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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-  3.2424796479760154e-01  3.0660370758054967e-01  2.8990116598452254e-01  2.7409841872609064e-01  2.5915454407883409e-01
-  2.4502968839369110e-01  2.3168512174254197e-01  2.1908328186436687e-01  2.0718780752542632e-01  1.9596356233750800e-01
-  1.8537665001230508e-01  1.7539442196444632e-01  1.6598547811304609e-01  1.5711966166996927e-01  1.4876804864444715e-01
-  1.4090293273673637e-01  1.3349780623990259e-01  1.2652733751724909e-01  1.1996734557434463e-01  1.1379477219856060e-01
-  1.0798765209582406e-01  1.0252508141368288e-01  9.7387185001678311e-02  9.2555082724584015e-02  8.8010855111109620e-02
-  8.3737508589961873e-02  7.9718940536826377e-02  7.5939904329596963e-02  7.2385974585237101e-02  6.9043512729294765e-02
-  6.5899633029043336e-02  6.2942169202580001e-02  6.0159641699440547e-02  5.7541225732930634e-02  5.5076720130546430e-02
-  5.2756517056398833e-02  5.0571572648238083e-02  4.8513378601664936e-02  4.6573934725081756e-02  4.4745722480991068e-02
-  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
-  2.5996698317105604e-02  2.5267475760840985e-02  2.4572125264713973e-02  2.3908509926274246e-02  2.3274635987705516e-02
-  2.2668643641204911e-02  2.2088798370316409e-02  2.1533482801290083e-02  2.1001189039288493e-02  2.0490511464994254e-02
-  2.0000139967999431e-02  1.9528853594166895e-02  1.9075514584991349e-02  1.8639062787818239e-02  1.8218510416650235e-02
-  1.7812937144080498e-02  1.7421485505751177e-02  1.7043356599549031e-02  1.6677806062561751e-02  1.6324140309613155e-02
-  1.5981713017976018e-02  1.5649921843605585e-02  1.5328205354974755e-02  1.5016040171312250e-02  1.4712938292708366e-02
-  1.4418444610242331e-02  1.4132134584901757e-02  1.3853612084676337e-02  1.3582507369821917e-02  1.3318475216818060e-02
-  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/CMakeLists.txt

@@ -52,8 +52,15 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
+endif()
+
+option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
+if(DISABLE_CXX11_REQUIREMENT)
+  add_definitions(-DLAMMPS_CXX98)
+# else()
+#  set(CMAKE_CXX_STANDARD 11)
 endif()
 
 # GNU compiler features
@@ -241,6 +248,7 @@ if(BUILD_OMP)
 endif()
 
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+  enable_language(C)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -315,13 +323,14 @@ endif()
 include(Packages/KSPACE)
 include(Packages/PYTHON)
 include(Packages/VORONOI)
-include(Packages/USER-SCAFACOS)
-include(Packages/USER-PLUMED)
+include(Packages/USER-COLVARS)
 include(Packages/USER-MOLFILE)
 include(Packages/USER-NETCDF)
-include(Packages/USER-SMD)
-include(Packages/USER-QUIP)
+include(Packages/USER-PLUMED)
 include(Packages/USER-QMMM)
+include(Packages/USER-QUIP)
+include(Packages/USER-SCAFACOS)
+include(Packages/USER-SMD)
 include(Packages/USER-VTK)
 include(Packages/KIM)
 include(Packages/LATTE)
@@ -411,8 +420,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
-  USER-QMMM)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
@@ -426,10 +434,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
-    elseif(PKG_LIB STREQUAL colvars)
-      target_compile_options(colvars PRIVATE -DLEPTON)
-      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
-      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
     endif()
@@ -589,6 +593,7 @@ if(BUILD_TOOLS)
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
   endif()
 
   enable_language(C)

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/Packages/KIM.cmake

@@ -1,4 +1,5 @@
 if(PKG_KIM)
+  set(KIM-API_MIN_VERSION 2.1)
   find_package(CURL)
   if(CURL_FOUND)
     include_directories(${CURL_INCLUDE_DIRS})
@@ -7,10 +8,17 @@ if(PKG_KIM)
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)
-    set(DOWNLOAD_KIM_DEFAULT OFF)
+    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 (NOT DOWNLOAD_KIM)
-      message(WARNING "KIM-API package not found.  We will download and build our own")
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
     endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
@@ -28,8 +36,8 @@ if(PKG_KIM)
       message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
     endif()
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
-      URL_MD5 6ac52e14ef52967fc7858220b208cba5
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -42,7 +50,7 @@ if(PKG_KIM)
     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 REQUIRED)
+    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
   endif()
   list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
   include_directories(${KIM-API_INCLUDE_DIRS})

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,15 +1,24 @@
 if(PKG_KOKKOS)
-  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
-  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/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)
-  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)
 
   set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
   set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
@@ -17,12 +26,15 @@ if(PKG_KOKKOS)
                          ${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)
 
@@ -38,6 +50,7 @@ if(PKG_KOKKOS)
   # 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)

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,4 +1,7 @@
 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

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-MOLFILE.cmake

@@ -1,4 +1,8 @@
 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})

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
-      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
+      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}

cmake/README.md

@@ -1798,6 +1798,32 @@ Requires installation of the Voro++ library
 </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

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/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "6 August 2019" "2019-08-06"
+.TH LAMMPS "30 October 2019" "2019-10-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

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

doc/src/Build_development.txt

@@ -50,7 +50,7 @@ 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. 
+developers can run the tests directly on their workstation.
 
 NOTE: this is incomplete and only represents a small subset of tests that we run
 

doc/src/Build_extras.txt

@@ -302,7 +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
 
@@ -642,30 +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
 
@@ -802,7 +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
@@ -849,15 +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_all.txt

@@ -124,6 +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

@@ -108,7 +108,7 @@ OPT.
 "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,

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

@@ -65,6 +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,
@@ -165,6 +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,

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/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_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_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/Errors_messages.txt

@@ -4791,6 +4791,22 @@ Self-explanatory. :dd
 
 This fix option cannot be used with point particles. :dd
 
+{Fix langevin gjf and respa are not compatible} :dt
+
+Self-explanatory. :dd
+
+{Fix langevin gjf cannot have period equal to dt/2} :dt
+
+If the period is equal to dt/2 then division by zero will happen. :dd
+
+{Fix langevin gjf should come before fix nve} :dt
+
+Self-explanatory. :dd
+
+{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt
+
+This option is not yet available. :dd
+
 {Fix langevin omega is not yet implemented with kokkos} :dt
 
 This option is not yet available. :dd

doc/src/Errors_warnings.txt

@@ -47,6 +47,11 @@ too far away. :dd
 
 Self-explanatory. :dd
 
+{Angles are defined but no angle style is set} :dt
+
+The topology contains angles, but there are no angle forces computed
+since there was no angle_style command. :dd
+
 {Atom style in data file differs from currently defined atom style} :dt
 
 Self-explanatory. :dd
@@ -73,6 +78,11 @@ short or the bond has blown apart and an atom is too far away. :dd
 
 Self-explanatory. :dd
 
+{Bonds are defined but no bond style is set} :dt
+
+The topology contains bonds, but there are no bond forces computed
+since there was no bond_style command. :dd
+
 {Bond/angle/dihedral extent > half of periodic box length} :dt
 
 This is a restriction because LAMMPS can be confused about which image
@@ -186,6 +196,11 @@ to check your simulation geometry. :dd
 
 Self-explanatory. :dd
 
+{Dihedrals are defined but no dihedral style is set} :dt
+
+The topology contains dihedrals, but there are no dihedral forces computed
+since there was no dihedral_style command. :dd
+
 {Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt
 
 If the fix changes the timestep, the dump dcd file will not
@@ -248,6 +263,10 @@ included one or more of the following: kspace, triclinic, a hybrid
 pair style, an eam pair style, or no "single" function for the pair
 style. :dd
 
+{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt
+
+This will most likely cause errors in kinetic fluctuations.
+
 {Fix property/atom mol or charge w/out ghost communication} :dt
 
 A model typically needs these properties defined for ghost atoms. :dd
@@ -348,6 +367,11 @@ to check your simulation geometry. :dd
 
 Self-explanatory. :dd
 
+{Impropers are defined but no improper style is set} :dt
+
+The topology contains impropers, but there are no improper forces computed
+since there was no improper_style command. :dd
+
 {Inconsistent image flags} :dt
 
 The image flags for a pair on bonded atoms appear to be inconsistent.
@@ -366,6 +390,11 @@ have fully consistent image flags, since some bonds will cross
 periodic boundaries and connect two atoms with the same image
 flag. :dd
 
+{Increasing communication cutoff for GPU style} :dt
+
+The pair style has increased the communication cutoff to be consistent with
+the communication cutoff requirements for this pair style when run on the GPU. :dd
+
 {KIM Model does not provide 'energy'; Potential energy will be zero} :dt
 
 Self-explanatory. :dd
@@ -403,6 +432,30 @@ This library function cannot be used if atom IDs are not defined or
 are not consecutively numbered, or if no atom map is defined.  See the
 atom_modify command for details about atom maps. :dd
 
+{Likewise 1-2 special neighbor interactions != 1.0} :dt
+
+The topology contains bonds, but there is no bond style defined
+and a 1-2 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the bond style. :dd
+
+{Likewise 1-3 special neighbor interactions != 1.0} :dt
+
+The topology contains angles, but there is no angle style defined
+and a 1-3 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the angle style. :dd
+
+{Likewise 1-4 special neighbor interactions != 1.0} :dt
+
+The topology contains dihedrals, but there is no dihedral style defined
+and a 1-4 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the dihedral style. :dd
+
 {Lost atoms via change_box: original %ld current %ld} :dt
 
 The command options you have used caused atoms to be lost. :dd

doc/src/Examples.txt

@@ -141,6 +141,7 @@ HEAT: compute thermal conductivity for LJ and water via fix ehex
 KAPPA: compute thermal conductivity via several methods
 MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
 SPIN: examples for features of the SPIN package
+UNITS: examples that run the same simulation in lj, real, metal units
 USER: examples for USER packages and USER-contributed commands
 VISCOSITY: compute viscosity via several methods :tb(s=:)
 

doc/src/Howto_chunk.txt

@@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
 spreads per-chunk values to each atom in the chunk, producing per-atom
 values as its output.  This can be useful for outputting per-chunk
 values to a per-atom "dump file"_dump.html.  Or for using an atom's
-associated chunk value in an "atom-style variable"_variable.html.
+associated chunk value in an "atom-style variable"_variable.html.  Or
+as input to the "fix ave/chunk"_fix_ave_chunk.html command to
+spatially average per-chunk values calculated by a per-chunk compute.
 
 The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
 peratom value across the atoms in each chunk to produce a value per
@@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes
 compute size all property/chunk cc1 count
 fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
 
-(6) An example of using a per-chunk value to apply per-atom forces to
+(6) An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the "compute
 chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
 
-(7) An example of using one set of per-chunk values for molecule
+(7) An example for using one set of per-chunk values for molecule
 chunks, to create a 2nd set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the "compute
 chunk/reduce"_compute_reduce_chunk.html command doc page.
+
+(8) An example for using one set of per-chunk values (dipole moment
+vectors) for molecule chunks, spreading the values to each atom in
+each chunk, then defining a second set of chunks as spatial bins, and
+using the "fix ave/chunk"_fix_ave_chunk.html command to calculate an
+average dipole moment vector for each bin.  This example is explained
+on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html
+command doc page.

doc/src/Howto_spins.txt

@@ -43,19 +43,19 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
-The command "fix setforce/spin"_fix_setforce.html allows to set the 
-components of the magnetic precession vectors (while erasing and 
-replacing the previously computed magnetic precession vectors on 
-the atom). 
-This command can be used to freeze the magnetic moment of certain 
-atoms in the simulation by zeroing their precession vector. 
+The command "fix setforce/spin"_fix_setforce.html allows to set the
+components of the magnetic precession vectors (while erasing and
+replacing the previously computed magnetic precession vectors on
+the atom).
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
 
 The command "fix nve/spin"_fix_nve_spin.html can be used to
-perform a symplectic integration of the combined dynamics of spins 
+perform a symplectic integration of the combined dynamics of spins
 and atomic motions.
 
 The minimization style "min/spin"_min_spin.html can be applied
-to the spins to perform a minimization of the spin configuration. 
+to the spins to perform a minimization of the spin configuration.
 
 
 All the computed magnetic properties can be output by two main

doc/src/Howto_viscosity.txt

@@ -83,7 +83,7 @@ variable    d equal $p*$s   # dump interval :pre
 
 # convert from LAMMPS real units to SI :pre
 
-variable    kB equal 1.3806504e-23    # \[J/K/] Boltzmann
+variable    kB equal 1.3806504e-23    # \[J/K\] Boltzmann
 variable    atm2Pa equal 101325.0
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15

doc/src/Howto_walls.txt

@@ -59,14 +59,15 @@ granular particles; all the other commands create smooth walls.
 "fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
 "fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
 "fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
+"fix wall/morse"_fix_wall.html - flat walls, with Morse potential
 "fix wall/region"_fix_wall_region.html - use region surface as wall
 "fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
 
-The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
-flat walls to move with a constant velocity, or oscillate in time.
-The "fix wall/region"_fix_wall_region.html command offers the most
-generality, since the region surface is treated as a wall, and the
-geometry of the region can be a simple primitive volume (e.g. a
+The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all
+allow the flat walls to move with a constant velocity, or oscillate in
+time.  The "fix wall/region"_fix_wall_region.html command offers the
+most generality, since the region surface is treated as a wall, and
+the geometry of the region can be a simple primitive volume (e.g. a
 sphere, or cube, or plane), or a complex volume made from the union
 and intersection of primitive volumes.  "Regions"_region.html can also
 specify a volume "interior" or "exterior" to the specified primitive

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="6 Aug 2019 version">
+<META NAME="docnumber" CONTENT="30 Oct 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-6 Aug 2019 version :c,h2
+30 Oct 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/PDF/pair_gayberne_extra.tex

@@ -48,8 +48,8 @@ $$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
 \mathbf{G}_2. $$
 
 Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
-(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by 
-the relative well depths (dimensionless energy scales 
+(\epsilon_{ia}^{-1/\mu}, \epsilon_{ib}^{-1/\mu}, \epsilon_{ic}^{-1/\mu})$
+be given by the relative well depths (dimensionless energy scales 
 inversely proportional to the well-depths of the respective 
 orthogonal configurations of the interacting molecules). The 
 $\chi$ orientation-dependent energy based on the user-specified 
@@ -62,8 +62,8 @@ $$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
 
 and
 
-$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
-\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
+$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 = \mathbf{B}_1 +
 \mathbf{B}_2. $$
 
 Here, we use the distance of closest approach approximation given by the
@@ -131,7 +131,7 @@ and
 
 $$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
 r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
-\times \mathbf{\iota} ). $$
+\times \mathbf{\iota} ) \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu}. $$
 
 For the derivative of the $\eta$ term, we were unable to find a matrix
 expression due to the determinant. Let $a_{mi}$ be the mth row of the

doc/src/Packages_details.txt

@@ -1746,11 +1746,12 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
-And a "dynamical_matrix" command to compute the dynamical matrix
-from finite differences.
+And a "dynamical_matrix"_dynamical_matrix.html as well as a
+"third_order"_third_order.html command to compute the dynamical matrix
+and third order tensor from finite differences.
 
 [Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
-and Charlie Sievers (UC Davis) for "dynamical_matrix"
+and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
 
 
 [Supporting info:]
@@ -1759,6 +1760,7 @@ src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
 "dynamical_matrix"_dynamical_matrix.html
+"third_order"_third_order.html
 examples/USER/phonon :ul
 
 :line

doc/src/Run_options.txt

@@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS.  By default
 Ng = 1 and Ns is not set.
 
 Depending on which flavor of MPI you are running, LAMMPS will look for
-one of these 3 environment variables
+one of these 4 environment variables
 
 SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MPT_LRANK (HPE MPI)
 MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
 OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
 

doc/src/Speed_kokkos.txt

@@ -46,14 +46,14 @@ software version 7.5 or later must be installed on your system. See
 the discussion for the "GPU package"_Speed_gpu.html for details of how
 to check and do this.
 
-NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library 
-is CUDA-aware. This is not always the case, especially when using 
-pre-compiled MPI libraries provided by a Linux distribution. This is not 
-a problem when using only a single GPU with a single MPI rank. When 
-running with multiple MPI ranks, you may see segmentation faults without 
-CUDA-aware MPI support. These can be avoided by adding the flags "-pk 
-kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by 
-using the command "package kokkos cuda/aware off"_package.html in the 
+NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
+is CUDA-aware. This is not always the case, especially when using
+pre-compiled MPI libraries provided by a Linux distribution. This is not
+a problem when using only a single GPU with a single MPI rank. When
+running with multiple MPI ranks, you may see segmentation faults without
+CUDA-aware MPI support. These can be avoided by adding the flags "-pk
+kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
+using the command "package kokkos cuda/aware off"_package.html in the
 input file.
 
 [Building LAMMPS with the KOKKOS package:]
@@ -110,10 +110,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
 back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
 the code thread-safe is removed.
 
-NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to 
-change the default "package kokkos"_package.html options. See its doc 
-page for details and default settings. Experimenting with its options 
-can provide a speed-up for specific calculations. For example: 
+NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
 
 mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
@@ -183,15 +183,15 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
 threads/task as Nt. The product of these two values should be N, i.e.
 256 or 264.
 
-NOTE: The default for the "package kokkos"_package.html command when 
-running on KNL is to use "half" neighbor lists and set the Newton flag 
-to "on" for both pairwise and bonded interactions. This will typically 
-be best for many-body potentials. For simpler pair-wise potentials, it 
-may be faster to use a "full" neighbor list with Newton flag to "off". 
-Use the "-pk kokkos" "command-line switch"_Run_options.html to change 
-the default "package kokkos"_package.html options. See its doc page for 
-details and default settings. Experimenting with its options can provide 
-a speed-up for specific calculations. For example: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on KNL is to use "half" neighbor lists and set the Newton flag
+to "on" for both pairwise and bonded interactions. This will typically
+be best for many-body potentials. For simpler pair-wise potentials, it
+may be faster to use a "full" neighbor list with Newton flag to "off".
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can provide
+a speed-up for specific calculations. For example:
 
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm :pre
@@ -206,19 +206,19 @@ supports.
 
 [Running on GPUs:]
 
-Use the "-k" "command-line switch"_Run_options.html to specify the 
-number of GPUs per node. Typically the -np setting of the mpirun command 
-should set the number of MPI tasks/node to be equal to the number of 
-physical GPUs on the node. You can assign multiple MPI tasks to the same 
-GPU with the KOKKOS package, but this is usually only faster if some 
-portions of the input script have not been ported to use Kokkos. In this 
-case, also packing/unpacking communication buffers on the host may give 
-speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS 
+Use the "-k" "command-line switch"_Run_options.html to specify the
+number of GPUs per node. Typically the -np setting of the mpirun command
+should set the number of MPI tasks/node to be equal to the number of
+physical GPUs on the node. You can assign multiple MPI tasks to the same
+GPU with the KOKKOS package, but this is usually only faster if some
+portions of the input script have not been ported to use Kokkos. In this
+case, also packing/unpacking communication buffers on the host may give
+speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
 is recommended in this scenario.
 
-Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be 
-avoided by using "-pk kokkos cuda/aware no"_package.html. As above for 
-multi-core CPUs (and no GPU), if N is the number of physical cores/node, 
+Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
+avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
+multi-core CPUs (and no GPU), if N is the number of physical cores/node,
 then the number of MPI tasks/node should not exceed N.
 
 -k on g Ng :pre
@@ -229,18 +229,18 @@ one or more nodes, each with two GPUs:
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
 mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
 
-NOTE: The default for the "package kokkos"_package.html command when 
-running on GPUs is to use "full" neighbor lists and set the Newton flag 
-to "off" for both pairwise and bonded interactions, along with threaded 
-communication. When running on Maxwell or Kepler GPUs, this will 
-typically be best. For Pascal GPUs, using "half" neighbor lists and 
-setting the Newton flag to "on" may be faster. For many pair styles, 
-setting the neighbor binsize equal to twice the CPU default value will 
-give speedup, which is the default when running on GPUs. Use the "-pk 
-kokkos" "command-line switch"_Run_options.html to change the default 
-"package kokkos"_package.html options. See its doc page for details and 
-default settings. Experimenting with its options can provide a speed-up 
-for specific calculations. For example: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on GPUs is to use "full" neighbor lists and set the Newton flag
+to "off" for both pairwise and bonded interactions, along with threaded
+communication. When running on Maxwell or Kepler GPUs, this will
+typically be best. For Pascal GPUs, using "half" neighbor lists and
+setting the Newton flag to "on" may be faster. For many pair styles,
+setting the neighbor binsize equal to twice the CPU default value will
+give speedup, which is the default when running on GPUs. Use the "-pk
+kokkos" "command-line switch"_Run_options.html to change the default
+"package kokkos"_package.html options. See its doc page for details and
+default settings. Experimenting with its options can provide a speed-up
+for specific calculations. For example:
 
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 

doc/src/Tools.txt

@@ -76,9 +76,10 @@ Post-processing tools :h3
 "pymol_asphere"_#pymol,
 "python"_#pythontools,
 "reax"_#reax_tool,
+"replica"_#replica,
 "smd"_#smd,
 "spin"_#spin,
-"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) 
 
 Miscellaneous tools :h3
 
@@ -86,6 +87,7 @@ Miscellaneous tools :h3
 "emacs"_#emacs,
 "i-pi"_#ipi,
 "kate"_#kate,
+"singularity"_#singularity_tool,
 "vim"_#vim :tb(c=5,ea=c,a=l)
 
 :line
@@ -485,6 +487,21 @@ README for more info on Pizza.py and how to use these scripts.
 
 :line
 
+replica tool :h4,link(replica)
+
+The tools/replica directory contains the reorder_remd_traj python script which
+can be used to reorder the replica trajectories (resulting from the use of the 
+temper command) according to temperature. This will produce discontinuous
+trajectories with all frames at the same temperature in each trajectory.
+Additional options can be used to calculate the canonical configurational
+log-weight for each frame at each temperature using the pymbar package. See
+the README.md file for further details. Try out the peptide example provided.
+
+This tool was written by (and is maintained by) Tanmoy Sanyal, 
+while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) 
+
+:line
+
 reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alone codes that can
@@ -515,17 +532,26 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 spin tool :h4,link(spin)
 
 The spin sub-directory contains a C file interpolate.c which can
-be compiled and used to perform a cubic polynomial interpolation of 
+be compiled and used to perform a cubic polynomial interpolation of
 the MEP following a GNEB calculation.
 
 See the README file in tools/spin/interpolate_gneb for more details.
 
 This tool was written by the SPIN package author, Julien
-Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei 
+Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
 Ivanov, at University of Iceland (ali5 at hi.is).
 
 :line
 
+singularity tool :h4,link(singularity_tool)
+
+The singularity sub-directory contains container definitions files
+that can be used to build container images for building and testing
+LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
+container software. Contributions for additional variants are welcome.
+
+:line
+
 vim tool :h4,link(vim)
 
 The files in the tools/vim directory are add-ons to the VIM editor
@@ -549,3 +575,4 @@ simulation.
 See the README file for details.
 
 These files were provided by Vikas Varshney (vv0210 at gmail.com)
+

doc/src/comm_modify.txt

@@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring
 processors and stored as properties of ghost atoms.
 
 NOTE: These options apply to the currently defined comm style.  When
-you specify a "comm_style"_comm_style.html command, all communication
-settings are restored to their default values, including those
+you specify a "comm_style"_comm_style.html or
+"read_restart"_read_restart.html command, all communication settings
+are restored to their default or stored values, including those
 previously reset by a comm_modify command.  Thus if your input script
-specifies a comm_style command, you should use the comm_modify command
-after it.
+specifies a comm_style or read_restart command, you should use the
+comm_modify command after it.
 
 The {mode} keyword determines whether a single or multiple cutoff
 distances are used to determine which atoms to communicate.

doc/src/commands_list.txt

@@ -108,6 +108,7 @@ Commands :h1
    thermo
    thermo_modify
    thermo_style
+   third_order
    timer
    timestep
    uncompute

doc/src/compute.txt

@@ -217,6 +217,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
+"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals
 "improper"_compute_improper.html - energy of each improper sub-style
 "improper/local"_compute_improper_local.html - angle of each improper
 "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
@@ -243,7 +244,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
 "pressure"_compute_pressure.html - total pressure and pressure tensor
 "pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
-"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field 
+"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
 "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
 "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
 "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
@@ -283,7 +284,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
 "stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
 "stress/tally"_compute_tally.html -
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle 
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
 "temp"_compute_temp.html - temperature of group of atoms
 "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
 "temp/body"_compute_temp_body.html - temperature of body particles

doc/src/compute_bond_local.txt

@@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 bond/local = style name of this compute command :l
 one or more values may be appended :l
-value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
+value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
   {dist} = bond distance
   {engpot} = bond potential energy
   {force} = bond force :pre
+  {fx},{fy},{fz} = components of bond force
   {engvib} = bond kinetic energy of vibration
   {engrot} = bond kinetic energy of rotation
   {engtrans} = bond kinetic energy of translation
@@ -38,6 +39,7 @@ keyword = {set} :l
 
 compute 1 all bond/local engpot
 compute 1 all bond/local dist engpot force :pre
+compute 1 all bond/local dist fx fy fz :pre
 compute 1 all angle/local dist v_distsq set dist d :pre
 
 [Description:]
@@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond.
 The value {force} is the magnitude of the force acting between the
 pair of atoms in the bond.
 
+The values {fx}, {fy}, and {fz} are the xyz components of
+{force} between the pair of atoms in the bond.
+
 The remaining properties are all computed for motion of the two atoms
 relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

doc/src/compute_chunk_spread_atom.txt

@@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
 [Description:]
 
 Define a calculation that "spreads" one or more per-chunk values to
-each atom in the chunk.  This can be useful for creating a "dump
-file"_dump.html where each atom lists info about the chunk it is in,
-e.g. for post-processing purposes.  It can also be used in "atom-style
-variables"_variable.html that need info about the chunk each atom is
-in.  Examples are given below.
+each atom in the chunk.  This can be useful in several scenarios:
+
+For creating a "dump file"_dump.html where each atom lists info about
+the chunk it is in, e.g. for post-processing purposes. :ulb,l
+
+To access chunk value in "atom-style variables"_variable.html that
+need info about the chunk each atom is in. :l
+
+To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
+average per-chunk values calculated by a per-chunk compute. :l,ule
+
+Examples are given below.
 
 In LAMMPS, chunks are collections of atoms defined by a "compute
 chunk/atom"_compute_chunk_atom.html command, which assigns each atom
@@ -148,6 +155,28 @@ thermo_style    custom step etotal press v_ave :pre
 
 :line
 
+Here is an example for using one set of chunks, defined for molecules,
+to compute the dipole moment vector for each chunk.  E.g. for water
+molecules. Then spreading those values to each atom in each chunk.
+Then defining a second set of chunks based on spatial bins.  And
+finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
+calculate an average dipole moment vector per spatial bin.
+
+compute       cmol all chunk/atom molecule
+compute       dipole all dipole/chunk cmol
+compute       spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
+compute       cspatial all chunk/atom bin/1d z lower 0.1 units reduced
+fix           ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
+
+Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
+per-atom values as input.  That is why the compute chunk/spread/atom
+command is used to assign per-chunk values to each atom in the chunk.
+If a molecule straddles bin boundaries, each of its atoms contributes
+in a weighted manner to the average dipole moment of the spatial bin
+it is in.
+
+:line
+
 [Output info:]
 
 This compute calculates a per-atom vector or array, which can be

doc/src/compute_coord_atom.txt

@@ -47,7 +47,7 @@ neighboring atoms, unless selected by type, type range, or group option,
 are included in the coordination number tally.
 
 The optional {group} keyword allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'. 
+contribute to the coordination number. Default setting is group 'all'.
 
 The {typeN} keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is

doc/src/compute_gyration_shape.txt

@@ -24,7 +24,7 @@ compute 1 molecule gyration/shape pe :pre
 
 Define a computation that calculates the eigenvalues of the gyration tensor of a
 group of atoms and three shape parameters. The computation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 The three computed shape parameters are the asphericity, b, the acylindricity, c,
 and the relative shape anisotropy, k:
@@ -84,3 +84,6 @@ package"_Build_package.html doc page for more info.
 :link(Theodorou)
 [(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
 
+:link(Mattice)
+[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. 
+

doc/src/compute_hma.txt

@@ -0,0 +1,184 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute hma command :h3
+
+[Syntax:]
+
+compute ID group-ID hma temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :l
+hma = style name of this compute command :l
+temp-ID = ID of fix that specifies the set temperature during canonical simulation :l
+keyword = {anharmonic} {u} {p Pharm} {cv} :l
+  {anharmonic} = compute will return anharmonic property values
+  {u} = compute will return potential energy
+  {p} = compute will return pressure.  the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
+  {cv} = compute will return the heat capacity :pre
+:ule
+
+[Examples:]
+
+compute 2 all hma 1 u
+compute 2 all hma 1 anharmonic u p 0.9
+compute 2 all hma 1 u cv :pre
+
+
+
+[Description:]
+
+Define a computation that calculates the properties of a solid (potential
+energy, pressure or heat capacity), using the harmonically-mapped averaging
+(HMA) method.
+This command yields much higher precision than the equivalent compute commands
+("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
+commands during a canonical simulation of an atomic crystal. Specifically,
+near melting HMA can yield averages of a given precision an order of magnitude
+faster than conventional methods, and this only improves as the temperatures is
+lowered.  This is particularly important for evaluating the free energy by
+thermodynamic integration, where the low-temperature contributions are the
+greatest source of statistical uncertainty.  Moreover, HMA has other
+advantages, including smaller potential-truncation effects, finite-size
+effects, smaller timestep inaccuracy, faster equilibration and shorter
+decorrelation time.
+
+HMA should not be used if atoms are expected to diffuse.  It is also
+restricted to simulations in the NVT ensemble.  While this compute may be
+used with any potential in LAMMPS, it will provide inaccurate results
+for potentials that do not go to 0 at the truncation distance;
+"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
+work fine, while "pair_lj"_pair_lj.html will perform poorly unless
+the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+this compute is restricted to those that implement the single_hessian method
+in Pair.  Implementing single_hessian in additional pair styles is simple.
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+buffalo.edu) if your desired pair style does not have this method.  This is
+the list of pair styles that currently implement pair_hessian:
+
+"lj_smooth_linear"_pair_lj_smooth_linear.html :l
+:ule
+
+In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
+averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
+by noise produced by the already-known harmonic behavior.
+A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
+
+\begin\{equation\}
+\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T  + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
+constant, \(T\) is the temperature, \(d\) is the
+dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the
+atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of
+pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
+
+The pressure is computed by the formula:
+
+\begin\{equation\}
+\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the
+difference between the harmonic and lattice pressure, \(P_\{vir\}\) is
+the virial pressure computed as the sum of pair, bond, angle, dihedral,
+improper, kspace (long-range), and fix contributions to the force on each
+atom, and \(k_B=1/k_B T\).  Although the method will work for any value of \(\Delta \hat P\)
+specified (use pressure "units"_units.html), the precision of the resultant
+pressure is sensitive to \(\Delta \hat P\); the precision tends to be
+best when \(\Delta \hat P\) is the actual the difference between the lattice
+pressure and harmonic pressure.
+
+\begin\{equation\}
+\left<C_V \right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left<
+U_\{HMA\}^2 \right> - \left<U_\{HMA\}\right>^2 \right) + \frac\{1\}\{4 T\}
+\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
+\end\{equation\}
+
+where \(\Phi\) is the Hessian matrix. The compute hma command
+computes the full expression for \(C_V\) except for the
+\(\left<U_\{HMA\}^2\right>^2\) in the variance term, which can be obtained by
+passing the {u} keyword; you must add this extra contribution to the \(C_V\)
+value reported by this compute.  The variance term can cause significant
+round-off error when computing \(C_V\).  To address this, the {anharmonic}
+keyword can be passed and/or the output format can be specified with more
+digits.
+
+thermo_modify format float '%22.15e' :pre
+
+The {anharmonic} keyword will instruct the compute to return anharmonic
+properties rather than the full properties, which include lattice, harmonic
+and anharmonic contributions.
+When using this keyword, the compute must be first active (it must be included
+via a "thermo_style custom"_thermo_style.html command) while the atoms are
+still at their lattice sites (before equilibration).
+
+The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or
+Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat
+("fix langevin"_fix_langevin.html)
+should be avoided as its extra forces interfere with the HMA implementation.
+
+
+
+NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
+The simulation should not be started before this command has been used in the input script.
+
+
+The following example illustrates the placement of this command in the input script:
+
+
+min_style cg
+minimize 1e-35 1e-15 50000 500000
+compute 1 all hma thermostatid u
+fix thermostatid all nvt temp 600.0 600.0 100.0 :pre
+
+
+
+NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
+
+
+NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
+
+An example input script that uses this compute is included in
+examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
+properties fluctuate less than the corresponding conventional properties.
+
+[Output info:]
+
+This compute calculates a global vector that includes the n properties
+requested as arguments to the command (the potential energy, pressure and/or heat
+capacity).  The elements of the vector can be accessed by indices 1-n by any
+command that uses global vector values as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output options.
+
+The vector values calculated by this compute are "extensive".  The
+scalar value will be in energy "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is enabled only
+if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+Usage restricted to canonical (NVT) ensemble simulation only.
+
+[Related commands:]
+
+"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
+
+"dynamical matrix"_dynamical_matrix.html provides a finite difference
+formulation of the hessian provided by Pair's single_hessian, which is used by
+this compute.
+
+[Default:] none
+
+:line
+
+:link(hma-Moustafa)
+[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation},
+"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303

doc/src/compute_orientorder_atom.txt

@@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
   {degrees} values = nlvalues, l1, l2,...
+  {wl} value = yes or no
+  {wl/hat} value = yes or no
   {components} value = ldegree  :pre
 
 :ule
@@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
 
 compute 1 all orientorder/atom
 compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
-compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
+compute 1 all orientorder/atom wl/hat yes
+compute 1 all orientorder/atom components 6 :pre
 
 [Description:]
 
@@ -48,7 +51,7 @@ neighbors of the central atom.
 The angles theta and phi are the standard spherical polar angles
 defining the direction of the bond vector {rij}.
 The second equation defines {Ql}, which is a
-rotationally invariant scalar quantity obtained by summing
+rotationally invariant non-negative amplitude obtained by summing
 over all the components of degree {l}.
 
 The optional keyword {cutoff} defines the distance cutoff
@@ -63,7 +66,7 @@ specified distance cutoff are used.
 
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
-parameters. This is followed by that number of integers giving the
+parameters. This is followed by that number of non-negative integers giving the
 degree of each order parameter. Because {Q}2 and all odd-degree order
 parameters are zero for atoms in cubic crystals (see
 "Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
@@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see
 = sqrt(7/3)/8 = 0.19094....  The numerical values of all order
 parameters up to {Q}12 for a range of commonly encountered
 high-symmetry structures are given in Table I of "Mickel et
-al."_#Mickel.
+al."_#Mickel, and these can be reproduced with this compute
+
+The optional keyword {wl} will output the third-order invariants {Wl}
+(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as
+for the {Ql} parameters. For the FCC crystal with {nnn} =12,
+{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...
+
+The optional keyword {wl/hat} will output the normalized third-order
+invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt)
+for the same degrees as for the {Ql} parameters. For the FCC crystal
+with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical
+values of {Wlhat} for a range of commonly encountered high-symmetry
+structures are given in Table I of "Steinhardt"_#Steinhardt, and these
+can be reproduced with this keyword.
 
 The optional keyword {components} will output the components of the
 normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
@@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2.
 
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
-{nnn} neighbors within the distance cutoff.
+{nnn} neighbors within the distance cutoff, unless {nnn} is NULL.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns,
 giving the {Ql} values for each atom, which are real numbers on the
 range 0 <= {Ql} <= 1.
 
+If the keyword {wl} is set to yes, then the {Wl} values for each
+atom will be added to the output array, which are real numbers.
+
+If the keyword {wl/hat} is set to yes, then the {Wl_hat}
+values for each atom will be added to the output array, which are real numbers.
+
 If the keyword {components} is set, then the real and imaginary parts
 of each component of (normalized) {Ybar_lm} will be added to the
 output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
@@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html
 [Default:]
 
 The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
-{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12,
+{wl} = no, {wl/hat} = no, and {components} off
 
 :line
 

doc/src/compute_pair_local.txt

@@ -64,6 +64,23 @@ which calculate the tangential force between two particles and return
 its components and magnitude acting on atom I for N = 1,2,3,4.  See
 individual pair styles for details.
 
+When using {pN} with pair style {hybrid}, the output will be the Nth
+quantity from the sub-style that computes the pairwise interaction
+(based on atom types).  If that sub-style does not define a {pN},
+the output will be 0.0.  The maximum allowed N is the maximum number
+of quantities provided by any sub-style.
+
+When using {pN} with pair style {hybrid/overlay} the quantities
+from all sub-styles that provide them are concatenated together
+into one long list. For example, if there are 3 sub-styles and
+2 of them have additional output (with 3 and 4 quantities,
+respectively), then 7 values ({p1} up to {p7}) are defined.
+The values {p1} to {p3} refer to quantities defined by the first
+of the two sub-styles.  Values {p4} to {p7} refer to quantities
+from the second of the two sub-styles.  If the referenced {pN}
+is not computed for the specific pairwise interaction (based on
+atom types), then the output will be 0.0.
+
 The value {dist} will be in distance "units"_units.html.  The value
 {eng} will be in energy "units"_units.html.  The values {force}, {fx},
 {fy}, and {fz} will be in force "units"_units.html.  The values {pN}
@@ -126,7 +143,7 @@ options.
 The output for {dist} will be in distance "units"_units.html.  The
 output for {eng} will be in energy "units"_units.html.  The output for
 {force}, {fx}, {fy}, and {fz} will be in force "units"_units.html.
-The outpur for {pN} will be in whatever units the pair style defines.
+The output for {pN} will be in whatever units the pair style defines.
 
 [Restrictions:] none
 

doc/src/compute_sna_atom.txt

@@ -196,7 +196,7 @@ for j1 in range(0,twojmax+1):
             if (j>=j1): print j1/2.,j2/2.,j/2. :pre
 
 NOTE: the {diagonal} keyword allowing other possible choices
-for the number of bispectrum components was removed in 2019, 
+for the number of bispectrum components was removed in 2019,
 since all potentials use the value of 3, corresponding to the
 above set of bispectrum components.
 

doc/src/compute_spin.txt

@@ -40,14 +40,14 @@ The simplest way to output the results of the compute spin calculation
 is to define some of the quantities as variables, and to use the thermo and
 thermo_style commands, for example:
 
-compute out_mag		all spin :pre
+compute out_mag         all spin :pre
 
-variable mag_z      	equal c_out_mag\[3\]
-variable mag_norm	equal c_out_mag\[4\]
-variable temp_mag      	equal c_out_mag\[6\] :pre
+variable mag_z          equal c_out_mag\[3\]
+variable mag_norm       equal c_out_mag\[4\]
+variable temp_mag       equal c_out_mag\[6\] :pre
 
-thermo          	10
-thermo_style    	custom step v_mag_z v_mag_norm v_temp_mag :pre
+thermo                  10
+thermo_style            custom step v_mag_z v_mag_norm v_temp_mag :pre
 
 This series of commands evaluates the total magnetization along z, the norm of
 the total magnetization, and the magnetic temperature. Three variables are

doc/src/computes.txt

@@ -47,6 +47,7 @@ Computes :h1
    compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
+   compute_hma
    compute_improper
    compute_improper_local
    compute_inertia_chunk

doc/src/create_bonds.txt

@@ -23,11 +23,14 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
     btype = bond type of new bond
     batom1,batom2 = atom IDs for two atoms in bond
   {single/angle} args = atype aatom1 aatom2 aatom3
-    atype = bond type of new angle
+    atype = angle type of new angle
     aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
   {single/dihedral} args = dtype datom1 datom2 datom3 datom4
-    dtype = bond type of new dihedral
-    datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre
+    dtype = dihedral type of new dihedral
+    datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
+  {single/improper} args = itype iatom1 iatom2 iatom3 iatom4
+    itype = improper type of new improper
+    iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {special} :l
   {special} value = {yes} or {no} :pre
@@ -38,51 +41,54 @@ keyword = {special} :l
 create_bonds many all all 1 1.0 1.2
 create_bonds many surf solvent 3 2.0 2.4
 create_bonds single/bond 1 1 2
-create_bonds single/angle 5 52 98 107 special no :pre
+create_bonds single/angle 5 52 98 107 special no
+create_bonds single/dihedral 2 4 19 27 101
+create_bonds single/improper 3 23 26 31 57 :pre
 
 [Description:]
 
 Create bonds between pairs of atoms that meet a specified distance
-criteria.  Or create a single bond, angle, or dihedral between 2, 3,
+criteria.  Or create a single bond, angle, dihedral or improper between 2, 3,
 or 4 specified atoms.
 
-The new bond (angle, dihedral) interactions will then be computed
-during a simulation by the bond (angle, dihedral) potential defined by
+The new bond (angle, dihedral, improper) interactions will then be computed
+during a simulation by the bond (angle, dihedral, improper) potential defined by
 the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
 "angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
 "dihedral_style"_dihedral_style.html,
-"dihedral_coeff"_dihedral_coeff.html commands.
+"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html,
+"improper_coeff"_improper_coeff.html commands.
 
 The {many} style is useful for adding bonds to a system, e.g. between
 nearest neighbors in a lattice of atoms, without having to enumerate
 all the bonds in the data file read by the "read_data"_read_data.html
 command.
 
-The {single} styles are useful for adding bonds, angles, dihedrals
+The {single} styles are useful for adding bonds, angles, dihedrals, impropers
 to a system incrementally, then continuing a simulation.
 
-Note that this command does not auto-create any angle or dihedral
+Note that this command does not auto-create any angle, dihedral or improper
 interactions when a bond is added.  Nor does it auto-create any bonds
-when an angle or dihedral is added.  Or auto-create any angles when a
-dihedral is added.  Thus the flexibility of this command is limited.
+when an angle, dihedral or improper is added.  Or auto-create any angles when a
+dihedral or improper is added.  Thus the flexibility of this command is limited.
 It can be used several times to create different types of bond at
 different distances.  But it cannot typically auto-create all the
-bonds or angles or dihedral that would normally be defined in a data
-file for a complex system of molecules.
+bonds or angles or dihedrals or impropers that would normally be defined in a
+data file for a complex system of molecules.
 
-NOTE: If the system has no bonds (angles, dihedrals) to begin with, or
-if more bonds per atom are being added than currently exist, then you
+NOTE: If the system has no bonds (angles, dihedrals, impropers) to begin with,
+or if more bonds per atom are being added than currently exist, then you
 must insure that the number of bond types and the maximum number of
 bonds per atom are set to large enough values.  And similarly for
-angles and dihedrals.  Otherwise an error may occur when too many
-bonds (angles, dihedrals) are added to an atom.  If the
+angles, dihedrals and impropers.  Otherwise an error may occur when too many
+bonds (angles, dihedrals, impropers) are added to an atom.  If the
 "read_data"_read_data.html command is used to define the system, these
 parameters can be set via the "bond types" and "extra bond per atom"
 fields in the header section of the data file.  If the
 "create_box"_create_box.html command is used to define the system,
 these 2 parameters can be set via its optional "bond/types" and
-"extra/bond/per/atom" arguments.  And similarly for angles and
-dihedrals.  See the doc pages for these 2 commands for details.
+"extra/bond/per/atom" arguments.  And similarly for angles, dihedrals and
+impropers.  See the doc pages for these 2 commands for details.
 
 :line
 
@@ -137,18 +143,25 @@ ordered linearly within the angle; the central atom is {aatom2}.
 {Atype} must be a value between 1 and the number of angle types
 defined.
 
-The {single/dihedral} style creates a single dihedral of type {btype}
-between two atoms with IDs {batom1} and {batom2}.  The ordering of the
-atoms is the same as in the {Dihedrals} section of a data file read by
-the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
-linearly within the dihedral.  {Dtype} must be a value between 1 and
+The {single/dihedral} style creates a single dihedral of type {dtype}
+between four atoms with IDs {datom1}, {datom2}, {datom3}, and {datom4}.  The
+ordering of the atoms is the same as in the {Dihedrals} section of a data file
+read by the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
+linearly within the dihedral.  {dtype} must be a value between 1 and
 the number of dihedral types defined.
 
+The {single/improper} style creates a single improper of type {itype}
+between four atoms with IDs {iatom1}, {iatom2}, {iatom3}, and {iatom4}.  The
+ordering of the atoms is the same as in the {Impropers} section of a data file
+read by the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
+linearly within the improper.  {itype} must be a value between 1 and
+the number of improper types defined.
+
 :line
 
 The keyword {special} controls whether an internal list of special
-bonds is created after one or more bonds, or a single angle or
-dihedral is added to the system.
+bonds is created after one or more bonds, or a single angle, dihedral or
+improper is added to the system.
 
 The default value is {yes}.  A value of {no} cannot be used
 with the {many} style.
@@ -161,16 +174,16 @@ see the "special_bonds"_special_bonds.html command for details.
 Thus if you are adding a few bonds or a large list of angles all at
 the same time, by using this command repeatedly, it is more efficient
 to only trigger the internal list to be created once, after the last
-bond (or angle, or dihedral) is added:
+bond (or angle, or dihedral, or improper) is added:
 
 create_bonds single/bond 5 52 98 special no
-create_bonds single/bond  5 73 74 special no
+create_bonds single/bond 5 73 74 special no
 ...
 create_bonds single/bond 5 17 386 special no
 create_bonds single/bond 4 112 183 special yes :pre
 
 Note that you MUST insure the internal list is re-built after the last
-bond (angle, dihedral) is added, before performing a simulation.
+bond (angle, dihedral, improper) is added, before performing a simulation.
 Otherwise pairwise interactions will not be properly excluded or
 weighted.  LAMMPS does NOT check that you have done this correctly.
 

doc/src/dihedral_harmonic.txt

@@ -8,6 +8,7 @@
 
 dihedral_style harmonic command :h3
 dihedral_style harmonic/intel command :h3
+dihedral_style harmonic/kk command :h3
 dihedral_style harmonic/omp command :h3
 
 [Syntax:]

doc/src/dump.txt

@@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
+{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l

doc/src/dump_modify.txt

@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {pbc} or {precision} or {region} or {refresh} or {scale} or {sfactor} or {sort} or {tfactor} or {thermo} or {thresh} or {time} or {units} or {unwrap} :l
   {append} arg = {yes} or {no}
   {at} arg = N
     N = index of frame written upon first dump
@@ -30,10 +30,10 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {fileper} arg = Np
     Np = write one file for every this many processors
   {first} arg = {yes} or {no}
+  {flush} arg = {yes} or {no}
   {format} args = {line} string, {int} string, {float} string, M string, or {none}
     string = C-style format string
     M = integer from 1 to N, where N = # of per-atom quantities being output
-  {flush} arg = {yes} or {no}
   {image} arg = {yes} or {no}
   {label} arg = string
     string = character string (e.g. BONDS) to use in header of dump local file
@@ -48,18 +48,20 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {refresh} arg = c_ID = compute ID that supports a refresh operation
   {scale} arg = {yes} or {no}
   {sfactor} arg = coordinate scaling factor (> 0.0)
-  {thermo} arg = {yes} or {no}
-  {tfactor} arg = time scaling factor (> 0.0)
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
      N = sort per-atom lines in ascending order by the Nth column
      -N = sort per-atom lines in descending order by the Nth column
+  {tfactor} arg = time scaling factor (> 0.0)
+  {thermo} arg = {yes} or {no}
+  {time} arg = {yes} or {no}
   {thresh} args = attribute operator value
     attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
     operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
     value = numeric value to compare to, or LAST
     these 3 args can be replaced by the word "none" to turn off thresholding
+  {units} arg = {yes} or {no}
   {unwrap} arg = {yes} or {no} :pre
 these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
 keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
@@ -620,6 +622,37 @@ threshold criterion is met.  Otherwise it is not met.
 
 :line
 
+The {time} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each frame will will
+contain two extra lines before the "ITEM: TIMESTEP" entry:
+
+ITEM: TIME
+\<elapsed time\> :pre
+
+This will output the current elapsed simulation time in current
+time units equivalent to the "thermo keyword"_thermo_style.html {time}.
+This is to simplify post-processing of trajectories using a variable time
+step, e.g. when using "fix dt/reset"_fix_dt_reset.html.
+The default setting is {no}.
+
+:line
+
+The {units} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each individual dump
+file will contain two extra lines at the very beginning with:
+
+ITEM: UNITS
+\<units style\> :pre
+
+This will output the current selected "units"_units.html style
+to the dump file and thus allows visualization and post-processing
+tools to determine the choice of units of the data in the dump file.
+The default setting is {no}.
+
+:line
+
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
 flags for each atom.  Unwrapped means that if the atom has passed through
@@ -924,6 +957,7 @@ scale = yes
 sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
 sort = id for dump styles {dcd}, {xtc}, and {xyz}
 thresh = none
+units = no
 unwrap = no :ul
 
 acolor = * red/green/blue/yellow/aqua/cyan

doc/src/dynamical_matrix.txt

@@ -30,14 +30,29 @@ dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
 
 [Description:]
 
-Calculate the dynamical matrix of the selected group.
+Calculate the dynamical matrix by finite difference of the selected group,
+
+:c,image(JPG/dynamical_matrix_dynmat.jpg)
+
+where D is the dynamical matrix and Phi is the force constant matrix defined by
+
+:c,image(JPG/dynamical_matrix_force_constant.jpg).
+
+The output for the dynamical matrix is printed three elements at a time. The
+three elements are the three beta elements for a respective i/alpha/j combination. 
+Each line is printed in order of j increasing first, alpha second, and i last.
+
+If the style eskm is selected, the dynamical matrix will be in units of inverse squared
+femtoseconds. These units will then conveniently leave frequencies in THz, where
+frequencies, represented as omega, can be calculated from
+
+:c, image(Eqs/dynamical_matrix_phonons.jpg)
 
 [Restrictions:]
 
-The command collects the entire dynamical matrix a single MPI rank,
-so the memory requirements can be very significant for large systems.
-
-This command assumes a periodic system.
+The command collects an array of nine times the number of atoms in a group
+on every single MPI rank, so the memory requirements can be very significant
+for large systems.
 
 This command is part of the USER-PHONON package.  It is only enabled if
 LAMMPS was built with that package.  See the "Build
@@ -47,6 +62,9 @@ package"_Build_package.html doc page for more info.
 
 "fix phonon"_fix_phonon.html
 
+"compute hma"_compute_hma.html uses an analytic formulation of the hessian
+provided by Pair's single_hessian.
+
 [Default:]
 
-The default settings are file = "dynmat.dyn", binary = no  
+The default settings are file = "dynmat.dyn", binary = no

doc/src/fix.txt

@@ -188,7 +188,7 @@ accelerated styles exist.
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
 "client/md"_fix_client_md.html - MD client for client/server simulations
 "cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
-"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
+"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
 "controller"_fix_controller.html - apply control loop feedback mechanism
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
@@ -221,7 +221,7 @@ accelerated styles exist.
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "hyper/global"_fix_hyper_global.html - global hyperdynamics
 "hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol 
+"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
 "indent"_fix_indent.html - impose force due to an indenter
 "ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
 "langevin"_fix_langevin.html - Langevin temperature control
@@ -244,7 +244,7 @@ accelerated styles exist.
 "mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
 "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
-"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
 "mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
@@ -327,7 +327,7 @@ accelerated styles exist.
 "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html - 
+"saed/vtk"_fix_saed_vtk.html -
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
 "shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
@@ -371,6 +371,7 @@ accelerated styles exist.
 "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
 "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
 "wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
+"wall/morse"_fix_wall.html - Morse potential wall
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall

doc/src/fix_bond_react.txt

@@ -186,20 +186,25 @@ reacting atoms.
 
 Some atoms in the pre-reacted template that are not reacting may have
 missing topology with respect to the simulation. For example, the
-pre-reacted template may contain an atom that would connect to the
-rest of a long polymer chain. These are referred to as edge atoms, and
-are also specified in the map file. When the pre-reaction template
-contains edge atoms, not all atoms, bonds, charges, etc. specified in
-the reaction templates will be updated. Specifically, topology that
-involves only atoms that are 'too near' to template edges will not be
-updated. The definition of 'too near the edge' depends on which
-interactions are defined in the simulation. If the simulation has
-defined dihedrals, atoms within two bonds of edge atoms are considered
-'too near the edge.' If the simulation defines angles, but not
-dihedrals, atoms within one bond of edge atoms are considered 'too
-near the edge.' If just bonds are defined, only edge atoms are
+pre-reacted template may contain an atom that, in the simulation, is
+currently connected to the rest of a long polymer chain. These are
+referred to as edge atoms, and are also specified in the map file. All
+pre-reaction template atoms should be linked to a bonding atom, via at
+least one path that does not involve edge atoms. When the pre-reaction
+template contains edge atoms, not all atoms, bonds, charges, etc.
+specified in the reaction templates will be updated. Specifically,
+topology that involves only atoms that are 'too near' to template
+edges will not be updated. The definition of 'too near the edge'
+depends on which interactions are defined in the simulation. If the
+simulation has defined dihedrals, atoms within two bonds of edge atoms
+are considered 'too near the edge.' If the simulation defines angles,
+but not dihedrals, atoms within one bond of edge atoms are considered
+'too near the edge.' If just bonds are defined, only edge atoms are
 considered 'too near the edge.'
 
+NOTE: Small molecules, i.e. ones that have all their atoms contained
+within the reaction templates, never have edge atoms.
+
 Note that some care must be taken when a building a molecule template
 for a given simulation. All atom types in the pre-reacted template
 must be the same as those of a potential reaction site in the
@@ -261,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword. The fourth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there is one type of constraint available, as discussed below.
+there are three types of constraints available, as discussed below.
 
 A sample map file is given below:
 
@@ -295,17 +300,47 @@ Equivalences :pre
 :line
 
 Any number of additional constraints may be specified in the
-Constraints section of the map file. Currently there is one type of
-additional constraint, of type 'distance', whose syntax is as follows:
+Constraints section of the map file. The constraint of type 'distance'
+has syntax as follows:
 
 distance {ID1} {ID2} {rmin} {rmax} :pre
 
 where 'distance' is the required keyword, {ID1} and {ID2} are
 pre-reaction atom IDs, and these two atoms must be separated by a
-distance between {rmin} and {rmax} for the reaction to occur. This
+distance between {rmin} and {rmax} for the reaction to occur.
+
+The constraint of type 'angle' has the following syntax:
+
+angle {ID1} {ID2} {ID3} {amin} {amax} :pre
+
+where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are
+pre-reaction atom IDs, and these three atoms must form an angle
+between {amin} and {amax} for the reaction to occur (where {ID2} is
+the central atom). Angles must be specified in degrees. This
 constraint can be used to enforce a certain orientation between
 reacting molecules.
 
+The constraint of type 'arrhenius' imposes an additional reaction
+probability according to the temperature-dependent Arrhenius equation:
+
+:c,image(Eqs/fix_bond_react.jpg)
+
+The Arrhenius constraint has the following syntax:
+
+arrhenius {A} {n} {E_a} {seed} :pre
+
+where 'arrhenius' is the required keyword, {A} is the pre-exponential
+factor, {n} is the exponent of the temperature dependence, {E_a} is
+the activation energy ("units"_units.html of energy), and {seed} is a
+random number seed. The temperature is defined as the instantaneous
+temperature averaged over all atoms in the reaction site, and is
+calculated in the same manner as for example
+"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no
+options for additional temperature averaging or velocity-biased
+temperature calculations. A uniform random number between 0 and 1 is
+generated using {seed}; if this number is less than the result of the
+Arrhenius equation above, the reaction is permitted to occur.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -381,7 +416,7 @@ will apply to all reactions.
 Computationally, each timestep this fix operates, it loops over
 neighbor lists (for bond-forming reactions) and computes distances
 between pairs of atoms in the list. It also communicates between
-neighboring processors to coordinate which bonds  are created and/or
+neighboring processors to coordinate which bonds are created and/or
 removed. All of these operations increase the cost of a timestep. Thus
 you should be cautious about invoking this fix too frequently.
 
@@ -392,10 +427,11 @@ local command.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart
-files"_restart.html, aside from internally-created per-atom
-properties. None of the "fix_modify"_fix_modify.html options are
-relevant to this fix.
+Cumulative reaction counts for each reaction are written to "binary
+restart files"_restart.html. These values are associated with the
+reaction name (react-ID). Additionally, internally-created per-atom
+properties are stored to allow for smooth restarts. None of the
+"fix_modify"_fix_modify.html options are relevant to this fix.
 
 This fix computes one statistic for each {react} argument that it
 stores in a global vector, of length 'number of react arguments', that
@@ -406,8 +442,8 @@ These is 1 quantity for each react argument:
 
 (1) cumulative # of reactions occurred :ul
 
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.  This fix is not invoked during "energy
+No parameter of this fix can be used with the {start/stop} keywords
+of the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
 When fix bond/react is 'unfixed,' all internally-created groups are
@@ -417,18 +453,20 @@ all other fixes that use any group created by fix bond/react.
 [Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if
-LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
+LAMMPS was built with that package.  See the
+"Build package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"fix bond/create"_fix_bond_create.html, "fix
-bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"fix bond/create"_fix_bond_create.html,
+"fix bond/break"_fix_bond_break.html,
+"fix bond/swap"_fix_bond_swap.html,
 "dump local"_dump.html, "special_bonds"_special_bonds.html
 
 [Default:]
 
-The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
+update_edges = none
 
 :line
 

doc/src/fix_controller.txt

@@ -31,7 +31,6 @@ cvar = name of control variable :l
 
 [Examples:]
 
-		
 fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
 fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
 fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre

doc/src/fix_langevin.txt

@@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
   {angmom} value = {no} or factor
     {no} = do not thermostat rotational degrees of freedom via the angular momentum
     factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
-  {gjf} value = {no} or {yes}
+  {gjf} value = {no} or {vfull} or {vhalf}
     {no} = use standard formulation
-    {yes} = use Gronbech-Jensen/Farago formulation
+    {vfull} = use Gronbech-Jensen/Farago formulation
+    {vhalf} = use 2GJ formulation
   {omega} value = {no} or {yes}
     {no} = do not thermostat rotational degrees of freedom via the angular velocity
     {yes} = do thermostat rotational degrees of freedom via the angular velocity
@@ -217,6 +218,10 @@ the particles.  As described below, this energy can then be printed
 out or added to the potential energy of the system to monitor energy
 conservation.
 
+NOTE: this accumulated energy does NOT include kinetic energy removed
+by the {zero} flag. LAMMPS will print a warning when both options are
+active.
+
 The keyword {zero} can be used to eliminate drift due to the
 thermostat. Because the random forces on different atoms are
 independent, they do not sum exactly to zero.  As a result, this fix
@@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
 described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
-distribution of atom positions.  It is implemented within LAMMPS, by
-changing how the random force is applied so that it is composed of
-the average of two random forces representing half-contributions from
-the previous and current time intervals.
+distribution of atom positions.
 
-In common with all methods based on Verlet integration, the
-discretized velocities generated by this method in conjunction with
-velocity-Verlet time integration are not exactly conjugate to the
-positions.  As a result the temperature (computed from the discretized
-velocities) will be systematically lower than the target temperature,
-by a small amount which grows with the timestep.  Nonetheless, the
-distribution of atom positions will still be consistent with the
+The current implementation provides the user with the option to output
+the velocity in one of two forms: {vfull} or {vhalf}, which replaces
+the outdated option {yes}. The {gjf} option {vfull} outputs the on-site
+velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
+is shown to be systematically lower than the target temperature by a small
+amount, which grows quadratically with the timestep.
+The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
+"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems,
+this velocity is shown to not have any statistical errors for any stable time step.
+An overview of statistically correct Boltzmann and Maxwell-Boltzmann
+sampling of true on-site and true half-step velocities is given in
+"Gronbech-Jensen"_#1Gronbech-Jensen.
+Regardless of the choice of output velocity, the sampling of the configurational
+distribution of atom positions is the same, and linearly consistent with the
 target temperature.
 
-As an example of using the {gjf} keyword, for molecules containing C-H
-bonds, configurational properties generated with dt = 2.5 fs and tdamp
-= 100 fs are indistinguishable from dt = 0.5 fs.  Because the velocity
-distribution systematically decreases with increasing timestep, the
-method should not be used to generate properties that depend on the
-velocity distribution, such as the velocity auto-correlation function
-(VACF). In this example, the velocity distribution at dt = 2.5fs
-generates an average temperature of 220 K, instead of 300 K.
-
 :line
 
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the
 
 This fix is not invoked during "energy minimization"_minimize.html.
 
-[Restrictions:] none
+[Restrictions:]
+
+For {gjf} do not choose damp=dt/2. {gjf} is not compatible
+with run_style respa. 
 
 [Related commands:]
 
@@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no.
 
 :link(Gronbech-Jensen)
 [(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
-(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
-185, 524 (2014)
+(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
+
+:link(2Gronbech-Jensen)
+[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
+
+:link(1Gronbech-Jensen)
+[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506

doc/src/fix_langevin_spin.txt

@@ -50,7 +50,7 @@ As an example:
 
 fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
 fix 2 all langevin/spin 300.0 0.01 21
-fix 3 all nve/spin lattice yes :pre
+fix 3 all nve/spin lattice moving :pre
 
 is correct, but defining a force/spin command after the langevin/spin command
 would give an error message.

doc/src/fix_neb_spin.txt

@@ -24,18 +24,18 @@ fix 1 active neb/spin 1.0
 [Description:]
 
 Add nudging forces to spins in the group for a multi-replica
-simulation run via the "neb/spin"_neb_spin.html command to perform a 
-geodesic nudged elastic band (GNEB) calculation for finding the 
+simulation run via the "neb/spin"_neb_spin.html command to perform a
+geodesic nudged elastic band (GNEB) calculation for finding the
 transition state.
-Hi-level explanations of GNEB are given with the 
-"neb/spin"_neb_spin.html command and on the 
-"Howto replica"_Howto_replica.html doc page.  
-The fix neb/spin command must be used with the "neb/spin" command and 
-defines how inter-replica nudging forces are computed.  A GNEB 
-calculation is divided in two stages. In the first stage n replicas 
-are relaxed toward a MEP until convergence.  In the second stage, the 
-climbing image scheme is enabled, so that the replica having the highest 
-energy relaxes toward the saddle point (i.e. the point of highest energy 
+Hi-level explanations of GNEB are given with the
+"neb/spin"_neb_spin.html command and on the
+"Howto replica"_Howto_replica.html doc page.
+The fix neb/spin command must be used with the "neb/spin" command and
+defines how inter-replica nudging forces are computed.  A GNEB
+calculation is divided in two stages. In the first stage n replicas
+are relaxed toward a MEP until convergence.  In the second stage, the
+climbing image scheme is enabled, so that the replica having the highest
+energy relaxes toward the saddle point (i.e. the point of highest energy
 along the MEP), and a second relaxation is performed.
 
 The nudging forces are calculated as explained in

doc/src/fix_nve_spin.txt

@@ -15,22 +15,26 @@ fix ID group-ID nve/spin keyword values :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 nve/spin = style name of this fix command :l
 keyword = {lattice} :l
-  {lattice} value = {no} or {yes} :pre
+  {lattice} value = {moving} or {frozen}
+    moving = integrate both spin and atomic degress of freedom
+    frozen = integrate spins on a fixed lattice :pre
 :ule
 
 [Examples:]
 
-fix 3 all nve/spin lattice yes
-fix 1 all nve/spin lattice no :pre
+fix 3 all nve/spin lattice moving
+fix 1 all nve/spin lattice frozen :pre
 
 [Description:]
 
 Perform a symplectic integration for the spin or spin-lattice system.
 
 The {lattice} keyword defines if the spins are integrated on a lattice
-of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
-
-By default (lattice = yes), a spin-lattice integration is performed.
+of fixed atoms (lattice = frozen), or if atoms are moving
+(lattice = moving).
+The first case corresponds to a spin dynamics calculation, and
+the second to a spin-lattice calculation.
+By default a spin-lattice integration is performed (lattice = moving).
 
 The {nve/spin} fix applies a Suzuki-Trotter decomposition to
 the equations of motion of the spin lattice system, following the scheme:
@@ -63,7 +67,9 @@ instead of "array" is also valid.
 
 "atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
 
-[Default:] none
+[Default:] 
+
+The option default is lattice = moving.
 
 :line
 

doc/src/fix_precession_spin.txt

@@ -21,7 +21,7 @@ style = {zeeman} or {anisotropy} or {cubic} :l
   {anisotropy} args = K x y z
     K = intensity of the magnetic anisotropy (in eV)
     x y z = vector direction of the anisotropy :pre
-  {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z 
+  {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
     K1 and K2c = intensity of the magnetic anisotropy (in eV)
     n1x to n3z = three direction vectors of the cubic anisotropy :pre
 :ule
@@ -55,24 +55,24 @@ with n defining the direction of the anisotropy, and K (in eV) its intensity.
 If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
 
 Style {cubic} is used to simulate a cubic anisotropy, with three
-possible easy axis for the magnetic spins in the defined group: 
+possible easy axis for the magnetic spins in the defined group:
 
 :c,image(Eqs/fix_spin_cubic.jpg)
 
-with K1 and K2c (in eV) the intensity coefficients and 
+with K1 and K2c (in eV) the intensity coefficients and
 n1, n2 and n3 defining the three anisotropic directions
-defined by the command (from n1x to n3z). 
-For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an 
+defined by the command (from n1x to n3z).
+For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
 iron type anisotropy (easy axis along the (001)-type cube
 edges), and K1 > 0 defines a nickel type anisotropy (easy axis
-along the (111)-type cube diagonals). 
+along the (111)-type cube diagonals).
 K2^c > 0 also defines easy axis along the (111)-type cube
 diagonals.
 See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
 anisotropies.
 
 In all cases, the choice of (x y z) only imposes the vector
-directions for the forces. Only the direction of the vector is 
+directions for the forces. Only the direction of the vector is
 important; it's length is ignored (the entered vectors are
 normalized).