybrid) #ifndef LMP_ANGLE_HYBRID_H #define LMP_ANGLE_HYBRID_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 6eb127fa58..3c92b852b3 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,10 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_zero.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/angle_zero.h b/src/angle_zero.h index b91be5c8d7..bc1ce0725f 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -20,7 +20,6 @@ AngleStyle(zero,AngleZero) #ifndef LMP_ANGLE_ZERO_H #define LMP_ANGLE_ZERO_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/atom.cpp b/src/atom.cpp index e5a982d620..24ad2d40da 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom.h" #include -#include -#include +#include #include #include -#include -#include "atom.h" #include "style_atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" @@ -27,15 +25,12 @@ #include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" -#include "thermo.h" #include "update.h" #include "domain.h" #include "group.h" #include "input.h" #include "variable.h" #include "molecule.h" -#include "atom_masks.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index e9cd590624..7949e327a9 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom.h" +#include +#include #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index d4bea15d0b..1ea085b869 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/atom_vec.h b/src/atom_vec.h index 87fb35d9c7..26c181be1e 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -14,8 +14,7 @@ #ifndef LMP_ATOM_VEC_H #define LMP_ATOM_VEC_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index af4b4e617d..25a28f1668 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 96cf0ec909..5e83946078 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_body.h" +#include +#include +#include "my_pool_chunk.h" #include "style_body.h" #include "body.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 4d02c4b3e0..38309648fb 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -21,7 +21,6 @@ AtomStyle(body,AtomVecBody) #define LMP_ATOM_VEC_BODY_H #include "atom_vec.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { @@ -112,7 +111,6 @@ class AtomVecBody : public AtomVec { void grow_bonus(); void copy_bonus(int, int); - //void check(int); }; } diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index fa3c99ca34..9f35d16ff0 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 7bb29bd6bc..5565b82a10 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -15,12 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include #include "atom_vec_ellipsoid.h" +#include #include "math_extra.h" #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 18f6fb567d..9e9dbc95f0 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_hybrid.h" +#include #include "atom.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index a027923a17..8129baccba 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -20,7 +20,6 @@ AtomStyle(hybrid,AtomVecHybrid) #ifndef LMP_ATOM_VEC_HYBRID_H #define LMP_ATOM_VEC_HYBRID_H -#include #include "atom_vec.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index ba59b3d17a..695ced13fd 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_line.h" +#include +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 2a77ec418b..75136503ea 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_sphere.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 45418b35fd..3b7bfe5377 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_tri.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/balance.cpp b/src/balance.cpp index 61ac895467..c3b6f7d3bf 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -18,11 +18,10 @@ //#define BALANCE_DEBUG 1 +#include "balance.h" #include #include -#include #include -#include "balance.h" #include "atom.h" #include "comm.h" #include "rcb.h" @@ -30,7 +29,6 @@ #include "domain.h" #include "force.h" #include "update.h" -#include "group.h" #include "modify.h" #include "fix_store.h" #include "imbalance.h" @@ -39,7 +37,6 @@ #include "imbalance_neigh.h" #include "imbalance_store.h" #include "imbalance_var.h" -#include "timer.h" #include "memory.h" #include "error.h" diff --git a/src/balance.h b/src/balance.h index 420031502a..424da33757 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,7 +20,6 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/body.cpp b/src/body.cpp index 78e2f5d71b..c0e58d3f4c 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "body.h" -#include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/body.h b/src/body.h index 59001620f8..44581b75f6 100644 --- a/src/body.h +++ b/src/body.h @@ -16,7 +16,6 @@ #include "pointers.h" #include "atom_vec_body.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { diff --git a/src/bond.cpp b/src/bond.cpp index edcd869425..bb54306280 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "bond.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/bond.h b/src/bond.h index 8fb7040832..b558a2a35e 100644 --- a/src/bond.h +++ b/src/bond.h @@ -14,8 +14,7 @@ #ifndef LMP_BOND_H #define LMP_BOND_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -48,6 +47,8 @@ class Bond : protected Pointers { virtual double equilibrium_distance(int) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double single(int, double, int, int, double &) = 0; virtual double memory_usage(); diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 567b1a4d00..3e20553cac 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "bond_deprecated.h" +#include #include "bond_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 65609b4b6e..2b365014cf 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "bond_hybrid.h" +#include #include #include -#include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" @@ -325,6 +324,7 @@ void BondHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -350,6 +350,7 @@ void BondHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_bond(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index e51d467ac1..19e4debfed 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -20,7 +20,6 @@ BondStyle(hybrid,BondHybrid) #ifndef LMP_BOND_HYBRID_H #define LMP_BOND_HYBRID_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 0847cf9e6b..9be37c13be 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,10 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_zero.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/bond_zero.h b/src/bond_zero.h index 9443ff0784..7cbd2b9a96 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -20,7 +20,6 @@ BondStyle(zero,BondZero) #ifndef LMP_BOND_ZERO_H #define LMP_BOND_ZERO_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/change_box.cpp b/src/change_box.cpp index b7d3cb245f..98119fb3bf 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "change_box.h" #include #include -#include #include -#include "change_box.h" #include "atom.h" #include "modify.h" #include "fix.h" diff --git a/src/citeme.cpp b/src/citeme.cpp index d021722671..c8745891cf 100644 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -12,9 +12,7 @@ ------------------------------------------------------------------------- */ #include "citeme.h" -#include "version.h" #include "universe.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/citeme.h b/src/citeme.h index 262b284337..c383ec2227 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -15,7 +15,6 @@ #define LMP_CITEME_H #include "pointers.h" -#include #include namespace LAMMPS_NS { @@ -29,7 +28,7 @@ class CiteMe : protected Pointers { private: FILE *fp; // opaque pointer to log.cite file object typedef std::set citeset; - citeset *cs; // registered set of publications + citeset *cs; // registered set of publications }; } diff --git a/src/comm.cpp b/src/comm.cpp index 052de93793..3f2138aacc 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -11,16 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "comm.h" #include #include #include -#include "comm.h" #include "universe.h" #include "atom.h" #include "atom_vec.h" #include "force.h" #include "pair.h" +#include "bond.h" #include "modify.h" +#include "neighbor.h" #include "fix.h" #include "compute.h" #include "domain.h" @@ -585,6 +587,82 @@ void Comm::set_proc_grid(int outflag) } } +/* ---------------------------------------------------------------------- + determine suitable communication cutoff. + this uses three inputs: 1) maximum neighborlist cutoff, 2) an estimate + based on bond lengths and bonded interaction styles present, and 3) a + user supplied communication cutoff. + the neighbor list cutoff (1) is *always* used, since it is a requirement + for neighborlists working correctly. the bond length based cutoff is + *only* used, if no pair style is defined and no user cutoff is provided. + otherwise, a warning is printed. if the bond length based estimate is + larger than what is used. + print a warning, if a user specified communication cutoff is overridden. +------------------------------------------------------------------------- */ + +double Comm::get_comm_cutoff() +{ + double maxcommcutoff, maxbondcutoff = 0.0; + + if (force->bond) { + int n = atom->nbondtypes; + for (int i = 1; i <= n; ++i) + maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i)); + + // apply bond length based heuristics. + + if (force->newton_bond) { + if (force->dihedral || force->improper) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } + } else { + if (force->dihedral || force->improper) { + maxbondcutoff *= 3.125; + } else if (force->angle) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } + } + maxbondcutoff += neighbor->skin; + } + + // always take the larger of max neighbor list and user specified cutoff + + maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax); + + // use cutoff estimate from bond length only if no user specified + // cutoff was given and no pair style present. Otherwise print a + // warning, if the estimated bond based cutoff is larger than what + // is currently used. + + if (!force->pair && (cutghostuser == 0.0)) { + maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); + } else { + if ((me == 0) && (maxbondcutoff > maxcommcutoff)) { + char mesg[256]; + snprintf(mesg,256,"Communication cutoff %g is shorter than a bond " + "length based estimate of %g. This may lead to errors.", + maxcommcutoff,maxbondcutoff); + error->warning(FLERR,mesg); + } + } + + // print warning if neighborlist cutoff overrides user cutoff + + if (me == 0) { + if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) { + char mesg[128]; + snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff); + error->warning(FLERR,mesg); + } + } + + return maxcommcutoff; +} + /* ---------------------------------------------------------------------- determine which proc owns atom with coord x[3] based on current decomp x will be in box (orthogonal) or lamda coords (triclinic) @@ -963,11 +1041,6 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs, return 0; // all nout_rvous are 0, no 2nd irregular } - - - - - // create procs and outbuf for All2all if necesary if (!outorder) { diff --git a/src/comm.h b/src/comm.h index 30360b1059..5978836da7 100644 --- a/src/comm.h +++ b/src/comm.h @@ -14,7 +14,7 @@ #ifndef LMP_COMM_H #define LMP_COMM_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -70,6 +70,8 @@ class Comm : protected Pointers { void set_processors(int, char **); // set 3d processor grid attributes virtual void set_proc_grid(int outflag = 1); // setup 3d grid of procs + double get_comm_cutoff(); // determine communication cutoff + virtual void setup() = 0; // setup 3d comm pattern virtual void forward_comm(int dummy = 0) = 0; // forward comm of atom coords virtual void reverse_comm() = 0; // reverse comm of forces @@ -237,6 +239,15 @@ Self-explanatory. E: Cannot put data on ring from NULL pointer +W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. + +The communication cutoff defaults to the maximum of what is inferred from pair and +bond styles (will be zero, if none are defined) and what is specified via +"comm_modify cutoff" (defaults to 0.0). If this results to 0.0, no ghost atoms will +be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in +interaction lists. To avoid, either define pair style zero with a suitable cutoff +or use comm_modify cutoff. + UNDOCUMENTED U: OMP_NUM_THREADS environment is not set. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 330551aaed..324e6dd7bf 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -15,27 +15,18 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "comm_brick.h" #include #include #include -#include -#include -#include "comm_brick.h" -#include "comm_tiled.h" -#include "universe.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "pair.h" #include "domain.h" #include "neighbor.h" -#include "group.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" -#include "math_extra.h" #include "error.h" #include "memory.h" @@ -175,7 +166,10 @@ void CommBrick::setup() int ntypes = atom->ntypes; double *prd,*sublo,*subhi; - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); if (triclinic == 0) { prd = domain->prd; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index d1d625445a..b3b77584a9 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "comm_tiled.h" -#include "comm_brick.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "force.h" #include "pair.h" #include "neighbor.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" #include "memory.h" #include "error.h" @@ -157,7 +155,11 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); + cutghost[0] = cutghost[1] = cutghost[2] = cut; if ((periodicity[0] && cut > prd[0]) || diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 13ecbc4b01..5a9beb28f7 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -14,6 +14,7 @@ #ifndef LMP_COMM_TILED_H #define LMP_COMM_TILED_H +#include #include "comm.h" namespace LAMMPS_NS { diff --git a/src/compute.cpp b/src/compute.cpp index 207f825ec8..cc92d2b5d3 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -11,15 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute.h" #include #include -#include "compute.h" -#include "atom.h" #include "domain.h" #include "force.h" -#include "comm.h" #include "group.h" #include "modify.h" #include "fix.h" diff --git a/src/compute.h b/src/compute.h index a023834368..38d001db6f 100644 --- a/src/compute.h +++ b/src/compute.h @@ -14,7 +14,7 @@ #ifndef LMP_COMPUTE_H #define LMP_COMPUTE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index e9f9ba2b6f..dee5fb214f 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -15,20 +15,17 @@ Contributing authors: Aidan P. Thompson (SNL) ------------------------------------------------------------------------- */ +#include "compute_adf.h" #include #include -#include #include -#include "compute_adf.h" #include "atom.h" #include "update.h" #include "force.h" #include "pair.h" -#include "domain.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_adf.h b/src/compute_adf.h index a7983b7173..f768013207 100644 --- a/src/compute_adf.h +++ b/src/compute_adf.h @@ -20,7 +20,6 @@ ComputeStyle(adf,ComputeADF) #ifndef LMP_COMPUTE_ADF_H #define LMP_COMPUTE_ADF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6c8c8e5d9a..e495ac6899 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,9 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_aggregate_atom.h" +#include #include #include -#include "compute_aggregate_atom.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 59945f5832..fc72a58453 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_angle.h" +#include +#include "angle.h" #include "update.h" #include "force.h" #include "angle_hybrid.h" diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 1196211665..b100824ea9 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_angle_local.h" #include #include -#include "compute_angle_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index a70eaaf49f..05ea963b82 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_angmom_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 896aaec9bd..5cc947c764 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_bond.h" +#include +#include "bond.h" #include "update.h" #include "force.h" #include "bond_hybrid.h" diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index ccdd3ee77c..d579772384 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_bond_local.h" #include #include -#include "compute_bond_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 5096879b32..18fc31390f 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -15,9 +15,8 @@ Contributing author: Michel Perez (U Lyon) for non-fcc lattices ------------------------------------------------------------------------- */ -#include -#include #include "compute_centro_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 61b653b375..92567101de 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -13,10 +13,13 @@ // NOTE: allow for bin center to be variables for sphere/cylinder +#include "compute_chunk_atom.h" #include +#include #include #include -#include "compute_chunk_atom.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -24,6 +27,7 @@ #include "region.h" #include "lattice.h" #include "modify.h" +#include "fix.h" #include "fix_store.h" #include "comm.h" #include "group.h" @@ -33,8 +37,6 @@ #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 3d0cea1add..51dad00c25 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_chunk_spread_atom.h" #include #include -#include "compute_chunk_spread_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 0c34b42671..ff227b3590 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_cluster_atom.h" +#include #include #include -#include -#include "compute_cluster_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index b8ad3f0f64..054798f637 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_cna_atom.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index ec66767245..c39911214c 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_com_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index e60a51832a..7a288afb43 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_contact_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" @@ -22,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 54f4c70c71..30747c1314 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_coord_atom.h" #include #include -#include -#include "compute_coord_atom.h" #include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 069fa73437..1db78b6bdf 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 3595b2eda3..e50903104a 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_dihedral.h" +#include #include "update.h" #include "force.h" +#include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 9efdd61cb8..ac2c884c3f 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_dihedral_local.h" #include #include -#include "compute_dihedral_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "update.h" #include "domain.h" #include "force.h" -#include "dihedral.h" #include "input.h" #include "variable.h" - #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index b0474b6359..3790da2035 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_dipole_chunk.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index d8f279058e..41db4db1d6 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -11,15 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_displace_atom.h" #include #include -#include "compute_displace_atom.h" #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "input.h" #include "variable.h" diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 31ed0aaba5..2a8588f061 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere.h" +#include #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index 999bc062c5..78664a912f 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index bb273f3bdb..f9b68dd217 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,8 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "compute_fragment_atom.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index dc9ab52f49..15f8a8f1aa 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_global_atom.h" #include #include -#include "compute_global_atom.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 17e8737350..c64db19fc1 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -16,10 +16,10 @@ K-space terms added by Stan Moore (BYU) ------------------------------------------------------------------------- */ +#include "compute_group_group.h" #include #include #include -#include "compute_group_group.h" #include "atom.h" #include "update.h" #include "force.h" @@ -33,7 +33,6 @@ #include "comm.h" #include "domain.h" #include "math_const.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0e29c0d667..bce0c0de85 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_gyration.h" +#include #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 6a23398aca..5677ce4b6a 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_gyration_chunk.h" +#include #include #include -#include "compute_gyration_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 0b37865034..c465a2ab02 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,14 +16,13 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ -#include -#include #include "compute_heat_flux.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "force.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 6d17ae15bd..96d4c47678 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_hexorder_atom.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index ac2a23e727..181771dcfb 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_improper.h" +#include #include "update.h" #include "force.h" +#include "improper.h" #include "improper_hybrid.h" #include "error.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index 2861850c79..e363749b67 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -11,16 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_improper_local.h" #include #include -#include "compute_improper_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "update.h" #include "domain.h" #include "force.h" -#include "improper.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index a33073c35a..be980a08ee 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_inertia_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index fb3c5a9695..c6ba478dcb 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke.h" +#include #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index c5506996da..102d6364ff 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 608d3e6b33..b15bb8e875 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_msd.h" +#include +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 1f974cc06c..8039a4fcd5 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_msd_chunk.h" +#include +#include #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 23447da602..327c64493f 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_omega_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 8a0a525fdc..266df575f9 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -16,10 +16,10 @@ Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_orientorder_atom.h" #include #include #include -#include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index df4f3a1ddb..e9a3faf723 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair.h" #include #include #include -#include "compute_pair.h" #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index c356a08be9..2018d929f3 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair_local.h" #include #include #include -#include "compute_pair_local.h" #include "atom.h" #include "update.h" #include "force.h" @@ -22,7 +22,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 5839ec2095..fd7b74b43a 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pe.h" #include #include -#include "compute_pe.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index 2f1dc5650e..274e1b05a6 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" @@ -24,7 +24,6 @@ #include "improper.h" #include "kspace.h" #include "modify.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 978cad0cad..75b729d9c0 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pressure.h" #include #include -#include -#include "compute_pressure.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 0b57840696..065e3eeb82 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_property_atom.h" #include #include -#include "compute_property_atom.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 489890e1cc..579c7cae3f 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_property_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index ddcf5913ca..651e1190b1 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_property_local.h" +#include #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index d49485b4ea..501a506c98 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -15,11 +15,10 @@ Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ +#include "compute_rdf.h" #include #include -#include #include -#include "compute_rdf.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_rdf.h b/src/compute_rdf.h index 52a93a38dd..85f6ce6ad2 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -20,7 +20,6 @@ ComputeStyle(rdf,ComputeRDF) #ifndef LMP_COMPUTE_RDF_H #define LMP_COMPUTE_RDF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 16dc84628a..8467554faa 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,17 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_reduce.h" #include #include #include -#include "compute_reduce.h" #include "atom.h" #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" #include "group.h" #include "input.h" #include "variable.h" diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index f31672ef74..3b68e20fcb 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_reduce_chunk.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 8e91a299e8..9074124a61 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_reduce_region.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index ac70e7dd15..67b60882f6 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_slice.h" +#include #include #include -#include "compute_slice.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index 5211f015ab..7c0ed9ef17 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_stress_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 70a7734593..402b84bb4b 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 396492e18d..0fa5bbbb8a 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_temp_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index c46a17497f..dc12e8f6db 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_com.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 280c17dd08..7d81a84bc4 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_deform.h" #include #include -#include "compute_temp_deform.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index ee72ba3e74..f5f29d9dc0 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_partial.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c7f0b28a6c..fce145848e 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_profile.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 36e7f51ce4..30f6701fcd 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_ramp.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "lattice.h" #include "memory.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 0c54aeb63c..4c0b925eb6 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_region.h" #include #include -#include "compute_temp_region.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 23e74634b5..786ef523ad 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_sphere.h" #include #include -#include "compute_temp_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" #include "domain.h" #include "modify.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index d9de99bcb2..35eef8fe10 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_torque_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index d46b8b5fa0..5123e3aab4 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_vacf.h" +#include +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index a6dd796c63..b0a8dbeee7 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_vcm_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "compute_chunk_atom.h" -#include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 52e4256fca..f6cff042fe 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "create_atoms.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -23,8 +22,6 @@ #include "modify.h" #include "force.h" #include "special.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "lattice.h" #include "region.h" diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index e19b565554..5b7c354595 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,9 +15,9 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ -#include -#include #include "create_bonds.h" +#include +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/create_box.cpp b/src/create_box.cpp index b5e37b759c..4a826cb691 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "create_box.h" +#include #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "domain.h" #include "region.h" #include "region_prism.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 41df167f07..e8d9c5d53b 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "delete_atoms.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index fe32bca879..c450f77ee7 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -11,14 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "delete_bonds.h" #include #include #include -#include "delete_bonds.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "neighbor.h" #include "comm.h" #include "force.h" #include "group.h" diff --git a/src/deprecated.cpp b/src/deprecated.cpp index b937482669..86af54fbfd 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -15,10 +15,9 @@ Contributing authors: Axel Kohlmeyer (Temple U), ------------------------------------------------------------------------- */ -#include #include "deprecated.h" +#include #include "comm.h" -#include "force.h" #include "error.h" #include "input.h" diff --git a/src/dihedral.cpp b/src/dihedral.cpp index adccf2a490..d2de841dd0 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -11,13 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dihedral.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "pair.h" -#include "suffix.h" #include "atom_masks.h" #include "memory.h" #include "error.h" diff --git a/src/dihedral.h b/src/dihedral.h index f1b42008bf..f7b0ad1c71 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -14,8 +14,7 @@ #ifndef LMP_DIHEDRAL_H #define LMP_DIHEDRAL_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -45,6 +44,8 @@ class Dihedral : protected Pointers { virtual void coeff(int, char **) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double memory_usage(); diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 70888ca76d..0205b1b887 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_deprecated.h" +#include #include "dihedral_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index f3e4823d53..6c0a4338ae 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "dihedral_hybrid.h" +#include #include #include -#include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" @@ -309,6 +308,7 @@ void DihedralHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -334,6 +334,7 @@ void DihedralHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_dihedral(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 0839fdfc61..2804060af4 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -20,7 +20,6 @@ DihedralStyle(hybrid,DihedralHybrid) #ifndef LMP_DIHEDRAL_HYBRID_H #define LMP_DIHEDRAL_HYBRID_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 8145d5f32d..daf46fe79a 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dihedral_zero.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index e7dbb0d3a5..e97f8f6641 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -24,7 +24,6 @@ DihedralStyle(zero,DihedralZero) #ifndef LMP_DIHEDRAL_ZERO_H #define LMP_DIHEDRAL_ZERO_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 7b29b1d3d5..dc94c3ed35 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "displace_atoms.h" +#include +#include +#include #include "atom.h" #include "modify.h" #include "domain.h" diff --git a/src/domain.cpp b/src/domain.cpp index 74d7560c31..372b264013 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -15,12 +15,10 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "domain.h" +#include +#include +#include #include "style_region.h" #include "atom.h" #include "atom_vec.h" @@ -37,13 +35,11 @@ #include "output.h" #include "thermo.h" #include "universe.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; #define BIG 1.0e20 #define SMALL 1.0e-4 diff --git a/src/domain.h b/src/domain.h index e131d07a1b..a0bda8ae72 100644 --- a/src/domain.h +++ b/src/domain.h @@ -15,9 +15,9 @@ #define LMP_DOMAIN_H #include -#include "pointers.h" #include #include +#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump.cpp b/src/dump.cpp index 8fa07a9cb2..57a8decbb0 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "dump.h" +#include +#include #include "atom.h" #include "irregular.h" #include "update.h" diff --git a/src/dump.h b/src/dump.h index 1c6a131f76..bc7fd2d5a5 100644 --- a/src/dump.h +++ b/src/dump.h @@ -14,9 +14,7 @@ #ifndef LMP_DUMP_H #define LMP_DUMP_H -#include -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 74583f4013..e2e77cfb77 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_atom.h" +#include #include "domain.h" #include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index ddd662c8a6..3430720b8c 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,18 +16,10 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dump_cfg.h" +#include #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "memory.h" #include "error.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 17ad4b89ef..ce83e442c9 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "dump_custom.h" #include #include -#include "dump_custom.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index 384e9089c0..254b371e22 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -16,12 +16,10 @@ Axel Kohlmeyer (Temple U), support for groups ------------------------------------------------------------------------- */ +#include "dump_dcd.h" #include -#include // requires C++-11 -#include #include #include -#include "dump_dcd.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index f0999f4276..4263b9801f 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 0d63d2e4cb..7e6bc0c44c 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_image.h" +#include #include #include -#include #include -#include "dump_image.h" #include "image.h" #include "atom.h" +#include "atom_vec.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "atom_vec_body.h" #include "body.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "force.h" #include "comm.h" #include "modify.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 8dc0554690..9f021a7b6a 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_local.h" #include #include #include -#include "dump_local.h" -#include "atom.h" #include "modify.h" #include "fix.h" #include "compute.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 59dfdc3d6e..ea67320d4a 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,13 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dump_movie.h" +#include #include "comm.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index fd52671d81..10ba10f995 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_xyz.h" +#include #include "atom.h" -#include "group.h" #include "error.h" #include "memory.h" #include "update.h" diff --git a/src/error.cpp b/src/error.cpp index cc80dcb4d8..656c957ee2 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "error.h" #include #include #include -#include "error.h" #include "universe.h" -#include "update.h" #include "output.h" #include "input.h" diff --git a/src/finish.cpp b/src/finish.cpp index 1baa6d6fda..9ab97ae410 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -11,16 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "finish.h" #include #include #include #include -#include -#include "finish.h" -#include "timer.h" -#include "universe.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -32,10 +28,10 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "output.h" #include "memory.h" #include "error.h" -#include "utils.h" +#include "timer.h" +#include "universe.h" #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 634bc2393d..e0cfeca1a9 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix.h" #include #include -#include "fix.h" #include "atom.h" #include "group.h" #include "force.h" -#include "comm.h" #include "atom_masks.h" #include "memory.h" #include "error.h" diff --git a/src/fix.h b/src/fix.h index 7eaff38bd3..7e55e96269 100644 --- a/src/fix.h +++ b/src/fix.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_H #define LMP_FIX_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 9a5b528747..8668690e1d 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_adapt.h" +#include #include "atom.h" #include "bond.h" #include "update.h" diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d66457a1f1..275ec2c846 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_addforce.h" +#include #include #include -#include "fix_addforce.h" #include "atom.h" #include "atom_masks.h" #include "update.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index c8cbad75c9..694df2bcf7 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_atom.h" #include #include -#include "fix_ave_atom.h" #include "atom.h" -#include "domain.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index e4baf6bda1..42aa282d53 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -20,7 +20,6 @@ FixStyle(ave/atom,FixAveAtom) #ifndef LMP_FIX_AVE_ATOM_H #define LMP_FIX_AVE_ATOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 7aed4dcbe7..45eb38f5c2 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_chunk.h" +#include #include #include #include -#include "fix_ave_chunk.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index 4dc1c1c246..dac5761ae8 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -20,7 +20,6 @@ FixStyle(ave/chunk,FixAveChunk) #ifndef LMP_FIX_AVE_CHUNK_H #define LMP_FIX_AVE_CHUNK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 5c95f20ec2..f65b53efc8 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,10 +17,11 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate.h" +#include #include #include #include -#include "fix_ave_correlate.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index ff20e8ba94..05fd6b6576 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate,FixAveCorrelate) #ifndef LMP_FIX_AVE_CORRELATE_H #define LMP_FIX_AVE_CORRELATE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 87da5222f0..5a5de6d0b6 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,15 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_histo.h" +#include #include #include #include -#include "fix_ave_histo.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 3616959c61..35bdfcfa7f 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -20,7 +20,6 @@ FixStyle(ave/histo,FixAveHisto) #ifndef LMP_FIX_AVE_HISTO_H #define LMP_FIX_AVE_HISTO_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index c78f4fa1e3..1f0d282e5d 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -14,21 +14,18 @@ /* ---------------------------------------------------------------------- Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ - -#include -#include -#include #include "fix_ave_histo_weight.h" +#include +#include +#include "fix.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index e5638e1215..6ec3ba5721 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -20,7 +20,6 @@ FixStyle(ave/histo/weight,FixAveHistoWeight) #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H #define LMP_FIX_AVE_HISTO_WEIGHT_H -#include #include "fix_ave_histo.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 50654b6561..05d556d0c8 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,10 +15,11 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_ave_time.h" +#include #include #include #include -#include "fix_ave_time.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index 62dfbad296..01228f9e55 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -20,7 +20,6 @@ FixStyle(ave/time,FixAveTime) #ifndef LMP_FIX_AVE_TIME_H #define LMP_FIX_AVE_TIME_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 1c87ba5785..8ad07780a9 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_aveforce.h" #include #include -#include -#include "fix_aveforce.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index ddaf42b49d..5ca1ec124a 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_balance.h" +#include #include "balance.h" #include "update.h" #include "atom.h" @@ -26,7 +25,6 @@ #include "modify.h" #include "fix_store.h" #include "rcb.h" -#include "timer.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/fix_balance.h b/src/fix_balance.h index 64383b5950..76cbea258a 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -20,7 +20,6 @@ FixStyle(balance,FixBalance) #ifndef LMP_FIX_BALANCE_H #define LMP_FIX_BALANCE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index a315330d14..c19ea918b4 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -15,10 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_box_relax.h" #include #include -#include -#include "fix_box_relax.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index eb7a794962..855869a574 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_controller.h" #include #include -#include "fix_controller.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 909ead3e2a..9d84c4bb62 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -15,10 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_deform.h" +#include +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 7db27152ba..0c212668b3 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index e4cf12d1ff..9af5a37675 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_drag.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 7566094b48..da4bdad827 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_dt_reset.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "integrate.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 986ded5d16..3edd24e9af 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_enforce2d.h" +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index b1ffa65e49..afb420df93 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_external.h" +#include #include "atom.h" #include "update.h" #include "memory.h" diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index bc10eb2807..14ba913c01 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_gravity.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 8a332bed95..d2eea9f781 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_group.h" +#include #include "group.h" #include "update.h" #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 5fda4c30d6..8ebb39f0e9 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_halt.h" +#include +#include +#include #include "update.h" #include "force.h" -#include "update.h" #include "input.h" #include "variable.h" #include "atom.h" diff --git a/src/fix_halt.h b/src/fix_halt.h index 372c915a7f..93c5e95078 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -20,7 +20,6 @@ FixStyle(halt,FixHalt) #ifndef LMP_FIX_HALT_H #define LMP_FIX_HALT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index f34845785c..67d445df92 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_heat.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "region.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index b8e07dfd53..04837ff39b 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -15,10 +15,10 @@ Contributing author: Ravi Agrawal (Northwestern U) ------------------------------------------------------------------------- */ +#include "fix_indent.h" +#include #include #include -#include -#include "fix_indent.h" #include "atom.h" #include "input.h" #include "variable.h" @@ -26,7 +26,6 @@ #include "lattice.h" #include "update.h" #include "modify.h" -#include "output.h" #include "respa.h" #include "error.h" #include "force.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 3f2ec20db0..a050e5a13a 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -16,11 +16,10 @@ Aidan Thompson (SNL) GJF formulation ------------------------------------------------------------------------- */ +#include "fix_langevin.h" #include #include #include -#include -#include "fix_langevin.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -28,8 +27,6 @@ #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "input.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index aea1a2a25b..c153ee65dd 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_lineforce.h" #include #include -#include -#include "fix_lineforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index fa39643a1b..df2dfb02a7 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_minimize.h" #include "atom.h" #include "domain.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 680251e670..a363cb8eac 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_momentum.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "group.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 0a5f506ab2..770c0fca6b 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_move.h" +#include +#include #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/fix_move.h b/src/fix_move.h index 5993d7d6e8..740b051be0 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -20,7 +20,6 @@ FixStyle(move,FixMove) #ifndef LMP_FIX_MOVE_H #define LMP_FIX_MOVE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 207c409596..5c740ae649 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -11,18 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_neigh_history.h" #include #include -#include -#include "fix_neigh_history.h" +#include "my_page.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "force.h" #include "pair.h" -#include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 601e8a55a2..51d03f5b12 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -21,7 +21,6 @@ FixStyle(NEIGH_HISTORY,FixNeighHistory) #define LMP_FIX_NEIGH_HISTORY_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index deca0ad83d..bb3fe7559c 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -15,11 +15,9 @@ Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nh.h" -#include "math_extra.h" +#include +#include #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index f176493242..1ff3fc2d4d 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "force.h" #include "domain.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 40265ef57c..7148b024de 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 3fcbe5e9c6..f64f144f34 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index d17577d68d..e856fafe2d 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 50ac990daf..9cbb17b0ca 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 959483230e..863ce5404d 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nve.h" +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 68ff0665a1..d63c736e73 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_nve_limit.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index d4fca9e676..022e8abe74 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nve_noforce.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index 0bee8b8685..c0fea17c2b 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_sphere.h" +#include +#include #include "atom.h" #include "domain.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" #include "error.h" #include "math_vector.h" diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7247612dd4..6f0d4c6c50 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index c7d23364a7..138794862a 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -15,9 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod.h" +#include #include "math_extra.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 44046699ba..fed3799011 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_sphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 45dc782fcf..a3f27277bd 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_planeforce.h" #include #include -#include -#include "fix_planeforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 95db004436..c090c554e2 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_press_berendsen.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" @@ -23,7 +22,6 @@ #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index f6db88114a..dc76fc39f9 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_print.h" +#include +#include #include "update.h" #include "input.h" #include "modify.h" diff --git a/src/fix_print.h b/src/fix_print.h index 37b6680aee..5644160220 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -20,7 +20,6 @@ FixStyle(print,FixPrint) #ifndef LMP_FIX_PRINT_H #define LMP_FIX_PRINT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index c89419f850..555114e4f9 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom.h" #include #include -#include "fix_property_atom.h" #include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "update.h" - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index 3c3178f4af..afedf9c12c 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_read_restart.h" #include "atom.h" #include "memory.h" diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 75b383d67a..f461e0fa52 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include #include "fix_recenter.h" +#include +#include #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 64461ba7ca..742dd5c58b 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_respa.h" +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 08485d65b3..5a0d4fb662 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -16,17 +16,16 @@ support for bond and angle restraints by Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ +#include "fix_restrain.h" +#include #include #include -#include -#include "fix_restrain.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" #include "comm.h" #include "respa.h" -#include "input.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index fc8b7aeb59..77c4bfbddc 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 328a0eeafd..510b194ab7 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_spring.h" +#include +#include #include "atom.h" #include "update.h" #include "respa.h" -#include "domain.h" #include "force.h" #include "group.h" #include "error.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 5b5d95b111..e14936a976 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_spring_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" #include "respa.h" -#include "domain.h" #include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 28c8969006..f1e68bffa4 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,10 +16,8 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_spring_rg.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 670883af41..c94f21b492 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ -#include -#include #include "fix_spring_self.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 9db65d0987..94c62c1850 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_store.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/fix_store.h b/src/fix_store.h index 5524770a97..437c14f0f7 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -20,7 +20,6 @@ FixStyle(STORE,FixStore) #ifndef LMP_FIX_STORE_H #define LMP_FIX_STORE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index a841714098..5c25f0e162 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_store_force.h" +#include #include "atom.h" #include "update.h" -#include "group.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index da899a173c..18dfa026d9 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_store_state.h" #include #include -#include "fix_store_state.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 55518015c4..be8922be4e 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_temp_berendsen.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 7bdf776355..f827c88f51 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -15,10 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_temp_csld.h" +#include +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 495a155113..55cbb60407 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,13 +16,12 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_temp_csvr.h" +#include +#include +#include #include "atom.h" #include "force.h" -#include "memory.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 11dfa6a5fc..a9d605d5ba 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_temp_rescale.h" +#include +#include #include "atom.h" #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 10315a750d..cfe9a9572e 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -16,11 +16,10 @@ Christian Burisch (Bochum Univeristy, Germany) ------------------------------------------------------------------------- */ +#include "fix_tmd.h" #include #include -#include #include -#include "fix_tmd.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_tmd.h b/src/fix_tmd.h index b6db41dd5a..f23a64a027 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -20,7 +20,6 @@ FixStyle(tmd,FixTMD) #ifndef LMP_FIX_TMD_H #define LMP_FIX_TMD_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 6387af7676..53093acbf6 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_vector.h" +#include +#include #include "update.h" #include "force.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index e845142322..bdd1e19976 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index e84d01191d..8ceafb4bfc 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall.h" -#include "atom.h" +#include +#include #include "input.h" #include "variable.h" #include "domain.h" diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 4dc067178a..6c6d5ec402 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_harmonic.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index a93f4dd699..5656cf113d 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -15,8 +15,8 @@ Contributing author: Jonathan Lee (Sandia) ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj1043.h" +#include #include "atom.h" #include "math_const.h" diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index 369ef78c97..e748e2ef13 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj126.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index ce5a06c81b..c0e81b60ee 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 8acba72035..bc3414d650 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_reflect.h" +#include #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index ff147d7446..c1a689d90a 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,18 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_region.h" +#include +#include +#include #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_const.h" diff --git a/src/force.cpp b/src/force.cpp index 2648358932..1a826b2843 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "force.h" #include #include #include -#include "force.h" #include "style_bond.h" #include "style_angle.h" #include "style_dihedral.h" #include "style_improper.h" #include "style_pair.h" #include "style_kspace.h" -#include "atom.h" #include "comm.h" #include "pair.h" #include "pair_hybrid.h" @@ -32,8 +31,6 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "group.h" -#include "memory.h" #include "error.h" #include "utils.h" diff --git a/src/force.h b/src/force.h index 227b9427c0..26a3ecdfb8 100644 --- a/src/force.h +++ b/src/force.h @@ -15,7 +15,6 @@ #define LMP_FORCE_H #include "pointers.h" -#include #include #include diff --git a/src/group.cpp b/src/group.cpp index 256bab7778..d119964ea1 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "group.h" #include #include -#include #include -#include -#include "group.h" +#include #include "domain.h" #include "atom.h" #include "force.h" diff --git a/src/group.h b/src/group.h index 962d37b32a..ec913f98bc 100644 --- a/src/group.h +++ b/src/group.h @@ -14,7 +14,6 @@ #ifndef LMP_GROUP_H #define LMP_GROUP_H -#include #include "pointers.h" #include diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index f612be9eeb..c3824b71fe 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -2,9 +2,7 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -#include -#include -#include +#include "hashlittle.h" // if the system defines the __BYTE_ORDER__ define, // we use it instead of guessing the platform @@ -142,7 +140,7 @@ acceptable. Do NOT use for cryptographic purposes. ------------------------------------------------------------------------------- */ -uint32_t hashlittle( const void *key, size_t length, uint32_t initval) +uint32_t LAMMPS_NS::hashlittle(const void *key, size_t length, uint32_t initval) { #ifndef PURIFY_HATES_HASHLITTLE diff --git a/src/hashlittle.h b/src/hashlittle.h index 7b57a35c80..75380d366b 100644 --- a/src/hashlittle.h +++ b/src/hashlittle.h @@ -2,4 +2,13 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -uint32_t hashlittle(const void *key, size_t length, uint32_t); +#ifndef LMP_HASHLITTLE_H +#define LMP_HASHLITTLE_H + +#include +#include + +namespace LAMMPS_NS { + uint32_t hashlittle(const void *key, size_t length, uint32_t); +} +#endif diff --git a/src/image.cpp b/src/image.cpp index 3df167bbf6..4a5009b8ed 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -15,12 +15,11 @@ Contributing author: Nathan Fabian (Sandia) ------------------------------------------------------------------------- */ +#include "image.h" #include #include #include -#include #include -#include "image.h" #include "math_extra.h" #include "random_mars.h" #include "math_const.h" @@ -29,7 +28,7 @@ #include "memory.h" #ifdef LAMMPS_JPEG -#include "jpeglib.h" +#include #endif #ifdef LAMMPS_PNG diff --git a/src/image.h b/src/image.h index 5672bf85c5..7df81425d9 100644 --- a/src/image.h +++ b/src/image.h @@ -15,7 +15,6 @@ #define LMP_IMAGE_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance.h b/src/imbalance.h index d3c3b9a642..0cc4ac844e 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,8 +14,7 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 2a55754da8..19f3915a11 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_neigh.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 6b69caf785..343d47b189 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_store.h" +#include #include "atom.h" -#include "input.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index a5fe538b8f..0831713204 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_time.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "timer.h" #include "error.h" diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index e089b1df0c..ba84ef01ef 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_var.h" +#include +#include #include "atom.h" #include "group.h" #include "input.h" @@ -20,9 +21,6 @@ #include "memory.h" #include "error.h" -// DEBUG -#include "update.h" - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/improper.cpp b/src/improper.cpp index 17e2df4e59..eefe3222ee 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "improper.h" #include "atom.h" #include "comm.h" diff --git a/src/improper.h b/src/improper.h index d940b43a13..c30079bb5e 100644 --- a/src/improper.h +++ b/src/improper.h @@ -14,8 +14,7 @@ #ifndef LMP_IMPROPER_H #define LMP_IMPROPER_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -45,6 +44,8 @@ class Improper : protected Pointers { virtual void coeff(int, char **) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double memory_usage(); diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 6f4d08764f..62a688527a 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_deprecated.h" +#include #include "improper_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 5fdcb42a96..730a75766c 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "improper_hybrid.h" +#include #include #include -#include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" @@ -306,6 +305,7 @@ void ImproperHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -331,6 +331,7 @@ void ImproperHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_improper(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index 89595ccfc4..3e5423b173 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -20,7 +20,6 @@ ImproperStyle(hybrid,ImproperHybrid) #ifndef LMP_IMPROPER_HYBRID_H #define LMP_IMPROPER_HYBRID_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 747dd57919..efa70c8ff5 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_zero.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/improper_zero.h b/src/improper_zero.h index 0a2290b6f7..1a70059070 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -20,7 +20,6 @@ ImproperStyle(zero,ImproperZero) #ifndef LMP_IMPROPER_ZERO_H #define LMP_IMPROPER_ZERO_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/info.cpp b/src/info.cpp index 25b9879408..67d6ece291 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,8 +16,14 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include #include "info.h" +#include +#include +#include +#include +#include +#include +#include #include "accelerator_kokkos.h" #include "atom.h" #include "comm.h" @@ -44,18 +50,12 @@ #include "error.h" #include "utils.h" -#include -#include -#include -#include - #ifdef _WIN32 #define PSAPI_VERSION 1 #include #include // requires C++-11 #include #else -#include #include #include #endif @@ -366,7 +366,7 @@ void Info::command(int narg, char **arg) if (comm->mode == 0) { fprintf(out,"Communication mode = single\n"); fprintf(out,"Communication cutoff = %g\n", - MAX(comm->cutghostuser,neighbor->cutneighmax)); + comm->get_comm_cutoff()); } if (comm->mode == 1) { diff --git a/src/input.cpp b/src/input.cpp index 8bf4fc12e1..6871ee23f5 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -11,15 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "input.h" #include -#include #include #include #include #include #include #include -#include "input.h" #include "style_command.h" #include "universe.h" #include "atom.h" @@ -52,10 +51,6 @@ #include "memory.h" #include "utils.h" -#ifdef _OPENMP -#include -#endif - #ifdef _WIN32 #include #endif diff --git a/src/input.h b/src/input.h index b86982cb39..4b274c17a9 100644 --- a/src/input.h +++ b/src/input.h @@ -14,7 +14,6 @@ #ifndef LMP_INPUT_H #define LMP_INPUT_H -#include #include "pointers.h" #include #include diff --git a/src/integrate.cpp b/src/integrate.cpp index d6b27e042d..545de849d5 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "integrate.h" #include "update.h" #include "force.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 1865f9cbf6..b67214df25 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "irregular.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/irregular.h b/src/irregular.h index d56bcb253d..3fdfe20b36 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -14,6 +14,7 @@ #ifndef LMP_IRREGULAR_H #define LMP_IRREGULAR_H +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/kspace.cpp b/src/kspace.cpp index 643cf22113..f9020416bf 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,9 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kspace.h" +#include +#include #include #include -#include "kspace.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/kspace.h b/src/kspace.h index 69f4ccb433..c04a0db989 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -14,7 +14,7 @@ #ifndef LMP_KSPACE_H #define LMP_KSPACE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #ifdef FFT_SINGLE typedef float FFT_SCALAR; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 1d62de2692..0b6490b4cf 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "kspace_deprecated.h" +#include #include "comm.h" #include "force.h" #include "error.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index f8d04c9323..5ddc1600a4 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -11,26 +11,28 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lammps.h" #include +#include #include +#include #include #include #include -#include "lammps.h" -#include "style_angle.h" -#include "style_atom.h" -#include "style_bond.h" -#include "style_command.h" -#include "style_compute.h" -#include "style_dihedral.h" -#include "style_dump.h" -#include "style_fix.h" -#include "style_improper.h" -#include "style_integrate.h" -#include "style_kspace.h" -#include "style_minimize.h" -#include "style_pair.h" -#include "style_region.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_atom.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_command.h" // IWYU pragma: keep +#include "style_compute.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_dump.h" // IWYU pragma: keep +#include "style_fix.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_integrate.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep +#include "style_region.h" // IWYU pragma: keep #include "universe.h" #include "input.h" #include "info.h" @@ -46,7 +48,7 @@ #include "output.h" #include "citeme.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" +#include "accelerator_omp.h" // IWYU pragma: keep #include "timer.h" #include "lmppython.h" #include "version.h" diff --git a/src/lammps.h b/src/lammps.h index e02d0c764a..dc2916f214 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,6 +14,7 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H +#include #include namespace LAMMPS_NS { diff --git a/src/lattice.cpp b/src/lattice.cpp index ee2fea2a75..98faf680e8 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lattice.h" #include #include #include -#include "lattice.h" #include "update.h" #include "domain.h" #include "comm.h" diff --git a/src/library.cpp b/src/library.cpp index a653b83adb..eabe5fd179 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -14,14 +14,12 @@ // C or Fortran style library interface to LAMMPS // customize by adding new LAMMPS-specific functions +#include "library.h" #include +#include #include #include -#include "library.h" -#include "lmptype.h" -#include "lammps.h" #include "universe.h" -#include "input.h" #include "atom_vec.h" #include "atom.h" #include "domain.h" diff --git a/src/library.h b/src/library.h index f6f8d9d75c..8b03bb3621 100644 --- a/src/library.h +++ b/src/library.h @@ -17,7 +17,9 @@ */ #include +#ifdef LAMMPS_BIGBIG #include /* for int64_t */ +#endif /* ifdefs allow this file to be included in a C program */ diff --git a/src/lmppython.cpp b/src/lmppython.cpp index 7c6a490c24..52abd93f10 100644 --- a/src/lmppython.cpp +++ b/src/lmppython.cpp @@ -12,7 +12,11 @@ ------------------------------------------------------------------------- */ #include "lmppython.h" +#if LMP_PYTHON +#include "python_impl.h" +#else #include "error.h" +#endif using namespace LAMMPS_NS; diff --git a/src/lmppython.h b/src/lmppython.h index afc21037fb..3d55c4827b 100644 --- a/src/lmppython.h +++ b/src/lmppython.h @@ -51,11 +51,6 @@ private: }; } - -#endif - -#if LMP_PYTHON -#include "python_impl.h" #endif /* ERROR/WARNING messages: diff --git a/src/lmptype.h b/src/lmptype.h index 12fa6cc4fb..8a596e9f83 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -48,10 +48,6 @@ namespace LAMMPS_NS { -// enum used for KOKKOS host/device flags - -enum ExecutionSpace{Host,Device}; - // reserve 2 hi bits in molecular system neigh list for special bonds flag // max local + ghost atoms per processor = 2^30 - 1 diff --git a/src/main.cpp b/src/main.cpp index 8eb5e4e543..b7f6adbdda 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -11,12 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "lammps.h" +#include #include "input.h" -#include "error.h" -#include -#include #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include diff --git a/src/math_extra.cpp b/src/math_extra.cpp index f7e5bb646b..797d210d0e 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "math_extra.h" #include #include -#include "math_extra.h" #define MAXJACOBI 50 diff --git a/src/math_extra.h b/src/math_extra.h index 85f57224cf..09b135c641 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -19,9 +19,6 @@ #define LMP_MATH_EXTRA_H #include -#include -#include -#include "error.h" namespace MathExtra { diff --git a/src/math_special.cpp b/src/math_special.cpp index 31567bdc77..bf11a1ad45 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,6 +1,6 @@ -#include -#include // requires C++-11 #include "math_special.h" +#include +#include // IWYU pragma: keep using namespace LAMMPS_NS; diff --git a/src/memory.cpp b/src/memory.cpp index b2f8a95b17..a513dde6c2 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "memory.h" +#include #include "error.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) diff --git a/src/memory.h b/src/memory.h index c5eddc7fe7..42c9bf6aba 100644 --- a/src/memory.h +++ b/src/memory.h @@ -14,7 +14,6 @@ #ifndef LMP_MEMORY_H #define LMP_MEMORY_H -#include "lmptype.h" #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/min.cpp b/src/min.cpp index 2a42a444a0..408954edb8 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,10 +19,10 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include -#include -#include #include "min.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 20e8cc30dd..ff318d23da 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_cg.h" #include #include -#include -#include "min_cg.h" -#include "atom.h" #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index a50071d562..b7f853afd2 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,15 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "min_fire.h" +#include +#include #include "universe.h" #include "atom.h" #include "force.h" #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 0c834fbeb4..dcfed10fef 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,11 +17,12 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ +#include "min_hftn.h" +#include #include #include #include "atom.h" #include "fix_minimize.h" -#include "min_hftn.h" #include "modify.h" #include "output.h" #include "pair.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index f93a56b09d..a7a10dcd51 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,19 +21,15 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include #include "min_linesearch.h" +#include +#include #include "atom.h" -#include "update.h" -#include "neighbor.h" -#include "domain.h" #include "modify.h" #include "fix_minimize.h" #include "pair.h" #include "output.h" #include "thermo.h" -#include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 8b48816355..04e72b046d 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -11,16 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_quickmin.h" #include #include -#include "min_quickmin.h" #include "universe.h" #include "atom.h" #include "force.h" #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 5d44437ca0..e4e159003f 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "min_sd.h" -#include "atom.h" +#include #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/minimize.cpp b/src/minimize.cpp index e27fffd74b..e1af924019 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "minimize.h" #include "domain.h" #include "update.h" diff --git a/src/modify.cpp b/src/modify.cpp index 7378ce55d2..109571d531 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "modify.h" +#include #include "style_compute.h" #include "style_fix.h" #include "atom.h" diff --git a/src/modify.h b/src/modify.h index 5ff81855fe..b736485196 100644 --- a/src/modify.h +++ b/src/modify.h @@ -14,7 +14,6 @@ #ifndef LMP_MODIFY_H #define LMP_MODIFY_H -#include #include "pointers.h" #include #include diff --git a/src/molecule.cpp b/src/molecule.cpp index 454459084a..38887ebb0c 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,9 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "molecule.h" +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" @@ -21,12 +23,10 @@ #include "comm.h" #include "domain.h" #include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 256 #define EPSILON 1.0e-7 diff --git a/src/mpiio.h b/src/mpiio.h index 4953ade185..0098fca0e1 100644 --- a/src/mpiio.h +++ b/src/mpiio.h @@ -23,7 +23,7 @@ #error "The MPIIO package cannot be compiled in serial with MPI STUBS" #endif -#include "restart_mpiio.h" +#include "restart_mpiio.h" // IWYU pragma: export #else diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index 8bf88d35bb..a313e45f05 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -43,6 +43,10 @@ public variables: #ifndef LAMMPS_MY_POOL_CHUNK_H #define LAMMPS_MY_POOL_CHUNK_H +#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#define LAMMPS_MEMALIGN 64 +#endif + #include namespace LAMMPS_NS { @@ -190,9 +194,17 @@ class MyPoolChunk { for (int i = oldpage; i < npage; i++) { whichbin[i] = ibin; +#if defined(LAMMPS_MEMALIGN) + void *ptr; + if (posix_memalign(&ptr, LAMMPS_MEMALIGN, + chunkperpage*chunksize[ibin]*sizeof(T))) + errorflag = 2; + pages[i] = (T *) ptr; +#else pages[i] = (T *) malloc(chunkperpage*chunksize[ibin]*sizeof(T)); size += chunkperpage*chunksize[ibin]; if (!pages[i]) errorflag = 2; +#endif } // reset free list for unused chunks on new pages diff --git a/src/nbin.cpp b/src/nbin.cpp index 3e50148a04..4838d1d63d 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "nbin.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 6bdb9beae6..31720cc78c 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "neigh_list.h" +#include "my_page.h" // IWYU pragma: keep #include "atom.h" #include "comm.h" -#include "update.h" -#include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "my_page.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/neigh_list.h b/src/neigh_list.h index 755a1bf134..aca11cd921 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -15,7 +15,6 @@ #define LMP_NEIGH_LIST_H #include "pointers.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0382624198..d38aed08c0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -15,11 +15,10 @@ Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "neighbor.h" #include #include -#include #include -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "nbin.h" @@ -48,8 +47,6 @@ #include "error.h" #include "utils.h" -#include - using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/neighbor.h b/src/neighbor.h index 3466dd426a..50de4b4c98 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -15,7 +15,6 @@ #define LMP_NEIGHBOR_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/npair.cpp b/src/npair.cpp index 24cdc7750a..b63135fad6 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "nbin.h" diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp index 9426d22ed3..0a522c628d 100644 --- a/src/npair_copy.cpp +++ b/src/npair_copy.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp index 94a6af129c..464dca9251 100644 --- a/src/npair_full_bin.cpp +++ b/src/npair_full_bin.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index db84733f1c..758fc7e42b 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_atomonly.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp index 2edd03cc9e..61b27dd99d 100644 --- a/src/npair_full_bin_ghost.cpp +++ b/src/npair_full_bin_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 9a2490ac5d..40ed2275be 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp index 1b404ffc94..76b66fd004 100644 --- a/src/npair_full_nsq.cpp +++ b/src/npair_full_nsq.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp index 1727b2905e..b20fa9b8ce 100644 --- a/src/npair_full_nsq_ghost.cpp +++ b/src/npair_full_nsq_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index 6da44b4a5c..a7fa3985ef 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_atomonly_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp index 4c44741ffe..65768918c9 100644 --- a/src/npair_half_bin_newtoff.cpp +++ b/src/npair_half_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp index 72ec15e66a..91fbf049cb 100644 --- a/src/npair_half_bin_newtoff_ghost.cpp +++ b/src/npair_half_bin_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp index 3a387870e3..fe388e1144 100644 --- a/src/npair_half_bin_newton.cpp +++ b/src/npair_half_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp index 169e710e0e..1f0e3c1187 100644 --- a/src/npair_half_bin_newton_tri.cpp +++ b/src/npair_half_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 07b5c87a6c..57dcf29cc7 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 3d90979329..a9293d3d64 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 909c69246b..c1d845cb38 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp index 06e8344332..db369687d0 100644 --- a/src/npair_half_nsq_newtoff.cpp +++ b/src/npair_half_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp index 1865061a8b..0a9b6d0f45 100644 --- a/src/npair_half_nsq_newtoff_ghost.cpp +++ b/src/npair_half_nsq_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp index 11c71d5609..69489915b2 100644 --- a/src/npair_half_nsq_newton.cpp +++ b/src/npair_half_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp index 0145771f4a..8c1d8d684f 100644 --- a/src/npair_half_respa_bin_newtoff.cpp +++ b/src/npair_half_respa_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp index 72a613204d..d2598fa1a4 100644 --- a/src/npair_half_respa_bin_newton.cpp +++ b/src/npair_half_respa_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp index add1cf6e5c..efe48d48e1 100644 --- a/src/npair_half_respa_bin_newton_tri.cpp +++ b/src/npair_half_respa_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp index c0e932f0ae..334ebb5ca8 100644 --- a/src/npair_half_respa_nsq_newtoff.cpp +++ b/src/npair_half_respa_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp index f7d161896d..7ecd02b0c5 100644 --- a/src/npair_half_respa_nsq_newton.cpp +++ b/src/npair_half_respa_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 021452028b..b9e44675ac 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index 760c09570a..93bcc25373 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index d831982ed6..39068c02bc 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 1c2fe5f3d5..6f169d0b6c 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index ce9f8ec186..d427c14809 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index 84816f07b2..6ff5433e88 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -12,12 +12,8 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index 371bbd33a8..0912cfe12f 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 1fe202537a..028041a947 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 1d4eda5354..68436654b2 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_respa.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index 67717ae576..436d21f76f 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 74a80e6d3d..cd674ff777 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index a042acd1c6..0540592cba 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on_oneside.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp index 0986c40dd4..b18d990bba 100644 --- a/src/nstencil_full_bin_2d.cpp +++ b/src/nstencil_full_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp index b6a2198132..46ec073ddd 100644 --- a/src/nstencil_full_bin_3d.cpp +++ b/src/nstencil_full_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp index bbbf1a4466..5ac19569c5 100644 --- a/src/nstencil_full_ghost_bin_2d.cpp +++ b/src/nstencil_full_ghost_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp index e9abca2174..6ee56516dc 100644 --- a/src/nstencil_full_ghost_bin_3d.cpp +++ b/src/nstencil_full_ghost_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index ed2ffe11dc..c69c53a761 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_2d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index c171bfadc5..df47c1e7e9 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_3d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp index e51db6fe7a..f3a6c5d08b 100644 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ b/src/nstencil_half_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d_newton.cpp index 9479bbf0c8..8fdc8f1aa9 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_newton_tri.cpp index 4f89b1c326..30d064fb29 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp index 433de400c2..e44a93d47d 100644 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ b/src/nstencil_half_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d_newton.cpp index 24c234c004..998ed28afe 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_newton_tri.cpp index 691ce0bb80..2aae44ceaf 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp index 4bb0ecafe2..6f9a7585fe 100644 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp index 1026b11542..6492fe4a4e 100644 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp index 567abe2878..63cd3fd524 100644 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ b/src/nstencil_half_multi_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d_newton.cpp index 5dc2c37148..f6f6c488a5 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_newton_tri.cpp index 59a5a1d19e..b44ab36ea0 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp index 72b882dddc..5a83c4e002 100644 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ b/src/nstencil_half_multi_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d_newton.cpp index 9a5d5cab65..5b0c7f9f63 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_newton_tri.cpp index 953beb3211..b25a0d0bdb 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 8a87a5d6e5..ca63b85328 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo.h" +#include #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 2a358c8ce5..e0c20609a1 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c82110cda5..a6fd900825 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index 15a8b658f3..8cbcf8bcbd 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 42e9e2303d..5309754554 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 5a1acd9191..1cbf5eed11 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index fa98658ad0..cd7b85aa19 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 9c94fb10f9..5af2d526e0 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 14749e6511..faac57aa51 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 8ea860c2e2..bce8ecf4bc 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index 6c478dec52..0cbecbf962 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 2c37668ca8..17e5d4cf62 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 953e010d89..a80fe60e1d 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/output.cpp b/src/output.cpp index 6253d7de37..193db9ae2a 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "output.h" +#include +#include #include "style_dump.h" #include "atom.h" #include "neighbor.h" @@ -26,7 +25,6 @@ #include "domain.h" #include "thermo.h" #include "modify.h" -#include "compute.h" #include "force.h" #include "dump.h" #include "write_restart.h" diff --git a/src/pair.cpp b/src/pair.cpp index 2b4863a54c..36194aec9b 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -15,24 +15,18 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include -#include -#include -#include #include "pair.h" +#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep +#include +#include #include "atom.h" #include "neighbor.h" -#include "neigh_list.h" #include "domain.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "modify.h" #include "compute.h" #include "suffix.h" #include "atom_masks.h" diff --git a/src/pair.h b/src/pair.h index 7481514dae..9ced2fa1c7 100644 --- a/src/pair.h +++ b/src/pair.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_H #define LMP_PAIR_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -61,7 +61,7 @@ class Pair : protected Pointers { int dispersionflag; // 1 if compatible with LJ/dispersion solver int tip4pflag; // 1 if compatible with TIP4P solver int dipoleflag; // 1 if compatible with dipole solver - int spinflag; // 1 if compatible with spin solver + int spinflag; // 1 if compatible with spin solver int reinitflag; // 1 if compatible with fix adapt and alike int tail_flag; // pair_modify flag for LJ tail correction diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 17731ebf0b..b94436b696 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,10 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_beck.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born.cpp b/src/pair_born.cpp index 78434c91f8..bd993acb56 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,11 +15,10 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 2e565897b5..f7e139c750 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,11 +16,9 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_dsf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 3bb0e39e57..f4d533bdb0 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,11 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index a3cf1a38d6..a94ce87891 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 094797694c..d05c139f71 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -15,10 +15,9 @@ Contributing author: Eduardo Bringa (LLNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_buck_coul_cut.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 196e064219..9e6f238eba 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index c8afdabb93..1b87a93701 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_debye.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index e487ff171c..22230182b0 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -16,11 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_dsf.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 282c855249..628f6a6b36 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "pair_coul_streitz.h" +#include #include -#include #include #include -#include "pair_coul_streitz.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -27,8 +27,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index dbf21b8bee..15c7839fc6 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,11 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 0b1342fb2d..058809eb80 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_deprecated.h" +#include #include "pair_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 914b4aee17..ec65eaafd6 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_dpd.h" +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 1207c954eb..15d7c90b27 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "pair_dpd_tstat.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 2d157d6cac..7fd3233f4c 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,15 +15,13 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gauss.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 9aff8a387a..762b9fe8fc 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -12,11 +12,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "pair_hybrid.h" +#include #include #include -#include "pair_hybrid.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index e313e16f18..074517a859 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -20,7 +20,6 @@ PairStyle(hybrid,PairHybrid) #ifndef LMP_PAIR_HYBRID_H #define LMP_PAIR_HYBRID_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 717c0de1d1..e67cb677af 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "pair_hybrid_overlay.h" #include #include -#include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index cefe9b87e0..c27038900d 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj96_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index fdbfca608f..7990952494 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,15 +16,12 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cubic.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 2a0fcde3a5..0302858adb 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 38a6e2c431..d4640bee3a 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index cc6e92b2e3..4ef533a743 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_lj_cut_coul_debye.h" +#include +#include #include "atom.h" #include "neigh_list.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index f114a5851f..778f9f2fb4 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -16,11 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_dsf.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 55aff0d7c5..00a5832529 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -15,19 +15,14 @@ Contributing author: Vishal Boddu (FAU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index d5c0a40f2d..a5184bc2f5 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_expand.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 1fdaefebe9..baef482ef9 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -15,15 +15,12 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 28dc8ec79b..c62944b6a1 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -15,11 +15,9 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs_coul_gromacs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index ecacadbffa..7c7eb51b53 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -15,10 +15,9 @@ Contributing author: Craig Maloney (UCSB) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_smooth.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 265828c4cf..a3e4aed2fe 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -15,10 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_smooth_linear.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 231832dc48..46657687f6 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_mie_cut.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index dca1834c14..d088f98bf4 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_morse.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 7602f7b925..6f821e684b 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_soft.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "update.h" #include "neigh_list.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index b1b6f45eda..9fcbc3ee9f 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -15,11 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table.h" #include #include #include #include -#include "pair_table.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 226fb6e7d9..8cc4d2796f 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -17,26 +17,18 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_ufm.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 913afbd5a1..e8775c9668 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_yukawa.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index 254a82ea64..199e4f0907 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -15,21 +15,12 @@ Contributing authors: Stephen Foiles, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_zbl.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -37,7 +28,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index 143808f598..403bd73944 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -15,11 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_zero.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pointers.h b/src/pointers.h index 44967f5135..2d528db392 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,9 +21,11 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" -#include -#include "lammps.h" +#include "lmptype.h" // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragme: export +#include // IWYU pragma: export +#include "lammps.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -34,6 +36,15 @@ namespace LAMMPS_NS { #define MIN(A,B) ((A) < (B) ? (A) : (B)) #define MAX(A,B) ((A) > (B) ? (A) : (B)) +// enum used for KOKKOS host/device flags + +enum ExecutionSpace{Host,Device}; + +// global forward declarations + +template class MyPoolChunk; +template class MyPage; + class Pointers { public: Pointers(LAMMPS *ptr) : diff --git a/src/procmap.cpp b/src/procmap.cpp index 8207b61f4c..1741e351fe 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,6 +16,12 @@ ------------------------------------------------------------------------- */ #include "procmap.h" +#include +#include +#include +#include +#include +#include #include "universe.h" #include "comm.h" #include "domain.h" @@ -23,9 +29,6 @@ #include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; #define MAXLINE 128 diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 464e640eab..9de5290d29 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -14,8 +14,8 @@ // Marsaglia random number generator // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990) -#include #include "random_mars.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/random_park.cpp b/src/random_park.cpp index fc00939bd4..e12e8a3a10 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -13,8 +13,8 @@ // Park/Miller RNG -#include #include "random_park.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 83cdccdf80..2cc70a2de9 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "rcb.h" #include #include -#include "rcb.h" #include "irregular.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; @@ -473,6 +472,24 @@ void RCB::compute(int dimension, int n, double **x, double *wt, valuehalf = valuehalf_select; if (ndot > 0) memcpy(dotmark,dotmark_select,ndot*sizeof(int)); + // special case for zero box width + // can occur when all dots are on corner vertices of this sub-box + // split box on longest dimension + // reset dotmark for that cut + + if (largest == 0.0) { + dim = 0; + if (hi[1]-lo[1] > hi[0]-lo[0]) dim = 1; + if (dimension == 3 && hi[2]-lo[2] > hi[dim]-lo[dim]) dim = 2; + valuehalf = 0.5* (lo[dim] + hi[dim]); + + for (j = 0; j < nlist; j++) { + i = dotlist[j]; + if (dots[i].x[dim] <= valuehalf) dotmark[i] = 0; + else dotmark[i] = 1; + } + } + // found median // store cut info only if I am procmid diff --git a/src/read_data.cpp b/src/read_data.cpp index 989f989269..1208ab4b43 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -15,19 +15,15 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" -#include -#include -#include -#include -#include #include "read_data.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "force.h" #include "molecule.h" #include "group.h" #include "comm.h" diff --git a/src/read_data.h b/src/read_data.h index 26ab6ff381..98de607f6b 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,7 +20,6 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 85e2312a42..7316a2f5cd 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -19,25 +19,19 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" +#include "read_dump.h" #include #include -#include -#include "read_dump.h" +#include #include "reader.h" #include "style_reader.h" #include "atom.h" #include "atom_vec.h" #include "update.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "comm.h" #include "force.h" #include "irregular.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "memory.h" #include "utils.h" diff --git a/src/read_dump.h b/src/read_dump.h index 3ee13f779c..6fb4f11ed1 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -23,7 +23,6 @@ CommandStyle(read_dump,ReadDump) #define LMP_READ_DUMP_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 6e156da837..3d2e2b6592 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "read_restart.h" #include #include -#include #include -#include "read_restart.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -23,7 +22,6 @@ #include "irregular.h" #include "update.h" #include "modify.h" -#include "fix.h" #include "fix_read_restart.h" #include "group.h" #include "force.h" diff --git a/src/read_restart.h b/src/read_restart.h index 23d6ec3fba..63adf37b22 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,7 +20,6 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/reader.cpp b/src/reader.cpp index 5292c9c992..ee032dc822 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "reader.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 60b7ecd764..fba613bdd3 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "reader_native.h" #include #include -#include "reader_native.h" #include "atom.h" #include "memory.h" #include "error.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 19f0ff2135..a5209956b9 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "reader_xyz.h" -#include "atom.h" +#include #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/region.cpp b/src/region.cpp index 6b49a2819b..7a676de1af 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "region.h" +#include +#include #include "update.h" #include "domain.h" #include "lattice.h" diff --git a/src/region.h b/src/region.h index 6a3806fed7..0dce004a5b 100644 --- a/src/region.h +++ b/src/region.h @@ -14,7 +14,7 @@ #ifndef LMP_REGION_H #define LMP_REGION_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/region_block.cpp b/src/region_block.cpp index e55c481189..8ea8b3f202 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_block.h" +#include #include "force.h" #include "domain.h" #include "math_extra.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 72f56a268f..3c7d0a29d8 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -15,10 +15,9 @@ Contributing author: Pim Schravendijk ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_cone.h" +#include +#include #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 7709c57aab..b2c06270d0 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_cylinder.h" +#include +#include #include "update.h" #include "domain.h" #include "input.h" diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index 87225959fa..a2e4e88393 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "region_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 96d3bed16c..fe074a6b4c 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_intersect.h" +#include #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index e67a2c85bd..85671357ef 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_plane.h" +#include #include "error.h" #include "force.h" diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 22fc504c37..b6c54c2fb9 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -15,10 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_prism.h" +#include #include "domain.h" #include "force.h" #include "math_extra.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8080ef5882..bf874ad311 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_sphere.h" +#include +#include #include "update.h" #include "input.h" #include "variable.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index 33ac6fedd7..be1fe6eeff 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_union.h" +#include #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 3c8f4a8aee..1617ab0313 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "replicate.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "force.h" #include "domain.h" #include "comm.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index 063ea882c2..3cd1c53628 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "rerun.h" +#include #include "read_dump.h" #include "domain.h" #include "update.h" diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index b2cf7a9bbc..857738e841 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "reset_ids.h" +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -28,7 +29,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} /* ---------------------------------------------------------------------- */ -void ResetIDs::command(int narg, char **/*arg*/) +void ResetIDs::command(int narg, char ** /* arg */) { if (domain->box_exist == 0) error->all(FLERR,"Reset_ids command before simulation box is defined"); diff --git a/src/respa.cpp b/src/respa.cpp index 6fa9959d78..a184756335 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -15,14 +15,14 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "respa.h" +#include #include "neighbor.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "fix.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -33,10 +33,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix_respa.h" #include "timer.h" -#include "memory.h" #include "error.h" #include "utils.h" #include "pair_hybrid.h" diff --git a/src/run.cpp b/src/run.cpp index beb71be52c..2c2f00a7a8 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "run.h" +#include #include "domain.h" #include "update.h" #include "force.h" diff --git a/src/set.cpp b/src/set.cpp index 00b2d8a9b0..3bf00063c5 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "set.h" #include #include -#include #include -#include "set.h" +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" @@ -26,9 +26,7 @@ #include "region.h" #include "group.h" #include "comm.h" -#include "neighbor.h" #include "force.h" -#include "pair.h" #include "input.h" #include "variable.h" #include "random_park.h" diff --git a/src/special.cpp b/src/special.cpp index 903794c0f6..3dd817bc7f 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "special.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" #include "comm.h" #include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom_masks.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/thermo.cpp b/src/thermo.cpp index bba867d195..3748ee77fe 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -15,12 +15,10 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" +#include "thermo.h" #include #include -#include #include -#include "thermo.h" #include "atom.h" #include "update.h" #include "comm.h" @@ -43,11 +41,8 @@ #include "kspace.h" #include "output.h" #include "timer.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "universe.h" - #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/thermo.h b/src/thermo.h index 8c32f24d3c..f2384e0ac3 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -18,9 +18,6 @@ namespace LAMMPS_NS { -class DumpNetCDF; -class DumpNetCDFMPIIO; - class Thermo : protected Pointers { friend class MinCG; // accesses compute_pe friend class DumpNetCDF; // accesses thermo properties diff --git a/src/timer.cpp b/src/timer.cpp index 65cb6ab5d8..0a5e56ab35 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -11,14 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "timer.h" #include #include #include -#include "timer.h" #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #ifdef _WIN32 #include diff --git a/src/universe.cpp b/src/universe.cpp index dba31f8b76..036b3a7e66 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "universe.h" #include #include #include #include -#include -#include "universe.h" #include "version.h" #include "error.h" #include "force.h" diff --git a/src/universe.h b/src/universe.h index 3073409b86..fd6655c749 100644 --- a/src/universe.h +++ b/src/universe.h @@ -14,7 +14,6 @@ #ifndef LMP_UNIVERSE_H #define LMP_UNIVERSE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/update.cpp b/src/update.cpp index f5e706e354..8a3e6f0d1d 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -11,23 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "update.h" +#include #include "integrate.h" #include "min.h" #include "style_integrate.h" #include "style_minimize.h" #include "neighbor.h" -#include "neigh_list.h" #include "force.h" #include "modify.h" #include "fix.h" -#include "domain.h" -#include "region.h" #include "compute.h" #include "output.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/utils.cpp b/src/utils.cpp index 4e39187f77..5e53a3a09d 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "utils.h" #include #include -#include "utils.h" #include "lammps.h" #include "error.h" diff --git a/src/variable.cpp b/src/variable.cpp index 63a425bcf5..3fffa11d5e 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,12 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "variable.h" +#include #include #include #include #include #include -#include "variable.h" #include "universe.h" #include "atom.h" #include "update.h" @@ -26,6 +27,7 @@ #include "region.h" #include "modify.h" #include "compute.h" +#include "input.h" #include "fix.h" #include "fix_store.h" #include "force.h" @@ -33,7 +35,6 @@ #include "thermo.h" #include "random_mars.h" #include "math_const.h" -#include "atom_masks.h" #include "lmppython.h" #include "memory.h" #include "info.h" diff --git a/src/variable.h b/src/variable.h index 512195bd14..a504da14ec 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,9 +14,7 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include #include "pointers.h" -#include "input.h" namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 95d820cc22..e5985884f8 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -11,14 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "velocity.h" +#include +#include #include "atom.h" -#include "update.h" #include "domain.h" #include "lattice.h" #include "input.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index fcba248d5f..8cd6fe940d 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet.h" +#include #include "neighbor.h" #include "domain.h" #include "comm.h" @@ -28,10 +28,7 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 9bf54b3c08..8e5b4fcb71 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_coeff.h" #include #include +#include #include -#include "write_coeff.h" #include "pair.h" #include "bond.h" #include "angle.h" diff --git a/src/write_coeff.h b/src/write_coeff.h index 569a615e6e..b995e60d63 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,7 +20,6 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_data.cpp b/src/write_data.cpp index decc92ea8c..3d788b9665 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_data.h" #include #include -#include "write_data.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "force.h" #include "pair.h" #include "bond.h" diff --git a/src/write_data.h b/src/write_data.h index 6f1bb2ec47..1c0f6b2a7c 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,7 +20,6 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 072680a8a5..31ceb4cbbf 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -15,15 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "write_dump.h" +#include +#include #include "style_dump.h" #include "dump.h" #include "dump_image.h" -#include "atom.h" #include "comm.h" -#include "group.h" -#include "input.h" #include "update.h" #include "error.h" #include "utils.h" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index e0e17cd292..4b84e790b8 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_restart.h" #include #include -#include "write_restart.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "group.h" #include "force.h" #include "pair.h" diff --git a/src/write_restart.h b/src/write_restart.h index c6202acbfd..e7cdc6a501 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,7 +20,6 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS {