Loading .github/CODEOWNERS 0 → 100644 +21 −0 Original line number Diff line number Diff line # This file contains file patterns that triggers automatic # code review requests from users that are owners of these files # Order matters, the last match has the highest precedence # library folders lib/colvars/* @giacomofiorin lib/compress/* @akohlmey lib/kokkos/* @stanmoore1 lib/molfile/* @akohlmey lib/qmmm/* @akohlmey lib/vtk/* @rbberger # packages src/KOKKOS @stanmoore1 src/USER-CGSDK @akohlmey src/USER-COLVARS @giacomofiorin src/USER-OMP @akohlmey src/USER-QMMM @akohlmey # tools tools/msi2lmp/* @akohlmey doc/src/Manual.txt +1 −1 Original line number Diff line number Diff line Loading @@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the "LAMMPS project on GitHub."_https://github.com/lammps/lammps The lammps.org domain, currently hosting "public continuous integration testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux RPM and Windows installer packages"_http://rpm.lammps.org is located RPM and Windows installer packages"_http://packages.lammps.org is located at Temple University and managed by Richard Berger, richard.berger at temple.edu. Loading doc/src/Section_errors.txt +4 −4 Original line number Diff line number Diff line Loading @@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd {New bond exceeded special list size in fix bond/create} :dt See the "special_bonds extra" command (or the "read_data extra/special/per/atom" command) See the "read_data extra/special/per/atom" command (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd Loading Loading @@ -9666,8 +9666,8 @@ you are running. :dd {Special list size exceeded in fix bond/create} :dt See the special_bonds extra command (or the read_data extra/special/per/atom command) See the "read_data extra/special/per/atom" command (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd Loading doc/src/Section_start.txt +33 −21 Original line number Diff line number Diff line Loading @@ -662,27 +662,25 @@ your own build system. Due to differences between the Windows OS and Windows system libraries to Unix-like environments like Linux or MacOS, when compiling for Windows a few adjustments may be needed: Do not set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable) Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable) Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable) Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul Since none of the current LAMMPS core developers has significant experience building executables on Windows, we are happy to distribute contributed instructions and modifications, but we cannot provide support for those. Since none of the current LAMMPS core developers has significant experience building executables on Windows, we are happy to distribute contributed instructions and modifications to improve the situation, but we cannot provide support for those. With the so-called "Anniversary Update" to Windows 10, there is a Ubuntu Linux subsystem available for Windows, that can be installed and then used to compile/install LAMMPS as if you are running on a Ubuntu Linux system instead of Windows. As an alternative, you can download "daily builds" (and some older versions) of the installer packages from "rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html. These executables are built with most optional packages and the download includes documentation, potential files, some tools and many examples, but no source code. As an alternative, you can download pre-compiled installer packages from "packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html. These executables are built with most optional packages included and the download includes documentation, potential files, some tools and many examples, but no source code. :line Loading Loading @@ -1095,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages. :line On a Windows box, you can skip making LAMMPS and simply download an installer package from "here"_http://rpm.lammps.org/windows.html installer package from "here"_http://packages.lammps.org/windows.html For running the non-MPI executable, follow these steps: Loading @@ -1107,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj] with the name of your LAMMPS input script. :l The serial executable includes support for multi-threading parallelization from the styles in the USER-OMP packages. To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp" :ule For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps: For the MPI version, which allows you to run LAMMPS under Windows with the more general message passing parallel library (LAMMPS has been designed from ground up to use MPI efficiently), follow these steps: Download and install "MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads for Windows. :ulb,l Download and install a compatible MPI library binary package: for 32-bit Windows "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi and for 64-bit Windows "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ulb,l The LAMMPS Windows installer packages will automatically adjust your path for the default location of this MPI package. After the installation of the MPICH software, it needs to be integrated into the system. of the MPICH2 software, it needs to be integrated into the system. For this you need to start a Command Prompt in {Administrator Mode} (right click on the icon and select it). Change into the MPICH2 installation directory, then into the subdirectory [bin] and execute Loading @@ -1137,7 +1144,7 @@ or mpiexec -np 4 lmp_mpi -in in.lj :pre replacing in.lj with the name of your LAMMPS input script. For the latter replacing [in.lj] with the name of your LAMMPS input script. For the latter case, you may be prompted to enter your password. :l In this mode, output may not immediately show up on the screen, so if Loading @@ -1149,6 +1156,11 @@ something like: lmp_mpi -in in.lj :pre And the parallel executable also includes OpenMP multi-threading, which can be combined with MPI using something like: mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre :ule :line Loading doc/src/fix_bond_create.txt +2 −3 Original line number Diff line number Diff line Loading @@ -150,10 +150,9 @@ atoms. Note that adding a single bond always adds a new 1st neighbor but may also induce *many* new 2nd and 3rd neighbors, depending on the molecular topology of your system. The "extra special per atom" parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3 size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 ways to do this. See the "read_data"_read_data.html or "create_box"_create_box.html or "special_bonds extra" commands for details. "create_box"_create_box.html commands for details. NOTE: Even if you do not use the {atype}, {dtype}, or {itype} keywords, the list of topological neighbors is updated for atoms Loading Loading
.github/CODEOWNERS 0 → 100644 +21 −0 Original line number Diff line number Diff line # This file contains file patterns that triggers automatic # code review requests from users that are owners of these files # Order matters, the last match has the highest precedence # library folders lib/colvars/* @giacomofiorin lib/compress/* @akohlmey lib/kokkos/* @stanmoore1 lib/molfile/* @akohlmey lib/qmmm/* @akohlmey lib/vtk/* @rbberger # packages src/KOKKOS @stanmoore1 src/USER-CGSDK @akohlmey src/USER-COLVARS @giacomofiorin src/USER-OMP @akohlmey src/USER-QMMM @akohlmey # tools tools/msi2lmp/* @akohlmey
doc/src/Manual.txt +1 −1 Original line number Diff line number Diff line Loading @@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the "LAMMPS project on GitHub."_https://github.com/lammps/lammps The lammps.org domain, currently hosting "public continuous integration testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux RPM and Windows installer packages"_http://rpm.lammps.org is located RPM and Windows installer packages"_http://packages.lammps.org is located at Temple University and managed by Richard Berger, richard.berger at temple.edu. Loading
doc/src/Section_errors.txt +4 −4 Original line number Diff line number Diff line Loading @@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd {New bond exceeded special list size in fix bond/create} :dt See the "special_bonds extra" command (or the "read_data extra/special/per/atom" command) See the "read_data extra/special/per/atom" command (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd Loading Loading @@ -9666,8 +9666,8 @@ you are running. :dd {Special list size exceeded in fix bond/create} :dt See the special_bonds extra command (or the read_data extra/special/per/atom command) See the "read_data extra/special/per/atom" command (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd Loading
doc/src/Section_start.txt +33 −21 Original line number Diff line number Diff line Loading @@ -662,27 +662,25 @@ your own build system. Due to differences between the Windows OS and Windows system libraries to Unix-like environments like Linux or MacOS, when compiling for Windows a few adjustments may be needed: Do not set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable) Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable) Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable) Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul Since none of the current LAMMPS core developers has significant experience building executables on Windows, we are happy to distribute contributed instructions and modifications, but we cannot provide support for those. Since none of the current LAMMPS core developers has significant experience building executables on Windows, we are happy to distribute contributed instructions and modifications to improve the situation, but we cannot provide support for those. With the so-called "Anniversary Update" to Windows 10, there is a Ubuntu Linux subsystem available for Windows, that can be installed and then used to compile/install LAMMPS as if you are running on a Ubuntu Linux system instead of Windows. As an alternative, you can download "daily builds" (and some older versions) of the installer packages from "rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html. These executables are built with most optional packages and the download includes documentation, potential files, some tools and many examples, but no source code. As an alternative, you can download pre-compiled installer packages from "packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html. These executables are built with most optional packages included and the download includes documentation, potential files, some tools and many examples, but no source code. :line Loading Loading @@ -1095,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages. :line On a Windows box, you can skip making LAMMPS and simply download an installer package from "here"_http://rpm.lammps.org/windows.html installer package from "here"_http://packages.lammps.org/windows.html For running the non-MPI executable, follow these steps: Loading @@ -1107,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj] with the name of your LAMMPS input script. :l The serial executable includes support for multi-threading parallelization from the styles in the USER-OMP packages. To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp" :ule For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps: For the MPI version, which allows you to run LAMMPS under Windows with the more general message passing parallel library (LAMMPS has been designed from ground up to use MPI efficiently), follow these steps: Download and install "MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads for Windows. :ulb,l Download and install a compatible MPI library binary package: for 32-bit Windows "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi and for 64-bit Windows "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ulb,l The LAMMPS Windows installer packages will automatically adjust your path for the default location of this MPI package. After the installation of the MPICH software, it needs to be integrated into the system. of the MPICH2 software, it needs to be integrated into the system. For this you need to start a Command Prompt in {Administrator Mode} (right click on the icon and select it). Change into the MPICH2 installation directory, then into the subdirectory [bin] and execute Loading @@ -1137,7 +1144,7 @@ or mpiexec -np 4 lmp_mpi -in in.lj :pre replacing in.lj with the name of your LAMMPS input script. For the latter replacing [in.lj] with the name of your LAMMPS input script. For the latter case, you may be prompted to enter your password. :l In this mode, output may not immediately show up on the screen, so if Loading @@ -1149,6 +1156,11 @@ something like: lmp_mpi -in in.lj :pre And the parallel executable also includes OpenMP multi-threading, which can be combined with MPI using something like: mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre :ule :line Loading
doc/src/fix_bond_create.txt +2 −3 Original line number Diff line number Diff line Loading @@ -150,10 +150,9 @@ atoms. Note that adding a single bond always adds a new 1st neighbor but may also induce *many* new 2nd and 3rd neighbors, depending on the molecular topology of your system. The "extra special per atom" parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3 size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 ways to do this. See the "read_data"_read_data.html or "create_box"_create_box.html or "special_bonds extra" commands for details. "create_box"_create_box.html commands for details. NOTE: Even if you do not use the {atype}, {dtype}, or {itype} keywords, the list of topological neighbors is updated for atoms Loading
