diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8f7ac9a6e7..7f212ac48e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -106,6 +106,8 @@ if(BUILD_LIB) endif() endif() +option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF) + if(NOT BUILD_EXE AND NOT BUILD_LIB) message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE") endif() @@ -222,6 +224,9 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI find_package(LAPACK) find_package(BLAS) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) + if(CMAKE_GENERATOR STREQUAL "Ninja") + status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support") + endif() enable_language(Fortran) file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) @@ -517,6 +522,19 @@ if(BUILD_EXE) set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1) +endif() + +if(BUILD_TOOLS) + add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp) + install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR}) + + # ninja-build currently does not support fortran. thus we skip building this tool + if(NOT CMAKE_GENERATOR STREQUAL "Ninja") + message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support") + enable_language(Fortran) + add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f) + target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) + endif() enable_language(C) get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE) @@ -525,7 +543,6 @@ if(BUILD_EXE) target_link_libraries(msi2lmp m) install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) - endif() include(Documentation) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 21ebd0f8e0..8815f73881 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -13,6 +13,9 @@ if(PKG_KIM) endif() option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT}) if(DOWNLOAD_KIM) + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool") + endif() message(STATUS "KIM-API download requested - we will build our own") enable_language(C) enable_language(Fortran) diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake index a709561562..de7116780b 100644 --- a/cmake/Modules/Packages/LATTE.cmake +++ b/cmake/Modules/Packages/LATTE.cmake @@ -11,6 +11,9 @@ if(PKG_LATTE) if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") endif() + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool") + endif() message(STATUS "LATTE download requested - we will build our own") include(ExternalProject) ExternalProject_Add(latte_build diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake index e8744bc192..b442580583 100644 --- a/cmake/Modules/Packages/MSCG.cmake +++ b/cmake/Modules/Packages/MSCG.cmake @@ -11,6 +11,9 @@ if(PKG_MSCG) if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7") endif() + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool") + endif() include(ExternalProject) if(NOT LAPACK_FOUND) set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a") diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 422527dd06..500558fc72 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -17,6 +17,9 @@ if(PKG_USER-PLUMED) option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT}) if(DOWNLOAD_PLUMED) + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool") + endif() if(BUILD_MPI) set(PLUMED_CONFIG_MPI "--enable-mpi") set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER}) diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/USER-SCAFACOS.cmake index adb002081f..475f2585c8 100644 --- a/cmake/Modules/Packages/USER-SCAFACOS.cmake +++ b/cmake/Modules/Packages/USER-SCAFACOS.cmake @@ -13,6 +13,9 @@ if(PKG_USER-SCAFACOS) endif() option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) if(DOWNLOAD_SCAFACOS) + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool") + endif() message(STATUS "ScaFaCoS download requested - we will build our own") include(ExternalProject) ExternalProject_Add(scafacos_build diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake index df4551b6e7..5ce974a7ae 100644 --- a/cmake/Modules/Packages/VORONOI.cmake +++ b/cmake/Modules/Packages/VORONOI.cmake @@ -7,6 +7,9 @@ if(PKG_VORONOI) endif() option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT}) if(DOWNLOAD_VORO) + if(CMAKE_GENERATOR STREQUAL "Ninja") + message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool") + endif() message(STATUS "Voro++ download requested - we will build our own") include(ExternalProject) diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 265c16e3d4..a16ba995a8 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -32,10 +32,18 @@ cmake \[options ...\] ../cmake # configuration with (command-line) cmake make # compilation :pre The cmake command will detect available features, enable selected -packages and options, and will generate the build environment. The make -command will then compile and link LAMMPS, producing (by default) an -executable called "lmp" and a library called "liblammps.a" in the -"build" folder. +packages and options, and will generate the build environment. By default +this build environment will be created for "Unix Makefiles" on most +platforms and particularly on Linux. However, alternate build tools +(e.g. Ninja) and support files for Integrated Development Environments +(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is +selected via the "-G" command line flag. For the rest of the documentation +we will assume that the build environment is generated for makefiles +and thus the make command will be used to compile and link LAMMPS as +indicated above, producing (by default) an executable called "lmp" and +a library called "liblammps.a" in the "build" folder. When generating +a build environment for the "Ninja" build tool, the build command would +be "ninja" instead of "make". If your machine has multiple CPU cores (most do these days), using a command like "make -jN" (with N being the number of available local diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index 6401be54e9..125eba1302 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -88,6 +88,8 @@ potentials only include the pair potential portion of the EAM interaction when used by this compute, not the embedding term. Also bonded or Kspace interactions do not contribute to this compute. +The computes in this package are not compatible with dynamic groups. + [Related commands:] {compute group/group}_compute_group_group.html, {compute diff --git a/examples/USER/misc/kolmogorov_crespi_full/CH.rebo b/examples/USER/misc/kolmogorov_crespi_full/CH.rebo new file mode 120000 index 0000000000..c5a6a40100 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_full/CH.rebo @@ -0,0 +1 @@ +../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene index 63ac92cb05..c3e59337de 100644 --- a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene +++ b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene @@ -18,7 +18,7 @@ group adsorbate type 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical +pair_coeff * * rebo CH.rebo NULL C # chemical pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.1 similarity index 59% rename from examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 rename to examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.1 index a06b3effdd..c74f9956a2 100644 --- a/examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 +++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (8 Mar 2018) +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors + special bonds CPU = 0.000353813 secs + read_data CPU = 0.0043292 secs mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups @@ -32,8 +35,8 @@ group adsorbate type 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 +pair_coeff * * rebo CH.rebo NULL C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings @@ -92,32 +95,32 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 - 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 - 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 - 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 - 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 - 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 - 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 - 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 - 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 - 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 - 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 -Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms + 0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 + 100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015 + 200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578 + 300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907 + 400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497 + 500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 + 600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092 + 700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565 + 800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926 + 900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640 + 1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 +Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms -Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 155.99 | 155.99 | 155.99 | 0.0 | 99.90 -Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00 +Pair | 103.59 | 103.59 | 103.59 | 0.0 | 99.87 +Bond | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05 -Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00 -Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02 -Other | | 0.02838 | | | 0.02 +Comm | 0.082476 | 0.082476 | 0.082476 | 0.0 | 0.08 +Output | 0.0010884 | 0.0010884 | 0.0010884 | 0.0 | 0.00 +Modify | 0.032938 | 0.032938 | 0.032938 | 0.0 | 0.03 +Other | | 0.01749 | | | 0.02 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -133,4 +136,4 @@ Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:02:36 +Total wall time: 0:01:43 diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.4 similarity index 59% rename from examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 rename to examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.4 index 58322f9ce0..b90ee7ee2e 100644 --- a/examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 +++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (8 Mar 2018) +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors + special bonds CPU = 0.000187874 secs + read_data CPU = 0.00234103 secs mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups @@ -32,8 +35,8 @@ group adsorbate type 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 +pair_coeff * * rebo CH.rebo NULL C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings @@ -92,32 +95,32 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 - 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 - 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 - 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 - 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 - 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 - 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 - 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 - 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 - 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 - 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 -Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms + 0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 + 100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015 + 200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578 + 300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907 + 400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497 + 500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 + 600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092 + 700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565 + 800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926 + 900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640 + 1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 +Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms -Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s +94.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36 -Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00 +Pair | 30.833 | 31.356 | 32.18 | 9.1 | 92.95 +Bond | 0.00026059 | 0.00029182 | 0.00031185 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54 -Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00 -Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03 -Other | | 0.02864 | | | 0.07 +Comm | 1.443 | 2.2722 | 2.8091 | 34.3 | 6.74 +Output | 0.00068855 | 0.00095087 | 0.0017185 | 0.0 | 0.00 +Modify | 0.010187 | 0.011709 | 0.015284 | 1.9 | 0.03 +Other | | 0.09241 | | | 0.27 Nlocal: 340 ave 344 max 334 min Histogram: 1 0 0 0 0 0 1 0 1 1 @@ -133,4 +136,4 @@ Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:42 +Total wall time: 0:00:33 diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 6f1dfc9982..31c54aee76 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -547,6 +547,18 @@ FixLbFluid::~FixLbFluid() } else { delete [] NodeArea; } + MPI_Type_free(&passxf); + MPI_Type_free(&passyf); + MPI_Type_free(&passzf); + MPI_Type_free(&passxu); + MPI_Type_free(&passyu); + MPI_Type_free(&passzu); + MPI_Type_free(&passxrho); + MPI_Type_free(&passyrho); + MPI_Type_free(&passzrho); + MPI_Type_free(&passxtemp); + MPI_Type_free(&passytemp); + MPI_Type_free(&passztemp); } int FixLbFluid::setmask() diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 69f0db0b23..3339e0555b 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -41,6 +41,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : vector_flag = 0; peratom_flag = 1; timeflag = 1; + dynamic_group_allow = 0; comm_reverse = size_peratom_cols = 3; extscalar = 1; diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 0f7979d7ed..2a5f724953 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -38,6 +38,7 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) : vector_flag = 1; timeflag = 1; + dynamic_group_allow = 0; comm_reverse = 7; extvector = 1; diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index bb0ff89b9e..5fabd4a77b 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -39,6 +39,7 @@ ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : vector_flag = 1; size_vector = 4; timeflag = 1; + dynamic_group_allow = 0; extvector = 1; peflag = 1; // we need Pair::ev_tally() to be run diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index de678f59b8..8e6703bde1 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -40,6 +40,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : vector_flag = 0; peratom_flag = 1; timeflag = 1; + dynamic_group_allow = 0; comm_reverse = size_peratom_cols = 2; extscalar = 1; diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index d769b61d9a..07d685a9c2 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -41,6 +41,7 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : vector_flag = 0; peratom_flag = 1; timeflag = 1; + dynamic_group_allow = 0; comm_reverse = size_peratom_cols = 6; extscalar = 0; diff --git a/src/lmptype.h b/src/lmptype.h index 20d29880ed..12fa6cc4fb 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -211,7 +211,7 @@ typedef int bigint; #elif defined(__INTEL_COMPILER) # define _noopt #elif defined(__GNUC__) -# if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4)) +# if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 9)) # define _noopt __attribute__((optimize("O0","no-var-tracking-assignments"))) # else # define _noopt __attribute__((optimize("O0"))) diff --git a/src/thermo.cpp b/src/thermo.cpp index 3e777edf82..f4ab7b0779 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -113,9 +113,11 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (strcmp(style,"one") == 0) { line = new char[256+6*64]; + memset(line,0,256+6*64); strcpy(line,ONE); } else if (strcmp(style,"multi") == 0) { line = new char[256+12*64]; + memset(line,0,256+12*64); strcpy(line,MULTI); lineflag = MULTILINE;