Merge pull request #1737 from akohlmey/next_patch_release

Step version string for next patch release

.github/CONTRIBUTING.md

@@ -68,7 +68,8 @@ How quickly your contribution will be integrated depends largely on how much eff
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
-* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers outside of <cstdio>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.

bench/POTENTIALS/CH.airebo

@@ -0,0 +1 @@
+../../potentials/CH.airebo

bench/POTENTIALS/CdTe.bop.table

@@ -0,0 +1 @@
+../../potentials/CdTe.bop.table

bench/POTENTIALS/Cu_u3.eam

@@ -1,305 +0,0 @@
-Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
-   29     63.550         3.6150    FCC
-  500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
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-  2.4502968839369110e-01  2.3168512174254197e-01  2.1908328186436687e-01  2.0718780752542632e-01  1.9596356233750800e-01
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-  6.5899633029043336e-02  6.2942169202580001e-02  6.0159641699440547e-02  5.7541225732930634e-02  5.5076720130546430e-02
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-  4.3021679522073253e-02  4.1395175224364866e-02  3.9859987214311721e-02  3.8410278881708670e-02  3.7040577866510604e-02
-  3.5745755503880039e-02  3.4521007208912380e-02  3.3361833779917971e-02  3.2264023597108116e-02  3.1223635691821294e-02
-  3.0236983660070216e-02  2.9300620393215571e-02  2.8411323597772320e-02  2.7566082075896281e-02  2.6762082737777249e-02
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-  1.5981713017976018e-02  1.5649921843605585e-02  1.5328205354974755e-02  1.5016040171312250e-02  1.4712938292708366e-02
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-  1.3061193172097418e-02  1.2810359927147186e-02  1.2565693807050415e-02  1.2326931365025051e-02  1.2093826075940506e-02
-  1.1866147122233661e-02  1.1643678266026136e-02  1.1426216801644407e-02  1.1213572583084475e-02  1.1005567121320226e-02
-  1.0802032746662471e-02  1.0602811831688208e-02  1.0407756070544782e-02  1.0216725810699157e-02  1.0029589433467268e-02
-  9.8462227798860602e-03  9.6665086187306404e-03  9.4903361536790021e-03  9.3176005668363371e-03  9.1482025960089031e-03
-  8.9820481433065535e-03  8.8190479128032462e-03  8.6591170751522117e-03  8.5021749571883021e-03  8.3481447546937537e-03
-  8.1969532666261724e-03  8.0485306492223962e-03  7.9028101885199598e-03  7.7597280899136256e-03  7.6192232834934315e-03
-  7.4812372439735375e-03  7.3457138241272979e-03  7.2125991007052359e-03  7.0818412319012813e-03  6.9533903254870300e-03
-  6.8271983168139705e-03  6.7032188559211503e-03  6.5814072030662141e-03  6.4617201320263939e-03  6.3441158405819764e-03
-  6.2285538676237207e-03  6.1149950163802147e-03  6.0034012832899109e-03  5.8937357920846312e-03  5.7859627326801166e-03
-  5.6800473044990030e-03  5.5759556638887986e-03  5.4736548753111791e-03  5.3731128660109428e-03  5.2742983838981461e-03
-  5.1771809583849582e-03  5.0817308639591330e-03  4.9879190862693046e-03  4.8957172905357560e-03  4.8050977921015592e-03
-  4.7160335289582467e-03  4.6284980360953021e-03  4.5424654215287241e-03  4.4579103438822931e-03  4.3748079913988880e-03
-  4.2931340622749670e-03  4.2128647462132407e-03  4.1339767071033873e-03  4.0564470667446839e-03  3.9802533895282599e-03
-  3.9053736680121076e-03  3.8317863093158128e-03  3.7594701222811860e-03  3.6884043053326127e-03  3.6185684349951674e-03
-  3.5499424550168301e-03  3.4825066660512660e-03  3.4162417158645347e-03  3.3511285900229004e-03  3.2871486030347646e-03
-  3.2242833899080170e-03  3.1625148980992668e-03  3.1018253798278661e-03  3.0421973847258310e-03  2.9836137528083811e-03
-  2.9260576077371064e-03  2.8695123503632708e-03  2.8139616525287708e-03  2.7593894511106498e-03  2.7057799422959966e-03
-  2.6531175760685227e-03  2.6013870509009052e-03  2.5505733086344240e-03  2.5006615295404683e-03  2.4516371275501436e-03
-  2.4034857456453340e-03  2.3561932514012535e-03  2.3097457326723414e-03  2.2641294934160616e-03  2.2193310496436136e-03
-  2.1753371254977782e-03  2.1321346494441173e-03  2.0897107505768314e-03  2.0480527550303662e-03  2.0071481824917164e-03
-  1.9669847428123305e-03  1.9275503327108034e-03  1.8888330325659355e-03  1.8508211032951805e-03  1.8135029833145980e-03
-  1.7768672855772646e-03  1.7409027946878666e-03  1.7055984640891586e-03  1.6709434133182904e-03  1.6369269253308227e-03
-  1.6035384438881917e-03  1.5707675710093030e-03  1.5386040644797400e-03  1.5070378354209296e-03  1.4760589459142243e-03
-  1.4456576066784674e-03  1.4158241748004133e-03  1.3865491515145517e-03  1.3578231800324136e-03  1.3296370434173130e-03
-  1.3019816625059188e-03  1.2748480938728074e-03  1.2482275278369870e-03  1.2221112865106742e-03  1.1964908218862064e-03
-  1.1713577139624703e-03  1.1467036689077198e-03  1.1225205172586891e-03  1.0988002121543120e-03  1.0755348276031765e-03
-  1.0527165567835728e-03  1.0303377103750150e-03  1.0083907149206553e-03  9.8686811121878604e-04  9.6576255274356815e-04
-  9.4506680409354657e-04  9.2477373946662708e-04  9.0487634116191706e-04  8.8536769810608137e-04  8.6624100440530968e-04
-  8.4748955791986991e-04  8.2910675886310736e-04  8.1108610842155551e-04  7.9342120739794852e-04  7.7610575487466887e-04
-  7.5913354689786591e-04  7.4249847518158968e-04  7.2619452583109687e-04  7.1021577808524222e-04  6.9455640307671332e-04
-  6.7921066261025093e-04  6.6417290795844214e-04  6.4943757867335500e-04  6.3499920141575628e-04  6.2085238879914031e-04
-  6.0699183824991856e-04  5.9341233088238896e-04  5.8010873038847818e-04  5.6707598194186137e-04  5.5430911111587280e-04
-  5.4180322281523891e-04  5.2955350022104025e-04  5.1755520374872563e-04  5.0580367001857793e-04  4.9429431083891986e-04
-  4.8302261220136561e-04  4.7198413328763435e-04  4.6117450548847222e-04  4.5058943143359842e-04  4.4022468403297037e-04
-  4.3007610552883886e-04  4.2013960655883260e-04  4.1041116522908330e-04  4.0088682619821882e-04  3.9156269977118005e-04
-  3.8243496100300207e-04  3.7349984881274514e-04  3.6475366510662147e-04  3.5619277391102898e-04  3.4781360051482253e-04
-  3.3961263062063513e-04  3.3158640950565685e-04  3.2373154119109092e-04  3.1604468762060252e-04  3.0852256784754707e-04
-  3.0116195723081836e-04  2.9395968663908575e-04  2.8691264166377101e-04  2.8001776184017647e-04  2.7327203987681688e-04
-  2.6667252089326854e-04  2.6021630166557681e-04  2.5390052988028163e-04  2.4772240339593181e-04  2.4167916951265550e-04
-  2.3576812424967210e-04  2.2998661163024531e-04  2.2433202297460642e-04  2.1880179620031078e-04  2.1339341513026532e-04
-  2.0810440880823181e-04  2.0293235082175821e-04  1.9787485863260665e-04  1.9292959291436311e-04  1.8809425689761319e-04
-  1.8336659572205580e-04  1.7874439579616125e-04  1.7422548416372047e-04  1.6980772787763936e-04  1.6548903338088530e-04
-  1.6126734589430591e-04  1.5714064881157744e-04  1.5310696310104604e-04  1.4916434671449329e-04  1.4531089400280153e-04
-  1.4154473513841234e-04  1.3786403554466153e-04  1.3426699533172857e-04  1.3075184873951283e-04  1.2731686358694039e-04
-  1.2396034072819674e-04  1.2068061351527565e-04  1.1747604726729168e-04  1.1434503874632306e-04  1.1128601563955686e-04
-  1.0829743604811193e-04  1.0537778798212988e-04  1.0252558886227753e-04  9.9739385027582898e-05  9.7017751249615057e-05
-  9.4359290252773662e-05  9.1762632240957511e-05  8.9226434430383569e-05  8.6749380588361721e-05  8.4330180578390864e-05
-  8.1967569911181246e-05  7.9660309301724484e-05  7.7407184232279429e-05  7.5207004521348451e-05  7.3058603898526649e-05
-  7.0960839585107720e-05  6.8912591880629977e-05  6.6912763755002085e-05  6.4960280446513426e-05  6.3054089065330086e-05
-  6.1193158202771814e-05  5.9376477546041213e-05  5.7603057498502742e-05  5.5871928805544500e-05  5.4182142185708361e-05
-  5.2532767967318744e-05  5.0922895730446966e-05  4.9351633954125953e-05  4.7818109668823321e-05  4.6321468114150300e-05
-  4.4860872401664663e-05  4.3435503182825573e-05  4.2044558321957873e-05  4.0687252574273750e-05  3.9362817268785450e-05
-  3.8070499996214428e-05  3.6809564301621984e-05  3.5579289382025496e-05  3.4378969788611451e-05  3.3207915133769052e-05
-  3.2065449802711312e-05  3.0950912669766876e-05  2.9863656819185611e-05  2.8803049270468119e-05  2.7768470708167169e-05
-  2.6759315216115260e-05  2.5774990015931323e-05  2.4814915209964844e-05  2.3878523528387922e-05  2.2965260080560611e-05
-  2.2074582110528148e-05  2.1205958756658535e-05  2.0358870815317476e-05  1.9532810508535560e-05  1.8727281255713447e-05
-  1.7941797449145505e-05  1.7175884233475961e-05  1.6429077288930018e-05  1.5700922618341645e-05  1.4990976337865471e-05
-  1.4298804471386687e-05  1.3623982748522034e-05  1.2966096406226424e-05  1.2324739993882115e-05  1.1699517181902770e-05
-  1.1090040573734860e-05  1.0495931521266495e-05  9.9168199435395021e-06  9.3523441487842465e-06  8.8021506596591475e-06
-  8.2658940417265321e-06  7.7432367350197678e-06  7.2338488887770244e-06  6.7374081991923703e-06  6.2535997501888662e-06
-  5.7821158571569505e-06  5.3226559136389283e-06  4.8749262408651290e-06  4.4386399401326240e-06  4.0135167480073166e-06
-  3.5992828942305738e-06  3.1956709623667747e-06  2.8024197531120341e-06  2.4192741502208947e-06  2.0459849890155880e-06
-  1.6823089274468580e-06  1.3280083196495871e-06  9.8285109196557868e-07  6.4661062138351467e-07  3.1906561636122974e-07
-  0.                      0.                      0.                      0.                      0.
-
-

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1 @@
+../../potentials/Cu_u3.eam

bench/POTENTIALS/Ni.adp

@@ -0,0 +1 @@
+../../potentials/Ni.adp

cmake/Modules/CodeCoverage.cmake

@@ -0,0 +1,28 @@
+###############################################################################
+# Coverage
+#
+# Requires latest gcovr (for GCC 8.1 support):#
+# pip install git+https://github.com/gcovr/gcovr.git
+###############################################################################
+if(ENABLE_COVERAGE)
+    find_program(GCOVR_BINARY gcovr)
+    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+
+    if(GCOVR_FOUND)
+        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+
+        add_custom_target(
+            gen_coverage_xml
+            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating XML Coverage Report..."
+        )
+
+        add_custom_target(
+            gen_coverage_html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating HTML Coverage Report..."
+        )
+    endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -0,0 +1,59 @@
+###############################################################################
+# Build documentation
+###############################################################################
+option(BUILD_DOC "Build LAMMPS documentation" OFF)
+if(BUILD_DOC)
+  include(ProcessorCount)
+  ProcessorCount(NPROCS)
+  find_package(PythonInterp 3 REQUIRED)
+
+  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
+  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
+  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+
+  add_custom_command(
+    OUTPUT docenv
+    COMMAND ${VIRTUALENV} docenv
+  )
+
+  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+
+  add_custom_command(
+    OUTPUT requirements.txt
+    DEPENDS docenv
+    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+  )
+
+  set(RST_FILES "")
+  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
+  file(MAKE_DIRECTORY ${RST_DIR})
+  foreach(TXT_FILE ${DOC_SOURCES})
+    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
+    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
+    list(APPEND RST_FILES ${RST_FILE})
+    add_custom_command(
+      OUTPUT ${RST_FILE}
+      DEPENDS requirements.txt docenv ${TXT_FILE}
+      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
+    )
+  endforeach()
+
+  add_custom_command(
+    OUTPUT html
+    DEPENDS ${RST_FILES}
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+  )
+
+  add_custom_target(
+    doc ALL
+    DEPENDS html
+    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
+  )
+
+  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+endif()

cmake/Modules/FindKIM-API.cmake

@@ -37,6 +37,26 @@
 # KIM-API-CMAKE_Fortran_COMPILER
 #
 
+function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
+  if(NOT EXISTS ${_version_hdr})
+    message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
+  endif()
+  foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)  
+    file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
+    if(_contents)
+      string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
+      if(${_${_var}} STREQUAL "")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
+      elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
+      endif()
+    else()
+      message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
+    endif()
+  endforeach()
+  set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
+endfunction()
+
 if(KIM-API_FIND_QUIETLY)
   set(REQ_OR_QUI "QUIET")
 else()
@@ -54,6 +74,12 @@ if(KIM-API_FOUND)
   pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
 endif()
 
+if(KIM-API_INCLUDEDIR)
+  _KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
+else()
+  set(KIM-API_VERSION 0)
+endif()
+
 # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE
-find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)

cmake/Modules/LAMMPSUtils.cmake

@@ -0,0 +1,71 @@
+# Utility functions
+function(list_to_bulletpoints result)
+    list(REMOVE_AT ARGV 0)
+    set(temp "")
+    foreach(item ${ARGV})
+        set(temp "${temp}* ${item}\n")
+    endforeach()
+    set(${result} "${temp}" PARENT_SCOPE)
+endfunction(list_to_bulletpoints)
+
+function(validate_option name values)
+    string(TOLOWER ${${name}} needle_lower)
+    string(TOUPPER ${${name}} needle_upper)
+    list(FIND ${values} ${needle_lower} IDX_LOWER)
+    list(FIND ${values} ${needle_upper} IDX_UPPER)
+    if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+        list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+        message(FATAL_ERROR "\n########################################################################\n"
+                            "Invalid value '${${name}}' for option ${name}\n"
+                            "\n"
+                            "Possible values are:\n"
+                            "${POSSIBLE_VALUE_LIST}"
+                            "########################################################################")
+    endif()
+endfunction(validate_option)
+
+function(get_lammps_version version_header variable)
+    file(READ ${version_header} line)
+    set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+    string(STRIP ${day} day)
+    string(STRIP ${month} month)
+    string(STRIP ${year} year)
+    list(FIND MONTHS "${month}" month)
+    string(LENGTH ${day} day_length)
+    string(LENGTH ${month} month_length)
+    if(day_length EQUAL 1)
+        set(day "0${day}")
+    endif()
+    if(month_length EQUAL 1)
+        set(month "0${month}")
+    endif()
+    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+function(check_for_autogen_files source_dir)
+    message(STATUS "Running check for auto-generated files from make-based build system")
+    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
+    foreach(_SRC ${SRC_AUTOGEN_FILES})
+      get_filename_component(FILENAME "${_SRC}" NAME)
+      if(EXISTS ${source_dir}/${FILENAME})
+        message(FATAL_ERROR "\n########################################################################\n"
+                              "Found header file(s) generated by the make-based build system\n"
+                              "\n"
+                              "Please run\n"
+                              "make -C ${source_dir} purge\n"
+                              "to remove\n"
+                              "########################################################################")
+      endif()
+    endforeach()
+endfunction()
+
+macro(pkg_depends PKG1 PKG2)
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
+    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+  endif()
+endmacro()

cmake/Modules/Packages/COMPRESS.cmake

@@ -0,0 +1,5 @@
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
+endif()

cmake/Modules/Packages/CORESHELL.cmake

@@ -0,0 +1,13 @@
+if(PKG_CORESHELL)
+    set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+    set(CORESHELL_SOURCES)
+    set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
+
+    # detects styles which have a CORESHELL version
+    RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+
+    get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+
+    list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+    include_directories(${CORESHELL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/GPU.cmake

@@ -0,0 +1,194 @@
+if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1")
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+    set(GPU_API_VALUES opencl cuda)
+    set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+    validate_option(GPU_API GPU_API_VALUES)
+    string(TOUPPER ${GPU_API} GPU_API)
+
+    set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+    set(GPU_PREC_VALUES double mixed single)
+    set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+    validate_option(GPU_PREC GPU_PREC_VALUES)
+    string(TOUPPER ${GPU_PREC} GPU_PREC)
+
+    if(GPU_PREC STREQUAL "DOUBLE")
+      set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "MIXED")
+      set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "SINGLE")
+      set(GPU_PREC_SETTING "SINGLE_SINGLE")
+    endif()
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+      endif()
+
+      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+      endif()
+      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+      if(CUDA_VERSION VERSION_GREATER "4.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER "5.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER "7.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER "8.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER "9.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+      endif()
+
+      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OPENCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
+      set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
+      validate_option(OCL_TUNE OCL_TUNE_VALUES)
+      string(TOUPPER ${OCL_TUNE} OCL_TUNE)
+
+      include(OpenCLUtils)
+      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+      )
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+      list(APPEND GPU_LIB_SOURCES
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+      )
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KIM.cmake

@@ -0,0 +1,57 @@
+if(PKG_KIM)
+  set(KIM-API_MIN_VERSION 2.1)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+  endif()
+  find_package(KIM-API QUIET)
+  if(KIM-API_FOUND)
+    if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
+      if ("${DOWNLOAD_KIM}" STREQUAL "")
+        message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\".  Default behavior set to download and build our own.")
+      endif()
+      set(DOWNLOAD_KIM_DEFAULT ON)
+    else()
+      set(DOWNLOAD_KIM_DEFAULT OFF)
+    endif()
+  else()
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
+    endif()
+    set(DOWNLOAD_KIM_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
+  if(DOWNLOAD_KIM)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
+    endif()
+    message(STATUS "KIM-API download requested - we will build our own")
+    include(CheckLanguage)
+    include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
+    ExternalProject_Add(kim_build
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
+    list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -0,0 +1,66 @@
+if(PKG_KOKKOS)
+  # TODO: this option needs to be documented when this works with a
+  # regular release version of KOKKOS, and a version compatibility check
+  # of external KOKKOS lib versus what the KOKKOS package needs is required.
+  option(EXTERNAL_KOKKOS "Build against external kokkos library")
+  if(EXTERNAL_KOKKOS)
+    find_package(Kokkos REQUIRED)
+    list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
+  else()
+    set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+    set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+    add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  
+    set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                            ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+    include_directories(${Kokkos_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS kokkos)
+  endif()
+  add_definitions(-DLMP_KOKKOS)
+
+  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+  if(PKG_KSPACE)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+  endif()
+
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+  # detects styles which have KOKKOS version
+  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
+
+  if(PKG_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
+  include_directories(${KOKKOS_PKG_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KSPACE.cmake

@@ -0,0 +1,42 @@
+if(PKG_KSPACE)
+  option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
+  set(FFTW "FFTW3")
+  if(FFT_SINGLE)
+    set(FFTW "FFTW3F")
+    add_definitions(-DFFT_SINGLE)
+  endif()
+  find_package(${FFTW} QUIET)
+  if(${FFTW}_FOUND)
+    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
+  else()
+    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
+  endif()
+  set(FFT_VALUES KISS FFTW3 MKL)
+  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+  validate_option(FFT FFT_VALUES)
+  string(TOUPPER ${FFT} FFT)
+
+  if(FFT STREQUAL "FFTW3")
+    find_package(${FFTW} REQUIRED)
+    add_definitions(-DFFT_FFTW3)
+    include_directories(${${FFTW}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+  elseif(FFT STREQUAL "MKL")
+    find_package(MKL REQUIRED)
+    add_definitions(-DFFT_MKL)
+    include_directories(${MKL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    # last option is KISSFFT
+    add_definitions(-DFFT_KISS)
+  endif()
+
+  set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
+  set(FFT_PACK_VALUES array pointer memcpy)
+  set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
+  validate_option(FFT_PACK FFT_PACK_VALUES)
+  if(NOT FFT_PACK STREQUAL "array")
+    string(TOUPPER ${FFT_PACK} FFT_PACK)
+    add_definitions(-DFFT_PACK_${FFT_PACK})
+  endif()
+endif()

cmake/Modules/Packages/LATTE.cmake

@@ -0,0 +1,38 @@
+if(PKG_LATTE)
+  enable_language(Fortran)
+  find_package(LATTE)
+  if(LATTE_FOUND)
+    set(DOWNLOAD_LATTE_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_LATTE_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
+  if(DOWNLOAD_LATTE)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
+    endif()
+    message(STATUS "LATTE download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+      URL_MD5 85ac414fdada2d04619c8f936344df14
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+      -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+      -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
+      -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -0,0 +1,32 @@
+if(PKG_MESSAGE)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
+  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+  add_library(cslib STATIC ${cslib_SOURCES})
+  if(BUILD_MPI)
+    target_compile_definitions(cslib PRIVATE -DMPI_YES)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+  else()
+    target_compile_definitions(cslib PRIVATE -DMPI_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+  endif()
+
+  if(MESSAGE_ZMQ)
+    target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+    find_package(ZMQ REQUIRED)
+    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+  else()
+    target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+  endif()
+
+  list(APPEND LAMMPS_LINK_LIBS cslib)
+  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()

cmake/Modules/Packages/MSCG.cmake

@@ -0,0 +1,45 @@
+if(PKG_MSCG)
+  find_package(GSL REQUIRED)
+  find_package(MSCG QUIET)
+  if(MSGC_FOUND)
+    set(DOWNLOAD_MSCG_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_MSCG_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+  if(DOWNLOAD_MSCG)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
+    endif()
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/OPT.cmake

@@ -0,0 +1,13 @@
+if(PKG_OPT)
+    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+    set(OPT_SOURCES)
+    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+
+    # detects styles which have OPT version
+    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+
+    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+
+    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+    include_directories(${OPT_SOURCES_DIR})
+endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -0,0 +1,6 @@
+if(PKG_PYTHON)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+endif()

cmake/Modules/Packages/QEQ.cmake

@@ -0,0 +1,20 @@
+# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
+if(PKG_QEQ)
+  set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+
+  if(NOT PKG_MANYBODY)
+    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+    list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+  foreach(MY_HEADER ${QEQ_HEADERS})
+    AddStyleHeader(${MY_HEADER} FIX)
+  endforeach()
+
+  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+  list(APPEND LIB_SOURCES ${QEQ_SOURCES})
+  include_directories(${QEQ_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -0,0 +1,42 @@
+if(PKG_USER-COLVARS)
+
+  set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+
+  file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+
+  # Build Lepton by default
+  set(COLVARS_LEPTON_DEFAULT ON)
+  # but not if C++11 is disabled per user request
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if(DISABLE_CXX11_REQUIREMENT)
+      set(COLVARS_LEPTON_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
+
+  # Verify that the user's choice is consistent
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
+      message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
+    endif()
+  endif()
+
+  if(COLVARS_LEPTON)
+    set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+    file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+    add_library(lepton STATIC ${LEPTON_SOURCES})
+    target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+  endif()
+
+  add_library(colvars STATIC ${COLVARS_SOURCES})
+  target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+  list(APPEND LAMMPS_LINK_LIBS colvars)
+
+  if(COLVARS_LEPTON)
+    list(APPEND LAMMPS_LINK_LIBS lepton)
+    target_compile_options(colvars PRIVATE -DLEPTON)
+    target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+  endif()
+
+endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -0,0 +1,8 @@
+if(PKG_USER-H5MD)
+  enable_language(C)
+
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-INTEL.cmake

@@ -0,0 +1,118 @@
+if(PKG_USER-INTEL)
+  check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
+  if(NOT FOUND_IMMINTRIN)
+    message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
+  endif()
+
+  add_definitions(-DLMP_USER_INTEL)
+
+  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+  set(INTEL_ARCH_VALUES cpu knl)
+  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
+
+  find_package(Threads QUIET)
+  if(Threads_FOUND)
+    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  else()
+    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  endif()
+  set(INTEL_LRT_VALUES none threads c++11)
+  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
+  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
+  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
+  if(INTEL_LRT_MODE STREQUAL "THREADS")
+    if(Threads_FOUND)
+      add_definitions(-DLMP_INTEL_USELRT)
+      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
+    else()
+      message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+    endif()
+  endif()
+  if(INTEL_LRT_MODE STREQUAL "C++11")
+    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
+  endif()
+
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    endif()
+  else()
+    message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  endif()
+
+  find_package(TBB QUIET)
+  if(TBB_FOUND)
+    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
+  else()
+    add_definitions(-DLMP_INTEL_NO_TBB)
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    endif()
+  endif()
+
+  find_package(MKL QUIET)
+  if(MKL_FOUND)
+    add_definitions(-DLMP_USE_MKL_RNG)
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
+  endif()
+
+  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
+    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  endif()
+
+  if(INTEL_ARCH STREQUAL "KNL")
+    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    endif()
+    set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
+    set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
+    add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
+    add_definitions(-DLMP_INTEL_OFFLOAD)
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+      endif()
+      include(CheckCXXCompilerFlag)
+      foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+        if(COMPILER_SUPPORTS${_FLAG})
+          add_compile_options(${_FLAG})
+        endif()
+      endforeach()
+    else()
+      add_compile_options(-O3 -ffast-math)
+    endif()
+  endif()
+
+  # collect sources
+  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+
+  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+  # detect styles which have a USER-INTEL version
+  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+
+  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+  if(PKG_KSPACE)
+    list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+    RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  endif()
+
+  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+  include_directories(${USER-INTEL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -0,0 +1,14 @@
+if(PKG_USER-MOLFILE)
+  if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
+    message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
+  endif()
+
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+  # no need to link with -ldl on windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS molfile)
+endif()

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -0,0 +1,6 @@
+if(PKG_USER-NETCDF)
+  find_package(NetCDF REQUIRED)
+  include_directories(${NETCDF_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+endif()

cmake/Modules/Packages/USER-OMP.cmake

@@ -0,0 +1,42 @@
+if(PKG_USER-OMP)
+    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+    add_definitions(-DLMP_USER_OMP)
+    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+
+    # detects styles which have USER-OMP version
+    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
+
+    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+    # manually add package dependent source files from USER-OMP that do not provide styles
+
+    if(PKG_ASPHERE)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+    endif()
+
+    if(PKG_RIGID)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+    endif()
+
+    if(PKG_USER-REAXC)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+    endif()
+
+    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+    include_directories(${USER-OMP_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -0,0 +1,91 @@
+if(PKG_USER-PLUMED)
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  set(PLUMED_LINK_LIBS "")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
+    endif()
+  endif()
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
+    endif()
+    if(BUILD_MPI)
+      set(PLUMED_CONFIG_MPI "--enable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+    else()
+      set(PLUMED_CONFIG_MPI "--disable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    endif()
+    if(BUILD_OMP)
+      set(PLUMED_CONFIG_OMP "--enable-openmp")
+    else()
+      set(PLUMED_CONFIG_OMP "--disable-openmp")
+    endif()
+    message(STATUS "PLUMED download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
+      URL_MD5 de30d6e7c2dcc0973298e24a6da24286
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                               --enable-modules=all
+                                               ${PLUMED_CONFIG_MPI}
+                                               ${PLUMED_CONFIG_OMP}
+                                               CXX=${PLUMED_CONFIG_CXX}
+                                               CC=${PLUMED_CONFIG_CC}
+    )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
+    endif()
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-QMMM.cmake

@@ -0,0 +1,9 @@
+if(PKG_USER-QMMM)
+  enable_language(Fortran)
+  enable_language(C)
+
+  message(WARNING "Building QMMM with CMake is still experimental")
+  find_package(QE REQUIRED)
+  include_directories(${QE_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
+endif()

cmake/Modules/Packages/USER-QUIP.cmake

@@ -0,0 +1,5 @@
+if(PKG_USER-QUIP)
+  enable_language(Fortran)
+  find_package(QUIP REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -0,0 +1,62 @@
+if(PKG_USER-SCAFACOS)
+  enable_language(Fortran)
+  enable_language(C)
+
+  find_package(GSL REQUIRED)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(SCAFACOS QUIET scafacos)
+    if(SCAFACOS_FOUND)
+      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
+    endif()
+  endif()
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
+  if(DOWNLOAD_SCAFACOS)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
+    endif()
+    message(STATUS "ScaFaCoS download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(scafacos_build
+      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+      URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
+                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                               --with-internal-fftw --with-internal-pfft
+                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                               FC=${CMAKE_MPI_Fortran_COMPILER}
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               F77=
+    )
+    ExternalProject_get_property(scafacos_build INSTALL_DIR)
+    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
+    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
+    list(APPEND LAMMPS_DEPS scafacos_build)
+    # list and order from pkg_config file of ScaFaCoS build
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
+    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(SCAFACOS REQUIRED scafacos)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+  endif()
+  include_directories(${SCAFACOS_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-SDPD.cmake

@@ -0,0 +1,13 @@
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-SMD.cmake

@@ -0,0 +1,28 @@
+if(PKG_USER-SMD)
+  find_package(Eigen3 NO_MODULE)
+  if(EIGEN3_FOUND)
+    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
+  if(DOWNLOAD_EIGEN3)
+    message(STATUS "Eigen3 download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
+    endif()
+  endif()
+  include_directories(${EIGEN3_INCLUDE_DIR})
+endif()

cmake/Modules/Packages/USER-VTK.cmake

@@ -0,0 +1,6 @@
+if(PKG_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${VTK_USE_FILE})
+  add_definitions(-DLAMMPS_VTK)
+  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
+endif()

cmake/Modules/Packages/VORONOI.cmake

@@ -0,0 +1,45 @@
+if(PKG_VORONOI)
+  find_package(VORO)
+  if(VORO_FOUND)
+    set(DOWNLOAD_VORO_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_VORO_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
+  if(DOWNLOAD_VORO)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
+    endif()
+    message(STATUS "Voro++ download requested - we will build our own")
+    include(ExternalProject)
+
+    if(BUILD_SHARED_LIBS)
+      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    else()
+      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    endif()
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
+
+    ExternalProject_Add(voro_build
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+      CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(voro_build SOURCE_DIR)
+    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS voro_build)
+  else()
+    find_package(VORO)
+    if(NOT VORO_FOUND)
+      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+    endif()
+  endif()
+  include_directories(${VORO_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+endif()

cmake/Modules/Testing.cmake

@@ -0,0 +1,52 @@
+###############################################################################
+# Testing
+###############################################################################
+option(ENABLE_TESTING "Enable testing" OFF)
+if(ENABLE_TESTING AND BUILD_EXE)
+  enable_testing()
+  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+
+  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
+    include(FetchContent)
+
+    FetchContent_Declare(lammps-testing
+      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
+    )
+
+    FetchContent_GetProperties(lammps-testing)
+    if(NOT lammps-testing_POPULATED)
+      message(STATUS "Downloading tests...")
+      FetchContent_Populate(lammps-testing)
+    endif()
+
+    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+  endif()
+
+  add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
+
+  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
+    message(STATUS "Running test discovery...")
+
+    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
+    foreach(script_path ${TEST_SCRIPTS})
+      get_filename_component(TEST_NAME ${script_path} EXT)
+      get_filename_component(SCRIPT_NAME ${script_path} NAME)
+      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+      set(TEST_NAME "test_core_${TEST_NAME}_serial")
+      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+    endforeach()
+    list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+    message(STATUS "Found ${NUM_TESTS} tests.")
+  endif()
+endif()

cmake/README.md

@@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Package-Specific Configuration Options](#package-specific-configuration-options)
          * [KSPACE Package](#kspace-package)
          * [MKL](#mkl)
-         * [FFTW2](#fftw2)
          * [FFTW3](#fftw3)
+         * [BLAS](#blas)
          * [LAPACK](#lapack)
          * [PYTHON Package](#python-package)
          * [GPU Package](#gpu-package)
+         * [MESSAGE Package](#message-package)
+         * [MSCG Package](#mscg-package)
          * [VORONOI Package](#voronoi-package)
+         * [USER-LATTE Package](#user-latte-package)
+         * [USER-PLUMED Package](#user-plumed-package)
+         * [USER-SCAFACOS Package](#user-scafacos-package)
          * [USER-SMD Package](#user-smd-package)
       * [Optional Features](#optional-features)
          * [zlib support](#zlib-support)
@@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases.
          * [Building with GNU Compilers](#building-with-gnu-compilers)
          * [Building with Intel Compilers](#building-with-intel-compilers)
          * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
-      * [Examples](#examples)
-
 
 ## Quick Start for the Impatient
 If you want to skip ahead and just run the compilation using `cmake`, please
@@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   <td>Controls if debugging symbols are added to the generated binaries</td>
   <td>
   <dl>
-  <dt><code>Release</code> (default)</dt>
+  <dt><code>RelWithDebInfo (default)</code></dt>
+  <dt><code>Release</code></dt>
   <dt><code>Debug</code></dt>
+  <dt><code>MinSizeRel</code></dt>
   </dl>
   </td>
 </tr>
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
+  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_MEMALIGN</code></td>
   <td>controls the alignment of blocks of memory allocated by LAMMPS</td>
@@ -271,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
 </tr>
 <tr>
   <td><code>LAMMPS_MACHINE</code></td>
-  <td>allows appending a machine suffix to the generate LAMMPS binary</td>
+  <td>allows appending a machine suffix to the generated LAMMPS binary</td>
+  <td>
+  <dl>
+    <dt>*none*  (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_LIB_SUFFIX</code></td>
+  <td>allows appending a suffix to the generated LAMMPS library</td>
   <td>
   <dl>
     <dt>*none*  (default)</dt>
@@ -319,8 +343,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
-  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td><code>BUILD_TOOLS</code></td>
+  <td>control whether to build LAMMPS tools</td>
   <td>
   <dl>
     <dt><code>off</code> (default)</dt>
@@ -561,23 +585,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_MEAM</code></td>
-  <td>
-<p>A pair style for the modified embedded atom (MEAM) potential.</p>
-
-<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
-which is a direct translation of the MEAM package to C++. USER-MEAMC contains
-additional optimizations making it run faster than MEAM on most machines, while
-providing the identical features and USER interface.</strong></p>
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_MISC</code></td>
   <td>
@@ -634,21 +641,6 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_REAX</code></td>
-  <td>
-  A pair style which wraps a Fortran library which implements the ReaxFF
-  potential, which is a universal reactive force field. See the USER-REAXC
-  package for an alternate implementation in C/C++. Also a fix reax/bonds
-  command for monitoring molecules as bonds are created and destroyed.
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_REPLICA</code></td>
   <td>
@@ -695,6 +687,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_SPIN</code></td>
+  <td>Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_SNAP</code></td>
   <td>
@@ -757,6 +759,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_MESSAGE</code></td>
+  <td>Commands to use LAMMPS as either a client or server and couple it to another application.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_MSCG</code></td>
   <td>
@@ -811,6 +823,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_VORONOI</code></td>
+  <td>
+  A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -825,6 +849,16 @@ providing the identical features and USER interface.</strong></p>
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>PKG_USER-ADIOS</code></td>
+  <td>ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-ATC</code></td>
   <td>
@@ -853,6 +887,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-BOCS</code></td>
+  <td>
+  This package provides fix bocs, a modified version of fix npt which includes the pressure correction to the barostat as outlined in: N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015).
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-CGDNA</code></td>
   <td>
@@ -1142,6 +1188,30 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-PLUMED</code></td>
+  <td>
+  The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the <code>fix plumed</code> command.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-PTM</code></td>
+  <td>
+  A <code>compute ptm/atom</code> command that calculates local structure characterization using the Polyhedral Template Matching methodology.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-QTB</code></td>
   <td>
@@ -1197,6 +1267,33 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-SCAFACOS</code></td>
+  <td>
+  A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-SDPD</code></td>
+  <td>
+  A pair style for smoothed dissipative particle dynamics (SDPD), which is an
+  extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal
+  fluctuations are important (see the USER-SPH package). Also two fixes for
+  moving and rigid body integration of SPH/SDPD particles (particles of
+  <code>atom_style meso</code>).</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-SMD</code></td>
   <td>
@@ -1280,6 +1377,23 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-YAFF</code></td>
+  <td>
+  Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
+  The expressions and their use are discussed in the following papers:
+  <ul>
+    <li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
+    <li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
+  </ul>
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1300,14 +1414,27 @@ providing the identical features and USER interface.</strong></p>
   <td><code>FFT</code></td>
   <td>
     <p>FFT library for KSPACE package</p>
-    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
+    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate
+    these libraries automatically. To control which one should be used please see
+    the options below for each FFT library.  Otherwise it will default to KISS
+    FFT.</p>
   </td>
   <td>
   <dl>
-    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
+    <dt><code>KISS</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>FFT_SINGLE</code></td>
+  <td>Use single-precision floating-point in FFT</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default = double precision)</dt>
+    <dt><code>on</code></dt>
   </dl>
   </td>
 </tr>
@@ -1325,60 +1452,6 @@ providing the identical features and USER interface.</strong></p>
 </tbody>
 </table>
 
-### MKL
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>MKL_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>MKL_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
-TODO static vs dynamic linking
-
-### FFTW2
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>FFTW2_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>FFTW2_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
 ### FFTW3
 
 <table>
@@ -1392,24 +1465,57 @@ TODO static vs dynamic linking
 <tbody>
 <tr>
   <td><code>FFTW3_INCLUDE_DIRS</code></td>
-  <td></td>
+  <td>path to FFTW3 include files</td>
   <td>
   </td>
 </tr>
 <tr>
   <td><code>FFTW3_LIBRARIES</code></td>
-  <td></td>
+  <td>list of paths to FFTW3 libraries</td>
   <td>
   </td>
 </tr>
 </tbody>
 </table>
 
+### MKL
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MKL_INCLUDE_DIRS</code></td>
+  <td>path to MKL include files</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MKL_LIBRARIES</code></td>
+  <td>list of paths to MKL libraries</td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### BLAS
+
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html)
+
 ### LAPACK
-TODO
+
+See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html)
 
 ### PYTHON Package
 
+See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html)
+
 ### USER-INTEL Package
 
 <table>
@@ -1499,10 +1605,11 @@ target API.
   <td>
   <dl>
     <dt><code>sm_20</code> (Fermi)</dt>
-    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_30</code> (Kepler) (default)</dt>
     <dt><code>sm_50</code> (Maxwell)</dt>
     <dt><code>sm_60</code> (Pascal)</dt>
     <dt><code>sm_70</code> (Volta)</dt>
+    <dt><code>sm_75</code> (Turing)</dt>
   </dl>
   </td>
 </tr>
@@ -1534,13 +1641,14 @@ target API.
 </tbody>
 </table>
 
-### VORONOI Package
+### KIM Package
 
-TODO
+Requires installation of the KIM library with API v2
 
-### USER-SMD Package
-
-Requires a Eigen3 installation
+If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside
+the CMake build directory. If the KIM library is already on your system (in a
+location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable
+so that `libkim-api` can be found.
 
 <table>
 <thead>
@@ -1551,9 +1659,349 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>DOWNLOAD_KIM</code></td>
+  <td>Download KIM API v2 and compile it as part of the build.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MESSAGE Package
+
+This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MESSAGE_ZMQ</code></td>
+  <td>Build with ZeroMQ support</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMQ_LIBRARY</code></td>
+  <td>
+    ZMQ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing ZMQ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MSCG Package
+
+Requires installation of the MSCG library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_MSCG</code></td>
+  <td>Download MSCG and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_LIBRARY</code></td>
+  <td>
+    MSCG library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing MSCG installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### VORONOI Package
+
+Requires installation of the Voro++ library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_VORO</code></td>
+  <td>Download Voro++ and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_LIBRARY</code></td>
+  <td>
+    Voro++ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing Voro++ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-COLVARS Package
+
+Requires a C++11 compiler to compile with the Lepton library included.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>COLVARS_LEPTON</code></td>
+  <td>Enable the use of the Lepton library inside the Colvars library.
+  <td>
+  <dl>
+    <dt><code>on</code> (default)</dt>
+    <dt><code>off</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-PLUMED Package
+
+Requires installation of the PLUMED library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_PLUMED</code></td>
+  <td>Download PLUMED and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PLUMED_MODE</code></td>
+  <td>
+    Determines the linkage mode for the PLUMED library.
+  </td>
+  <td>
+  <dl>
+    <dt><code>static</code> (default)</dt>
+    <dt><code>shared</code></dt>
+    <dt><code>runtime</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-SMD Package
+
+Requires installation of the Eigen3 library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_EIGEN3</code></td>
+  <td>Download Eigen3 and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>EIGEN3_INCLUDE_DIR</code></td>
-  <td></td>
+  <td>
+    Provide include directory of existing Eigen3 installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+
+### USER-SCAFACOS Package
+
+To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/)
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_SCAFACOS</code></td>
+  <td>Download SCAFACOS and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_LIBRARY</code></td>
+  <td>
+    SCAFACOS library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_INCLUDE_DIR</code></td>
+  <td>
+    SCAFACOS include directory (only needed if at custom location)
+  </td>
   <td>
   </td>
 </tr>
@@ -1791,5 +2239,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL
 cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
+## LAMMPS Developer Options
 
-## Examples
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>ENABLE_TESTING</code></td>
+  <td>Control wheather to add tests via CTest</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_SOURCE_DIR</code></td>
+  <td>Custom location of lammps-testing repository (optional). If not specified it will download it via Git</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_GIT_TAG</code></td>
+  <td>If lammps-testing repository is cloned, this is the tag/commit that will be checked out</td>
+  <td>
+  <dl>
+    <dt><code>master</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_COVERAGE</code></td>
+  <td>Enables code coverage support via gcov and adds a gcovr build target to generate a coverage report.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_ADDRESS</code></td>
+  <td>Enables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_UNDEFINED</code></td>
+  <td>Enables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_THREAD</code></td>
+  <td>Enables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>

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

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

cmake/presets/mingw-cross.cmake

@@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
                  USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
                  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
-                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -14,4 +14,4 @@ endforeach()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

cmake/presets/most.cmake

@@ -4,10 +4,10 @@
 
 set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
-        PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
+        PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
         USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
         USER-DRUDE USER-FEP USER-MEAMC USER-MESO
-        USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
+        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
         USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})

doc/Makefile

@@ -69,6 +69,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		doc_anchor_check src/*.txt ;\
+		env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)

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 <cstring>` or `#include <mpi.h>`) 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 <cstdlib>` or
+`#include <cctypes>`).  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 <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### 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`, cstdlib, 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.
+

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "31 May 2019" "2019-05-31"
+.TH LAMMPS "30 October 2019" "2019-10-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build.txt

@@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page.
    Build_package
    Build_extras
    Build_windows
+   Build_development
 
 END_RST -->
 
@@ -41,7 +42,8 @@ END_RST -->
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
 "Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+"Notes for building LAMMPS on Windows"_Build_windows.html
+"Development build options (CMake only)"_Build_development.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

doc/src/Build_basics.txt

@@ -51,7 +51,7 @@ Serial build (see src/MAKE/Makefile.serial):
 
 MPI_INC =       -I../STUBS
 MPI_PATH =      -L../STUBS
-MPI_LIB =	-lmpi_stubs :pre
+MPI_LIB =       -lmpi_stubs :pre
 
 For a parallel build, if MPI is installed on your system in the usual
 place (e.g. under /usr/local), you do not need to specify the 3
@@ -183,17 +183,17 @@ want.
 
 Parallel build (see src/MAKE/Makefile.mpi):
 
-CC =		mpicxx
-CCFLAGS =	-g -O3
-LINK =		mpicxx
-LINKFLAGS =	-g -O :pre
+CC =            mpicxx
+CCFLAGS =       -g -O3
+LINK =          mpicxx
+LINKFLAGS =     -g -O :pre
 
 Serial build (see src/MAKE/Makefile.serial):
 
-CC =		g++
-CCFLAGS =	-g -O3
-LINK =		g++
-LINKFLAGS =	-g -O :pre
+CC =            g++
+CCFLAGS =       -g -O3
+LINK =          g++
+LINKFLAGS =     -g -O :pre
 
 The "compiler/linker settings" section of a Makefile.machine lists
 compiler and linker settings for your C++ compiler, including
@@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface.
 
 -D BUILD_EXE=value           # yes (default) or no
 -D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+-D BUILD_SHARED_LIBS=value   # yes or no (default)
+-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value :pre
+
 
 Setting BUILD_EXE=no will not produce an executable.  Setting
 BUILD_LIB=yes will produce a static library named liblammps.a.
 Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so.
+shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
+libraries will be named liblammps_name.a or liblammps_name.so instead.
 
 [Traditional make]:
 
@@ -310,6 +314,30 @@ current LAMMPS version (HTML and PDF files), from the website
 
 :line
 
+Build LAMMPS tools :h4,link(tools)
+
+Some tools described in "Auxiliary tools"_Tools.html can be built directly
+using CMake or Make.
+
+[CMake variable]:
+
+-D BUILD_TOOLS=value       # yes or no (default) :pre
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+[Traditional make]:
+
+cd lammps/tools
+make all              # build all binaries of tools
+make binary2txt       # build only binary2txt tool
+make chain            # build only chain tool
+make micelle2d        # build only micelle2d tool
+make thermo_extract   # build only thermo_extract tool
+:pre
+
+:line
+
+
 Install LAMMPS after a build :h4,link(install)
 
 After building LAMMPS, you may wish to copy the LAMMPS executable of

doc/src/Build_cmake.txt

@@ -32,10 +32,18 @@ cmake \[options ...\] ../cmake     # configuration with (command-line) cmake
 make                             # compilation :pre
 
 The cmake command will detect available features, enable selected
-packages and options, and will generate the build environment.  The make
-command will then compile and link LAMMPS, producing (by default) an
-executable called "lmp" and a library called "liblammps.a" in the
-"build" folder.
+packages and options, and will generate the build environment.  By default
+this build environment will be created for "Unix Makefiles" on most
+platforms and particularly on Linux.  However, alternate build tools
+(e.g. Ninja) and support files for Integrated Development Environments
+(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+selected via the "-G" command line flag. For the rest of the documentation
+we will assume that the build environment is generated for makefiles
+and thus the make command will be used to compile and link LAMMPS as
+indicated above, producing (by default) an executable called "lmp" and
+a library called "liblammps.a" in the "build" folder.  When generating
+a build environment for the "Ninja" build tool, the build command would
+be "ninja" instead of "make".
 
 If your machine has multiple CPU cores (most do these days), using a
 command like "make -jN" (with N being the number of available local
@@ -44,11 +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
@@ -106,7 +120,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
--D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
 -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir

doc/src/Build_development.txt

@@ -0,0 +1,86 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Development build options (CMake only) :h3
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+:line
+
+Verify compilation flags :h4,link(compilation)
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+make VERBOSE=1 :pre
+
+:line
+
+Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
+code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
+language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+:pre
+
+:line
+
+Code Coverage and Testing :h4,link(testing)
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation.
+
+NOTE: this is incomplete and only represents a small subset of tests that we run
+
+-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+:pre
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+make test
+:pre
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+make test               # run tests first!
+make gen_coverage_html  # generate coverage report in HTML format
+make gen_coverage_xml   # generate coverage report in XML format
+:pre
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+pip install git+https://github.com/gcovr/gcovr.git :pre
+:pre

doc/src/Build_extras.txt

@@ -88,7 +88,7 @@ which GPU hardware to build for.
                           # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
 -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
                           # value = sm_XX, see below
-                          # default is Cuda-compiler dependent, but typically sm_20
+                          # default is sm_30
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
                           # value = yes (default) or no
@@ -172,22 +172,17 @@ KIM package :h4,link(kim)
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that downloading and installing
-the KIM API library with all its models, may take a long time (10s of
-minutes to hours) to build.  Of course you only need to do that once.
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+See the list of all KIM models here: https://openkim.org/browse/models
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+(Also note that when downloading and installing from source
+the KIM API library with all its models, may take a long time (tens of
+minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
@@ -307,7 +302,7 @@ files.
 
 KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
 export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC =		mpicxx :pre
+CC =            mpicxx :pre
 
 :line
 
@@ -359,6 +354,9 @@ be installed on your system.
 [CMake build]:
 
 -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+-D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+:pre
 
 [Traditional make]:
 
@@ -371,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args:
 make lib-message               # print help message
 make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
 make lib-message args="-s"     # build as serial lib with no ZMQ support
+:pre
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an
@@ -643,30 +642,61 @@ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 USER-COLVARS package :h4,link(user-colvars)
 
+This package includes into the LAMMPS distribution the Colvars library, which
+can be built for the most part with all major versions of the C++ language.
+
+A few of the most recent features require C++11 support.  In particular, the
+library is optionally built together with the
+"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
+included in the LAMMPS distribution.  Lepton implements the
+"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
+feature, and requires C++11 support.
+
+See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
+C++11-only features.
+
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-COLVARS=yes".
+This is the recommended build recipe: no additional settings are normally
+needed besides "-D PKG_USER-COLVARS=yes".
+
+Building and linking of Lepton (or other C++11-only features) is enabled
+automatically when compilation is carried out with C++11 support, and disabled
+otherwise.  Optionally, Lepton build may be manually controlled with the flag
+"-D COLVARS_LEPTON=yes|no".
 
 [Traditional make]:
 
-Before building LAMMPS, you must build the COLVARS library in
-lib/colvars.  You can do this manually if you prefer; follow the
-instructions in lib/colvars/README.  You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/colvars/Install.py script with the specified args:
+Before building LAMMPS, one must build the Colvars library in lib/colvars.
+
+This can be done manually in the same folder by using or adapting one of the
+provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+
+In general, it is safer to use build setting consistent with the rest of
+LAMMPS.  This is best carried out from the LAMMPS src directory using a
+command like these, which simply invoke the lib/colvars/Install.py script with
+the specified args:
 
 make lib-colvars                      # print help message
 make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
 make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
 
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank).  If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
+The "machine" argument of the "-m" flag is used to find a Makefile.machine to
+use as build recipe.  If it does not already exist in lib/colvars, it will be
+auto-generated by using compiler flags consistent with those parsed from the
+core LAMMPS makefiles.
+
+Optional flags may be specified as environment variables:
+
+COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+
+The build should produce two files: the library lib/colvars/libcolvars.a
+(which also includes Lepton objects if enabled) and the specification file
+lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+not need to be edited.
+
 
 :line
 
@@ -803,7 +833,7 @@ dir, using a command like these, which simply invoke the
 lib/h5md/Install.py script with the specified args:
 
 make lib-h5md                     # print help message
-make lib-hm5d args="-m h5cc"      # build with h5cc compiler :pre
+make lib-h5md args="-m h5cc"      # build with h5cc compiler :pre
 
 The build should produce two files: lib/h5md/libch5md.a and
 lib/h5md/Makefile.lammps.  The latter is copied from an existing
@@ -850,15 +880,15 @@ additional information.
 For CPUs:
 
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
-CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
 LIB =           -ltbbmalloc :pre
 
 For KNLs:
 
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
 LIB =           -ltbbmalloc :pre
 
 :line

doc/src/Build_settings.txt

@@ -12,6 +12,7 @@ Optional build settings :h3
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
+"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
 "FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
 "Size of LAMMPS data types"_#size
 "Read or write compressed files"_#gzip
@@ -23,6 +24,33 @@ explain how to do this for building both with CMake and make.
 
 :line
 
+C++11 standard compliance test :h4,link(cxx11)
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to switch.  To determine the impact of requiring C++11,
+we have added a simple compliance test to the source code, that will cause
+the compilation to abort, if C++11 compliance is not available or enabled.
+To bypass this check, you need to change a setting in the makefile or
+when calling CMake.
+
+[CMake variable]:
+
+-D DISABLE_CXX11_REQUIREMENT=yes :pre
+
+You can set additional C++ compiler flags (beyond those selected by CMake)
+through the CMAKE_CXX_FLAGS variable. Example for CentOS 7:
+
+-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_CXX98 :pre
+
+:line
+
 FFT library :h4,link(fft)
 
 When the KSPACE package is included in a LAMMPS build, the

doc/src/Commands.txt

@@ -33,6 +33,11 @@ commands in it are used to define a LAMMPS simulation.
    Commands_bond
    Commands_kspace
 
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
+
 END_RST -->
 
 <!-- HTML_ONLY -->
@@ -49,5 +54,7 @@ END_RST -->
 "Bond, angle, dihedral, improper commands"_Commands_bond.html
 "KSpace solvers"_Commands_kspace.html  :all(b)
 
+"Removed commands and packages"_Commands_removed.html  :all(b)
+
 <!-- END_HTML_ONLY -->
 

doc/src/Commands_all.txt

@@ -50,11 +50,11 @@ An alphabetic list of all general LAMMPS commands.
 "dump"_dump.html,
 "dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dump_modify"_dump_modify.html,
 "dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
@@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
-"kim_query"_kim_query.html,
+"kim_init"_kim_commands.html,
+"kim_interactions"_kim_commands.html,
+"kim_query"_kim_commands.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -122,6 +124,7 @@ An alphabetic list of all general LAMMPS commands.
 "thermo"_thermo.html,
 "thermo_modify"_thermo_modify.html,
 "thermo_style"_thermo_style.html,
+"third_order"_third_order.html,
 "timer"_timer.html,
 "timestep"_timestep.html,
 "uncompute"_uncompute.html,

doc/src/Commands_bond.txt

@@ -28,8 +28,12 @@ OPT.
 
 "none"_bond_none.html,
 "zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
-
+"hybrid"_bond_hybrid.html,
+,
+,
+,
+,
+,
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
@@ -56,8 +60,12 @@ OPT.
 
 "none"_angle_none.html,
 "zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
-
+"hybrid"_angle_hybrid.html,
+,
+,
+,
+,
+,
 "charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
 "class2/p6"_angle_class2.html,
@@ -89,14 +97,18 @@ OPT.
 
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
-
+"hybrid"_dihedral_hybrid.html,
+,
+,
+,
+,
+,
 "charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
 "fourier (io)"_dihedral_fourier.html,
-"harmonic (io)"_dihedral_harmonic.html,
+"harmonic (iko)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
@@ -117,8 +129,12 @@ OPT.
 
 "none"_improper_none.html,
 "zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
-
+"hybrid"_improper_hybrid.html,
+,
+,
+,
+,
+,
 "class2 (ko)"_improper_class2.html,
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,

doc/src/Commands_compute.txt

@@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
+"gyration/shape"_compute_gyration_shape.html,
 "heat/flux"_compute_heat_flux.html,
 "heat/flux/tally"_compute_tally.html,
 "hexorder/atom"_compute_hexorder_atom.html,
@@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "meso/e/atom"_compute_meso_e_atom.html,
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
+"momentum"_compute_momentum.html,
 "msd"_compute_msd.html,
 "msd/chunk"_compute_msd_chunk.html,
 "msd/nongauss"_compute_msd_nongauss.html,

doc/src/Commands_fix.txt

@@ -232,6 +232,7 @@ OPT.
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
 "wall/lj93 (k)"_fix_wall.html,
+"wall/morse"_fix_wall.html,
 "wall/piston"_fix_wall_piston.html,
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,

doc/src/Commands_pair.txt

@@ -27,8 +27,11 @@ OPT.
 "none"_pair_none.html,
 "zero"_pair_zero.html,
 "hybrid (k)"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
-
+"hybrid/overlay (k)"_pair_hybrid.html,
+,
+,
+,
+,
 "adp (o)"_pair_adp.html,
 "agni (o)"_pair_agni.html,
 "airebo (io)"_pair_airebo.html,
@@ -62,6 +65,7 @@ OPT.
 "colloid (go)"_pair_colloid.html,
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
+"cosine/squared"_pair_cosine_squared.html,
 "coul/cut (gko)"_pair_coul.html,
 "coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
@@ -162,6 +166,7 @@ OPT.
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
 "lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
 "lj96/cut (go)"_pair_lj96.html,
+"local/density"_pair_local_density.html,
 "lubricate (o)"_pair_lubricate.html,
 "lubricate/poly (o)"_pair_lubricate.html,
 "lubricateU"_pair_lubricateU.html,
@@ -219,6 +224,8 @@ OPT.
 "sph/rhosum"_pair_sph_rhosum.html,
 "sph/taitwater"_pair_sph_taitwater.html,
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dipole/cut"_pair_spin_dipole.html,
+"spin/dipole/long"_pair_spin_dipole.html,
 "spin/dmi"_pair_spin_dmi.html,
 "spin/exchange"_pair_spin_exchange.html,
 "spin/magelec"_pair_spin_magelec.html,

doc/src/Commands_removed.txt

@@ -0,0 +1,66 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+Removed commands and packages :h3
+
+This page lists LAMMPS commands and packages that have been removed from
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
+
+Fix ave/spatial and fix ave/spatial/sphere :h4
+
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the "compute chunk/atom"_compute_chunk_atom.html command
+and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
+Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
+
+MEAM package :h4
+
+The MEAM package has been removed since it was superseded by the
+"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
+the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+which removes several restrictions (e.g. there can be multiple instances
+in hybrid pair styles) and allows for some optimizations leading
+to better performance.  The new pair style "meam/c"_pair_meamc.html has
+the exact same syntax as the old "meam" pair style and thus pair style
+"meam"_pair_meamc.html is an alias to the new style and backward
+compatibility of old inputs is preserved.
+
+REAX package :h4
+
+The REAX package has been removed since it was superseded by the
+"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via USER-OMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
+
+USER-CUDA package :h4
+
+The USER-CUDA package had been removed, since it had been unmaintained
+for a long time and had known bugs and problems.  Significant parts of
+the design were transferred to the
+"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
+performance characteristics on Nvidia GPUs. Both, the KOKKOS
+and the "GPU package"_Package_details.html#PKG-GPU are maintained
+and allow running LAMMPS with GPU acceleration.
+
+restart2data tool :h4
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands "read_restart"_read_restart.html and
+"write_data"_write_data.html can be used to the same effect.  For added
+convenience this conversion can also be triggered by "command line
+flags"_Run_options.html

doc/src/Eqs/angle_class2_p6.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/angle_cosine_buck6d.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/compute_shape_parameters.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ c = l_z - 0.5(l_y+l_x) \\
+ b = l_y - l_x \\
+ k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Eqs/fix_bond_react.tex

@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Eqs/improper_inversion_harmonic.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left(\theta - \theta_0\right)^2
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/norm_inf.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    || \vec{F} ||_{inf} 
+    = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, 
+    |F_N^1|, |F_N^2|, |F_N^3|\right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/norm_max.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    % \left| \left| \vec{F} \right| \right|_2 
+    || \vec{F} ||_{max} 
+    = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/norm_two.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    % \left| \left| \vec{F} \right| \right|_2 
+    || \vec{F} ||_{2} 
+    = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_agni.tex

@@ -0,0 +1,18 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  F_i^u & = & \sum_t^{N_t}\alpha_t \cdot \exp\left[-\frac{\left(d_{i,t}^u\right)^2}{2l^2}\right] \\
+  d_{i,t}^u & = & \left|\left| V_i^u(\eta) - V_t^u(\eta) \right|\right| \\
+  V_i^u(\eta) & = & \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\
+  f_d\left(r_{ij}\right) & = & \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right]
+\end{eqnarray*}
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_buck6d.tex

@@ -1,6 +1,7 @@
 \documentclass[12pt]{article}
 
 \begin{document}
+\pagestyle{empty}
 
 \begin{eqnarray*}
   E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\

doc/src/Eqs/pair_cosine_squared.tex

@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{align*}
+E = 
+\begin{cases}
+-\epsilon& \quad r < \sigma \\
+-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
+0& \quad r \geq r_c
+\end{cases}
+\end{align*}
+
+\end{document}

doc/src/Eqs/pair_cosine_squared_wca.tex

@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       2\left(\frac{\sigma}{r}\right)^6 + 1\right]
+                       , \quad r < \sigma
+$$
+
+\end{document}

doc/src/Eqs/pair_coul_gauss.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_kolmogorov_crespi_full.tex

@@ -27,7 +27,7 @@
   V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
   \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
   \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 \end{eqnarray*}
 \endgroup
 \end{document}

doc/src/Eqs/pair_local_density_energy.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ U_{LD} = \sum_i F(\rho_i)
+$$
+
+
+\end{document}
+~                  

doc/src/Eqs/pair_local_density_energy_implement.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] 
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_energy_multi.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U_{LD} = \sum_i a_\alpha F(\rho_i)
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_indicator_func.tex

@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+
+\begin{document}
+\[
+  \varphi(r) = 
+    \begin{cases}
+       1 & r \le R_1 \\
+       c_0 + c_2r^2 + c_4r^4 + c_6r^6  & r \in (R_1, R_2) \\
+       0 & r \ge R_2
+  \end{cases}
+\]
+
+\end{document}

doc/src/Eqs/pair_local_density_ld.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i = \sum_{j \neq i} \varphi(r_{ij})
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_ld_implement.tex

@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_ld_multi.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
+$$
+
+\end{document}

doc/src/Eqs/pair_spin_dipole.tex

@@ -0,0 +1,42 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,graphics,bm,setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \mathcal{H}_{\rm long}= 
+    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} 
+    \sum_{i,j,i\neq j}^{N}
+    \frac{g_i g_j}{r_{ij}^3}
+    \Big(3 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{i}\right) 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{j}\right) 
+    -\bm{s}_i\cdot\bm{s}_j \Big)
+    \nonumber
+  \end{equation}
+  \begin{equation}
+    \bm{\omega}_i = 
+    \frac{\mu_0 (\mu_B)^2}{4\pi\hbar}\sum_{j}
+    \frac{g_i g_j}{r_{ij}^3}
+    \, \Big(
+    3\,(\bm{e}_{ij}\cdot\bm{s}_{j})\bm{e}_{ij}
+    -\bm{s}_{j} \Big) \nonumber
+  \end{equation}
+  \begin{equation}
+    \bm{F}_i =
+    \frac{3\, \mu_0 (\mu_B)^2}{4\pi} \sum_j
+    \frac{g_i g_j}{r_{ij}^4}
+    \Big[\big( (\bm{s}_i\cdot\bm{s}_j) 
+    -5(\bm{e}_{ij}\cdot\bm{s}_i)
+    (\bm{e}_{ij}\cdot\bm{s}_j)\big) \bm{e}_{ij}+
+    \big(
+    (\bm{e}_{ij}\cdot\bm{s}_i)\bm{s}_j+
+    (\bm{e}_{ij}\cdot\bm{s}_j)\bm{s}_i
+    \big)
+    \Big]
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}