diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake index ec7a739785..95bb707e86 100644 --- a/cmake/Modules/LAMMPSInterfacePlugin.cmake +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -6,6 +6,9 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) "Please remove CMakeCache.txt and CMakeFiles first.") endif() +set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty" + CACHE STRING "URL for thirdparty package downloads") + # global LAMMPS/plugin build settings set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder") if(NOT LAMMPS_SOURCE_DIR) @@ -78,6 +81,13 @@ function(get_newest_file path variable) set(${variable} ${_bestfile} PARENT_SCOPE) endfunction() +# get LAMMPS version date +function(get_lammps_version version_header variable) + file(STRINGS ${version_header} line REGEX LAMMPS_VERSION) + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}") + set(${variable} "${date}" PARENT_SCOPE) +endfunction() + ################################################################################# # LAMMPS C++ interface. We only need the header related parts except on windows. add_library(lammps INTERFACE) @@ -89,6 +99,7 @@ endif() ################################################################################ # MPI configuration if(NOT CMAKE_CROSSCOMPILING) + set(MPI_CXX_SKIP_MPICXX TRUE) find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) else() diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index cf3d19c720..7f23a6f777 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -47,8 +47,8 @@ if(DOWNLOAD_KOKKOS) list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}") include(ExternalProject) - set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball") - set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" CACHE STRING "MD5 checksum of KOKKOS tarball") + set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball") + set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball") mark_as_advanced(KOKKOS_URL) mark_as_advanced(KOKKOS_MD5) ExternalProject_Add(kokkos_build @@ -72,7 +72,7 @@ if(DOWNLOAD_KOKKOS) add_dependencies(LAMMPS::KOKKOSCORE kokkos_build) add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build) elseif(EXTERNAL_KOKKOS) - find_package(Kokkos 3.6.00 REQUIRED CONFIG) + find_package(Kokkos 3.6.01 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) target_link_libraries(lmp PRIVATE Kokkos::kokkos) else() diff --git a/cmake/Modules/Packages/MDI.cmake b/cmake/Modules/Packages/MDI.cmake index 88859f0285..1a14d5273a 100644 --- a/cmake/Modules/Packages/MDI.cmake +++ b/cmake/Modules/Packages/MDI.cmake @@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al if(DOWNLOAD_MDI) message(STATUS "MDI download requested - we will build our own") - set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball") - set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball") + set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball") + set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball") mark_as_advanced(MDI_URL) mark_as_advanced(MDI_MD5) enable_language(C) @@ -44,7 +44,7 @@ if(DOWNLOAD_MDI) ExternalProject_Add(mdi_build URL ${MDI_URL} URL_MD5 ${MDI_MD5} - CMAKE_ARGS ${CMAKE_REQUEST_PIC} + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} @@ -54,6 +54,7 @@ if(DOWNLOAD_MDI) -Dlanguage=C -Dlibtype=STATIC -Dmpi=${MDI_USE_MPI} + -Dplugins=ON -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS} UPDATE_COMMAND "" INSTALL_COMMAND "" diff --git a/cmake/Modules/Packages/ML-HDNNP.cmake b/cmake/Modules/Packages/ML-HDNNP.cmake index f52d7ca6f3..f71d08f3ab 100644 --- a/cmake/Modules/Packages/ML-HDNNP.cmake +++ b/cmake/Modules/Packages/ML-HDNNP.cmake @@ -44,7 +44,9 @@ if(DOWNLOAD_N2P2) else() # get path to MPI include directory get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES) - set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}") + foreach (_INCL ${N2P2_MPI_INCLUDE}) + set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -I${_INCL}") + endforeach() endif() # prefer GNU make, if available. N2P2 lib seems to need it. @@ -75,7 +77,7 @@ if(DOWNLOAD_N2P2) UPDATE_COMMAND "" CONFIGURE_COMMAND "" PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp - BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS} + BUILD_COMMAND ${N2P2_MAKE} -C /src -f makefile libnnpif ${N2P2_BUILD_OPTIONS} BUILD_ALWAYS YES INSTALL_COMMAND "" BUILD_IN_SOURCE 1 diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 61c5e83eda..bb0c3e9c2a 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -138,6 +138,8 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`smd/vol ` * :doc:`snap ` * :doc:`sna/atom ` + * :doc:`sna/grid ` + * :doc:`sna/grid/local ` * :doc:`snad/atom ` * :doc:`snav/atom ` * :doc:`sph/e/atom ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 7dc3f324b4..e7a9f71b79 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -103,7 +103,7 @@ OPT. * :doc:`lb/viscous ` * :doc:`lineforce ` * :doc:`manifoldforce ` - * :doc:`mdi/aimd ` + * :doc:`mdi/qm ` * :doc:`meso/move ` * :doc:`mol/swap ` * :doc:`momentum (k) ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index f902b40b29..11334ea2d1 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -194,7 +194,7 @@ OPT. * :doc:`lubricateU/poly ` * :doc:`mdpd ` * :doc:`mdpd/rhosum ` - * :doc:`meam ` + * :doc:`meam (k) ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` * :doc:`mesocnt ` diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 2d588a1b77..ab06ac523c 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations. *More than one compute sna/atom* Self-explanatory. +*More than one compute sna/grid* + Self-explanatory. + +*More than one compute sna/grid/local* + Self-explanatory. + *More than one compute snad/atom* Self-explanatory. diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index f5aab0be22..14bef1a546 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -5,9 +5,9 @@ Client/server coupling of two (or more) codes is where one code is the "client" and sends request messages (data) to one (or more) "server" code(s). A server responds to each request with a reply message (data). This enables two (or more) codes to work in tandem to perform -a simulation. LAMMPS can act as either a client or server code; it -does this by using the `MolSSI Driver Interface (MDI) library -`_, +a simulation. In this context, LAMMPS can act as either a client or +server code. It does this by using the `MolSSI Driver Interface (MDI) +library `_, developed by the `Molecular Sciences Software Institute (MolSSI) `_, which is supported by the :ref:`MDI ` package. @@ -63,22 +63,39 @@ The package also provides a :doc:`mdi plugin ` command which enables LAMMPS to operate as an MDI driver and load an MDI engine as a plugin library. -The package also has a `fix mdi/aimd ` command in which -LAMMPS operates as an MDI driver to perform *ab initio* MD simulations -in conjunction with a quantum mechanics code. Its post_force() method -illustrates how a driver issues MDI commands to another code. This -command can be used to couple to an MDI engine which is either a -stand-alone code or a plugin library. +The package also has a `fix mdi/qm ` command in which +LAMMPS operates as an MDI driver in conjunction with a quantum +mechanics code as an MDI engine. The post_force() method of the +fix_mdi_qm.cpp file shows how a driver issues MDI commands to another +code. This command can be used to couple to an MDI engine which is +either a stand-alone code or a plugin library. + +As explained on the `fix mdi/qm ` command doc page, it can +be used to perform *ab initio* MD simulations or energy minimizations, +or to evaluate the quantum energy and forces for a series of +independent systems. The examples/mdi directory has example input +scripts for all of these use cases. ---------- The examples/mdi directory contains Python scripts and LAMMPS input script which use LAMMPS as either an MDI driver or engine or both. -Three example use cases are provided: +Currently, 5 example use cases are provided: -* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver - and one as an engine. As an engine, LAMMPS is a surrogate for a - quantum code. +* Run ab initio MD (AIMD) using 2 instances of LAMMPS. As a driver + LAMMPS performs the timestepping in either NVE or NPT mode. As an + engine, LAMMPS computes forces and is a surrogate for a quantum + code. + +* As a driver, LAMMPS runs an MD simulation. Every N steps it passes + the current snapshot to an MDI engine to evaluate the energy, + virial, and peratom forces. As the engine LAMMPS is a surrogate for + a quantum code. + +* As a driver, LAMMPS loops over a series of data files and passes the + configuration to an MDI engine to evaluate the energy, virial, and + peratom forces. As the engine LAMMPS is a surrogate for a quantum + code. * A Python script driver invokes a sequence of unrelated LAMMPS calculations. Calculations can be single-point energy/force @@ -91,20 +108,22 @@ Three example use cases are provided: Note that in any of these example where LAMMPS is used as an engine, an actual QM code (which supports MDI) could be used in its place, -without modifying other code or scripts, except to specify the name of -the QM code. +without modifying the input scripts or launch commands, except to +specify the name of the QM code. -The examples/mdi/README file explains how to launch both driver and +The examples/mdi/Run.sh file illustrates how to launch both driver and engine codes so that they communicate using the MDI library via either -MPI or sockets. +MPI or sockets. Or using the engine as a stand-alone code or plugin +library. ------------- -Currently there are two quantum DFT codes which have direct MDI -support, `Quantum ESPRESSO (QE) `_ -and `INQ `_. There are also -several QM codes which have indirect support through QCEngine or i-PI. -The former means they require a wrapper program (QCEngine) with MDI +Currently there are at least two quantum DFT codes which have direct +MDI support, `Quantum ESPRESSO (QE) +`_ and `INQ +`_. There are also several QM +codes which have indirect support through QCEngine or i-PI. The +former means they require a wrapper program (QCEngine) with MDI support which writes/read files to pass data to the quantum code itself. The list of QCEngine-supported and i-PI-supported quantum codes is on the `MDI webpage diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index 5cabf63de3..3c97628179 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -68,7 +68,8 @@ liquid Ar via the GK formalism: # Sample LAMMPS input script for viscosity of liquid Ar units real - variable T equal 86.4956 + variable T equal 200.0 # run temperature + variable Tinit equal 250.0 # equilibration temperature variable V equal vol variable dt equal 4.0 variable p equal 400 # correlation length @@ -99,12 +100,14 @@ liquid Ar via the GK formalism: # equilibration and thermalization - velocity all create $T 102486 mom yes rot yes dist gaussian - fix NVT all nvt temp $T $T 10 drag 0.2 + velocity all create ${Tinit} 102486 mom yes rot yes dist gaussian + fix NVT all nvt temp ${Tinit} ${Tinit} 10 drag 0.2 run 8000 # viscosity calculation, switch to NVE if desired + velocity all create $T 102486 mom yes rot yes dist gaussian + fix NVT all nvt temp $T $T 10 drag 0.2 #unfix NVT #fix NVE all nve @@ -122,7 +125,7 @@ liquid Ar via the GK formalism: run 100000 variable v equal (v_v11+v_v22+v_v33)/3.0 variable ndens equal count(all)/vol - print "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3" + print "average viscosity: $v [Pa.s] @ $T K, ${ndens} atoms/A^3" The fifth method is related to the above Green-Kubo method, but uses the Einstein formulation, analogous to the Einstein @@ -131,9 +134,9 @@ time-integrated momentum fluxes play the role of Cartesian coordinates, whose mean-square displacement increases linearly with time at sufficiently long times. -The sixth is periodic perturbation method. It is also a non-equilibrium MD method. -However, instead of measure the momentum flux in response of applied velocity gradient, -it measures the velocity profile in response of applied stress. +The sixth is the periodic perturbation method, which is also a non-equilibrium MD method. +However, instead of measuring the momentum flux in response to an applied velocity gradient, +it measures the velocity profile in response to applied stress. A cosine-shaped periodic acceleration is added to the system via the :doc:`fix accelerate/cos ` command, and the :doc:`compute viscosity/cos` command is used to monitor the diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b5d704190e..59922bd939 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1479,7 +1479,7 @@ the :doc:`Build extras ` page. * lib/mdi/README * :doc:`Howto MDI ` * :doc:`mdi ` -* :doc:`fix mdi/aimd ` +* :doc:`fix mdi/qm ` * examples/PACKAGES/mdi ---------- @@ -1801,6 +1801,8 @@ computes which analyze attributes of the potential. * src/ML-SNAP: filenames -> commands * :doc:`pair_style snap ` * :doc:`compute sna/atom ` +* :doc:`compute sna/grid ` +* :doc:`compute sna/grid/local ` * :doc:`compute snad/atom ` * :doc:`compute snav/atom ` * examples/snap diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 6fdedbbb95..508c440e78 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -284,6 +284,8 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`smd/vol ` - per-particle volumes and their sum in Smooth Mach Dynamics * :doc:`snap ` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials * :doc:`sna/atom ` - bispectrum components for each atom +* :doc:`sna/grid ` - global array of bispectrum components on a regular grid +* :doc:`sna/grid/local ` - local array of bispectrum components on a regular grid * :doc:`snad/atom ` - derivative of bispectrum components for each atom * :doc:`snav/atom ` - virial contribution from bispectrum components for each atom * :doc:`sph/e/atom ` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 37705ff005..fdff250e24 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -2,6 +2,8 @@ .. index:: compute snad/atom .. index:: compute snav/atom .. index:: compute snap +.. index:: compute sna/grid +.. index:: compute sna/grid/local compute sna/atom command ======================== @@ -15,6 +17,12 @@ compute snav/atom command compute snap command ==================== +compute sna/grid command +======================== + +compute sna/grid/local command +============================== + Syntax """""" @@ -24,6 +32,9 @@ Syntax compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID sna/grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID sna/grid/local nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... * ID, group-ID are documented in :doc:`compute ` command * sna/atom = style name of this compute command @@ -32,6 +43,7 @@ Syntax * twojmax = band limit for bispectrum components (non-negative integer) * R_1, R_2,... = list of cutoff radii, one for each type (distance units) * w_1, w_2,... = list of neighbor weights, one for each type +* nx, ny, nz = number of grid points in x, y, and z directions (positive integer) * zero or more keyword/value pairs may be appended * keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag* @@ -81,6 +93,7 @@ Examples compute snap all snap 1.4 0.95 6 2.0 1.0 compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1 compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3 + compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0 Description """"""""""" @@ -215,6 +228,46 @@ command: See section below on output for a detailed explanation of the data layout in the global array. +The compute *sna/grid* and *sna/grid/local* commands calculate +bispectrum components for a regular grid of points. +These are calculated from the local density of nearby atoms *i'* +around each grid point, as if there was a central atom *i* +at the grid point. This is useful for characterizing fine-scale +structure in a configuration of atoms, and it is used +in the `MALA package `_ +to build machine-learning surrogates for finite-temperature Kohn-Sham +density functional theory (:ref:`Ellis et al. `) +Neighbor atoms not in the group do not contribute to the +bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}` +assumes that *i* has the same type as the neighbor atom *i'*. + +Compute *sna/grid* calculates a global array containing bispectrum +components for a regular grid of points. +The grid is aligned with the current box dimensions, with the +first point at the box origin, and forming a regular 3d array with +*nx*, *ny*, and *nz* points in the x, y, and z directions. For triclinic +boxes, the array is congruent with the periodic lattice vectors +a, b, and c. The array contains one row for each of the +:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest, +then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*, +and *z* coordinates of the grid point, followed by the bispectrum +components. See section below on output for a detailed explanation of the data +layout in the global array. + +Compute *sna/grid/local* calculates bispectrum components of a regular +grid of points similarly to compute *sna/grid* described above. +However, because the array is local, it contains only rows for grid points +that are local to the processor sub-domain. The global grid +of :math:`nx \times ny \times nz` points is still laid out in space the same as for *sna/grid*, +but grid points are strictly partitioned, so that every grid point appears in +one and only one local array. The array contains one row for each of the +local grid points, looping over the global index *ix* fastest, +then *iy*, and *iz* slowest. Each row of the array contains +the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*, +and *z* coordinates of the grid point, followed by the bispectrum +components. See section below on output for a detailed explanation of the data +layout in the global array. + The value of all bispectrum components will be zero for atoms not in the group. Neighbor atoms not in the group do not contribute to the bispectrum of atoms in the group. @@ -428,6 +481,21 @@ number of columns in the global array generated by *snap* are 31, and 931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N* is the total number of atoms. +Compute *sna/grid* evaluates a global array. +The array contains one row for each of the +:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest, +then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*, +and *z* coordinates of the grid point, followed by the bispectrum +components. + +Compute *sna/grid/local* evaluates a local array. +The array contains one row for each of the +local grid points, looping over the global index *ix* fastest, +then *iy*, and *iz* slowest. Each row of the array contains +the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*, +and *z* coordinates of the grid point, followed by the bispectrum +components. + If the *quadratic* keyword value is set to 1, then additional columns are generated, corresponding to the products of all distinct pairs of bispectrum components. If the number of bispectrum components is *K*, @@ -509,8 +577,7 @@ The optional keyword defaults are *rmin0* = 0, .. _Thompson20141: -**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint -available at `arXiv:1409.3880 `_ +**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316, (2015). .. _Bartok20101: @@ -531,4 +598,8 @@ of Angular Momentum, World Scientific, Singapore (1987). .. _Cusentino2020: -**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020) +**(Cusentino)** Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020) + +.. _Ellis2021: + +**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021) diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 4d272c940b..4417e186ec 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -27,6 +27,9 @@ dump command :doc:`dump custom/adios ` command ============================================= +:doc:`dump cfg/uef ` command +========================================== + Syntax """""" @@ -36,7 +39,7 @@ Syntax * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be dumped -* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* +* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* * N = dump every this many timesteps * file = name of file to write dump info to * args = list of arguments for a particular style @@ -47,22 +50,23 @@ Syntax *atom/gz* args = none *atom/zstd* args = none *atom/mpiio* args = none - *atom/adios* args = none, discussed on :doc:`dump atom/adios ` doc page + *atom/adios* args = none, discussed on :doc:`dump atom/adios ` page *cfg* args = same as *custom* args, see below *cfg/gz* args = same as *custom* args, see below *cfg/zstd* args = same as *custom* args, see below *cfg/mpiio* args = same as *custom* args, see below + *cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef ` page *custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below - *custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios ` doc page + *custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios ` page *dcd* args = none - *h5md* args = discussed on :doc:`dump h5md ` doc page - *image* args = discussed on :doc:`dump image ` doc page + *h5md* args = discussed on :doc:`dump h5md ` page + *image* args = discussed on :doc:`dump image ` page *local*, *local/gz*, *local/zstd* args = see below - *molfile* args = discussed on :doc:`dump molfile ` doc page - *movie* args = discussed on :doc:`dump image ` doc page - *netcdf* args = discussed on :doc:`dump netcdf ` doc page - *netcdf/mpiio* args = discussed on :doc:`dump netcdf ` doc page - *vtk* args = same as *custom* args, see below, also :doc:`dump vtk ` doc page + *molfile* args = discussed on :doc:`dump molfile ` page + *movie* args = discussed on :doc:`dump image ` page + *netcdf* args = discussed on :doc:`dump netcdf ` page + *netcdf/mpiio* args = discussed on :doc:`dump netcdf ` page + *vtk* args = same as *custom* args, see below, also :doc:`dump vtk ` page *xtc* args = none *xyz* args = none *xyz/gz* args = none @@ -155,7 +159,7 @@ timesteps in one of several styles. The *image* and *movie* styles are the exception: the *image* style renders a JPG, PNG, or PPM image file of the atom configuration every N timesteps while the *movie* style combines and compresses them into a movie file; both are discussed in -detail on the :doc:`dump image ` doc page. The timesteps on +detail on the :doc:`dump image ` page. The timesteps on which dump output is written can also be controlled by a variable. See the :doc:`dump_modify every ` command. @@ -194,7 +198,7 @@ or multiple smaller files). For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by atom ID is on by default. See the :doc:`dump_modify ` -doc page for details. +page for details. The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical in command syntax to the corresponding styles without @@ -204,7 +208,7 @@ alternative approach to writing compressed files via a pipe, as done by the regular dump styles, which may be required on clusters where the interface to the high-speed network disallows using the fork() library call (which is needed for a pipe). For the remainder of this -doc page, you should thus consider the *atom* and *atom/gz* styles +page, you should thus consider the *atom* and *atom/gz* styles (etc) to be inter-changeable, with the exception of the required filename suffix. @@ -218,7 +222,7 @@ As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in -parallel via the MPI-IO library. For the remainder of this doc page, +parallel via the MPI-IO library. For the remainder of this page, you should thus consider the *atom* and *atom/mpiio* styles (etc) to be inter-changeable. The one exception is how the filename is specified for the MPI-IO styles, as explained below. @@ -664,7 +668,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are the non-orthogonal vectors of the simulation box edges, as discussed -on the :doc:`Howto triclinic ` doc page. +on the :doc:`Howto triclinic ` page. Use *xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has @@ -787,7 +791,7 @@ more info. The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are part of the MPIIO package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` -doc page for more info. +page for more info. The *xtc*, *dcd* and *yaml* styles are part of the EXTRA-DUMP package. They are only enabled if LAMMPS was built with that package. See the @@ -797,12 +801,12 @@ Related commands """""""""""""""" :doc:`dump atom/adios `, :doc:`dump custom/adios `, -:doc:`dump h5md `, :doc:`dump image `, -:doc:`dump molfile `, :doc:`dump_modify `, -:doc:`undump ` +:doc:`dump cfg/uef `, :doc:`dump h5md `, +:doc:`dump image `, :doc:`dump molfile `, +:doc:`dump_modify `, :doc:`undump `, :doc:`write_dump ` Default """"""" The defaults for the *image* and *movie* styles are listed on the -:doc:`dump image ` doc page. +:doc:`dump image ` page. diff --git a/doc/src/fix.rst b/doc/src/fix.rst index b0ec47fbe6..ad3fbef77b 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -246,7 +246,7 @@ accelerated styles exist. * :doc:`lb/viscous ` - * :doc:`lineforce ` - constrain atoms to move in a line * :doc:`manifoldforce ` - restrain atoms to a manifold during minimization -* :doc:`mdi/aimd ` - LAMMPS operates as driver for ab initio MD (AIMD) via the MolSSI Driver Interface (MDI) +* :doc:`mdi/qm ` - LAMMPS operates as driver for a quantum code via the MolSSI Driver Interface (MDI) * :doc:`meso/move ` - move mesoscopic SPH/SDPD particles in a prescribed fashion * :doc:`mol/swap ` - Monte Carlo atom type swapping with a molecule * :doc:`momentum ` - zero the linear and/or angular momentum of a group of atoms diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index f75d44e3a4..8a6315fa48 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -116,13 +116,6 @@ potential energy of the system as part of :doc:`thermodynamic output `. The default setting for this fix is :doc:`fix_modify energy yes `. -The :doc:`fix_modify ` *virial* option is supported by -this fix to add the contribution compute by LATTE to the global -pressure of the system via the :doc:`compute pressure -` command. This can be accessed by -:doc:`thermodynamic output `. The default setting for -this fix is :doc:`fix_modify virial yes `. - The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution computed by LATTE to the global pressure of the system as part of :doc:`thermodynamic output @@ -137,7 +130,7 @@ energy discussed above. The scalar value calculated by this fix is No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. -The DFTB forces computed by LATTE via this fix are imposed during an +The DFTB forces computed by LATTE via this fix are used during an energy minimization, invoked by the :doc:`minimize ` command. diff --git a/doc/src/fix_mdi_aimd.rst b/doc/src/fix_mdi_aimd.rst deleted file mode 100644 index 9ab2a933ed..0000000000 --- a/doc/src/fix_mdi_aimd.rst +++ /dev/null @@ -1,93 +0,0 @@ -.. index:: fix mdi/aimd - -fix mdi/aimd command -====================== - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID mdi/aimd keyword - -* ID, group-ID are documented in :doc:`fix ` command -* mdi/aimd = style name of this fix command - -Examples -"""""""" - -.. code-block:: LAMMPS - - fix 1 all mdi/aimd - -Description -""""""""""" - -This command enables LAMMPS to act as a client with another server -code to couple the two codes together to perform ab initio MD (AIMD) -simulations. - -More specifically, this command causes LAMMPS to begin using the `MDI -Library `_ -to run as an MDI driver (client), which sends MDI commands to an -external MDI engine code (server) which in the case of AIMD is a -quantum mechanics (QM) code, or could be LAMMPS itself, acting as a -surrogate for a QM code. See the :doc:`Howto mdi ` page -for more information about how LAMMPS can operate as either an MDI -driver or engine. - -The examples/mdi directory contains input scripts performing AIMD in -this manner with LAMMPS acting as both a driver and an engine -(surrogate for a QM code). The examples/mdi/README file explains how -to launch both driver and engine codes so that they communicate using -the MDI library via either MPI or sockets. Any QM code that supports -MDI could be used in place of LAMMPS acting as a QM surrogate. See -the :doc:`Howto mdi ` page for a current list (March 2022) -of such QM codes. - -The engine code can run either as a stand-alone code, launched at the -same time as LAMMPS, or as a plugin library. See the :doc:`mdi plugin -` command for how to trigger LAMMPS to load the plugin library. -Again, the examples/mdi/README file explains how to launch both driver -and engine codes so that engine is used in plugin mode. - ----------- - -This fix performs the timestepping portion of an AIMD simulation. -Both LAMMPS and the engine code (QM or LAMMPS) should define the same -system (simulation box, atoms and their types) in their respective -input scripts. LAMMPS then begins its timestepping. - -At the point in each timestep when LAMMPS needs the force on each -atom, it communicates with the engine code. It sends the current -simulation box size and shape (if they change dynamically, e.g. during -an NPT simulation), and the current atom coordinates. The engine code -computes quantum forces on each atom and returns them to LAMMPS. If -LAMMPS also needs the system energy and/or virial, it requests those -values from the engine code as well. - -Restrictions -"""""""""""" - -This command is part of the MDI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package -` page for more info. - -To use LAMMPS as an MDI driver in conjunction with other MDI-enabled -atomistic codes, the :doc:`units ` command should be used to -specify *real* or *metal* units. This will ensure the correct unit -conversions between LAMMPS and MDI units, which the other codes will -also perform in their preferred units. - -LAMMPS can also be used as an MDI driver in other unit choices it -supports, e.g. *lj*, but then no unit conversion is performed. - -Related commands -"""""""""""""""" - -:doc:`mdi engine ` - -Default -""""""" - -none diff --git a/doc/src/fix_mdi_qm.rst b/doc/src/fix_mdi_qm.rst new file mode 100644 index 0000000000..ca47db5e7a --- /dev/null +++ b/doc/src/fix_mdi_qm.rst @@ -0,0 +1,276 @@ +.. index:: fix mdi/qm + +fix mdi/qm command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID mdi/qm keyword + +* ID, group-ID are documented in :doc:`fix ` command +* mdi/qm = style name of this fix command +* zero or more keyword/value pairs may be appended +* keyword = *virial* or *add* or *every* or *connect* or *elements* + + .. parsed-literal:: + + *virial* args = *yes* or *no* + yes = request virial tensor from server code + no = do not request virial tensor from server code + *add* args = *yes* or *no* + yes = add returned value from server code to LAMMPS quantities + no = do not add returned values to LAMMPS quantities + *every* args = Nevery + Nevery = request values from server code once every Nevery steps + *connect* args = *yes* or *no* + yes = perform a one-time connection to the MDI engine code + no = do not perform the connection operation + *elements* args = N_1 N_2 ... N_ntypes + N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all mdi/qm + fix 1 all mdi/qm virial yes + fix 1 all mdi/qm add no every 100 elements 13 29 + +Description +""""""""""" + +This command enables LAMMPS to act as a client with another server +code that will compute the total energy, per-atom forces, and total +virial for atom conformations and simulation box size/shapes that +LAMMPS sends it. + +Typically the server code will be a quantum mechanics (QM) code, hence +the name of the fix. However this is not required, the server code +could be another classical molecular dynamics code or LAMMPS itself. +The server code must support use of the `MDI Library +`_ as +explained below. + +These are example use cases for this fix, discussed further below: + +* perform an ab initio MD (AIMD) simulation with quantum forces +* perform an energy minimization with quantum forces +* perform a nudged elastic band (NEB) calculation with quantum forces +* perform a QM calculation for a series of independent systems which LAMMPS reads or generates + +The code coupling performed by this command is done via the `MDI +Library `_. +LAMMPS runs as an MDI driver (client), and sends MDI commands to an +external MDI engine code (server), e.g. a QM code which has support +for MDI. See the :doc:`Howto mdi ` page for more +information about how LAMMPS can operate as either an MDI driver or +engine. + +The examples/mdi directory contains input scripts using this fix in +the various use cases discussed below. In each case, two instances of +LAMMPS are used, once as an MDI driver, once as an MDI engine +(surrogate for a QM code). The examples/mdi/README file explains how +to launch two codes so that they communicate via the MDI library using +either MPI or sockets. Any QM code that supports MDI could be used in +place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi +` page for a current list (March 2022) of such QM codes. + +Note that an engine code can support MDI in either or both of two +modes. It can be used as a stand-alone code, launched at the same +time as LAMMPS. Or it can be used as a plugin library, which LAMMPS +loads. See the :doc:`mdi plugin ` command for how to trigger +LAMMPS to load a plugin library. The examples/mdi/README file +explains how to launch the two codes in either mode. + +---------- + +The *virial* keyword setting of yes or no determines whether +LAMMPS will request the QM code to also compute and return +a 6-element symmetric virial tensor for the system. + +The *add* keyword setting of *yes* or *no* determines whether the +energy and forces and virial returned by the QM code will be added to +the LAMMPS internal energy and forces and virial or not. If the +setting is *no* then the default :doc:`fix_modify energy ` +and :doc:`fix_modify virial ` settings are also set to +*no* and your input scripts should not set them to yes. See more +details on these fix_modify settings below. + +Whatever the setting for the *add* keyword, the QM energy, forces, and +virial will be stored by the fix, so they can be accessed by other +commands. See details below. + +The *every* keyword determines how often the QM code will be invoked +during a dynamics run with the current LAMMPS simulation box and +configuration of atoms. The QM code will be called once every +*Nevery* timesteps. + +The *connect* keyword determines whether this fix performs a one-time +connection to the QM code. The default is *yes*. The only time a +*no* is needed is if this command is used multiple times in an input +script. E.g. if it used inside a loop which also uses the :doc:`clear +` command to destroy the system (including any defined fixes). +See the examples/mdi/in.series.driver script as an example of this, +where LAMMPS is using the QM code to compute energy and forces for a +series of system configurations. In this use case *connect no* +is used along with the :doc:`mdi connect and exit ` command +to one-time initiate/terminate the connection outside the loop. + +The *elements* keyword allows specification of what element each +LAMMPS atom type corresponds to. This is specified by the atomic +number of the element, e.g. 13 for Al. An atomic number must be +specified for each of the ntypes LAMMPS atom types. Ntypes is +typically specified via the create_box command or in the data file +read by the read_data command. If this keyword is not specified, then +this fix will send the LAMMPS atom type for each atom to the MDI +engine. If both the LAMMPS driver and the MDI engine are initialized +so that atom type values are consistent in both codes, then the +*elements* keyword is not needed. Otherwise the keyword can be used +to insure the two codes are consistent in their definition of atomic +species. + +---------- + +The following 3 example use cases are illustrated in the examples/mdi +directory. See its README file for more details. + +(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy +minimization with QM forces, or a multi-replica NEB calculation, use +*add yes* and *every 1* (the defaults). This is so that every time +LAMMPS needs energy and forces, the QM code will be invoked. + +Both LAMMPS and the QM code should define the same system (simulation +box, atoms and their types) in their respective input scripts. Note +that on this scenario, it may not be necessary for LAMMPS to define a +pair style or use a neighbor list. + +LAMMPS will then perform the timestepping or minimization iterations +for the simulation. At the point in each timestep or iteration when +LAMMPS needs the force on each atom, it communicates with the engine +code. It sends the current simulation box size and shape (if they +change dynamically, e.g. during an NPT simulation), and the current +atom coordinates. The engine code computes quantum forces on each +atom and the total energy of the system and returns them to LAMMPS. + +Note that if the AIMD simulation is an NPT or NPH model, or the energy +minimization includes :doc:`fix box relax ` to +equilibrate the box size/shape, then LAMMPS computes a pressure. This +means the *virial* keyword should be set to *yes* so that the QM +contribution to the pressure can be included. + +(2) To run dynamics with a LAMMPS interatomic potential, and evaluate +the QM energy and forces once every 1000 steps, use *add no* and +*every 1000*. This could be useful for using an MD run to generate +randomized configurations which are then passed to the QM code to +produce training data for a machine learning potential. A :doc:`dump +custom ` command could be invoked every 1000 steps to dump the +atom coordinates and QM forces to a file. Likewise the QM energy and +virial could be output with the :doc:`thermo_style custom +` command. + +(3) To do a QM evaluation of energy and forces for a series of *N* +independent systems (simulation box and atoms), use *add no* and +*every 1*. Write a LAMMPS input script which loops over the *N* +systems. See the :doc:`Howto multiple ` doc page for +details on looping and removing old systems. The series of systems +could be initialized by reading them from data files with +:doc:`read_data ` commands. Or, for example, by using the +:doc:`lattice ` , :doc:`create_atoms `, +:doc:`delete_atoms `, and/or :doc:`displace_atoms +random ` commands to generate a series of different +systems. At the end of the loop perform :doc:`run 0 ` and +:doc:`write_dump ` commands to invoke the QM code and +output the QM energy and forces. As in (2) this be useful to produce +QM data for training a machine learning potential. + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files +`. + +The :doc:`fix_modify ` *energy* option is supported by +this fix to add the potential energy computed by the QM code to the +global potential energy of the system as part of :doc:`thermodynamic +output `. The default setting for this fix is +:doc:`fix_modify energy yes `, unless the *add* keyword is +set to *no*, in which case the default setting is *no*. + +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution computed by the QM code to the global +pressure of the system as part of :doc:`thermodynamic output +`. The default setting for this fix is :doc:`fix_modify +virial yes `, unless the *add* keyword is set to *no*, in +which case the default setting is *no*. + +This fix computes a global scalar which can be accessed by various +:doc:`output commands `. The scalar is the energy +returned by the QM code. The scalar value calculated by this fix is +"extensive". + +This fix also computes a global vector with of length 6 which contains +the symmetric virial tensor values returned by the QM code. It can +likewise be accessed by various :doc:`output commands `. + +The ordering of values in the symmetric virial tensor is as follows: +vxx, vyy, vzz, vxy, vxz, vyz. The values will be in pressure +:doc:`units `. + +This fix also computes a peratom array with 3 columns which contains +the peratom forces returned by the QM code. It can likewise be +accessed by various :doc:`output commands `. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +Assuming the *add* keyword is set to *yes* (the default), the forces +computed by the QM code are used during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the potential energy associated with the QM forces to + be included in the total potential energy of the system (the + quantity being minimized), you MUST not disable the + :doc:`fix_modify ` *energy* option for this fix, which + means the *add* keyword should also be set to *yes* (the default). + + +Restrictions +"""""""""""" + +This command is part of the MDI package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +The QM code does not currently compute and return per-atom energy or +per-atom virial contributions. So they will not show up as part of +the calculations performed by the :doc:`compute pe/atom +` or :doc:`compute stress/atom ` +commands. + +To use LAMMPS as an MDI driver in conjunction with other MDI-enabled +codes (MD or QM codes), the :doc:`units ` command should be +used to specify *real* or *metal* units. This will ensure the correct +unit conversions between LAMMPS and MDI units. The other code will +also perform similar unit conversions into its preferred units. + +LAMMPS can also be used as an MDI driver in other unit choices it +supports, e.g. *lj*, but then no unit conversion is performed. + +Related commands +"""""""""""""""" + +:doc:`mdi plugin `, :doc:`mdi engine ` + +Default +""""""" + +The default for the optional keywords are virial = no, add = yes, +every = 1, connect = yes. diff --git a/doc/src/if.rst b/doc/src/if.rst index 08ec6f2c3e..91b001fbdc 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -156,27 +156,28 @@ and Boolean operators: Each A and B is a number or string or a variable reference like $a or ${abc}, or A or B can be another Boolean expression. -If a variable is used it can produce a number when evaluated, like an -:doc:`equal-style variable `. Or it can produce a string, -like an :doc:`index-style variable `. For an individual -Boolean operator, A and B must both be numbers or must both be -strings. You cannot compare a number to a string. +Note that all variables used will be substituted for before the +Boolean expression in evaluated. A variable can produce a number, +like an :doc:`equal-style variable `. Or it can produce a +string, like an :doc:`index-style variable `. + +The Boolean operators "==" and "!=" can operate on a pair or strings +or numbers. They cannot compare a number to a string. All the other +Boolean operations can only operate on numbers. Expressions are evaluated left to right and have the usual C-style precedence: the unary logical NOT operator "!" has the highest precedence, the 4 relational operators "<", "<=", ">", and ">=" are next; the two remaining relational operators "==" and "!=" are next; then the logical AND operator "&&"; and finally the logical OR -operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have the -lowest precedence. Parenthesis can be used to group one or more +operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have +the lowest precedence. Parenthesis can be used to group one or more portions of an expression and/or enforce a different order of evaluation than what would occur with the default precedence. When the 6 relational operators (first 6 in list above) compare 2 numbers, they return either a 1.0 or 0.0 depending on whether the -relationship between A and B is TRUE or FALSE. When the 6 relational -operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or -FALSE, but the comparison is done by the C function strcmp(). +relationship between A and B is TRUE or FALSE. When the 3 logical operators (last 3 in list above) compare 2 numbers, they also return either a 1.0 or 0.0 depending on whether the @@ -190,8 +191,16 @@ returns 1.0 if its argument is 0.0, else it returns 0.0. The 3 logical operators can only be used to operate on numbers, not on strings. -The overall Boolean expression produces a TRUE result if the result is -non-zero. If the result is zero, the expression result is FALSE. +The overall Boolean expression produces a TRUE result if the numeric +result is non-zero. If the result is zero, the expression result is +FALSE. + +.. note:: + + If the Boolean expression is a single numeric value with no Boolean + operators, it will be FALSE if the value = 0.0, otherwise TRUE. If + the Boolean expression is a single string, an error message will be + issued. ---------- diff --git a/doc/src/mdi.rst b/doc/src/mdi.rst index 3a6f0234fc..b5ee0098bd 100644 --- a/doc/src/mdi.rst +++ b/doc/src/mdi.rst @@ -8,21 +8,26 @@ Syntax .. parsed-literal:: - mdi mode args + mdi option args -* mode = *engine* or *plugin* +* option = *engine* or *plugin* or *connect* or *exit* .. parsed-literal:: - *engine* args = none - *plugin* args = name keyword value keyword value + *engine* args = zero or more keyword arg pairs + keywords = *elements* + *elements* args = N_1 N_2 ... N_ntypes + N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types + *plugin* args = name keyword value keyword value ... name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded + keyword/value pairs in any order, some are required, some are optional keywords = *mdi* or *infile* or *extra* or *command* - *mdi* value = args passed to MDI for driver to operate with plugins - *infile* value = filename the engine will read at start-up + *mdi* value = args passed to MDI for driver to operate with plugins (required) + *infile* value = filename the engine will read at start-up (optional) *extra* value = aditional command-line args to pass to engine library when loaded - *command* value = a LAMMPS input script command to execute - + *command* value = a LAMMPS input script command to execute (required) + *connect* args = none + *exit* args = none Examples """""""" @@ -30,26 +35,19 @@ Examples .. code-block:: LAMMPS mdi engine + mdi engine elements 13 29 mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" & infile in.aimd.engine extra "-log log.aimd.engine.plugin" & command "run 5" + mdi connect + mdi exit Description """"""""""" -This command implements two high-level operations within LAMMPS to use -the `MDI Library -` for -coupling to other codes in a client/server protocol. - -The *engine* mode enables LAMMPS to act as an MDI engine (server), -responding to requests from an MDI driver (client) code. - -The *plugin* mode enables LAMMPS to act as an MDI driver (client), and -load the MDI engine (server) code as a library plugin. In this case -the MDI engine is a library plugin. It can also be a stand-alone -code, launched separately from LAMMPS, in which case the mdi plugin -command is not used. +This command implements operations within LAMMPS to use the `MDI +Library ` +for coupling to other codes in a client/server protocol. See the Howto MDI doc page for a discussion of all the different ways 2 or more codes can interact via MDI. @@ -61,6 +59,22 @@ stand-alone code or as a plugin. The README file in that directory shows how to launch and couple codes for all the 4 usage modes, and so they communicate via the MDI library using either MPI or sockets. +The scripts in that directory illustrate the use of all the options +for this command. + +The *engine* option enables LAMMPS to act as an MDI engine (server), +responding to requests from an MDI driver (client) code. + +The *plugin* option enables LAMMPS to act as an MDI driver (client), +and load the MDI engine (server) code as a library plugin. In this +case the MDI engine is a library plugin. An MDI engine can also be a +stand-alone code, launched separately from LAMMPS, in which case the +mdi plugin command is not used. + +The *connect* and *exit* options are only used when LAMMPS is acting +as an MDI driver. As explained below, these options are normally not +needed, except for a specific kind of use case. + ---------- The *mdi engine* command is used to make LAMMPS operate as an MDI @@ -100,6 +114,8 @@ commands, which are described further below. - Send/request charge on each atom (N values) * - >COORDS or ELEMENTS + - Send elements (atomic numbers) for each atom (N values) * - FORCES or TOLERANCE - Send 4 tolerance parameters for next MD minimization via OPTG command * - >TYPES or VELOCITIES or COORDS command), then LAMMPS will do a more expensive operation to migrate atoms to new processors as needed and - re-neighbor. If the >NATOMS or >TYPES commands have been sent - (since the previous >COORDS command), then LAMMPS assumes the - system is new and re-initializes an entirely new simulation. + re-neighbor. If the >NATOMS or >TYPES or >ELEMENTS commands have + been sent (since the previous >COORDS command), then LAMMPS assumes + the system is new and re-initializes an entirely new simulation. + +.. note:: + + The >TYPES or >ELEMENTS commands are how the MDI driver tells the + LAMMPS engine which LAMMPS atom type to assign to each atom. If + both the MDI driver and the LAMMPS engine are initialized so that + atom type values are consistent in both codes, then the >TYPES + command can be used. If not, the optional *elements* keyword can + be used to specify what element each LAMMPS atom type corresponds + to. This is specified by the atomic number of the element, e.g. 13 + for Al. An atomic number must be specified for each of the ntypes + LAMMPS atom types. Ntypes is typically specified via the + create_box command or in the data file read by the read_data + command. In this has been done, the MDI driver can send an + >ELEMENTS command to the LAMMPS driver with the atomic number of + each atom. The MD and OPTG commands perform an entire MD simulation or energy minimization (to convergence) with no communication from the driver @@ -270,7 +302,7 @@ The *command* keyword is required. It specifies a LAMMPS input script command (as a single argument in quotes if it is multiple words). Once the plugin library is launched, LAMMPS will execute this command. Other previously-defined commands in the input script, such as the -:doc:`fix mdi/aimd ` command, should perform MDI +:doc:`fix mdi/qm ` command, should perform MDI communication with the engine, while the specified *command* executes. Note that if *command* is an :doc:`include ` command, then it could specify a filename with multiple LAMMPS commands. @@ -284,6 +316,31 @@ could specify a filename with multiple LAMMPS commands. "mdi plugin" command could then load the same library plugin or a different one if desired. +---------- + +The *mdi connect* and *mdi exit* commands are only used when LAMMPS is +operating as an MDI driver. And when other LAMMPS command(s) which +send MDI commands and associated data to/from the MDI engine are not +able to initiate and terminate the connection to the engine code. + +The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm +` command. If it is only used once in an input script +then it can initiate and terminate the connection. But if it is being +issued multiple times, e.g. in a loop that issues a :doc:`clear +` command, then it cannot initiate or terminate the connection +multiple times. Instead, the *mdi connect* and *mdi exit* commands +should be used outside the loop to initiate or terminate the connection. + +See the examples/mdi/in.series.driver script for an example of how +this is done. The LOOP in that script is reading a series of data +file configurations and passing them to an MDI engine (e.g. quantum +code) for energy and force evaluation. A *clear* command inside the +loop wipes out the current system so a new one can be defined. This +operation also destroys all fixes. So the :doc:`fix mdi/qm +` command is issued once per loop iteration. Note that it +includes a "connect no" option which disables the initiate/terminate +logic within that fix. + Restrictions """""""""""" @@ -304,7 +361,7 @@ supports, e.g. *lj*, but then no unit conversion is performed. Related commands """""""""""""""" -:doc:`fix mdi/aimd ` +:doc:`fix mdi/qm ` Default """"""" diff --git a/doc/src/package.rst b/doc/src/package.rst index 8f9a65b2cc..0810bd5b6b 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -71,7 +71,7 @@ Syntax *no_affinity* values = none *kokkos* args = keyword value ... zero or more keyword/value pairs may be appended - keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *gpu/aware* or *pair/only* + keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only* *neigh* value = *full* or *half* full = full neighbor list half = half neighbor list built in thread-safe manner @@ -96,6 +96,7 @@ Syntax *comm/pair/forward* value = *no* or *device* *comm/fix/forward* value = *no* or *device* *comm/reverse* value = *no* or *host* or *device* + *comm/pair/reverse* value = *no* or *device* no = perform communication pack/unpack in non-KOKKOS mode host = perform pack/unpack on host (e.g. with OpenMP threading) device = perform pack/unpack on device (e.g. on GPU) @@ -500,7 +501,7 @@ rule of thumb may give too large a binsize and the default should be overridden with a smaller value. The *comm* and *comm/exchange* and *comm/forward* and *comm/pair/forward* -and *comm/fix/forward* and comm/reverse* +and *comm/fix/forward* and *comm/reverse* and *comm/pair/reverse* keywords determine whether the host or device performs the packing and unpacking of data when communicating per-atom data between processors. "Exchange" communication happens only on timesteps that neighbor lists @@ -521,9 +522,16 @@ packing/unpacking data for the communication. A value of *host* means to use the host, typically a multi-core CPU, and perform the packing/unpacking in parallel with threads. A value of *device* means to use the device, typically a GPU, to perform the packing/unpacking -operation. If a value of *host* is used for the *comm/pair/forward* or -*comm/fix/forward* keyword, it will be automatically be changed to *no* -since these keywords don't support *host* mode. +operation. + +For the *comm/pair/forward* or *comm/fix/forward* or *comm/pair/reverse* +keywords, if a value of *host* is used it will be automatically +be changed to *no* since these keywords don't support *host* mode. The +value of *no* will also always be used when running on the CPU, i.e. setting +the value to *device* will have no effect if the pair/fix style is +running on the CPU. For the *comm/fix/forward* or *comm/pair/reverse* +keywords, not all styles support *device* mode and in that case will run +in *no* mode instead. The optimal choice for these keywords depends on the input script and the hardware used. The *no* value is useful for verifying that the diff --git a/doc/src/pair_meam.rst b/doc/src/pair_meam.rst index afa89e10ca..eac8449b21 100644 --- a/doc/src/pair_meam.rst +++ b/doc/src/pair_meam.rst @@ -1,8 +1,11 @@ .. index:: pair_style meam +.. index:: pair_style meam/kk pair_style meam command ========================= +Accelerator Variants: *meam/kk* + Syntax """""" @@ -347,6 +350,12 @@ Most published MEAM parameter sets use the default values *attrac* = *repulse* = Setting *repuls* = *attrac* = *delta* corresponds to the form used in several recent published MEAM parameter sets, such as :ref:`(Valone) ` +---------- + +.. include:: accel_styles.rst + +---------- + .. note:: The default form of the *erose* expression in LAMMPS was corrected diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index cce6e92d05..77a1da6643 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -373,6 +373,7 @@ Caltech Camilloni Camiloni Campana +Cangi Cao Capolungo Caro @@ -2681,6 +2682,7 @@ polyhedra Polym polymorphism popen +Popoola Popov popstore Poresag @@ -2824,6 +2826,7 @@ radians Rafferty rahman Rahman +Rajamanickam Ralf Raman ramped @@ -3676,13 +3679,19 @@ vx Vx vxcm vxmu +vxx +vxy +vxz vy Vy vycm +vyy +vyz vz Vz vzcm vzi +vzz Waals Wadley wallstyle diff --git a/examples/PACKAGES/pace/plugin/CMakeLists.txt b/examples/PACKAGES/pace/plugin/CMakeLists.txt index f4068a03c9..6ad9c791ba 100644 --- a/examples/PACKAGES/pace/plugin/CMakeLists.txt +++ b/examples/PACKAGES/pace/plugin/CMakeLists.txt @@ -31,6 +31,23 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows") if(CMAKE_CROSSCOMPILING) set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") endif() + + get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION) + find_program(MAKENSIS_PATH makensis) + if(MAKENSIS_PATH) + execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico + ${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR}) + if(BUILD_MPI) + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis + DEPENDS paceplugin + BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe) + else() + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis + COMMAND ${CMAKE_COMMAND} -E echo ${PWD} + DEPENDS paceplugin lammps.ico lammps-text-logo-wide.bmp paceplugin.nsis + BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}.exe) + endif() + endif() else() set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic") endif() diff --git a/examples/mdi/README b/examples/mdi/README index fd459e6670..c6267a7abb 100644 --- a/examples/mdi/README +++ b/examples/mdi/README @@ -2,10 +2,11 @@ These are examples that work the MDI package in LAMMPS which uses the MolSSI MDI library for coupling codes together and communicating between them with MDI messages. -In MDI lingo, one code is the driver and another code is the engine. -The 2 codes can be written in any language; C++ (LAMMPS) and Python -are illustrated here. The 2 codes can each be stand-alone codes, in -which case they can be run on different numbers of processors. The 2 +Within the MDI context, one code is the driver and another code is +the engine. The 2 codes can be written in any language; C++ (LAMMPS) +and Python are illustrated here. The 2 codes can each be stand-alone +codes, in which case they can be run on different numbers of processors. +The 2 codes can communicate either via TCP (sockets) or via MPI. For the TCP case, the driver and engine need to be launched separately, e.g. in 2 windows on your desktop machine. For the MPI case, a single @@ -19,87 +20,99 @@ LAMMPS supports operating in all these MDI modes. It can be an engine operating either as a stand-alone code or as a plugin. It can also be a driver and couple to an engine that is either a stand-alone code or a plugin. Examples for all these use cases are in this directory. -The example commands below illustrate how to run all the variants. +The Run.sh file shows how run in all the modes. Type "sh Run.sh" +to try them all out. -To use LAMMPS as a plugin engine, you must build it as a shared library. -Something like this, which also builds the normal LAMMPS executable -lmp_mpi: +To use LAMMPS as a plugin engine, you must build it as a shared +library. Something like this with make, which also builds the normal +LAMMPS executable lmp_mpi: cd src make yes-mdi make mode=shlib mpi -To use the serial_driver.py example you will need Python 3 with Numpy -and mpi4py available in your Python. Make sure LAMMPS and Python are -using same the same version of MPI. +------------------------------------------------- + +Examples 4 and 5 use Python scripts as MDI drivers. For this you will +need Python 3 with Numpy and mpi4py installed. Make sure LAMMPS and +Python/mpi4py are using same the same version of MPI. + +You will also need MDI installed in your Python. You cannot use the +LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a +static library, not shared, which Python requires. + +You can install MDI in your Python via conda: + +% conda install -c conda-forge pymdi=1.4.1 + +or via pip: + +% pip install pymdi==1.4.1 + +It is likely fine to leave off the version number, to get the latest +MDI version. But to be safe, 1.4.1 is the version LAMMPS is currently +using. + +------------------------------------------------- + +5 example use-cases are explained below. + +In the first 3 examples, results running with MDI should be identical +to running without MDI (alone log files). Example #4 has no non-MDI +run. Example #5 results should match the non-MDI run of example #1. + +------------------------------------------------- + +* Example #1 = run ab initio MD (AIMD) + +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code. + +You can compare the thermo output in log.aimd.alone.1 to the thermo output in +any of the log.aimd.driver* files. It should be identical. + +Note that the "alone" and "driver" input scripts have options for +running in NVE vs NPT Comment in/out the appropriate line to make +change. Nothing needs to be changed in the "engine" scripts. ------------------------------------------------- ------------------------------------------------- -* Example #1 = run ab inito MD (AIMD) - Two instances of LAMMPS operate as a driver and engine - As an engine, LAMMPS is a surrogate for a quantum code +* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run -Note that the 2 input scripts in.aimd.alone and in.aimd.driver -have an option for running in NVE vs NPT mode. Comment in/out -the appropriate line to change modes. Nothing needs to be -changed in the in.aimd.engine or in.aimd.engine.plugin scripts. +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code ---- +You can compare the thermo output in log.snapshot.alone.1 to the +thermo output in any of the log.snapshot.driver* files. It should be +identical. -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI - -% lmp_mpi < in.aimd.alone - -With MDI, the thermo output of the driver should match the thermo -output of the in.aimd.alone script. - ---- - -Run with TCP: 1 proc each - -% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver - -% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine - ---- - -Run with TCP: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver - -% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine - ---- - -Run with MPI: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine - ---- - -Run in plugin mode: 1 proc - -% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin +You can compare the dumped forces in dump.snapshot.alone.1 to the +forces in any of the dump.snapshot.* files. They should be identical, +although at step 0 the forces are "zero" and may be epsilon different. ------------------------------------------------- ------------------------------------------------- -* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations - Each calculation can be a single-point evaluation, MD run, or minimization +* Example #3 = run LAMMPS, compute QM forces on series of independent systems + +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code + +You can compare the thermo output in log.series.alone.1 to the thermo +output in any of the log.series.driver* files. It should be +identical. + +You can compare the dumped forces in dump.series.alone.1 to the forces +in any of the dump.series.* files. They should be identical, + +------------------------------------------------- +------------------------------------------------- + +* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations + +Each calculation can be a single-point evaluation, MD run, or +minimization The sequence_driver.py code allows for optional switches in addition to -mdi (required) and the -plugin and -plugin_args switches which are @@ -128,101 +141,31 @@ copied here: # -seed 12345 # random number seed > 0, default = 12345 ---- - -Run with TCP: 1 proc each - -% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" - -% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence - ---- - -Run with TCP: 2 proc + 4 procs - -% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" - -% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence - ---- - -Run with MPI: 2 procs + 4 procs - -% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence - ---- - -Run in plugin mode: 1 proc - -% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence" - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence" +You can compare the thermo output in any of the log.sequence.engine.* +files. It should be identical. ------------------------------------------------- ------------------------------------------------- -* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines - First LAMMPS instance performs the MD timestepping - Second LAMMPS instance is surrogate QM = computes forces +* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines + +First LAMMPS instance performs the MD timestepping. Second LAMMPS +instance is surrogate QM to compute forces. The aimd_driver.py code allows for an optional switch in addition to -mdi (required) and the -plugin and -plugin_args swiches which are used to link to the 2 engines as a plugin libraries. The example run commands below use the default values of the optional switch. The -switch is also explained the top of the file; the info is copied -here: +switch is also explained the top of the file; the info is copied here: -# -nsteps 5 -# number of timesteps in dynamics runs, default = 5 +# -nsteps 10 +# number of timesteps in dynamics runs, default = 10 ---- +This calculation is the same as Example #1 with a LAMMPS driver and a +LAMMPS engine. Now there is a Python driver and two LAMMPS engines. -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI +You can compare the thermo output in log.aimd.alone.1 output to the +thermo output is any of the log.sequence.engine.* files. It should be +identical for the Total Energy printed out by the Python driver script. -% lmp_mpi < in.aimd.alone - -With MDI, the driver prints the QM and Total energies. These should -match the PotEng and TotEng output of the in.aimd.alone script. - ---- - -Run with TCP: 1 proc each - -% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" - -% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm - -% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with TCP: 2 procs + 2 procs + 3 procs - -% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" - -% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm - -% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with MPI: 2 procs + 2 procs + 3 procs - -% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm +E.g. Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166 diff --git a/examples/mdi/Run.sh b/examples/mdi/Run.sh new file mode 100644 index 0000000000..3b70a8bf79 --- /dev/null +++ b/examples/mdi/Run.sh @@ -0,0 +1,256 @@ +# Run all the examples + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 1 = run ab initio MD (AIMD) + +# --- + +# Run without MDI + +lmp_mpi -log log.aimd.alone.1 < in.aimd.alone + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin +mv log.aimd.engine.plugin log.aimd.engine.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin +mv log.aimd.engine.plugin log.aimd.engine.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 2 = run LAMMPS, compute QM forces on snapshots from a long run + +# --- + +# Run without MDI + +lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone +mv dump.snapshot.alone dump.snapshot.alone.1 + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.tcp.1 + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.tcp.4 + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.mpi.1 + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.mpi.4 + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin +mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1 +mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin +mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3 +mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 3 = run LAMMPS, compute QM forces on series of independent systems + +# --- + +# Run without MDI + +lmp_mpi -log log.series.alone.1 < in.series.alone +mv dump.series.alone dump.series.alone.1 + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine +mv dump.series.driver dump.series.driver.tcp.1 + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine +mv dump.series.driver dump.series.driver.tcp.4 + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine +mv dump.series.driver dump.series.driver.mpi.1 + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine +mv dump.series.driver dump.series.driver.mpi.4 + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin +mv log.series.engine.plugin log.series.engine.plugin.1 +mv dump.series.driver.plugin dump.series.driver.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin +mv log.series.engine.plugin log.series.engine.plugin.3 +mv dump.series.driver.plugin dump.series.driver.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 4 = Python driver runs a sequence of unrelated LAMMPS calculations + +# --- + +# Run with TCP: 1 proc each + +python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" & + +lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python + +# --- + +# Run with TCP: 2 proc + 4 procs + +mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" & + +mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python + +# --- + +# Run with MPI: 2 procs + 4 procs + +mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python + +# --- + +# Run in plugin mode: 1 proc + +python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 5 = run AIMD with Python driver code and 2 LAMMPS instances as engines + +# --- + +# Run with TCP: 1 proc each + +python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.1 & + +lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimdpy.mm & + +lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimdpy.qm + +# --- + +# Run with TCP: 2 procs + 2 procs + 3 procs + +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.2 & + +mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.2 -in in.aimdpy.mm & + +mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.3 -in in.aimdpy.qm + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.1 -in in.aimdpy.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.1 -in in.aimdpy.qm > log.aimdpy.driver.mpi.1 + +# --- + +# Run with MPI: 2 procs + 2 procs + 3 procs + +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.2 -in in.aimdpy.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.3 -in in.aimdpy.qm > log.aimdpy.driver.mpi.2 diff --git a/examples/mdi/aimd_driver.py b/examples/mdi/aimd_driver.py index ee493ea31e..062d680a1f 100644 --- a/examples/mdi/aimd_driver.py +++ b/examples/mdi/aimd_driver.py @@ -23,8 +23,8 @@ # -plugin_args arglist # args to add when launching plugin library, only when using plugin mode # enclose arglist in quotes if multiple words -# -nsteps 5 -# number of timesteps, default = 5 +# -nsteps 10 +# number of timesteps, default = 10 import sys import mdi @@ -182,7 +182,7 @@ mdiarg = "" plugin = "" plugin_args = "" -nsteps = 5 +nsteps = 10 # parse command-line args diff --git a/examples/mdi/data.series.0.7 b/examples/mdi/data.series.0.7 new file mode 100644 index 0000000000..641d8b07c9 --- /dev/null +++ b/examples/mdi/data.series.0.7 @@ -0,0 +1,1018 @@ +LAMMPS data file via write_data, version 2 Jun 2022, timestep = 0 + +500 atoms +1 atom types + +0 8.939035350965677 xlo xhi +0 8.939035350965677 ylo yhi +0 8.939035350965677 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.8939035350965676 0.8939035350965676 0 0 0 0 +3 1 0.8939035350965676 0 0.8939035350965676 0 0 0 +4 1 0 0.8939035350965676 0.8939035350965676 0 0 0 +5 1 1.7878070701931352 0 0 0 0 0 +6 1 2.6817106052897026 0.8939035350965676 0 0 0 0 +7 1 2.6817106052897026 0 0.8939035350965676 0 0 0 +8 1 1.7878070701931352 0.8939035350965676 0.8939035350965676 0 0 0 +9 1 3.5756141403862705 0 0 0 0 0 +10 1 4.469517675482838 0.8939035350965676 0 0 0 0 +11 1 4.469517675482838 0 0.8939035350965676 0 0 0 +12 1 3.5756141403862705 0.8939035350965676 0.8939035350965676 0 0 0 +13 1 5.363421210579405 0 0 0 0 0 +14 1 6.257324745675973 0.8939035350965676 0 0 0 0 +15 1 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4.25859 -4.73277 0.116077 +381 1 0.149236 6.9327 4.88187 0.301354 -7.8021 16.5737 +382 1 1.06612 7.54377 5.19235 6.17987 -18.0682 -12.1896 +383 1 0.908663 6.67909 5.83913 1.89859 7.5565 8.00921 +384 1 8.3967 7.73373 5.73713 17.5958 -22.201 25.7152 +385 1 2.09262 6.53099 4.7967 1.84262 19.7267 -15.5304 +386 1 2.6809 7.4184 4.97144 1.84587 -3.02643 6.66108 +387 1 2.76451 6.5131 6.02372 26.4927 9.3308 7.09081 +388 1 1.89235 7.21971 6.07993 -5.61302 23.442 -46.1583 +389 1 3.56452 6.91614 5.29782 1.29026 -2.451 2.37678 +390 1 4.22056 7.80764 5.23329 -2.48711 -3.82055 1.83806 +391 1 4.29263 6.77471 6.12925 7.35038 5.5119 -5.7056 +392 1 2.85273 7.60961 6.07343 16.4578 1.27697 -7.39815 +393 1 4.81773 6.56695 4.97715 -1.40117 8.33727 3.10183 +394 1 5.78811 7.39325 5.43254 7.66799 3.74746 -17.7564 +395 1 5.91597 6.55237 6.07292 -10.3134 0.875812 3.19143 +396 1 5.1536 7.54901 6.2302 -8.62748 1.72241 13.4381 +397 1 6.84976 6.76387 5.09828 -3.19969 2.83039 -4.79256 +398 1 7.54117 7.72913 5.1763 -12.4453 -25.3207 -11.2598 +399 1 7.70324 6.72981 5.83369 -19.5261 3.79708 -10.3274 +400 1 6.77336 7.41197 5.93794 -9.93531 -0.946567 -12.2979 +401 1 8.22949 8.35705 6.76928 1.64244 -1.45449 1.77988 +402 1 0.72004 0.832942 6.72959 22.4465 -5.361 -6.29847 +403 1 0.883022 0.0931191 7.57241 -5.23405 -15.4407 -5.32038 +404 1 0.0468789 0.82113 7.48906 -16.6351 2.71194 14.972 +405 1 2.03902 8.21121 6.63645 7.11775 -8.1199 -7.72414 +406 1 2.8098 1.35985 6.35749 11.4457 2.58538 -2.95276 +407 1 2.39096 8.06897 7.6788 1.19633 7.68608 5.18448 +408 1 1.75996 0.580686 7.28683 6.89284 15.6237 4.36189 +409 1 3.24708 7.93738 6.98795 5.84043 19.9452 -24.3758 +410 1 4.23919 0.919929 6.46503 -1.07654 -9.91612 -5.08402 +411 1 3.90772 0.424381 7.41946 37.0812 -23.6824 -3.45202 +412 1 2.91871 0.505987 7.33506 -26.0302 7.74114 -11.0468 +413 1 4.92803 0.11282 7.09764 -8.28234 1.33652 -4.84063 +414 1 5.89475 1.0043 6.70526 7.29393 0.830325 27.9656 +415 1 5.8956 8.35718 7.44426 -3.02776 0.024361 13.8614 +416 1 4.71342 1.28665 7.29701 10.263 5.35948 11.5905 +417 1 6.8248 0.0574117 7.01961 11.7828 1.29904 -9.90689 +418 1 7.52034 1.04303 6.65362 -4.17639 -6.17679 3.43381 +419 1 7.73603 8.17986 7.79994 1.7859 4.36245 -17.9939 +420 1 7.13318 0.752429 7.78463 13.3591 3.5282 -5.71599 +421 1 8.39243 1.66394 6.67161 -0.134672 7.39125 4.10576 +422 1 0.854509 2.49412 6.65204 0.887161 -2.38052 0.586225 +423 1 1.18138 1.63924 7.31791 -41.6971 -18.352 25.0151 +424 1 0.0943458 2.334 7.66786 0.324396 10.57 -15.5201 +425 1 1.87867 1.74452 6.645 -1.95754 3.46436 -44.2754 +426 1 2.63684 2.47303 6.52845 -8.45632 -20.7999 4.28943 +427 1 2.51699 1.47554 7.37579 1.92109 3.65888 22.6814 +428 1 1.82876 2.39767 7.50566 14.4123 21.9409 0.136363 +429 1 3.78398 2.21463 6.57246 -2.68631 2.13236 -0.792617 +430 1 4.46308 3.07592 6.43555 -3.89191 7.33892 -9.13636 +431 1 3.59875 1.35397 7.20413 -9.98874 22.9069 2.08665 +432 1 3.19396 2.3577 7.56493 -2.6719 3.09783 -0.16421 +433 1 5.06299 2.1644 6.37533 -2.58633 -2.00836 2.79809 +434 1 5.67119 3.15784 6.34996 -0.566548 -6.83481 -5.10746 +435 1 5.66575 1.97666 7.57441 -14.7077 -20.3342 4.08546 +436 1 4.67442 2.64884 7.36908 -6.67424 -36.8328 0.644107 +437 1 6.68154 1.59605 7.24042 -18.9747 -1.14386 -19.0037 +438 1 7.52504 2.47849 6.70825 -1.30537 -8.16455 -5.2397 +439 1 7.60687 1.7083 7.61907 22.0172 -9.53549 -2.5479 +440 1 6.29708 2.66318 7.23348 12.1765 11.0009 -15.9537 +441 1 0.116615 3.32613 6.70965 -8.35482 -2.36763 -31.1169 +442 1 0.754871 4.30259 6.64315 -6.49201 3.33528 -9.76479 +443 1 0.673999 3.30917 7.54182 21.55 -11.008 11.6004 +444 1 8.2904 4.07274 7.4316 9.5379 25.3171 7.28976 +445 1 1.3832 3.4915 6.68441 -1.24784 -22.5622 2.29536 +446 1 2.09272 4.19927 6.89939 7.14914 10.3433 -0.646722 +447 1 2.38812 3.48925 7.75082 -1.53849 -4.15299 -0.56146 +448 1 0.98545 4.31304 7.66307 5.8465 7.34467 12.6645 +449 1 3.01955 3.30623 6.95327 13.2113 8.86686 7.49164 +450 1 4.09943 3.91395 7.09298 -2.48303 5.76893 1.33505 +451 1 4.01094 3.20608 7.89765 -2.70921 2.34384 1.12391 +452 1 3.37728 4.06259 7.97546 3.1883 6.31048 -16.9835 +453 1 4.95274 4.06193 6.44472 -50.262 -12.0969 -14.4258 +454 1 5.82886 4.19415 6.78586 51.8922 14.3443 21.8961 +455 1 5.38346 3.34165 7.34475 16.015 22.8896 8.36611 +456 1 5.08561 4.4601 7.63447 17.0994 -9.93497 -11.4722 +457 1 6.63523 3.51978 6.68288 11.156 -6.22589 -13.2585 +458 1 7.56324 4.26511 6.59456 -1.25309 2.63878 0.745103 +459 1 7.65852 3.28844 7.34661 -10.7372 -4.25374 3.64969 +460 1 6.81691 4.07739 7.53042 5.20496 31.087 -1.8792 +461 1 0.0305913 5.07954 6.63961 -13.4152 -0.334577 -15.0347 +462 1 0.755373 5.9128 6.63716 6.29428 -4.8245 9.83099 +463 1 0.228688 5.17338 7.63443 6.77209 -15.3569 2.77515 +464 1 0.0239769 6.1789 7.50959 5.71025 13.0173 8.45368 +465 1 1.62736 5.16876 6.26262 -1.95267 15.3222 16.2267 +466 1 2.58882 5.57631 6.81228 -21.3734 15.7914 -12.1527 +467 1 2.44828 4.86387 7.63128 0.635145 -14.9061 -0.714387 +468 1 1.59901 5.57209 7.51534 -11.1496 -3.28487 -5.03165 +469 1 3.34619 4.96263 7.08932 17.4571 -30.3367 -0.525226 +470 1 4.2543 5.71212 7.1129 9.72931 3.13017 -7.54215 +471 1 4.20945 4.90695 7.86069 -23.7666 -21.5851 -7.20856 +472 1 3.30097 5.87496 7.52978 -1.62077 18.6793 20.7743 +473 1 5.31869 5.1825 6.70313 -6.70115 -5.30598 20.424 +474 1 6.1285 5.9705 7.04356 -55.8752 -30.7828 -22.045 +475 1 6.19989 5.01385 7.64593 -24.2843 -27.8512 -0.0723503 +476 1 5.23737 5.71302 7.75618 7.88564 -2.82129 -5.95862 +477 1 6.57282 5.00818 6.64579 3.73801 7.56977 2.57742 +478 1 7.65968 6.07456 6.846 -10.6673 -6.72159 -16.2973 +479 1 7.41458 5.08419 7.34751 2.79575 -2.58892 1.26995 +480 1 6.72257 5.83109 7.80136 50.7146 16.6992 29.5346 +481 1 0.0723308 6.76891 6.47705 11.6111 8.10298 22.8191 +482 1 1.02933 7.74537 6.50218 -6.26193 -3.88943 1.15511 +483 1 0.947055 6.70337 7.58592 -5.51835 -14.0139 4.24362 +484 1 0.0848928 7.36532 7.45176 -1.87156 3.22591 1.0451 +485 1 1.56902 6.60766 6.76327 -14.013 -31.9293 15.0177 +486 1 2.40361 7.17234 6.95829 30.5527 12.991 8.35655 +487 1 2.29885 6.36291 7.58786 1.80834 5.53646 4.44151 +488 1 1.553 7.54602 7.43994 -8.27629 2.11355 -7.51923 +489 1 3.47111 6.73135 6.78593 -6.0772 1.66346 11.0677 +490 1 4.24975 7.49747 6.97664 2.8759 -9.15152 10.7243 +491 1 4.10179 6.68273 7.72108 -3.71491 1.8557 -11.1514 +492 1 3.18945 7.41445 7.81539 11.7129 -34.8369 22.2868 +493 1 5.09069 6.56162 6.92242 0.709322 1.72009 4.70344 +494 1 6.15914 7.53992 6.80488 -4.25562 -6.4834 8.29409 +495 1 6.17817 6.79535 7.72789 -19.4606 -0.130997 -26.8387 +496 1 5.10104 7.47088 7.65047 -2.76834 -2.47532 -11.4779 +497 1 6.74018 6.65599 6.74814 32.1985 25.9827 -14.7809 +498 1 7.41102 7.54832 6.72723 12.7336 -14.2037 26.5422 +499 1 7.28837 6.72521 7.66327 11.2322 2.95469 4.78999 +500 1 6.81386 7.67069 7.84231 -16.9841 5.08288 -4.95949 diff --git a/examples/mdi/in.aimd.alone b/examples/mdi/in.aimd.alone index e2857c5704..9332730af4 100644 --- a/examples/mdi/in.aimd.alone +++ b/examples/mdi/in.aimd.alone @@ -29,4 +29,4 @@ fix 1 all nve thermo_style custom step temp pe etotal press vol thermo 1 -run 5 +run 10 diff --git a/examples/mdi/in.aimd.driver b/examples/mdi/in.aimd.driver index 5ee23ebe8d..652048b6c4 100644 --- a/examples/mdi/in.aimd.driver +++ b/examples/mdi/in.aimd.driver @@ -23,10 +23,9 @@ fix 1 all nve # NPT #fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes +fix 2 all mdi/qm virial yes thermo_style custom step temp pe etotal press vol thermo 1 -run 5 +run 10 diff --git a/examples/mdi/in.aimd.driver.plugin b/examples/mdi/in.aimd.driver.plugin index d8c7fdde62..a021f12b07 100644 --- a/examples/mdi/in.aimd.driver.plugin +++ b/examples/mdi/in.aimd.driver.plugin @@ -23,12 +23,11 @@ fix 1 all nve # NPT #fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes +fix 2 all mdi/qm virial yes thermo_style custom step temp pe etotal press vol thermo 1 -mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" & +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" & infile in.aimd.engine extra "-log log.aimd.engine.plugin" & - command "run 5" + command "run 10" diff --git a/examples/mdi/in.aimd.engine b/examples/mdi/in.aimd.engine index 11d22c750e..a64d166a24 100644 --- a/examples/mdi/in.aimd.engine +++ b/examples/mdi/in.aimd.engine @@ -1,16 +1,11 @@ # 3d Lennard-Jones melt - MDI engine script -variable x index 5 -variable y index 5 -variable z index 5 - units lj atom_style atomic -lattice fcc 0.8442 -region box block 0 $x 0 $y 0 $z +lattice fcc 1.0 +region box block 0 1 0 1 0 1 create_box 1 box -create_atoms 1 box mass 1 1.0 pair_style lj/cut 2.5 @@ -19,4 +14,7 @@ pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes +thermo_style custom step temp pe etotal press vol +thermo 1 + mdi engine diff --git a/examples/mdi/in.aimd.mm b/examples/mdi/in.aimdpy.mm similarity index 100% rename from examples/mdi/in.aimd.mm rename to examples/mdi/in.aimdpy.mm diff --git a/examples/mdi/in.aimd.qm b/examples/mdi/in.aimdpy.qm similarity index 100% rename from examples/mdi/in.aimd.qm rename to examples/mdi/in.aimdpy.qm diff --git a/examples/mdi/in.sequence b/examples/mdi/in.sequence.python similarity index 99% rename from examples/mdi/in.sequence rename to examples/mdi/in.sequence.python index c094326ae7..6f28922a66 100644 --- a/examples/mdi/in.sequence +++ b/examples/mdi/in.sequence.python @@ -19,3 +19,4 @@ fix 1 all nve thermo 10 mdi engine + diff --git a/examples/mdi/in.series.alone b/examples/mdi/in.series.alone new file mode 100644 index 0000000000..2e17468507 --- /dev/null +++ b/examples/mdi/in.series.alone @@ -0,0 +1,37 @@ +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + + displace_atoms all random 0.1 0.1 0.1 48294 + + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + compute 1 all pressure NULL virial + + thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + + run 0 + + write_dump all custom dump.series.alone & + id type x y z fx fy fz modify sort id append yes + + clear + +next rho + +jump SELF LOOP diff --git a/examples/mdi/in.series.driver b/examples/mdi/in.series.driver new file mode 100644 index 0000000000..267df465fc --- /dev/null +++ b/examples/mdi/in.series.driver @@ -0,0 +1,39 @@ +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +mdi connect + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + + displace_atoms all random 0.1 0.1 0.1 48294 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 + + write_dump all custom dump.series.driver & + id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + +mdi exit diff --git a/examples/mdi/in.series.driver.plugin b/examples/mdi/in.series.driver.plugin new file mode 100644 index 0000000000..f1189940b4 --- /dev/null +++ b/examples/mdi/in.series.driver.plugin @@ -0,0 +1,38 @@ +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + + displace_atoms all random 0.1 0.1 0.1 48294 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" & + infile in.series.engine & + extra "-log log.series.engine.plugin" & + command "run 0" + + write_dump all custom dump.series.driver.plugin & + id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP diff --git a/examples/mdi/in.series.engine b/examples/mdi/in.series.engine new file mode 100644 index 0000000000..f3293e048d --- /dev/null +++ b/examples/mdi/in.series.engine @@ -0,0 +1,17 @@ +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +region box block 0 1 0 1 0 1 +create_box 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine diff --git a/examples/mdi/in.snapshot.alone b/examples/mdi/in.snapshot.alone new file mode 100644 index 0000000000..7633dcaae3 --- /dev/null +++ b/examples/mdi/in.snapshot.alone @@ -0,0 +1,28 @@ +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +compute 1 all pressure NULL virial + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.alone & + id type x y z fx fy fz +dump_modify 1 sort id + +run 300 diff --git a/examples/mdi/in.snapshot.driver b/examples/mdi/in.snapshot.driver new file mode 100644 index 0000000000..78205efb0f --- /dev/null +++ b/examples/mdi/in.snapshot.driver @@ -0,0 +1,33 @@ +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver & + id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +run 300 pre no post no every 100 & + "print 'QM eng = $(f_2/atoms)'" & + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" diff --git a/examples/mdi/in.snapshot.driver.plugin b/examples/mdi/in.snapshot.driver.plugin new file mode 100644 index 0000000000..37f0fba2f9 --- /dev/null +++ b/examples/mdi/in.snapshot.driver.plugin @@ -0,0 +1,42 @@ +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +read_data data.snapshot + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver.plugin & + id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" & + infile in.snapshot.engine & + extra "-log log.snapshot.engine.plugin" & + command """ + run 300 pre no post no every 100 + "print 'QM eng = $(f_2/atoms)'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + """ diff --git a/examples/mdi/in.snapshot.engine b/examples/mdi/in.snapshot.engine new file mode 100644 index 0000000000..f3293e048d --- /dev/null +++ b/examples/mdi/in.snapshot.engine @@ -0,0 +1,17 @@ +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +region box block 0 1 0 1 0 1 +create_box 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine diff --git a/examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 b/examples/mdi/log.17Jun22.aimd.alone.1 similarity index 50% rename from examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 rename to examples/mdi/log.17Jun22.aimd.alone.1 index 5fa3743530..c7b0f2c492 100644 --- a/examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 +++ b/examples/mdi/log.17Jun22.aimd.alone.1 @@ -1,4 +1,4 @@ -LAMMPS (17 Feb 2022) +LAMMPS (2 Jun 2022) # 3d Lennard-Jones melt - MDI driver script variable x index 5 @@ -39,8 +39,8 @@ fix 1 all nve thermo_style custom step temp pe etotal press vol thermo 1 -run 5 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +run 10 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -54,37 +54,42 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 0.00919691 on 1 procs for 10 steps with 500 atoms -Performance: 505739.085 tau/day, 1170.692 timesteps/s -73.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 469723.136 tau/day, 1087.322 timesteps/s +98.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04 -Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49 -Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53 -Other | | 6.054e-05 | | | 1.42 +Pair | 0.0066536 | 0.0066536 | 0.0066536 | 0.0 | 72.35 +Neigh | 0.0017906 | 0.0017906 | 0.0017906 | 0.0 | 19.47 +Comm | 0.0002554 | 0.0002554 | 0.0002554 | 0.0 | 2.78 +Output | 0.00029976 | 0.00029976 | 0.00029976 | 0.0 | 3.26 +Modify | 9.8718e-05 | 9.8718e-05 | 9.8718e-05 | 0.0 | 1.07 +Other | | 9.887e-05 | | | 1.08 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1956 ave 1956 max 1956 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 19500 ave 19500 max 19500 min +Neighs: 19396 ave 19396 max 19396 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 19500 -Ave neighs/atom = 39 -Neighbor list builds = 0 +Total # of neighbors = 19396 +Ave neighs/atom = 38.792 +Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.driver.mpi.1 b/examples/mdi/log.17Jun22.aimd.driver.mpi.1 new file mode 100644 index 0000000000..e06ca0ada1 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.mpi.1 @@ -0,0 +1,83 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 0.0078442 on 1 procs for 10 steps with 500 atoms + +Performance: 550725.026 tau/day, 1274.826 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.592e-06 | 1.592e-06 | 1.592e-06 | 0.0 | 0.02 +Comm | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.34 +Output | 0.00021168 | 0.00021168 | 0.00021168 | 0.0 | 2.70 +Modify | 0.0075488 | 0.0075488 | 0.0075488 | 0.0 | 96.23 +Other | | 5.544e-05 | | | 0.71 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.driver.mpi.3 b/examples/mdi/log.17Jun22.aimd.driver.mpi.3 new file mode 100644 index 0000000000..e2f228ca6c --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.mpi.3 @@ -0,0 +1,83 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 0.00523112 on 3 procs for 10 steps with 500 atoms + +Performance: 825827.658 tau/day, 1911.638 timesteps/s +98.8% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 5.95e-07 | 1.7073e-06 | 3.907e-06 | 0.0 | 0.03 +Comm | 3.8259e-05 | 6.2707e-05 | 7.5974e-05 | 0.0 | 1.20 +Output | 0.00017543 | 0.00021238 | 0.00028075 | 0.0 | 4.06 +Modify | 0.004815 | 0.0048289 | 0.0048521 | 0.0 | 92.31 +Other | | 0.0001254 | | | 2.40 + +Nlocal: 166.667 ave 176 max 150 min +Histogram: 1 0 0 0 0 0 0 0 0 2 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.driver.plugin.1 b/examples/mdi/log.17Jun22.aimd.driver.plugin.1 new file mode 100644 index 0000000000..73779fc350 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.plugin.1 @@ -0,0 +1,84 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10" +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 0.00940117 on 1 procs for 10 steps with 500 atoms + +Performance: 459517.175 tau/day, 1063.697 timesteps/s +96.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.9e-06 | 1.9e-06 | 1.9e-06 | 0.0 | 0.02 +Comm | 3.0131e-05 | 3.0131e-05 | 3.0131e-05 | 0.0 | 0.32 +Output | 0.00030359 | 0.00030359 | 0.00030359 | 0.0 | 3.23 +Modify | 0.0090041 | 0.0090041 | 0.0090041 | 0.0 | 95.78 +Other | | 6.144e-05 | | | 0.65 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.driver.plugin.3 b/examples/mdi/log.17Jun22.aimd.driver.plugin.3 new file mode 100644 index 0000000000..7bb02f5f35 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.plugin.3 @@ -0,0 +1,84 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10" +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 0.00613177 on 3 procs for 10 steps with 500 atoms + +Performance: 704527.327 tau/day, 1630.850 timesteps/s +99.2% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.93e-07 | 1.8723e-06 | 3.996e-06 | 0.0 | 0.03 +Comm | 4.4254e-05 | 7.4628e-05 | 9.321e-05 | 0.0 | 1.22 +Output | 0.00019476 | 0.00024309 | 0.00032745 | 0.0 | 3.96 +Modify | 0.005637 | 0.0056559 | 0.0056903 | 0.0 | 92.24 +Other | | 0.0001563 | | | 2.55 + +Nlocal: 166.667 ave 176 max 150 min +Histogram: 1 0 0 0 0 0 0 0 0 2 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.driver.tcp.1 b/examples/mdi/log.17Jun22.aimd.driver.tcp.1 new file mode 100644 index 0000000000..db7413cc9e --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.tcp.1 @@ -0,0 +1,83 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 2.41182 on 1 procs for 10 steps with 500 atoms + +Performance: 1791.180 tau/day, 4.146 timesteps/s +0.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 2.596e-06 | 2.596e-06 | 2.596e-06 | 0.0 | 0.00 +Comm | 4.9627e-05 | 4.9627e-05 | 4.9627e-05 | 0.0 | 0.00 +Output | 0.00063707 | 0.00063707 | 0.00063707 | 0.0 | 0.03 +Modify | 2.411 | 2.411 | 2.411 | 0.0 | 99.97 +Other | | 0.0001146 | | | 0.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.17Jun22.aimd.driver.tcp.3 b/examples/mdi/log.17Jun22.aimd.driver.tcp.3 new file mode 100644 index 0000000000..43910d1a25 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.driver.tcp.3 @@ -0,0 +1,83 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +# NVE +fix 1 all nve +# NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 + +fix 2 all mdi/qm virial yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +run 10 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp PotEng TotEng Press Volume + 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 + 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 + 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 + 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 + 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 + 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 + 6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671 + 7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671 + 8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671 + 9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671 + 10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671 +Loop time of 2.39983 on 3 procs for 10 steps with 500 atoms + +Performance: 1800.127 tau/day, 4.167 timesteps/s +66.7% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 3.75e-07 | 1.3583e-06 | 2.574e-06 | 0.0 | 0.00 +Comm | 5.4167e-05 | 0.00010938 | 0.00015338 | 0.0 | 0.00 +Output | 0.00030885 | 0.00042099 | 0.00064497 | 0.0 | 0.02 +Modify | 2.3988 | 2.3989 | 2.3989 | 0.0 | 99.96 +Other | | 0.0004276 | | | 0.02 + +Nlocal: 166.667 ave 176 max 150 min +Histogram: 1 0 0 0 0 0 0 0 0 2 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/mdi/log.17Jun22.aimd.engine.mpi.1 b/examples/mdi/log.17Jun22.aimd.engine.mpi.1 new file mode 100644 index 0000000000..cb2e94c705 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.mpi.1 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.engine.mpi.4 b/examples/mdi/log.17Jun22.aimd.engine.mpi.4 new file mode 100644 index 0000000000..6d390106ce --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.mpi.4 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.engine.plugin.1 b/examples/mdi/log.17Jun22.aimd.engine.plugin.1 new file mode 100644 index 0000000000..cb2e94c705 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.plugin.1 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.engine.plugin.3 b/examples/mdi/log.17Jun22.aimd.engine.plugin.3 new file mode 100644 index 0000000000..cd227cffd0 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.plugin.3 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 3 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 3 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimd.engine.tcp.1 b/examples/mdi/log.17Jun22.aimd.engine.tcp.1 new file mode 100644 index 0000000000..9b1ae4a9e1 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.tcp.1 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.17Jun22.aimd.engine.tcp.4 b/examples/mdi/log.17Jun22.aimd.engine.tcp.4 new file mode 100644 index 0000000000..7bca369d96 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimd.engine.tcp.4 @@ -0,0 +1,55 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +thermo_style custom step temp pe etotal press vol +thermo 1 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes + Step Temp PotEng TotEng Press Volume + 0 0 -6.7733681 -6.7733681 -6.2353173 592.27671 + 1 0 -6.7699814 -6.7699814 -6.2120481 592.27671 + 2 0 -6.7596844 -6.7596844 -6.1418368 592.27671 + 3 0 -6.7420029 -6.7420029 -6.0231905 592.27671 + 4 0 -6.7161132 -6.7161132 -5.8534999 592.27671 + 5 0 -6.6808361 -6.6808361 -5.6291449 592.27671 + 6 0 -6.6344152 -6.6344152 -5.3453369 592.27671 + 7 0 -6.5752633 -6.5752633 -4.9977496 592.27671 + 8 0 -6.502724 -6.502724 -4.5844158 592.27671 + 9 0 -6.4153971 -6.4153971 -4.103842 592.27671 + 10 0 -6.3153532 -6.3153532 -3.5633405 592.27671 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.17Jun22.aimdpy.driver.mpi.1 b/examples/mdi/log.17Jun22.aimdpy.driver.mpi.1 new file mode 100644 index 0000000000..c0e8df8217 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.driver.mpi.1 @@ -0,0 +1,77 @@ +LAMMPS (2 Jun 2022) +LAMMPS (2 Jun 2022) +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.000 seconds +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 +Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769 +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 +Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 +Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 + 2 1.430825 0 0 2.141945 1.2054866 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 +Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 +Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 +Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 +Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 +Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 0 -6.502724 0 -6.502724 -4.5844158 +Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 0 -6.4153971 0 -6.4153971 -4.103842 +Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 +Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:00 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimdpy.driver.mpi.2 b/examples/mdi/log.17Jun22.aimdpy.driver.mpi.2 new file mode 100644 index 0000000000..7c839dc2d4 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.driver.mpi.2 @@ -0,0 +1,77 @@ +LAMMPS (2 Jun 2022) +LAMMPS (2 Jun 2022) +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 2 MPI processor grid +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.000 seconds +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 +Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769 +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 +Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 +Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 + 2 1.430825 0 0 2.141945 1.2054866 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 +Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 +Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 +Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 +Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 +Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 0 -6.502724 0 -6.502724 -4.5844158 +Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 0 -6.4153971 0 -6.4153971 -4.103842 +Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 +Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:00 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 b/examples/mdi/log.17Jun22.aimdpy.driver.tcp.1 similarity index 54% rename from examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 rename to examples/mdi/log.17Jun22.aimdpy.driver.tcp.1 index 2205a0f051..6ae0d7b714 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 +++ b/examples/mdi/log.17Jun22.aimdpy.driver.tcp.1 @@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 +Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773 +Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617 +Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654 +Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158 +Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 b/examples/mdi/log.17Jun22.aimdpy.driver.tcp.2 similarity index 54% rename from examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 rename to examples/mdi/log.17Jun22.aimdpy.driver.tcp.2 index 2205a0f051..6ae0d7b714 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 +++ b/examples/mdi/log.17Jun22.aimdpy.driver.tcp.2 @@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 +Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773 +Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617 +Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654 +Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158 +Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166 diff --git a/examples/mdi/log.17Jun22.aimdpy.mm.mpi.1 b/examples/mdi/log.17Jun22.aimdpy.mm.mpi.1 new file mode 100644 index 0000000000..2b9251e6fd --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.mm.mpi.1 @@ -0,0 +1,49 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +mdi engine +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 1.430825 0 0 2.141945 1.2054866 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimdpy.mm.mpi.2 b/examples/mdi/log.17Jun22.aimdpy.mm.mpi.2 new file mode 100644 index 0000000000..cb46801dac --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.mm.mpi.2 @@ -0,0 +1,49 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +mdi engine +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 1.430825 0 0 2.141945 1.2054866 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.aimdpy.mm.tcp.1 b/examples/mdi/log.17Jun22.aimdpy.mm.tcp.1 new file mode 100644 index 0000000000..a23fcbac53 --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.mm.tcp.1 @@ -0,0 +1,49 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +mdi engine +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 1.430825 0 0 2.141945 1.2054866 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.17Jun22.aimdpy.mm.tcp.2 b/examples/mdi/log.17Jun22.aimdpy.mm.tcp.2 new file mode 100644 index 0000000000..fab47d094f --- /dev/null +++ b/examples/mdi/log.17Jun22.aimdpy.mm.tcp.2 @@ -0,0 +1,49 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +mdi engine +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 2.15568 1.2132167 + 1 1.4377309 0 0 2.1522832 1.211305 + 2 1.430825 0 0 2.141945 1.2054866 + 3 1.4189655 0 0 2.1241913 1.1954949 + 4 1.4016029 0 0 2.0981995 1.1808667 + 5 1.3779738 0 0 2.0628267 1.1609589 + 6 1.3471497 0 0 2.016683 1.1349892 + 7 1.3081237 0 0 1.9582612 1.1021094 + 8 1.2599751 0 0 1.8861828 1.0615437 + 9 1.2021373 0 0 1.7995995 1.0128146 + 10 1.1347688 0 0 1.6987489 0.95605588 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 b/examples/mdi/log.17Jun22.aimdpy.qm.mpi.1 similarity index 53% rename from examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 rename to examples/mdi/log.17Jun22.aimdpy.qm.mpi.1 index e75a12c948..f365e18542 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 +++ b/examples/mdi/log.17Jun22.aimdpy.qm.mpi.1 @@ -1,4 +1,4 @@ -LAMMPS (17 Feb 2022) +LAMMPS (2 Jun 2022) # 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py variable x index 5 @@ -20,7 +20,7 @@ Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) create_atoms 1 box Created 500 atoms using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.000 seconds mass 1 1.0 pair_style lj/cut 2.5 @@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes mdi engine WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,11 +45,16 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 + 8 0 -6.502724 0 -6.502724 -4.5844158 + 9 0 -6.4153971 0 -6.4153971 -4.103842 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 b/examples/mdi/log.17Jun22.aimdpy.qm.mpi.3 similarity index 54% rename from examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 rename to examples/mdi/log.17Jun22.aimdpy.qm.mpi.3 index 5d6702100c..87501440b7 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 +++ b/examples/mdi/log.17Jun22.aimdpy.qm.mpi.3 @@ -1,4 +1,4 @@ -LAMMPS (17 Feb 2022) +LAMMPS (2 Jun 2022) # 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py variable x index 5 @@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes mdi engine WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,11 +45,16 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 + 8 0 -6.502724 0 -6.502724 -4.5844158 + 9 0 -6.4153971 0 -6.4153971 -4.103842 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 b/examples/mdi/log.17Jun22.aimdpy.qm.tcp.1 similarity index 53% rename from examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 rename to examples/mdi/log.17Jun22.aimdpy.qm.tcp.1 index 8750392def..1dd64c4beb 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 +++ b/examples/mdi/log.17Jun22.aimdpy.qm.tcp.1 @@ -1,4 +1,4 @@ -LAMMPS (17 Feb 2022) +LAMMPS (2 Jun 2022) # 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py variable x index 5 @@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes mdi engine WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,11 +45,16 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 + 8 0 -6.502724 0 -6.502724 -4.5844158 + 9 0 -6.4153971 0 -6.4153971 -4.103842 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 b/examples/mdi/log.17Jun22.aimdpy.qm.tcp.3 similarity index 53% rename from examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 rename to examples/mdi/log.17Jun22.aimdpy.qm.tcp.3 index cd5d443e65..2006741b75 100644 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 +++ b/examples/mdi/log.17Jun22.aimdpy.qm.tcp.3 @@ -1,4 +1,4 @@ -LAMMPS (17 Feb 2022) +LAMMPS (2 Jun 2022) # 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py variable x index 5 @@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes mdi engine WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,11 +45,16 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -6.7699814 0 -6.7699814 -6.2120481 + 2 0 -6.7596844 0 -6.7596844 -6.1418368 + 3 0 -6.7420029 0 -6.7420029 -6.0231905 + 4 0 -6.7161132 0 -6.7161132 -5.8534999 + 5 0 -6.6808361 0 -6.6808361 -5.6291449 + 6 0 -6.6344152 0 -6.6344152 -5.3453369 + 7 0 -6.5752633 0 -6.5752633 -4.9977496 + 8 0 -6.502724 0 -6.502724 -4.5844158 + 9 0 -6.4153971 0 -6.4153971 -4.103842 + 10 0 -6.3153532 0 -6.3153532 -3.5633405 +Total wall time: 0:00:02 diff --git a/examples/mdi/log.17Jun22.sequence.engine.mpi.1 b/examples/mdi/log.17Jun22.sequence.engine.mpi.1 new file mode 100644 index 0000000000..78a5fe3cb6 --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.mpi.1 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.sequence.engine.mpi.4 b/examples/mdi/log.17Jun22.sequence.engine.mpi.4 new file mode 100644 index 0000000000..856166696c --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.mpi.4 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.sequence.engine.plugin.1 b/examples/mdi/log.17Jun22.sequence.engine.plugin.1 new file mode 100644 index 0000000000..78a5fe3cb6 --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.plugin.1 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.sequence.engine.plugin.3 b/examples/mdi/log.17Jun22.sequence.engine.plugin.3 new file mode 100644 index 0000000000..4cb140028a --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.plugin.3 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 1 by 3 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 3 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 3 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 3 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.sequence.engine.tcp.1 b/examples/mdi/log.17Jun22.sequence.engine.tcp.1 new file mode 100644 index 0000000000..78a5fe3cb6 --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.tcp.1 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.sequence.engine.tcp.4 b/examples/mdi/log.17Jun22.sequence.engine.tcp.4 new file mode 100644 index 0000000000..856166696c --- /dev/null +++ b/examples/mdi/log.17Jun22.sequence.engine.tcp.4 @@ -0,0 +1,90 @@ +LAMMPS (2 Jun 2022) +# MDI engine script to process a series of evaulate, run, minimize commands + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +thermo 10 + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.9713146 0 -2.4947521 3.1253597 + 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 + 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 + 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 + 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 + 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 + 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 + 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 + 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 + 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 + 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -4.1934138 0 -2.7168513 0.72358299 + 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 + 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 + 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 + 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 + 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 + 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 + 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 + 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 + 90 1.219283 -4.5483185 0 -2.747971 0.17898549 + 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 +delete_atoms group all +Deleted 64 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 1 -3.8524214 0 -2.3758589 4.6814052 + 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 + 20 1.1791601 -4.117932 0 -2.3768284 3.8565 + 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 + 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 + 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 + 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 + 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 + 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 + 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 + 100 1.43934 -4.5009545 0 -2.375679 3.0923444 + +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.alone.1 b/examples/mdi/log.17Jun22.series.alone.1 new file mode 100644 index 0000000000..3e44a5c950 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.alone.1 @@ -0,0 +1,248 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + compute 1 all pressure NULL virial + + thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 2.729e-06 on 1 procs for 0 steps with 500 atoms + +109.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.729e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 15687 ave 15687 max 15687 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15687 +Ave neighs/atom = 31.374 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + compute 1 all pressure NULL virial + + thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.135 | 3.135 | 3.135 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 1.434e-06 on 1 procs for 0 steps with 500 atoms + +139.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.434e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18734 ave 18734 max 18734 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18734 +Ave neighs/atom = 37.468 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + compute 1 all pressure NULL virial + + thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 1.483e-06 on 1 procs for 0 steps with 500 atoms + +134.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.483e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 20023 ave 20023 max 20023 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 20023 +Ave neighs/atom = 40.046 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes + + clear + +next rho + +jump SELF LOOP +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.mpi.1 b/examples/mdi/log.17Jun22.series.driver.mpi.1 new file mode 100644 index 0000000000..4b109f8724 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.mpi.1 @@ -0,0 +1,213 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +mdi connect + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 1.919e-06 on 1 procs for 0 steps with 500 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.919e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 1.141e-06 on 1 procs for 0 steps with 500 atoms + +87.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.141e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.002 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 1.019e-06 on 1 procs for 0 steps with 500 atoms + +98.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.019e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + +mdi exit +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.mpi.3 b/examples/mdi/log.17Jun22.series.driver.mpi.3 new file mode 100644 index 0000000000..9c042f4194 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.mpi.3 @@ -0,0 +1,213 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +mdi connect + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 4.00933e-06 on 3 procs for 0 steps with 500 atoms + +91.5% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 4.009e-06 | | |100.00 + +Nlocal: 166.667 ave 177 max 150 min +Histogram: 1 0 0 0 0 0 0 0 1 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 3.11833e-06 on 3 procs for 0 steps with 500 atoms + +117.6% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.118e-06 | | |100.00 + +Nlocal: 166.667 ave 178 max 150 min +Histogram: 1 0 0 0 0 0 0 1 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 3 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 2.85467e-06 on 3 procs for 0 steps with 500 atoms + +140.1% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.855e-06 | | |100.00 + +Nlocal: 166.667 ave 181 max 150 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + +mdi exit +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.plugin.1 b/examples/mdi/log.17Jun22.series.driver.plugin.1 new file mode 100644 index 0000000000..13dd0f0f23 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.plugin.1 @@ -0,0 +1,212 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 2.359e-06 on 1 procs for 0 steps with 500 atoms + +127.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.359e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 1.468e-06 on 1 procs for 0 steps with 500 atoms + +204.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.468e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 1.378e-06 on 1 procs for 0 steps with 500 atoms + +145.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.378e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.plugin.3 b/examples/mdi/log.17Jun22.series.driver.plugin.3 new file mode 100644 index 0000000000..e32b35738f --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.plugin.3 @@ -0,0 +1,212 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 3.50867e-06 on 3 procs for 0 steps with 500 atoms + +114.0% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.509e-06 | | |100.00 + +Nlocal: 166.667 ave 177 max 150 min +Histogram: 1 0 0 0 0 0 0 0 1 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 3.225e-06 on 3 procs for 0 steps with 500 atoms + +82.7% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.225e-06 | | |100.00 + +Nlocal: 166.667 ave 178 max 150 min +Histogram: 1 0 0 0 0 0 0 1 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 3 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 2.713e-06 on 3 procs for 0 steps with 500 atoms + +98.3% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.713e-06 | | |100.00 + +Nlocal: 166.667 ave 181 max 150 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.tcp.1 b/examples/mdi/log.17Jun22.series.driver.tcp.1 new file mode 100644 index 0000000000..852f08a622 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.tcp.1 @@ -0,0 +1,213 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +mdi connect + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 3.017e-06 on 1 procs for 0 steps with 500 atoms + +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.017e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 1.977e-06 on 1 procs for 0 steps with 500 atoms + +101.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.977e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 2.042e-06 on 1 procs for 0 steps with 500 atoms + +97.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.042e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + +mdi exit +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.driver.tcp.3 b/examples/mdi/log.17Jun22.series.driver.tcp.3 new file mode 100644 index 0000000000..5b2395c275 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.driver.tcp.3 @@ -0,0 +1,213 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +variable rho index 0.7 0.8 0.9 + +mdi connect + +label LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.7 +Reading data file ... + orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366 +Loop time of 9.08933e-06 on 3 procs for 0 steps with 500 atoms + +95.3% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.089e-06 | | |100.00 + +Nlocal: 166.667 ave 177 max 150 min +Histogram: 1 0 0 0 0 0 0 0 1 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.8 +Reading data file ... + orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971 +Loop time of 3.63567e-06 on 3 procs for 0 steps with 500 atoms + +100.9% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.636e-06 | | |100.00 + +Nlocal: 166.667 ave 178 max 150 min +Histogram: 1 0 0 0 0 0 0 1 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + + units lj + atom_style atomic + + read_data data.series.${rho} + read_data data.series.0.9 +Reading data file ... + orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069) + 3 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + + displace_atoms all random 0.1 0.1 0.1 48294 +Displacing atoms ... + + neighbor 0.3 bin + neigh_modify delay 0 every 1 check yes + + fix 1 all mdi/qm add no virial yes connect no + variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3 + + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes + Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3] + 0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696 +Loop time of 3.806e-06 on 3 procs for 0 steps with 500 atoms + +105.1% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.806e-06 | | |100.00 + +Nlocal: 166.667 ave 181 max 150 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes + + clear + +next rho + +jump SELF LOOP + +mdi exit +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.mpi.1 b/examples/mdi/log.17Jun22.series.engine.mpi.1 new file mode 100644 index 0000000000..f644edc8d1 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.mpi.1 @@ -0,0 +1,58 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -5.200819 0 -5.200819 -4.5647906 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.0419499 0 -6.0419499 -4.2737827 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.mpi.4 b/examples/mdi/log.17Jun22.series.engine.mpi.4 new file mode 100644 index 0000000000..3561f4d232 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.mpi.4 @@ -0,0 +1,58 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -5.200819 0 -5.200819 -4.5647906 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.0419499 0 -6.0419499 -4.2737827 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.plugin.1 b/examples/mdi/log.17Jun22.series.engine.plugin.1 new file mode 100644 index 0000000000..322b40ad0e --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.plugin.1 @@ -0,0 +1,42 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.plugin.3 b/examples/mdi/log.17Jun22.series.engine.plugin.3 new file mode 100644 index 0000000000..861a422e6b --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.plugin.3 @@ -0,0 +1,42 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 3 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 3 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.105 | 3.107 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.tcp.1 b/examples/mdi/log.17Jun22.series.engine.tcp.1 new file mode 100644 index 0000000000..f644edc8d1 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.tcp.1 @@ -0,0 +1,58 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -5.200819 0 -5.200819 -4.5647906 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.0419499 0 -6.0419499 -4.2737827 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.series.engine.tcp.4 b/examples/mdi/log.17Jun22.series.engine.tcp.4 new file mode 100644 index 0000000000..3561f4d232 --- /dev/null +++ b/examples/mdi/log.17Jun22.series.engine.tcp.4 @@ -0,0 +1,58 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -5.200819 0 -5.200819 -4.5647906 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.0419499 0 -6.0419499 -4.2737827 +delete_atoms group all +Deleted 500 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.4477578 0 -6.4477578 -1.5268553 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.alone.1 b/examples/mdi/log.17Jun22.snapshot.alone.1 new file mode 100644 index 0000000000..44c39554f6 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.alone.1 @@ -0,0 +1,82 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +compute 1 all pressure NULL virial + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.alone id type x y z fx fy fz +dump_modify 1 sort id + +run 300 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.159268 on 1 procs for 300 steps with 500 atoms + +Performance: 813725.152 tau/day, 1883.623 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10659 | 0.10659 | 0.10659 | 0.0 | 66.93 +Neigh | 0.038637 | 0.038637 | 0.038637 | 0.0 | 24.26 +Comm | 0.0053144 | 0.0053144 | 0.0053144 | 0.0 | 3.34 +Output | 0.0048583 | 0.0048583 | 0.0048583 | 0.0 | 3.05 +Modify | 0.002043 | 0.002043 | 0.002043 | 0.0 | 1.28 +Other | | 0.001821 | | | 1.14 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1898 ave 1898 max 1898 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18744 ave 18744 max 18744 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.mpi.1 b/examples/mdi/log.17Jun22.snapshot.driver.mpi.1 new file mode 100644 index 0000000000..cf15f32e9b --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.mpi.1 @@ -0,0 +1,105 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.003 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.052449 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734575789 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.0497171 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7528640103266583949 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.0506296 on 1 procs for 100 steps with 500 atoms + +Performance: 853255.432 tau/day, 1975.128 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.032111 | 0.032111 | 0.032111 | 0.0 | 63.42 +Neigh | 0.012403 | 0.012403 | 0.012403 | 0.0 | 24.50 +Comm | 0.0016352 | 0.0016352 | 0.0016352 | 0.0 | 3.23 +Output | 0.001556 | 0.001556 | 0.001556 | 0.0 | 3.07 +Modify | 0.0023767 | 0.0023767 | 0.0023767 | 0.0 | 4.69 +Other | | 0.0005478 | | | 1.08 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1898 ave 1898 max 1898 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18744 ave 18744 max 18744 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7527974697327088904 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.mpi.3 b/examples/mdi/log.17Jun22.snapshot.driver.mpi.3 new file mode 100644 index 0000000000..8382b128e1 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.mpi.3 @@ -0,0 +1,105 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.0242313 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734558025 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.0269411 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.752864010326673494 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.022648 on 3 procs for 100 steps with 500 atoms + +Performance: 1907449.463 tau/day, 4415.392 timesteps/s +100.0% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0091419 | 0.010422 | 0.011089 | 0.9 | 46.02 +Neigh | 0.0036491 | 0.0040749 | 0.0043554 | 0.5 | 17.99 +Comm | 0.004713 | 0.0056035 | 0.0073471 | 1.6 | 24.74 +Output | 0.00062782 | 0.00063348 | 0.00064461 | 0.0 | 2.80 +Modify | 0.0013385 | 0.0013655 | 0.0013943 | 0.1 | 6.03 +Other | | 0.0005485 | | | 2.42 + +Nlocal: 166.667 ave 175 max 157 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 1254.33 ave 1264 max 1246 min +Histogram: 1 0 0 1 0 0 0 0 0 1 +Neighs: 6248 ave 6632 max 5774 min +Histogram: 1 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.752797469732716884 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.plugin.1 b/examples/mdi/log.17Jun22.snapshot.driver.plugin.1 new file mode 100644 index 0000000000..4d140820c8 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.plugin.1 @@ -0,0 +1,118 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """ + run 300 pre no post no every 100 + "print 'QM eng = $(f_2/atoms)'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + """ + + run 300 pre no post no every 100 + "print 'QM eng = $(f_2/atoms)'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.0623265 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734575789 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.0498825 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7528640103266583949 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.050109 on 1 procs for 100 steps with 500 atoms + +Performance: 862120.560 tau/day, 1995.649 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031747 | 0.031747 | 0.031747 | 0.0 | 63.36 +Neigh | 0.012304 | 0.012304 | 0.012304 | 0.0 | 24.55 +Comm | 0.0016113 | 0.0016113 | 0.0016113 | 0.0 | 3.22 +Output | 0.0015529 | 0.0015529 | 0.0015529 | 0.0 | 3.10 +Modify | 0.0023537 | 0.0023537 | 0.0023537 | 0.0 | 4.70 +Other | | 0.0005398 | | | 1.08 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1898 ave 1898 max 1898 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18744 ave 18744 max 18744 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7527974697327088904 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.plugin.3 b/examples/mdi/log.17Jun22.snapshot.driver.plugin.3 new file mode 100644 index 0000000000..bb39f53598 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.plugin.3 @@ -0,0 +1,118 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """ + run 300 pre no post no every 100 + "print 'QM eng = $(f_2/atoms)'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + """ + + run 300 pre no post no every 100 + "print 'QM eng = $(f_2/atoms)'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.0245664 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734442562 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566498001 -0.48020228608205661747 -0.33571704057970125357 -0.43928725961523629184 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.0221302 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7528640103266690531 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957305301251 -0.51524577748319111414 -0.27940441114042025017 -0.42108499009554783976 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.0224519 on 3 procs for 100 steps with 500 atoms + +Performance: 1924114.069 tau/day, 4453.968 timesteps/s +100.0% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0096043 | 0.010493 | 0.011044 | 0.6 | 46.74 +Neigh | 0.0037658 | 0.0041299 | 0.004422 | 0.4 | 18.39 +Comm | 0.0048946 | 0.0055617 | 0.0068824 | 1.3 | 24.77 +Output | 0.00063471 | 0.00063884 | 0.00064691 | 0.0 | 2.85 +Modify | 0.0010632 | 0.0010754 | 0.0010895 | 0.0 | 4.79 +Other | | 0.0005531 | | | 2.46 + +Nlocal: 166.667 ave 175 max 157 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 1254.33 ave 1264 max 1246 min +Histogram: 1 0 0 1 0 0 0 0 0 1 +Neighs: 6248 ave 6632 max 5774 min +Histogram: 1 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7527974697327239895 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315521697958 -0.24280603320323956851 -0.42189158691169470483 -0.59061971935071611028 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.tcp.1 b/examples/mdi/log.17Jun22.snapshot.driver.tcp.1 new file mode 100644 index 0000000000..905e53e8e4 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.tcp.1 @@ -0,0 +1,105 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.004 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.276735 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734575789 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.276667 on 1 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7528640103266583949 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.278602 on 1 procs for 100 steps with 500 atoms + +Performance: 155060.058 tau/day, 358.935 timesteps/s +26.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.049067 | 0.049067 | 0.049067 | 0.0 | 17.61 +Neigh | 0.01894 | 0.01894 | 0.01894 | 0.0 | 6.80 +Comm | 0.0026936 | 0.0026936 | 0.0026936 | 0.0 | 0.97 +Output | 0.002919 | 0.002919 | 0.002919 | 0.0 | 1.05 +Modify | 0.20406 | 0.20406 | 0.20406 | 0.0 | 73.24 +Other | | 0.0009253 | | | 0.33 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1898 ave 1898 max 1898 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18744 ave 18744 max 18744 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7527974697327088904 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536 +Total wall time: 0:00:01 diff --git a/examples/mdi/log.17Jun22.snapshot.driver.tcp.3 b/examples/mdi/log.17Jun22.snapshot.driver.tcp.3 new file mode 100644 index 0000000000..554c942b73 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.driver.tcp.3 @@ -0,0 +1,105 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI driver script + +units lj +atom_style atomic + +read_data data.snapshot +Reading data file ... + orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) + 1 by 1 by 3 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities + read_data CPU = 0.005 seconds + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all mdi/qm add no every 100 virial yes + +compute 1 all pressure NULL virial +variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3 + +thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] + +thermo 100 + +dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3] +dump_modify 1 sort id + +run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173 + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 +Loop time of 0.271725 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.7579933325734558025 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726 + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 +Loop time of 0.275711 on 3 procs for 100 steps with 500 atoms + +print 'QM eng = $(f_2/atoms)' +QM eng = -5.752864010326673494 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051 + Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3] + 200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499 + 300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972 +Loop time of 0.27674 on 3 procs for 100 steps with 500 atoms + +Performance: 156103.145 tau/day, 361.350 timesteps/s +71.1% CPU use with 3 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0086137 | 0.01236 | 0.019756 | 4.7 | 4.47 +Neigh | 0.003253 | 0.0047355 | 0.0075676 | 2.9 | 1.71 +Comm | 0.0065383 | 0.016521 | 0.021738 | 5.5 | 5.97 +Output | 0.0011823 | 0.0011972 | 0.0012111 | 0.0 | 0.43 +Modify | 0.24066 | 0.24076 | 0.24093 | 0.0 | 87.00 +Other | | 0.001171 | | | 0.42 + +Nlocal: 166.667 ave 175 max 157 min +Histogram: 1 0 0 0 0 0 1 0 0 1 +Nghost: 1254.33 ave 1264 max 1246 min +Histogram: 1 0 0 1 0 0 0 0 0 1 +Neighs: 6248 ave 6632 max 5774 min +Histogram: 1 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 18744 +Ave neighs/atom = 37.488 +Neighbor list builds = 31 +Dangerous builds = 0 +print 'QM eng = $(f_2/atoms)' +QM eng = -5.752797469732716884 +print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])' +QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663 +Total wall time: 0:00:01 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.mpi.1 b/examples/mdi/log.17Jun22.snapshot.engine.mpi.1 new file mode 100644 index 0000000000..1480d238f0 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.mpi.1 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.mpi.3 b/examples/mdi/log.17Jun22.snapshot.engine.mpi.3 new file mode 100644 index 0000000000..0be8b75f70 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.mpi.3 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.plugin.1 b/examples/mdi/log.17Jun22.snapshot.engine.plugin.1 new file mode 100644 index 0000000000..1480d238f0 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.plugin.1 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.plugin.3 b/examples/mdi/log.17Jun22.snapshot.engine.plugin.3 new file mode 100644 index 0000000000..d1344cccbd --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.plugin.3 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 3 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 3 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:00 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.tcp.1 b/examples/mdi/log.17Jun22.snapshot.engine.tcp.1 new file mode 100644 index 0000000000..4deaa0d0f1 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.tcp.1 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 1 by 1 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 1 by 1 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:01 diff --git a/examples/mdi/log.17Jun22.snapshot.engine.tcp.4 b/examples/mdi/log.17Jun22.snapshot.engine.tcp.4 new file mode 100644 index 0000000000..2af1319e58 --- /dev/null +++ b/examples/mdi/log.17Jun22.snapshot.engine.tcp.4 @@ -0,0 +1,45 @@ +LAMMPS (2 Jun 2022) +# 3d Lennard-Jones melt - MDI engine script + +units lj +atom_style atomic + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011) + 1 by 2 by 2 MPI processor grid +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +mdi engine +delete_atoms group all +Deleted 0 atoms, new total = 0 + 1 by 2 by 2 MPI processor grid +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -6.7733681 0 -6.7733681 -6.2353173 + 1 0 -5.7579933 0 -5.7579933 -0.4184022 + 2 0 -5.752864 0 -5.752864 -0.40524506 + 3 0 -5.7527975 0 -5.7527975 -0.41843911 +Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 deleted file mode 100644 index d817aed5a3..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms - -Performance: 731582.413 tau/day, 1693.478 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43 -Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58 -Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98 -Other | | 3e-05 | | | 1.02 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 deleted file mode 100644 index eaf806cfc9..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms - -Performance: 684416.574 tau/day, 1584.298 timesteps/s -99.5% CPU use with 3 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17 -Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92 -Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88 -Other | | 0.0001272 | | | 4.03 - -Nlocal: 166.667 ave 200 max 150 min -Histogram: 2 0 0 0 0 0 0 0 0 1 -Nghost: 55.3333 ave 92 max 32 min -Histogram: 1 1 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -3 -Ave neighs/atom = -0.006 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 deleted file mode 100644 index dea662c157..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 +++ /dev/null @@ -1,80 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd plugin -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5" -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms - -Performance: 544685.246 tau/day, 1260.845 timesteps/s -98.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40 -Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91 -Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89 -Other | | 3.184e-05 | | | 0.80 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 deleted file mode 100644 index ff9e2dd8f5..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 +++ /dev/null @@ -1,80 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd plugin -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5" -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms - -Performance: 752045.581 tau/day, 1740.846 timesteps/s -99.1% CPU use with 3 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36 -Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21 -Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42 -Other | | 8.637e-05 | | | 3.01 - -Nlocal: 166.667 ave 200 max 150 min -Histogram: 2 0 0 0 0 0 0 0 0 1 -Nghost: 55.3333 ave 92 max 32 min -Histogram: 1 1 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -3 -Ave neighs/atom = -0.006 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 deleted file mode 100644 index 1ff358e269..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms - -Performance: 1792.736 tau/day, 4.150 timesteps/s -0.1% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00 -Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02 -Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97 -Other | | 6.184e-05 | | | 0.01 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:08 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 deleted file mode 100644 index 6abf6b3928..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms - -Performance: 1800.259 tau/day, 4.167 timesteps/s -66.7% CPU use with 3 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 4.604e-06 | 4.8462e-05 | 7.527e-05 | 0.0 | 0.00 -Output | 0.00015266 | 0.00020593 | 0.00031177 | 0.0 | 0.02 -Modify | 1.1993 | 1.1994 | 1.1994 | 0.0 | 99.96 -Other | | 0.0002123 | | | 0.02 - -Nlocal: 166.667 ave 200 max 150 min -Histogram: 2 0 0 0 0 0 0 0 0 1 -Nghost: 55.3333 ave 92 max 32 min -Histogram: 1 1 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -3 -Ave neighs/atom = -0.006 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:08 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 deleted file mode 100644 index 615dae0578..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 b/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 deleted file mode 100644 index 88d5c66892..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 deleted file mode 100644 index 615dae0578..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 deleted file mode 100644 index fb8034972f..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 deleted file mode 100644 index 72becb2bba..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 b/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 deleted file mode 100644 index 3154bd0b27..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 deleted file mode 100644 index 741e8a1dfe..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 +++ /dev/null @@ -1,5 +0,0 @@ -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 deleted file mode 100644 index 741e8a1dfe..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 +++ /dev/null @@ -1,5 +0,0 @@ -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 deleted file mode 100644 index 55825ab30a..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 deleted file mode 100644 index 4c636b8486..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 deleted file mode 100644 index 7eb94ac4c6..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:11 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 deleted file mode 100644 index 6d253ee790..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:11 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 deleted file mode 100644 index 17e040d0d7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 deleted file mode 100644 index e634b156b8..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 b/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 deleted file mode 100644 index 17e040d0d7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 b/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 deleted file mode 100644 index ada69c6ca7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 2 by 2 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 deleted file mode 100644 index df8d258715..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 3 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 3 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 3 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 3 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 b/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 deleted file mode 100644 index ada69c6ca7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 2 by 2 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/sequence_driver.py b/examples/mdi/sequence_driver.py index f15b2d4921..33dcf61b70 100644 --- a/examples/mdi/sequence_driver.py +++ b/examples/mdi/sequence_driver.py @@ -155,7 +155,7 @@ def perform_tasks(world,mdicomm,dummy): # request virial tensor mdi.MDI_Send_command("/lib/libmpi.a) + else() + ExternalProject_Add(mpi4win_build + URL ${MPICH2_WIN32_DEVEL_URL} + URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmpi.a) + endif() + + ExternalProject_get_property(mpi4win_build SOURCE_DIR) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + add_library(MPI::MPI_CXX UNKNOWN IMPORTED) + set_target_properties(MPI::MPI_CXX PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include" + INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX") + add_dependencies(MPI::MPI_CXX mpi4win_build) + + # set variables for status reporting at the end of CMake run + set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include") + set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX") + set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a") + else() + find_package(MPI REQUIRED) + option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) + if(LAMMPS_LONGLONG_TO_LONG) + target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG) + endif() endif() target_link_libraries(lammps INTERFACE MPI::MPI_CXX) else() diff --git a/examples/snap/in.grid.snap b/examples/snap/in.grid.snap new file mode 100644 index 0000000000..08c95a004f --- /dev/null +++ b/examples/snap/in.grid.snap @@ -0,0 +1,94 @@ +# Demonstrate calculation of SNAP bispectrum descriptors on a grid + +# CORRECTNESS: The two atom positions coincide with two of +# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8]. +# The same is true for compute grid/local c_mygridlocal[8][4-11]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +units metal +atom_modify map hash + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice custom $a & + a1 1 0 0 & + a2 0 1 0 & + a3 0 0 1 & + basis 0 0 0 & + basis 0.5 0.5 0.5 & + +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string & + "${rcutfac} ${rfac0} ${twojmax} ${radelem} & + ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} & + bzeroflag ${bzero} switchflag ${switch}" + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} & + ${snap_options} +compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} & + ${snap_options} + +# define output + +variable B5atom equal c_b[2][5] +variable B5grid equal c_mygrid[8][8] + +variable rmse_global equal "sqrt( & + (c_mygrid[8][1] - x[2])^2 + & + (c_mygrid[8][2] - y[2])^2 + & + (c_mygrid[8][3] - z[2])^2 + & + (c_mygrid[8][4] - c_b[2][1])^2 + & + (c_mygrid[8][5] - c_b[2][2])^2 + & + (c_mygrid[8][6] - c_b[2][3])^2 + & + (c_mygrid[8][7] - c_b[2][4])^2 + & + (c_mygrid[8][8] - c_b[2][5])^2 & + )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal c_mygridlocal[*] +dump 2 all custom 1000 dump.batom id x y z c_b[*] + +# run + +run 0 + diff --git a/examples/snap/in.grid.tri b/examples/snap/in.grid.tri new file mode 100644 index 0000000000..5283957eb8 --- /dev/null +++ b/examples/snap/in.grid.tri @@ -0,0 +1,114 @@ +# Demonstrate calculation of SNAP bispectrum +# descriptors on a grid for triclinic cell + +# This triclinic cell has 6 times the volume of the single +# unit cell used by in.grid +# and contains 12 atoms. It is a 3x2x1 supercell +# with each unit cell containing 2 atoms and the +# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1]. +# The grid is listed in x-fastest order + +# CORRECTNESS: The atom positions coincide with certain +# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8] +# and c_b[7][1-5] should match c_mygrid[13][4-8]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal.tri + +# Initialize simulation + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +variable nrepx equal 3*${nrep} +variable nrepy equal 2*${nrep} +variable nrepz equal 1*${nrep} + +variable ngridx equal 3*${ngrid} +variable ngridy equal 2*${ngrid} +variable ngridz equal 1*${ngrid} + +units metal +atom_modify map hash sort 0 0 + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrepx} +variable ny equal ${nrepy} +variable nz equal ${nrepz} + +boundary p p p + +lattice custom $a & + a1 1 0 0 & + a2 1 1 0 & + a3 1 1 1 & + basis 0 0 0 & + basis 0.0 0.0 0.5 & + spacing 1 1 1 + +box tilt large +region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string & + "${rcutfac} ${rfac0} ${twojmax} ${radelem} & + ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} & + bzeroflag ${bzero} switchflag ${switch}" + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} & + ${snap_options} +compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} & + ${snap_options} + +# define output + +variable B5atom equal c_b[7][5] +variable B5grid equal c_mygrid[13][8] + +# do not compare x,y,z because assignment of ids +# to atoms is not unnique for different processor grids + +variable rmse_global equal "sqrt( & + (c_mygrid[13][4] - c_b[7][1])^2 + & + (c_mygrid[13][5] - c_b[7][2])^2 + & + (c_mygrid[13][6] - c_b[7][3])^2 + & + (c_mygrid[13][7] - c_b[7][4])^2 + & + (c_mygrid[13][8] - c_b[7][5])^2 & + )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*] +dump 2 all custom 1000 dump.batom.tri id x y z c_b[*] + +# run + +run 0 + diff --git a/examples/snap/log.15Jun22.grid.snap.g++.1 b/examples/snap/log.15Jun22.grid.snap.g++.1 new file mode 100644 index 0000000000..ec2026b16e --- /dev/null +++ b/examples/snap/log.15Jun22.grid.snap.g++.1 @@ -0,0 +1,159 @@ +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task +# Demonstrate calculation of SNAP bispectrum descriptors on a grid + +# CORRECTNESS: The two atom positions coincide with two of +# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8]. +# The same is true for compute grid/local c_mygridlocal[8][4-11]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +units metal +atom_modify map hash + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 1 +variable ny equal ${nrep} +variable ny equal 1 +variable nz equal ${nrep} +variable nz equal 1 + +boundary p p p + +lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 +lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 1 0 ${ny} 0 ${nz} +region box block 0 1 0 1 0 ${nz} +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.316 3.316 3.316) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +2 atoms in group snapgroup +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}" +4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_style zero 4.67637 +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 2 2 ${snap_options} +compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# define output + +variable B5atom equal c_b[2][5] +variable B5grid equal c_mygrid[8][8] + +variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][5])^2 )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal c_mygridlocal[*] +dump 2 all custom 1000 dump.batom id x y z c_b[*] + +# run + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.67637 + ghost atom cutoff = 6.67637 + binsize = 3.338185, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.127 | 7.127 | 7.127 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 9.1551336e-16 +Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms + +139.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.43e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 339 ave 339 max 339 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 64 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 128 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/snap/log.15Jun22.grid.snap.g++.4 b/examples/snap/log.15Jun22.grid.snap.g++.4 new file mode 100644 index 0000000000..5be17ada7d --- /dev/null +++ b/examples/snap/log.15Jun22.grid.snap.g++.4 @@ -0,0 +1,160 @@ +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task +# Demonstrate calculation of SNAP bispectrum descriptors on a grid + +# CORRECTNESS: The two atom positions coincide with two of +# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8]. +# The same is true for compute grid/local c_mygridlocal[8][4-11]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +units metal +atom_modify map hash + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 1 +variable ny equal ${nrep} +variable ny equal 1 +variable nz equal ${nrep} +variable nz equal 1 + +boundary p p p + +lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 +lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 1 0 ${ny} 0 ${nz} +region box block 0 1 0 1 0 ${nz} +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.316 3.316 3.316) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316) + create_atoms CPU = 0.001 seconds + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +2 atoms in group snapgroup +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}" +4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_style zero 4.67637 +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options} +compute mygrid all sna/grid grid 2 2 2 ${snap_options} +compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options} +compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# define output + +variable B5atom equal c_b[2][5] +variable B5grid equal c_mygrid[8][8] + +variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][5])^2 )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal c_mygridlocal[*] +dump 2 all custom 1000 dump.batom id x y z c_b[*] + +# run + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.67637 + ghost atom cutoff = 6.67637 + binsize = 3.338185, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970) +Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.631 | 7.139 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 1.6316879e-15 +Loop time of 2.57125e-06 on 4 procs for 0 steps with 2 atoms + +107.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.571e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 274.5 ave 275 max 274 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 16 ave 40 max 0 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +FullNghs: 32 ave 64 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 128 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/snap/log.15Jun22.grid.tri.g++.1 b/examples/snap/log.15Jun22.grid.tri.g++.1 new file mode 100644 index 0000000000..e26315235b --- /dev/null +++ b/examples/snap/log.15Jun22.grid.tri.g++.1 @@ -0,0 +1,192 @@ +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task +# Demonstrate calculation of SNAP bispectrum +# descriptors on a grid for triclinic cell + +# This triclinic cell has 6 times the volume of the single +# unit cell used by in.grid +# and contains 12 atoms. It is a 3x2x1 supercell +# with each unit cell containing 2 atoms and the +# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1]. +# The grid is listed in x-fastest order + +# CORRECTNESS: The atom positions coincide with certain +# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8] +# and c_b[7][1-5] should match c_mygrid[13][4-8]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal.tri + +# Initialize simulation + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +variable nrepx equal 3*${nrep} +variable nrepx equal 3*1 +variable nrepy equal 2*${nrep} +variable nrepy equal 2*1 +variable nrepz equal 1*${nrep} +variable nrepz equal 1*1 + +variable ngridx equal 3*${ngrid} +variable ngridx equal 3*2 +variable ngridy equal 2*${ngrid} +variable ngridy equal 2*2 +variable ngridz equal 1*${ngrid} +variable ngridz equal 1*2 + +units metal +atom_modify map hash sort 0 0 + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrepx} +variable nx equal 3 +variable ny equal ${nrepy} +variable ny equal 2 +variable nz equal ${nrepz} +variable nz equal 1 + +boundary p p p + +lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 +lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 +Lattice spacing in x,y,z = 3.316 3.316 3.316 + +box tilt large +region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 1 2 ${nz} ${nz} +region box prism 0 3 0 2 0 1 2 1 ${nz} +region box prism 0 3 0 2 0 1 2 1 1 +create_box 1 box +Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) +WARNING: Triclinic box skew is large (src/domain.cpp:224) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 12 atoms + using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +12 atoms in group snapgroup +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}" +4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_style zero 4.67637 +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 ${ngridy} ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 4 ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 4 2 ${snap_options} +compute mygrid all sna/grid grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 2 ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# define output + +variable B5atom equal c_b[7][5] +variable B5grid equal c_mygrid[13][8] + +# do not compare x,y,z because assignment of ids +# to atoms is not unnique for different processor grids + +variable rmse_global equal "sqrt( (c_mygrid[13][4] - c_b[7][1])^2 + (c_mygrid[13][5] - c_b[7][2])^2 + (c_mygrid[13][6] - c_b[7][3])^2 + (c_mygrid[13][7] - c_b[7][4])^2 + (c_mygrid[13][8] - c_b[7][5])^2 )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*] +dump 2 all custom 1000 dump.batom.tri id x y z c_b[*] + +# run + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.67637 + ghost atom cutoff = 6.67637 + binsize = 3.338185, bins = 6 3 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard + (2) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.183 | 7.183 | 7.183 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 7.2262471e-14 +Loop time of 1.414e-06 on 1 procs for 0 steps with 12 atoms + +70.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.414e-06 | | |100.00 + +Nlocal: 12 ave 12 max 12 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 604 ave 604 max 604 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 384 ave 384 max 384 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 768 ave 768 max 768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 768 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/snap/log.15Jun22.grid.tri.g++.4 b/examples/snap/log.15Jun22.grid.tri.g++.4 new file mode 100644 index 0000000000..cee3ce7f12 --- /dev/null +++ b/examples/snap/log.15Jun22.grid.tri.g++.4 @@ -0,0 +1,192 @@ +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task +# Demonstrate calculation of SNAP bispectrum +# descriptors on a grid for triclinic cell + +# This triclinic cell has 6 times the volume of the single +# unit cell used by in.grid +# and contains 12 atoms. It is a 3x2x1 supercell +# with each unit cell containing 2 atoms and the +# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1]. +# The grid is listed in x-fastest order + +# CORRECTNESS: The atom positions coincide with certain +# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8] +# and c_b[7][1-5] should match c_mygrid[13][4-8]. +# Local arrays can not be access directly in the script, +# but they are printed out to file dump.blocal.tri + +# Initialize simulation + +variable nrep index 1 +variable a index 3.316 +variable ngrid index 2 + +variable nrepx equal 3*${nrep} +variable nrepx equal 3*1 +variable nrepy equal 2*${nrep} +variable nrepy equal 2*1 +variable nrepz equal 1*${nrep} +variable nrepz equal 1*1 + +variable ngridx equal 3*${ngrid} +variable ngridx equal 3*2 +variable ngridy equal 2*${ngrid} +variable ngridy equal 2*2 +variable ngridz equal 1*${ngrid} +variable ngridz equal 1*2 + +units metal +atom_modify map hash sort 0 0 + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrepx} +variable nx equal 3 +variable ny equal ${nrepy} +variable ny equal 2 +variable nz equal ${nrepz} +variable nz equal 1 + +boundary p p p + +lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 +lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 +Lattice spacing in x,y,z = 3.316 3.316 3.316 + +box tilt large +region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz} +region box prism 0 3 0 2 0 1 2 ${nz} ${nz} +region box prism 0 3 0 2 0 1 2 1 ${nz} +region box prism 0 3 0 2 0 1 2 1 1 +create_box 1 box +Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) +WARNING: Triclinic box skew is large (src/domain.cpp:224) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 12 atoms + using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# define atom compute and grid compute + +group snapgroup type 1 +12 atoms in group snapgroup +variable twojmax equal 2 +variable rcutfac equal 4.67637 +variable rfac0 equal 0.99363 +variable rmin0 equal 0 +variable wj equal 1 +variable radelem equal 0.5 +variable bzero equal 0 +variable quadratic equal 0 +variable switch equal 1 + +variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}" +4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch} +4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# build zero potential to satisfy compute sna/atom + +pair_style zero ${rcutfac} +pair_style zero 4.67637 +pair_coeff * * + +# define atom and grid computes + +compute b all sna/atom ${snap_options} +compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 ${ngridy} ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 4 ${ngridz} ${snap_options} +compute mygrid all sna/grid grid 6 4 2 ${snap_options} +compute mygrid all sna/grid grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 +compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 ${ngridz} ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 2 ${snap_options} +compute mygridlocal all sna/grid/local grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1 + +# define output + +variable B5atom equal c_b[7][5] +variable B5grid equal c_mygrid[13][8] + +# do not compare x,y,z because assignment of ids +# to atoms is not unnique for different processor grids + +variable rmse_global equal "sqrt( (c_mygrid[13][4] - c_b[7][1])^2 + (c_mygrid[13][5] - c_b[7][2])^2 + (c_mygrid[13][6] - c_b[7][3])^2 + (c_mygrid[13][7] - c_b[7][4])^2 + (c_mygrid[13][8] - c_b[7][5])^2 )" + +thermo_style custom step v_B5atom v_B5grid v_rmse_global + +# this is the only way to view the local grid + +dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*] +dump 2 all custom 1000 dump.batom.tri id x y z c_b[*] + +# run + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.67637 + ghost atom cutoff = 6.67637 + binsize = 3.338185, bins = 6 3 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard + (2) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 1.9367585e-14 +Loop time of 2.65825e-06 on 4 procs for 0 steps with 12 atoms + +84.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.658e-06 | | |100.00 + +Nlocal: 3 ave 4 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 459 ave 460 max 458 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 96 ave 128 max 64 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 192 ave 256 max 128 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 768 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index dfbe22edde..a908507704 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,21 @@ # Change Log +## [3.6.01](https://github.com/kokkos/kokkos/tree/3.6.01) (2022-05-23) +[Full Changelog](https://github.com/kokkos/kokkos/compare/3.6.00...3.6.01) + +### Bug Fixes: +- Fix Threads: Fix serial resizing scratch space (3.6.01 cherry-pick) [\#5109](https://github.com/kokkos/kokkos/pull/5109) +- Fix ScatterMin/ScatterMax to use proper atomics (3.6.01 cherry-pick) [\#5046](https://github.com/kokkos/kokkos/pull/5046) +- Fix allocating large Views [\#4907](https://github.com/kokkos/kokkos/pull/4907) +- Fix bounds errors with Kokkos::sort [\#4980](https://github.com/kokkos/kokkos/pull/4980) +- Fix HIP version when printing the configuration [\#4872](https://github.com/kokkos/kokkos/pull/4872) +- Fixed `_CUDA_ARCH__` to `__CUDA_ARCH__` for CUDA LDG [\#4893](https://github.com/kokkos/kokkos/pull/4893) +- Fixed an incorrect struct initialization [\#5028](https://github.com/kokkos/kokkos/pull/5028) +- Fix racing condition in `HIPParallelLaunch` [\#5008](https://github.com/kokkos/kokkos/pull/5008) +- Avoid deprecation warnings with `OpenMPExec::validate_partition` [\#4982](https://github.com/kokkos/kokkos/pull/4982) +- Make View self-assignment not produce double-free [\#5024](https://github.com/kokkos/kokkos/pull/5024) + + ## [3.6.00](https://github.com/kokkos/kokkos/tree/3.6.00) (2022-02-18) [Full Changelog](https://github.com/kokkos/kokkos/compare/3.5.00...3.6.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index e1c6893725..b0a54118a0 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -136,7 +136,7 @@ ENDIF() set(Kokkos_VERSION_MAJOR 3) set(Kokkos_VERSION_MINOR 6) -set(Kokkos_VERSION_PATCH 00) +set(Kokkos_VERSION_PATCH 01) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index aa5f7c98f8..755831452b 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -12,7 +12,7 @@ endif KOKKOS_VERSION_MAJOR = 3 KOKKOS_VERSION_MINOR = 6 -KOKKOS_VERSION_PATCH = 00 +KOKKOS_VERSION_PATCH = 01 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) # Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Threads,Serial diff --git a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp index cde5e6857e..ce97de9b7d 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -422,54 +422,34 @@ class BinSort { template struct BinOp1D { - int max_bins_; - double mul_; - typename KeyViewType::const_value_type range_; - typename KeyViewType::const_value_type min_; + int max_bins_ = {}; + double mul_ = {}; + double min_ = {}; - BinOp1D() - : max_bins_(0), - mul_(0.0), - range_(typename KeyViewType::const_value_type()), - min_(typename KeyViewType::const_value_type()) {} + BinOp1D() = default; // Construct BinOp with number of bins, minimum value and maxuimum value BinOp1D(int max_bins__, typename KeyViewType::const_value_type min, typename KeyViewType::const_value_type max) : max_bins_(max_bins__ + 1), - // Cast to int64_t to avoid possible overflow when using integer - mul_(std::is_integral::value - ? 1.0 * max_bins__ / (int64_t(max) - int64_t(min)) - : 1.0 * max_bins__ / (max - min)), - range_(max - min), - min_(min) { + // Cast to double to avoid possible overflow when using integer + mul_(static_cast(max_bins__) / + (static_cast(max) - static_cast(min))), + min_(static_cast(min)) { // For integral types the number of bins may be larger than the range // in which case we can exactly have one unique value per bin // and then don't need to sort bins. if (std::is_integral::value && - static_cast(range_) <= static_cast(max_bins__)) { + (static_cast(max) - static_cast(min)) <= + static_cast(max_bins__)) { mul_ = 1.; } } // Determine bin index from key value - template < - class ViewType, - std::enable_if_t::value, - bool> = true> + template KOKKOS_INLINE_FUNCTION int bin(ViewType& keys, const int& i) const { - return int(mul_ * (keys(i) - min_)); - } - - // Determine bin index from key value - template < - class ViewType, - std::enable_if_t::value, - bool> = true> - KOKKOS_INLINE_FUNCTION int bin(ViewType& keys, const int& i) const { - // The cast to int64_t is necessary because otherwise HIP returns the wrong - // result. - return int(mul_ * (int64_t(keys(i)) - int64_t(min_))); + return static_cast(mul_ * (static_cast(keys(i)) - min_)); } // Return maximum bin index + 1 @@ -486,10 +466,9 @@ struct BinOp1D { template struct BinOp3D { - int max_bins_[3]; - double mul_[3]; - typename KeyViewType::non_const_value_type range_[3]; - typename KeyViewType::non_const_value_type min_[3]; + int max_bins_[3] = {}; + double mul_[3] = {}; + double min_[3] = {}; BinOp3D() = default; @@ -498,15 +477,15 @@ struct BinOp3D { max_bins_[0] = max_bins__[0]; max_bins_[1] = max_bins__[1]; max_bins_[2] = max_bins__[2]; - mul_[0] = 1.0 * max_bins__[0] / (max[0] - min[0]); - mul_[1] = 1.0 * max_bins__[1] / (max[1] - min[1]); - mul_[2] = 1.0 * max_bins__[2] / (max[2] - min[2]); - range_[0] = max[0] - min[0]; - range_[1] = max[1] - min[1]; - range_[2] = max[2] - min[2]; - min_[0] = min[0]; - min_[1] = min[1]; - min_[2] = min[2]; + mul_[0] = static_cast(max_bins__[0]) / + (static_cast(max[0]) - static_cast(min[0])); + mul_[1] = static_cast(max_bins__[1]) / + (static_cast(max[1]) - static_cast(min[1])); + mul_[2] = static_cast(max_bins__[2]) / + (static_cast(max[2]) - static_cast(min[2])); + min_[0] = static_cast(min[0]); + min_[1] = static_cast(min[1]); + min_[2] = static_cast(min[2]); } template @@ -596,9 +575,9 @@ std::enable_if_t::value> sort( // TODO: figure out better max_bins then this ... int64_t max_bins = view.extent(0) / 2; if (std::is_integral::value) { - // Cast to int64_t to avoid possible overflow when using integer - int64_t const max_val = result.max_val; - int64_t const min_val = result.min_val; + // Cast to double to avoid possible overflow when using integer + auto const max_val = static_cast(result.max_val); + auto const min_val = static_cast(result.min_val); // using 10M as the cutoff for special behavior (roughly 40MB for the count // array) if ((max_val - min_val) < 10000000) { @@ -606,6 +585,10 @@ std::enable_if_t::value> sort( sort_in_bins = false; } } + if (std::is_floating_point::value) { + KOKKOS_ASSERT(std::isfinite(static_cast(result.max_val) - + static_cast(result.min_val))); + } BinSort bin_sort( view, CompType(max_bins, result.min_val, result.max_val), sort_in_bins); diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index a03847f2b2..9108731c15 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -353,6 +353,55 @@ void test_issue_1160_impl() { } } +template +void test_issue_4978_impl() { + Kokkos::View element_("element", 9); + + auto h_element = Kokkos::create_mirror_view(element_); + + h_element(0) = LLONG_MIN; + h_element(1) = 0; + h_element(2) = 3; + h_element(3) = 2; + h_element(4) = 1; + h_element(5) = 3; + h_element(6) = 6; + h_element(7) = 4; + h_element(8) = 3; + + ExecutionSpace exec; + Kokkos::deep_copy(exec, element_, h_element); + + Kokkos::sort(exec, element_); + + Kokkos::deep_copy(exec, h_element, element_); + exec.fence(); + + ASSERT_EQ(h_element(0), LLONG_MIN); + ASSERT_EQ(h_element(1), 0); + ASSERT_EQ(h_element(2), 1); + ASSERT_EQ(h_element(3), 2); + ASSERT_EQ(h_element(4), 3); + ASSERT_EQ(h_element(5), 3); + ASSERT_EQ(h_element(6), 3); + ASSERT_EQ(h_element(7), 4); + ASSERT_EQ(h_element(8), 6); +} + +template +void test_sort_integer_overflow() { + // array with two extrema in reverse order to expose integer overflow bug in + // bin calculation + T a[2] = {Kokkos::Experimental::finite_max::value, + Kokkos::Experimental::finite_min::value}; + auto vd = Kokkos::create_mirror_view_and_copy( + ExecutionSpace(), Kokkos::View(a)); + Kokkos::sort(vd, /*force using Kokkos bin sort*/ true); + auto vh = Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), vd); + EXPECT_TRUE(std::is_sorted(vh.data(), vh.data() + 2)) + << "view (" << vh[0] << ", " << vh[1] << ") is not sorted"; +} + //---------------------------------------------------------------------------- template @@ -376,6 +425,11 @@ void test_issue_1160_sort() { test_issue_1160_impl(); } +template +void test_issue_4978_sort() { + test_issue_4978_impl(); +} + template void test_sort(unsigned int N) { test_1D_sort(N); @@ -385,6 +439,10 @@ void test_sort(unsigned int N) { test_dynamic_view_sort(N); #endif test_issue_1160_sort(); + test_issue_4978_sort(); + test_sort_integer_overflow(); + test_sort_integer_overflow(); + test_sort_integer_overflow(); } } // namespace Impl } // namespace Test diff --git a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp index 024b4618a4..e4dd9531fc 100644 --- a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp +++ b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp @@ -369,18 +369,6 @@ struct ScatterValue(&dest, dest_old, dest_new); - success = ((dest_new - dest_old) / dest_old <= 1e-15); - } - } - KOKKOS_INLINE_FUNCTION void join(ValueType& dest, const ValueType& src) const { atomic_prod(&dest, src); @@ -440,21 +428,9 @@ struct ScatterValue src) ? src : dest_old; - dest_new = - Kokkos::atomic_compare_exchange(&dest, dest_old, dest_new); - success = ((dest_new - dest_old) / dest_old <= 1e-15); - } - } - KOKKOS_INLINE_FUNCTION void join(ValueType& dest, const ValueType& src) const { - atomic_min(dest, src); + atomic_min(&dest, src); } KOKKOS_INLINE_FUNCTION @@ -511,21 +487,9 @@ struct ScatterValue(&dest, dest_old, dest_new); - success = ((dest_new - dest_old) / dest_old <= 1e-15); - } - } - KOKKOS_INLINE_FUNCTION void join(ValueType& dest, const ValueType& src) const { - atomic_max(dest, src); + atomic_max(&dest, src); } KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/containers/src/Kokkos_Vector.hpp b/lib/kokkos/containers/src/Kokkos_Vector.hpp index 88721bd89e..eddb878003 100644 --- a/lib/kokkos/containers/src/Kokkos_Vector.hpp +++ b/lib/kokkos/containers/src/Kokkos_Vector.hpp @@ -162,7 +162,7 @@ class vector : public DualView { } DV::sync_host(); DV::modify_host(); - if (it < begin() || it > end()) + if (std::less<>()(it, begin()) || std::less<>()(end(), it)) Kokkos::abort("Kokkos::vector::insert : invalid insert iterator"); if (count == 0) return it; ptrdiff_t start = std::distance(begin(), it); @@ -189,27 +189,21 @@ class vector : public DualView { iterator>::type insert(iterator it, InputIterator b, InputIterator e) { ptrdiff_t count = std::distance(b, e); - if (count == 0) return it; DV::sync_host(); DV::modify_host(); - if (it < begin() || it > end()) + if (std::less<>()(it, begin()) || std::less<>()(end(), it)) Kokkos::abort("Kokkos::vector::insert : invalid insert iterator"); - bool resized = false; - if ((size() == 0) && (it == begin())) { - resize(count); - it = begin(); - resized = true; - } ptrdiff_t start = std::distance(begin(), it); auto org_size = size(); - if (!resized) resize(size() + count); - it = begin() + start; + + // Note: resize(...) invalidates it; use begin() + start instead + resize(size() + count); std::copy_backward(begin() + start, begin() + org_size, begin() + org_size + count); - std::copy(b, e, it); + std::copy(b, e, begin() + start); return begin() + start; } diff --git a/lib/kokkos/containers/unit_tests/TestVector.hpp b/lib/kokkos/containers/unit_tests/TestVector.hpp index 57b92c38f8..c093c7b0c9 100644 --- a/lib/kokkos/containers/unit_tests/TestVector.hpp +++ b/lib/kokkos/containers/unit_tests/TestVector.hpp @@ -172,6 +172,23 @@ struct test_vector_insert { run_test(a); check_test(a, size); } + { test_vector_insert_into_empty(size); } + } + + void test_vector_insert_into_empty(const size_t size) { + using Vector = Kokkos::vector; + { + Vector a; + Vector b(size); + a.insert(a.begin(), b.begin(), b.end()); + ASSERT_EQ(a.size(), size); + } + + { + Vector c; + c.insert(c.begin(), size, Scalar{}); + ASSERT_EQ(c.size(), size); + } } }; diff --git a/lib/kokkos/core/src/CMakeLists.txt b/lib/kokkos/core/src/CMakeLists.txt index 88cca93f3c..793e07a841 100644 --- a/lib/kokkos/core/src/CMakeLists.txt +++ b/lib/kokkos/core/src/CMakeLists.txt @@ -8,6 +8,7 @@ KOKKOS_INCLUDE_DIRECTORIES( INSTALL (DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/" DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN desul/src EXCLUDE PATTERN "*.inc" PATTERN "*.inc_*" diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp index 294be2774b..aaa9ea8ad4 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp @@ -1007,6 +1007,15 @@ void CudaSpaceInitializer::print_configuration(std::ostream &msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } // namespace Kokkos #else diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp index 61563a0100..dec6ef15e1 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp @@ -139,7 +139,7 @@ struct CudaLDGFetch { template KOKKOS_INLINE_FUNCTION ValueType operator[](const iType& i) const { -#if defined(__CUDA_ARCH__) && (350 <= _CUDA_ARCH__) +#if defined(__CUDA_ARCH__) && (350 <= __CUDA_ARCH__) AliasType v = __ldg(reinterpret_cast(&m_ptr[i])); return *(reinterpret_cast(&v)); #else diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp index 4a6a3ba99e..a8a0496afe 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp @@ -132,7 +132,8 @@ void HIPInternal::print_configuration(std::ostream &s) const { s << "macro KOKKOS_ENABLE_HIP : defined" << '\n'; #if defined(HIP_VERSION) s << "macro HIP_VERSION = " << HIP_VERSION << " = version " - << HIP_VERSION / 100 << "." << HIP_VERSION % 100 << '\n'; + << HIP_VERSION_MAJOR << '.' << HIP_VERSION_MINOR << '.' << HIP_VERSION_PATCH + << '\n'; #endif for (int i = 0; i < dev_info.m_hipDevCount; ++i) { @@ -467,7 +468,6 @@ void HIPInternal::finalize() { } char *HIPInternal::get_next_driver(size_t driverTypeSize) const { - std::lock_guard const lock(m_mutexWorkArray); if (d_driverWorkArray == nullptr) { KOKKOS_IMPL_HIP_SAFE_CALL( hipHostMalloc(&d_driverWorkArray, diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp index 384b7ffd67..70b979e00a 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp @@ -490,6 +490,8 @@ struct HIPParallelLaunch< KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); + std::lock_guard const lock(hip_instance->m_mutexWorkArray); + // Invoke the driver function on the device DriverType *d_driver = reinterpret_cast( hip_instance->get_next_driver(sizeof(DriverType))); diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp index f334d93412..e9cfbf99f7 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Locks.cpp @@ -56,8 +56,7 @@ namespace Kokkos { #ifdef KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE namespace Impl { -__device__ __constant__ HIPLockArrays g_device_hip_lock_arrays = {nullptr, - nullptr, 0}; +__device__ __constant__ HIPLockArrays g_device_hip_lock_arrays = {nullptr, 0}; } #endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp index 6ade677fa8..776b7c6abe 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp @@ -464,6 +464,15 @@ void HIPSpaceInitializer::print_configuration(std::ostream& msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } // namespace Kokkos //============================================================================== diff --git a/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp b/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp index acf2224f02..623c7da025 100644 --- a/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp +++ b/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp @@ -199,6 +199,15 @@ void HPXSpaceInitializer::print_configuration(std::ostream &msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } // namespace Kokkos #else diff --git a/lib/kokkos/core/src/Kokkos_Cuda.hpp b/lib/kokkos/core/src/Kokkos_Cuda.hpp index 6305a1fa5d..0063b1cd1e 100644 --- a/lib/kokkos/core/src/Kokkos_Cuda.hpp +++ b/lib/kokkos/core/src/Kokkos_Cuda.hpp @@ -260,6 +260,7 @@ template <> struct DeviceTypeTraits { /// \brief An ID to differentiate (for example) Serial from OpenMP in Tooling static constexpr DeviceType id = DeviceType::Cuda; + static int device_id(const Cuda& exec) { return exec.cuda_device(); } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_HIP_Space.hpp b/lib/kokkos/core/src/Kokkos_HIP_Space.hpp index 1371d21d38..68869a6074 100644 --- a/lib/kokkos/core/src/Kokkos_HIP_Space.hpp +++ b/lib/kokkos/core/src/Kokkos_HIP_Space.hpp @@ -571,6 +571,9 @@ namespace Experimental { template <> struct DeviceTypeTraits { static constexpr DeviceType id = DeviceType::HIP; + static int device_id(const Kokkos::Experimental::HIP& exec) { + return exec.hip_device(); + } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_HPX.hpp b/lib/kokkos/core/src/Kokkos_HPX.hpp index d2ae9c0ec2..9238ca30a7 100644 --- a/lib/kokkos/core/src/Kokkos_HPX.hpp +++ b/lib/kokkos/core/src/Kokkos_HPX.hpp @@ -500,6 +500,7 @@ namespace Experimental { template <> struct DeviceTypeTraits { static constexpr DeviceType id = DeviceType::HPX; + static int device_id(const Kokkos::Experimental::HPX &) { return 0; } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_OpenMP.hpp b/lib/kokkos/core/src/Kokkos_OpenMP.hpp index 5d76e689f2..767e5b9324 100644 --- a/lib/kokkos/core/src/Kokkos_OpenMP.hpp +++ b/lib/kokkos/core/src/Kokkos_OpenMP.hpp @@ -179,6 +179,7 @@ namespace Experimental { template <> struct DeviceTypeTraits { static constexpr DeviceType id = DeviceType::OpenMP; + static int device_id(const OpenMP&) { return 0; } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_OpenMPTarget.hpp b/lib/kokkos/core/src/Kokkos_OpenMPTarget.hpp index f394f32408..373dc3d9c7 100644 --- a/lib/kokkos/core/src/Kokkos_OpenMPTarget.hpp +++ b/lib/kokkos/core/src/Kokkos_OpenMPTarget.hpp @@ -130,6 +130,9 @@ template <> struct DeviceTypeTraits<::Kokkos::Experimental::OpenMPTarget> { static constexpr DeviceType id = ::Kokkos::Profiling::Experimental::DeviceType::OpenMPTarget; + static int device_id(const Kokkos::Experimental::OpenMPTarget&) { + return omp_get_default_device(); + } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_SYCL.hpp b/lib/kokkos/core/src/Kokkos_SYCL.hpp index 02095ff7b3..e29093db32 100644 --- a/lib/kokkos/core/src/Kokkos_SYCL.hpp +++ b/lib/kokkos/core/src/Kokkos_SYCL.hpp @@ -182,6 +182,9 @@ template <> struct DeviceTypeTraits { /// \brief An ID to differentiate (for example) Serial from OpenMP in Tooling static constexpr DeviceType id = DeviceType::SYCL; + static int device_id(const Kokkos::Experimental::SYCL& exec) { + return exec.sycl_device(); + } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_Serial.hpp b/lib/kokkos/core/src/Kokkos_Serial.hpp index 9aada48bf6..b2e524c374 100644 --- a/lib/kokkos/core/src/Kokkos_Serial.hpp +++ b/lib/kokkos/core/src/Kokkos_Serial.hpp @@ -226,6 +226,7 @@ namespace Experimental { template <> struct DeviceTypeTraits { static constexpr DeviceType id = DeviceType::Serial; + static int device_id(const Serial&) { return 0; } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/Kokkos_Threads.hpp b/lib/kokkos/core/src/Kokkos_Threads.hpp index 45a2d0e326..5879209f12 100644 --- a/lib/kokkos/core/src/Kokkos_Threads.hpp +++ b/lib/kokkos/core/src/Kokkos_Threads.hpp @@ -175,6 +175,7 @@ namespace Experimental { template <> struct DeviceTypeTraits { static constexpr DeviceType id = DeviceType::Threads; + static int device_id(const Threads&) { return 0; } }; } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp index d2283d456f..66dbbacce9 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp @@ -67,8 +67,9 @@ __thread int t_openmp_hardware_id = 0; __thread Impl::OpenMPExec *t_openmp_instance = nullptr; #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -void OpenMPExec::validate_partition(const int nthreads, int &num_partitions, - int &partition_size) { +void OpenMPExec::validate_partition_impl(const int nthreads, + int &num_partitions, + int &partition_size) { if (nthreads == 1) { num_partitions = 1; partition_size = 1; @@ -506,6 +507,15 @@ void OpenMPSpaceInitializer::print_configuration(std::ostream &msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } // namespace Kokkos #else diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.hpp index 2f647af77e..ede24d1094 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Exec.hpp @@ -93,7 +93,11 @@ class OpenMPExec { #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 KOKKOS_DEPRECATED static void validate_partition(const int nthreads, int& num_partitions, - int& partition_size); + int& partition_size) { + validate_partition_impl(nthreads, num_partitions, partition_size); + } + static void validate_partition_impl(const int nthreads, int& num_partitions, + int& partition_size); #endif private: @@ -179,8 +183,8 @@ KOKKOS_DEPRECATED void OpenMP::partition_master(F const& f, int num_partitions, Exec* prev_instance = Impl::t_openmp_instance; - Exec::validate_partition(prev_instance->m_pool_size, num_partitions, - partition_size); + Exec::validate_partition_impl(prev_instance->m_pool_size, num_partitions, + partition_size); OpenMP::memory_space space; diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp index 907e4e9efe..45aacd7258 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp @@ -72,7 +72,7 @@ class SYCLInternal { bool force_shrink = false); uint32_t impl_get_instance_id() const; - int m_syclDev = -1; + int m_syclDev = 0; size_t m_maxWorkgroupSize = 0; uint32_t m_maxConcurrency = 0; diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp index 8a7c49871b..9682564ee0 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp +++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp @@ -399,27 +399,68 @@ bool ThreadsExec::wake() { //---------------------------------------------------------------------------- +void ThreadsExec::execute_resize_scratch_in_serial() { + const unsigned begin = s_threads_process.m_pool_base ? 1 : 0; + + auto deallocate_scratch_memory = [](ThreadsExec &exec) { + if (exec.m_scratch) { + using Record = + Kokkos::Impl::SharedAllocationRecord; + Record *const r = Record::get_record(exec.m_scratch); + exec.m_scratch = nullptr; + Record::decrement(r); + } + }; + if (s_threads_process.m_pool_base) { + for (unsigned i = s_thread_pool_size[0]; begin < i;) { + deallocate_scratch_memory(*s_threads_exec[--i]); + } + } + + s_current_function = &first_touch_allocate_thread_private_scratch; + s_current_function_arg = &s_threads_process; + + // Make sure function and arguments are written before activating threads. + memory_fence(); + + for (unsigned i = s_thread_pool_size[0]; begin < i;) { + ThreadsExec &th = *s_threads_exec[--i]; + + th.m_pool_state = ThreadsExec::Active; + + wait_yield(th.m_pool_state, ThreadsExec::Active); + } + + if (s_threads_process.m_pool_base) { + deallocate_scratch_memory(s_threads_process); + s_threads_process.m_pool_state = ThreadsExec::Active; + first_touch_allocate_thread_private_scratch(s_threads_process, nullptr); + s_threads_process.m_pool_state = ThreadsExec::Inactive; + } + + s_current_function_arg = nullptr; + s_current_function = nullptr; + + // Make sure function and arguments are cleared before proceeding. + memory_fence(); +} + +//---------------------------------------------------------------------------- + void *ThreadsExec::root_reduce_scratch() { return s_threads_process.reduce_memory(); } -void ThreadsExec::execute_resize_scratch(ThreadsExec &exec, const void *) { - using Record = Kokkos::Impl::SharedAllocationRecord; - - if (exec.m_scratch) { - Record *const r = Record::get_record(exec.m_scratch); - - exec.m_scratch = nullptr; - - Record::decrement(r); - } - +void ThreadsExec::first_touch_allocate_thread_private_scratch(ThreadsExec &exec, + const void *) { exec.m_scratch_reduce_end = s_threads_process.m_scratch_reduce_end; exec.m_scratch_thread_end = s_threads_process.m_scratch_thread_end; if (s_threads_process.m_scratch_thread_end) { // Allocate tracked memory: { + using Record = + Kokkos::Impl::SharedAllocationRecord; Record *const r = Record::allocate(Kokkos::HostSpace(), "Kokkos::thread_scratch", s_threads_process.m_scratch_thread_end); @@ -461,7 +502,7 @@ void *ThreadsExec::resize_scratch(size_t reduce_size, size_t thread_size) { s_threads_process.m_scratch_reduce_end = reduce_size; s_threads_process.m_scratch_thread_end = reduce_size + thread_size; - execute_resize_scratch(s_threads_process, nullptr); + execute_resize_scratch_in_serial(); s_threads_process.m_scratch = s_threads_exec[0]->m_scratch; } @@ -845,6 +886,15 @@ void ThreadsSpaceInitializer::print_configuration(std::ostream &msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } /* namespace Kokkos */ //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp index 561b1ce292..d17f417bbc 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp @@ -123,12 +123,15 @@ class ThreadsExec { static void global_unlock(); static void spawn(); - static void execute_resize_scratch(ThreadsExec &, const void *); + static void first_touch_allocate_thread_private_scratch(ThreadsExec &, + const void *); static void execute_sleep(ThreadsExec &, const void *); ThreadsExec(const ThreadsExec &); ThreadsExec &operator=(const ThreadsExec &); + static void execute_resize_scratch_in_serial(); + public: KOKKOS_INLINE_FUNCTION int pool_size() const { return m_pool_size; } KOKKOS_INLINE_FUNCTION int pool_rank() const { return m_pool_rank; } diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp index 4e0e81405f..d526682056 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp @@ -118,11 +118,14 @@ template constexpr uint32_t device_id_root() { constexpr auto device_id = static_cast(DeviceTypeTraits::id); - return (device_id << num_instance_bits); + return (device_id << (num_instance_bits + num_device_bits)); } template inline uint32_t device_id(ExecutionSpace const& space) noexcept { - return device_id_root() + space.impl_instance_id(); + return device_id_root() + + (DeviceTypeTraits::device_id(space) + << num_instance_bits) + + space.impl_instance_id(); } } // namespace Experimental } // namespace Tools diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial.cpp b/lib/kokkos/core/src/impl/Kokkos_Serial.cpp index c49e838d8f..e5917eb59d 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Serial.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Serial.cpp @@ -233,6 +233,15 @@ void SerialSpaceInitializer::print_configuration(std::ostream& msg, } } // namespace Impl + +#ifdef KOKKOS_ENABLE_CXX14 +namespace Tools { +namespace Experimental { +constexpr DeviceType DeviceTypeTraits::id; +} +} // namespace Tools +#endif + } // namespace Kokkos #else diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp index 09f7af0918..f606a39839 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp @@ -1005,15 +1005,15 @@ struct ViewOffset< /* Cardinality of the domain index space */ KOKKOS_INLINE_FUNCTION constexpr size_type size() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } /* Span of the range space */ KOKKOS_INLINE_FUNCTION constexpr size_type span() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { @@ -1026,23 +1026,24 @@ struct ViewOffset< return m_dim.N0; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_2() const { - return m_dim.N0 * m_dim.N1; + return size_type(m_dim.N0) * m_dim.N1; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_3() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_4() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_5() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_6() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5; } KOKKOS_INLINE_FUNCTION constexpr size_type stride_7() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6; } // Stride with [ rank ] value is the total length @@ -1288,8 +1289,8 @@ struct ViewOffset< /* Cardinality of the domain index space */ KOKKOS_INLINE_FUNCTION constexpr size_type size() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } /* Span of the range space */ @@ -1633,15 +1634,15 @@ struct ViewOffset< /* Cardinality of the domain index space */ KOKKOS_INLINE_FUNCTION constexpr size_type size() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } /* Span of the range space */ KOKKOS_INLINE_FUNCTION constexpr size_type span() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { @@ -1916,14 +1917,14 @@ struct ViewOffset< /* Cardinality of the domain index space */ KOKKOS_INLINE_FUNCTION constexpr size_type size() const { - return m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * m_dim.N5 * - m_dim.N6 * m_dim.N7; + return size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * + m_dim.N5 * m_dim.N6 * m_dim.N7; } /* Span of the range space */ KOKKOS_INLINE_FUNCTION constexpr size_type span() const { - return size() > 0 ? m_dim.N0 * m_stride : 0; + return size() > 0 ? size_type(m_dim.N0) * m_stride : 0; } KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { @@ -2066,27 +2067,29 @@ struct ViewOffset< stride(/* 2 <= rank */ m_dim.N1 * (dimension_type::rank == 2 - ? 1 + ? size_t(1) : m_dim.N2 * (dimension_type::rank == 3 - ? 1 + ? size_t(1) : m_dim.N3 * (dimension_type::rank == 4 - ? 1 + ? size_t(1) : m_dim.N4 * (dimension_type::rank == 5 - ? 1 + ? size_t(1) : m_dim.N5 * (dimension_type:: rank == 6 - ? 1 + ? size_t( + 1) : m_dim.N6 * (dimension_type:: rank == 7 - ? 1 + ? size_t( + 1) : m_dim .N7)))))))) { } @@ -2447,8 +2450,8 @@ struct ViewOffset { constexpr size_type size() const { return dimension_type::rank == 0 ? 1 - : m_dim.N0 * m_dim.N1 * m_dim.N2 * m_dim.N3 * m_dim.N4 * - m_dim.N5 * m_dim.N6 * m_dim.N7; + : size_type(m_dim.N0) * m_dim.N1 * m_dim.N2 * m_dim.N3 * + m_dim.N4 * m_dim.N5 * m_dim.N6 * m_dim.N7; } private: diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewTracker.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewTracker.hpp index fe3651886b..972b1b6d9a 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewTracker.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewTracker.hpp @@ -91,6 +91,7 @@ struct ViewTracker { template KOKKOS_INLINE_FUNCTION void assign(const View& vt) noexcept { + if (this == reinterpret_cast(&vt.m_track)) return; KOKKOS_IF_ON_HOST(( if (view_traits::is_managed && Kokkos::Impl::SharedAllocationRecord< void, void>::tracking_enabled()) { @@ -102,6 +103,7 @@ struct ViewTracker { KOKKOS_INLINE_FUNCTION ViewTracker& operator=( const ViewTracker& rhs) noexcept { + if (this == &rhs) return *this; KOKKOS_IF_ON_HOST(( if (view_traits::is_managed && Kokkos::Impl::SharedAllocationRecord< void, void>::tracking_enabled()) { diff --git a/lib/kokkos/core/unit_test/TestViewAPI.hpp b/lib/kokkos/core/unit_test/TestViewAPI.hpp index 21602be086..83efae6170 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI.hpp @@ -1087,6 +1087,20 @@ class TestViewAPI { dView4_unmanaged unmanaged_dx = dx; ASSERT_EQ(dx.use_count(), 1); + // Test self assignment +#if defined(__clang__) +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wself-assign-overloaded" +#endif + dx = dx; // copy-assignment operator +#if defined(__clang__) +#pragma GCC diagnostic pop +#endif + ASSERT_EQ(dx.use_count(), 1); + dx = reinterpret_cast( + dx); // conversion assignment operator + ASSERT_EQ(dx.use_count(), 1); + dView4_unmanaged unmanaged_from_ptr_dx = dView4_unmanaged( dx.data(), dx.extent(0), dx.extent(1), dx.extent(2), dx.extent(3)); diff --git a/lib/kokkos/core/unit_test/TestViewAPI_e.hpp b/lib/kokkos/core/unit_test/TestViewAPI_e.hpp index d4f484a530..d1d38022a7 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_e.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_e.hpp @@ -240,6 +240,35 @@ struct TestViewOverloadResolution { TEST(TEST_CATEGORY, view_overload_resolution) { TestViewOverloadResolution::test_function_overload(); } + +template +struct TestViewAllocationLargeRank { + using ViewType = Kokkos::View; + + KOKKOS_FUNCTION void operator()(int) const { + size_t idx = v.extent(0) - 1; + auto& lhs = v(idx, idx, idx, idx, idx, idx, idx, idx); + lhs = 42; // This is where it segfaulted + } + + ViewType v; +}; + +TEST(TEST_CATEGORY, view_allocation_large_rank) { + using ExecutionSpace = typename TEST_EXECSPACE::execution_space; + using MemorySpace = typename TEST_EXECSPACE::memory_space; + constexpr int dim = 16; + using FunctorType = TestViewAllocationLargeRank; + typename FunctorType::ViewType v("v", dim, dim, dim, dim, dim, dim, dim, dim); + + Kokkos::parallel_for(Kokkos::RangePolicy(0, 1), + FunctorType{v}); + typename FunctorType::ViewType v_single(v.data() + v.size() - 1, 1, 1, 1, 1, + 1, 1, 1, 1); + auto result = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace{}, v_single); + ASSERT_EQ(result(0, 0, 0, 0, 0, 0, 0, 0), 42); +} } // namespace Test #include diff --git a/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp b/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp index 08863232ed..bb1d3156f5 100644 --- a/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp +++ b/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp @@ -238,13 +238,10 @@ TEST(kokkosp, test_id_gen) { using Kokkos::Tools::Experimental::DeviceTypeTraits; test_wrapper([&]() { Kokkos::DefaultExecutionSpace ex; - auto id = device_id(ex); - auto id_ref = identifier_from_devid(id); - auto success = (id_ref.instance_id == ex.impl_instance_id()) && - (id_ref.device_id == - static_cast( - DeviceTypeTraits::id)); - ASSERT_TRUE(success); + auto id = device_id(ex); + auto id_ref = identifier_from_devid(id); + ASSERT_EQ(DeviceTypeTraits::id, id_ref.type); + ASSERT_EQ(id_ref.instance_id, ex.impl_instance_id()); }); } @@ -253,6 +250,7 @@ TEST(kokkosp, test_id_gen) { */ TEST(kokkosp, test_kernel_sequence) { test_wrapper([&]() { + Kokkos::DefaultExecutionSpace ex; auto root = Kokkos::Tools::Experimental::device_id_root< Kokkos::DefaultExecutionSpace>(); std::vector expected{ @@ -260,11 +258,10 @@ TEST(kokkosp, test_kernel_sequence) { {"named_instance", FencePayload::distinguishable_devices::no, root + num_instances}, {"test_kernel", FencePayload::distinguishable_devices::no, - root + num_instances} + Kokkos::Tools::Experimental::device_id(ex)} }; expect_fence_events(expected, [=]() { - Kokkos::DefaultExecutionSpace ex; TestFunctor tf; ex.fence("named_instance"); Kokkos::parallel_for( diff --git a/lib/kokkos/master_history.txt b/lib/kokkos/master_history.txt index e174b47f67..41c755a8a8 100644 --- a/lib/kokkos/master_history.txt +++ b/lib/kokkos/master_history.txt @@ -27,3 +27,4 @@ tag: 3.4.00 date: 04:26:2021 master: 1fb0c284 release: 5d7738d6 tag: 3.4.01 date: 05:20:2021 master: 4b97a22f release: 410b15c8 tag: 3.5.00 date: 11:19:2021 master: c28a8b03 release: 21b879e4 tag: 3.6.00 date: 04:14:2022 master: 2834f94a release: 6ea708ff +tag: 3.6.01 date: 06:16:2022 master: b52f8c83 release: afe9b404 diff --git a/lib/mdi/Install.py b/lib/mdi/Install.py index a439da34d2..5452853b82 100644 --- a/lib/mdi/Install.py +++ b/lib/mdi/Install.py @@ -34,12 +34,12 @@ make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (usi # settings -version = "1.3.2" +version = "1.4.1" url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version # known checksums for different MDI versions. used to validate the download. checksums = { \ - '1.3.2' : '836f5da400d8cff0f0e4435640f9454f', \ + '1.4.1' : 'f9505fccd4c79301a619f6452dad4ad9', \ } # print error message or help @@ -177,7 +177,7 @@ try: except: n_cpus = 1 -print("Building lib%s.so ..." % lib) +print("Building lib%s.a ..." % lib) cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT) print(txt.decode('UTF-8')) @@ -201,10 +201,10 @@ makefile_lammps.write(str(rpath_option) + "\n") makefile_lammps.close() -shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.so*" % lib) ) +shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.a" % lib) ) if len(shared_files) > 0: print("Build was successful") else: - error("Build of lib/%s/lib%s.so was NOT successful" % (lib,lib)) + error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib)) if has_extramake and not os.path.exists("Makefile.lammps"): print("lib/%s/Makefile.lammps was NOT created" % lib) diff --git a/lib/mdi/Makefile.g++ b/lib/mdi/Makefile.g++ deleted file mode 100644 index 15cc9c3a3b..0000000000 --- a/lib/mdi/Makefile.g++ +++ /dev/null @@ -1,18 +0,0 @@ -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.empty - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - mkdir -p build - cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ ../MDI_Library; make - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ CLEAN ------ - -clean: - -rm *.o *.h $(LIB) - -rm -r build diff --git a/lib/mdi/Makefile.gcc b/lib/mdi/Makefile.gcc index ef8a96f5ad..3653f77a2f 100644 --- a/lib/mdi/Makefile.gcc +++ b/lib/mdi/Makefile.gcc @@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty lib: $(OBJ) mkdir -p build - cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=gcc ../MDI_Library; make + cd build && cmake -D libtype=STATIC -D language=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D mpi=ON -D plugins=ON -D python_plugins=ON -D CMAKE_C_COMPILER=gcc ../MDI_Library && make @cp $(EXTRAMAKE) Makefile.lammps # ------ CLEAN ------ diff --git a/lib/mdi/Makefile.icc b/lib/mdi/Makefile.icc index d70ff28f97..615ebf9070 100644 --- a/lib/mdi/Makefile.icc +++ b/lib/mdi/Makefile.icc @@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty lib: $(OBJ) mkdir -p build - cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icc ../MDI_Library; make + cd build && cmake -D libtype=STATIC -D language=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D mpi=ON -D plugins=ON -D python_plugins=ON -D CMAKE_C_COMPILER=icc ../MDI_Library && make @cp $(EXTRAMAKE) Makefile.lammps # ------ CLEAN ------ diff --git a/lib/mdi/Makefile.lammps.empty b/lib/mdi/Makefile.lammps.empty index 3aabe162d2..01c8fe0b70 100644 --- a/lib/mdi/Makefile.lammps.empty +++ b/lib/mdi/Makefile.lammps.empty @@ -1,5 +1,7 @@ # Settings that the LAMMPS build will import when this package library is used -mdi_SYSINC = -mdi_SYSLIB = -mdi_SYSPATH = \ No newline at end of file +mdi_python_SYSLIB = $(shell which python3-config > /dev/null 2>&1 && python3-config --ldflags --embed > /dev/null 2>&1 && python3-config --ldflags --embed || (which python3-config > /dev/null 2>&1 && python3-config --ldflags || :) ) + +mdi_SYSINC = +mdi_SYSLIB = $(mdi_python_SYSLIB) +mdi_SYSPATH = diff --git a/lib/mdi/Makefile.mpi b/lib/mdi/Makefile.mpi index cff60f5e0b..4274f3e0e8 100644 --- a/lib/mdi/Makefile.mpi +++ b/lib/mdi/Makefile.mpi @@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty lib: $(OBJ) mkdir -p build - cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=mpicc -D CMAKE_CXX_COMPILER=mpicxx ../MDI_Library; make + cd build && cmake -D libtype=STATIC -D language=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D mpi=ON -D plugins=ON -D python_plugins=ON -D CMAKE_C_COMPILER=mpicc ../MDI_Library && make @cp $(EXTRAMAKE) Makefile.lammps # ------ CLEAN ------ diff --git a/src/.gitignore b/src/.gitignore index 220cd621db..4c1cf49b3b 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -173,12 +173,20 @@ /pair_tdpd.cpp /pair_tdpd.h +/compute_grid.cpp +/compute_grid.h +/compute_grid_local.cpp +/compute_grid_local.h /compute_sna_atom.cpp /compute_sna_atom.h /compute_snad_atom.cpp /compute_snad_atom.h /compute_snav_atom.cpp /compute_snav_atom.h +/compute_sna_grid.cpp +/compute_sna_grid.h +/compute_sna_grid_local.cpp +/compute_sna_grid_local.h /compute_snap.cpp /compute_snap.h /openmp_snap.h diff --git a/src/Depend.sh b/src/Depend.sh index 8046fd2636..98f3e5de4f 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -127,6 +127,10 @@ if (test $1 = "MANYBODY") then depend OPENMP fi +if (test $1 = "MEAM") then + depend KOKKOS +fi + if (test $1 = "MOLECULE") then depend EXTRA-MOLECULE depend GPU diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 022da7855a..314205ea3e 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -182,6 +182,13 @@ action kokkos_base.h action kokkos_base_fft.h fft3d.h action kokkos_few.h action kokkos_type.h +action meam_kokkos.h meam.h +action meam_dens_final_kokkos.h meam_dens_final.cpp +action meam_dens_init_kokkos.h meam_dens_init.cpp +action meam_force_kokkos.h meam_force.cpp +action meam_funcs_kokkos.h meam_funcs.cpp +action meam_impl_kokkos.h meam_impl.cpp +action meam_setup_done_kokkos.h meam_setup_done.cpp action memory_kokkos.h action modify_kokkos.cpp action modify_kokkos.h @@ -287,6 +294,8 @@ action pair_lj_gromacs_kokkos.cpp pair_lj_gromacs.cpp action pair_lj_gromacs_kokkos.h pair_lj_gromacs.h action pair_lj_sdk_kokkos.cpp pair_lj_sdk.cpp action pair_lj_sdk_kokkos.h pair_lj_sdk.h +action pair_meam_kokkos.cpp pair_meam.cpp +action pair_meam_kokkos.h pair_meam.h action pair_morse_kokkos.cpp action pair_morse_kokkos.h action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 18de4d46cb..dd37d1a838 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -1391,6 +1391,9 @@ int AtomVecAngleKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int n int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, ExecutionSpace space) { const size_t elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom; + + while (nlocal + nrecv/elements >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecAngleKokkos_UnpackExchangeFunctor diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 891ebb51c2..0a78b42227 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -649,6 +649,8 @@ struct AtomVecAtomicKokkos_UnpackExchangeFunctor { /* ---------------------------------------------------------------------- */ int AtomVecAtomicKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,ExecutionSpace space) { + while (nlocal + nrecv/11 >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecAtomicKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 3655d894c9..ea70f15dcb 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -845,6 +845,9 @@ int AtomVecBondKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, ExecutionSpace space) { const size_t elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom; + + while (nlocal + nrecv/elements >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecBondKokkos_UnpackExchangeFunctor diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 7de36ffd5d..3c0e1d46bb 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -774,6 +774,8 @@ struct AtomVecChargeKokkos_UnpackExchangeFunctor { int AtomVecChargeKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv, int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, ExecutionSpace space) { + while (nlocal + nrecv/12 >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecChargeKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index cf7ad9d533..1b7ccd97d0 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -1505,6 +1505,8 @@ struct AtomVecDPDKokkos_UnpackExchangeFunctor { /* ---------------------------------------------------------------------- */ int AtomVecDPDKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,ExecutionSpace space) { + while (nlocal + nrecv/17 >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecDPDKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index b75c33e046..7322a75b11 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -1186,6 +1186,9 @@ int AtomVecFullKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr ExecutionSpace space) { const size_t elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom; + + while (nlocal + nrecv/elements >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecFullKokkos_UnpackExchangeFunctor diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index c4e75c1da7..123adedbdf 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -1594,6 +1594,9 @@ int AtomVecMolecularKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,i ExecutionSpace space) { const size_t elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom; + + while (nlocal + nrecv/elements >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecMolecularKokkos_UnpackExchangeFunctor diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 0b722e8563..206d6c832c 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -2341,6 +2341,8 @@ struct AtomVecSphereKokkos_UnpackExchangeFunctor { /* ---------------------------------------------------------------------- */ int AtomVecSphereKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,ExecutionSpace space) { + while (nlocal + nrecv/16 >= nmax) grow(0); + if (space == Host) { k_count.h_view(0) = nlocal; AtomVecSphereKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 039c08f31c..7722241756 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -863,6 +863,8 @@ struct AtomVecSpinKokkos_UnpackExchangeFunctor { int AtomVecSpinKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv, int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, ExecutionSpace space) { + while (nlocal + nrecv/15 >= nmax) grow(0); + if(space == Host) { k_count.h_view(0) = nlocal; AtomVecSpinKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 4883838273..fea5864225 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -109,6 +109,7 @@ void CommKokkos::init() exchange_comm_classic = lmp->kokkos->exchange_comm_classic; forward_comm_classic = lmp->kokkos->forward_comm_classic; forward_pair_comm_classic = lmp->kokkos->forward_pair_comm_classic; + reverse_pair_comm_classic = lmp->kokkos->reverse_pair_comm_classic; forward_fix_comm_classic = lmp->kokkos->forward_fix_comm_classic; reverse_comm_classic = lmp->kokkos->reverse_comm_classic; exchange_comm_on_host = lmp->kokkos->exchange_comm_on_host; @@ -478,12 +479,13 @@ void CommKokkos::forward_comm_device(Pair *pair) int nsize = pair->comm_forward; KokkosBase* pairKKBase = dynamic_cast(pair); + int nmax = max_buf_pair; for (iswap = 0; iswap < nswap; iswap++) { - int n = MAX(max_buf_pair,nsize*sendnum[iswap]); - n = MAX(n,nsize*recvnum[iswap]); - if (n > max_buf_pair) - grow_buf_pair(n); + nmax = MAX(nmax,nsize*sendnum[iswap]); + nmax = MAX(nmax,nsize*recvnum[iswap]); } + if (nmax > max_buf_pair) + grow_buf_pair(nmax); for (iswap = 0; iswap < nswap; iswap++) { @@ -545,8 +547,76 @@ void CommKokkos::grow_buf_fix(int n) { void CommKokkos::reverse_comm(Pair *pair) { - k_sendlist.sync(); - CommBrick::reverse_comm(pair); + if (pair->execution_space == Host || !pair->reverse_comm_device || reverse_pair_comm_classic) { + k_sendlist.sync(); + CommBrick::reverse_comm(pair); + } else { + k_sendlist.sync(); + reverse_comm_device(pair); + } +} + +template +void CommKokkos::reverse_comm_device(Pair *pair) +{ + int iswap,n; + MPI_Request request; + DAT::tdual_xfloat_1d k_buf_tmp; + + KokkosBase* pairKKBase = dynamic_cast(pair); + + int nsize = MAX(pair->comm_reverse,pair->comm_reverse_off); + + int nmax = max_buf_pair; + for (iswap = 0; iswap < nswap; iswap++) { + nmax = MAX(nmax,nsize*sendnum[iswap]); + nmax = MAX(nmax,nsize*recvnum[iswap]); + } + if (nmax > max_buf_pair) + grow_buf_pair(nmax); + + for (iswap = nswap-1; iswap >= 0; iswap--) { + + // pack buffer + + n = pairKKBase->pack_reverse_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send_pair); + DeviceType().fence(); + + // exchange with another proc + // if self, set recv buffer to send buffer + + double* buf_send_pair; + double* buf_recv_pair; + if (lmp->kokkos->gpu_aware_flag) { + buf_send_pair = k_buf_send_pair.view().data(); + buf_recv_pair = k_buf_recv_pair.view().data(); + } else { + k_buf_send_pair.modify(); + k_buf_send_pair.sync(); + buf_send_pair = k_buf_send_pair.h_view.data(); + buf_recv_pair = k_buf_recv_pair.h_view.data(); + } + + if (sendproc[iswap] != me) { + if (sendnum[iswap]) + MPI_Irecv(buf_recv_pair,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); + if (recvnum[iswap]) + MPI_Send(buf_send_pair,n,MPI_DOUBLE,recvproc[iswap],0,world); + if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); + + if (!lmp->kokkos->gpu_aware_flag) { + k_buf_recv_pair.modify(); + k_buf_recv_pair.sync(); + } + k_buf_tmp = k_buf_recv_pair; + } else k_buf_tmp = k_buf_send_pair; + + // unpack buffer + + pairKKBase->unpack_reverse_comm_kokkos(sendnum[iswap],k_sendlist, + iswap,k_buf_tmp); + DeviceType().fence(); + } } void CommKokkos::forward_comm(Dump *dump) diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h index 3fcce82e2c..80736c1f92 100644 --- a/src/KOKKOS/comm_kokkos.h +++ b/src/KOKKOS/comm_kokkos.h @@ -27,6 +27,7 @@ class CommKokkos : public CommBrick { bool exchange_comm_classic; bool forward_comm_classic; bool forward_pair_comm_classic; + bool reverse_pair_comm_classic; bool forward_fix_comm_classic; bool reverse_comm_classic; bool exchange_comm_on_host; @@ -58,6 +59,7 @@ class CommKokkos : public CommBrick { template void forward_comm_device(int dummy); template void reverse_comm_device(); template void forward_comm_device(Pair *pair); + template void reverse_comm_device(Pair *pair); template void forward_comm_device(Fix *fix, int size=0); template void exchange_device(); template void borders_device(); diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 18f05fa281..3ecce0d75d 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -91,6 +91,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) exchange_comm_changed = 0; forward_comm_changed = 0; forward_pair_comm_changed = 0; + reverse_pair_comm_changed = 0; forward_fix_comm_changed = 0; reverse_comm_changed = 0; @@ -239,7 +240,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) newtonflag = 0; exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 0; - forward_pair_comm_classic = forward_fix_comm_classic = 0; + forward_pair_comm_classic = reverse_pair_comm_classic = forward_fix_comm_classic = 0; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } else { @@ -253,7 +254,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) newtonflag = 1; exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 1; - forward_pair_comm_classic = forward_fix_comm_classic = 1; + forward_pair_comm_classic = reverse_pair_comm_classic = forward_fix_comm_classic = 1; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } @@ -394,17 +395,17 @@ void KokkosLMP::accelerator(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); if (strcmp(arg[iarg+1],"no") == 0) { exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 1; - forward_pair_comm_classic = forward_fix_comm_classic = 1; + forward_pair_comm_classic = reverse_pair_comm_classic = forward_fix_comm_classic = 1; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } else if (strcmp(arg[iarg+1],"host") == 0) { exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 0; - forward_pair_comm_classic = forward_fix_comm_classic = 1; + forward_pair_comm_classic = reverse_pair_comm_classic = forward_fix_comm_classic = 1; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 1; } else if (strcmp(arg[iarg+1],"device") == 0) { exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 0; - forward_pair_comm_classic = forward_fix_comm_classic = 0; + forward_pair_comm_classic = reverse_pair_comm_classic = forward_fix_comm_classic = 0; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); @@ -441,6 +442,14 @@ void KokkosLMP::accelerator(int narg, char **arg) else error->all(FLERR,"Illegal package kokkos command"); forward_pair_comm_changed = 0; iarg += 2; + } else if (strcmp(arg[iarg],"comm/pair/reverse") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); + if (strcmp(arg[iarg+1],"no") == 0) reverse_pair_comm_classic = 1; + else if (strcmp(arg[iarg+1],"host") == 0) reverse_pair_comm_classic = 1; + else if (strcmp(arg[iarg+1],"device") == 0) reverse_pair_comm_classic = 0; + else error->all(FLERR,"Illegal package kokkos command"); + reverse_pair_comm_changed = 0; + iarg += 2; } else if (strcmp(arg[iarg],"comm/fix/forward") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); if (strcmp(arg[iarg+1],"no") == 0) forward_fix_comm_classic = 1; @@ -515,6 +524,10 @@ void KokkosLMP::accelerator(int narg, char **arg) forward_pair_comm_classic = 1; forward_pair_comm_changed = 1; } + if (reverse_pair_comm_classic == 0) { + reverse_pair_comm_classic = 1; + reverse_pair_comm_changed = 1; + } if (forward_fix_comm_classic == 0) { forward_fix_comm_classic = 1; forward_fix_comm_changed = 1; @@ -540,6 +553,10 @@ void KokkosLMP::accelerator(int narg, char **arg) forward_pair_comm_classic = 0; forward_pair_comm_changed = 0; } + if (reverse_pair_comm_changed) { + reverse_pair_comm_classic = 0; + reverse_pair_comm_changed = 0; + } if (forward_fix_comm_changed) { forward_fix_comm_classic = 0; forward_fix_comm_changed = 0; diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 07d172e524..1cecd69c5f 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -30,6 +30,7 @@ class KokkosLMP : protected Pointers { int exchange_comm_classic; int forward_comm_classic; int forward_pair_comm_classic; + int reverse_pair_comm_classic; int forward_fix_comm_classic; int reverse_comm_classic; int exchange_comm_on_host; @@ -38,6 +39,7 @@ class KokkosLMP : protected Pointers { int exchange_comm_changed; int forward_comm_changed; int forward_pair_comm_changed; + int reverse_pair_comm_changed; int forward_fix_comm_changed; int reverse_comm_changed; int nthreads,ngpus; diff --git a/src/KOKKOS/kokkos_base.h b/src/KOKKOS/kokkos_base.h index f18d55eec2..c593f0ae60 100644 --- a/src/KOKKOS/kokkos_base.h +++ b/src/KOKKOS/kokkos_base.h @@ -29,6 +29,10 @@ class KokkosBase { int, int *) {return 0;}; virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d &) {} + virtual int pack_reverse_comm_kokkos(int, int, DAT::tdual_xfloat_1d &) {return 0;}; + virtual void unpack_reverse_comm_kokkos(int, DAT::tdual_int_2d, + int, DAT::tdual_xfloat_1d &) {} + // Fix virtual int pack_forward_comm_fix_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d &, diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index 89f6586581..84c584a5cc 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -477,59 +477,3 @@ double MathSpecialKokkos::erfcx_y100(const double y100) return 1.0; } /* erfcx_y100 */ -/* optimizer friendly implementation of exp2(x). - * - * strategy: - * - * split argument into an integer part and a fraction: - * ipart = floor(x+0.5); - * fpart = x - ipart; - * - * compute exp2(ipart) from setting the ieee754 exponent - * compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[ - * - * the result becomes: exp2(x) = exp2(ipart) * exp2(fpart) - */ - -/* IEEE 754 double precision floating point data manipulation */ -typedef union -{ - double f; - uint64_t u; - struct {int32_t i0,i1;} s; -} udi_t; - -static const double fm_exp2_q[] = { -/* 1.00000000000000000000e0, */ - 2.33184211722314911771e2, - 4.36821166879210612817e3 -}; -static const double fm_exp2_p[] = { - 2.30933477057345225087e-2, - 2.02020656693165307700e1, - 1.51390680115615096133e3 -}; - -double MathSpecialKokkos::exp2_x86(double x) -{ - double ipart, fpart, px, qx; - udi_t epart; - - ipart = floor(x+0.5); - fpart = x - ipart; - epart.s.i0 = 0; - epart.s.i1 = (((int) ipart) + 1023) << 20; - - x = fpart*fpart; - - px = fm_exp2_p[0]; - px = px*x + fm_exp2_p[1]; - qx = x + fm_exp2_q[0]; - px = px*x + fm_exp2_p[2]; - qx = qx*x + fm_exp2_q[1]; - - px = px * fpart; - - x = 1.0 + 2.0*(px/(qx-px)); - return epart.f*x; -} diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h index 802d1c2979..35a8bf56c5 100644 --- a/src/KOKKOS/math_special_kokkos.h +++ b/src/KOKKOS/math_special_kokkos.h @@ -22,79 +22,233 @@ namespace LAMMPS_NS { namespace MathSpecialKokkos { + /*! Fast tabulated factorial function + * + * This function looks up pre-computed factorial values for arguments of n = 0 + * to a maximum of 167, which is the maximal value representable by a double + * precision floating point number. For other values of n a NaN value is returned. + * + * \param n argument (valid: 0 <= n <= 167) + * \return value of n! as double precision number or NaN */ + + extern double factorial(const int n); + + /* optimizer friendly implementation of exp2(x). + * + * strategy: + * + * split argument into an integer part and a fraction: + * ipart = floor(x+0.5); + * fpart = x - ipart; + * + * compute exp2(ipart) from setting the ieee754 exponent + * compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[ + * + * the result becomes: exp2(x) = exp2(ipart) * exp2(fpart) + */ + + /* IEEE 754 double precision floating point data manipulation */ + typedef union + { + double f; + uint64_t u; + struct {int32_t i0,i1;} s; + } udi_t; + + /* double precision constants */ + #define FM_DOUBLE_LOG2OFE 1.4426950408889634074 + + /*! Fast implementation of 2^x without argument checks for little endian CPUs + * + * This function implements an optimized version of pow(2.0, x) that does not + * check for valid arguments and thus may only be used where arguments are well + * behaved. The implementation makes assumptions about the layout of double + * precision floating point numbers in memory and thus will only work on little + * endian CPUs. If little endian cannot be safely detected, the result of + * calling pow(2.0, x) will be returned. This function also is the basis for + * the fast exponential fm_exp(x). + * + * \param x argument + * \return value of 2^x as double precision number */ + + KOKKOS_INLINE_FUNCTION + static double exp2_x86(double x) + { + #if defined(__BYTE_ORDER__) && (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__) + double ipart, fpart, px, qx; + udi_t epart; + + const double fm_exp2_q[2] = { + /* 1.00000000000000000000e0, */ + 2.33184211722314911771e2, + 4.36821166879210612817e3 + }; + const double fm_exp2_p[3] = { + 2.30933477057345225087e-2, + 2.02020656693165307700e1, + 1.51390680115615096133e3 + }; + + ipart = floor(x+0.5); + fpart = x - ipart; + epart.s.i0 = 0; + epart.s.i1 = (((int) ipart) + 1023) << 20; + + x = fpart*fpart; + + px = fm_exp2_p[0]; + px = px*x + fm_exp2_p[1]; + qx = x + fm_exp2_q[0]; + px = px*x + fm_exp2_p[2]; + qx = qx*x + fm_exp2_q[1]; + + px = px * fpart; + + x = 1.0 + 2.0*(px/(qx-px)); + return epart.f*x; + #else + return pow(2.0, x); + #endif + } + + /*! Fast implementation of exp(x) for little endian CPUs + * + * This function implements an optimized version of exp(x) for little endian CPUs. + * It calls the exp2_x86(x) function with a suitable prefactor to x to return exp(x). + * The implementation makes assumptions about the layout of double + * precision floating point numbers in memory and thus will only work on little + * endian CPUs. If little endian cannot be safely detected, the result of + * calling the exp(x) implementation in the standard math library will be returned. + * + * \param x argument + * \return value of e^x as double precision number */ + + KOKKOS_INLINE_FUNCTION + static double fm_exp(double x) + { + #if defined(__BYTE_ORDER__) && (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__) + if (x < -1022.0/FM_DOUBLE_LOG2OFE) return 0; + if (x > 1023.0/FM_DOUBLE_LOG2OFE) return INFINITY; + return exp2_x86(FM_DOUBLE_LOG2OFE * x); + #else + return ::exp(x); + #endif + } + // support function for scaled error function complement extern double erfcx_y100(const double y100); - // fast 2**x function without argument checks for little endian CPUs - extern double exp2_x86(double x); - - // scaled error function complement exp(x*x)*erfc(x) for coul/long styles + /*! Fast scaled error function complement exp(x*x)*erfc(x) for coul/long styles + * + * This is a portable fast implementation of exp(x*x)*erfc(x) that can be used + * in coul/long pair styles as a replacement for the polynomial expansion that + * is/was widely used. Unlike the polynomial expansion, that is only accurate + * at the level of single precision floating point it provides full double precision + * accuracy, but at comparable speed (unlike the erfc() implementation shipped + * with GNU standard math library). + * + * \param x argument + * \return value of e^(x*x)*erfc(x) */ static inline double my_erfcx(const double x) { - if (x >= 0.0) return erfcx_y100(400.0/(4.0+x)); - else return 2.0*exp(x*x) - erfcx_y100(400.0/(4.0-x)); + if (x >= 0.0) + return erfcx_y100(400.0 / (4.0 + x)); + else + return 2.0 * exp(x * x) - erfcx_y100(400.0 / (4.0 - x)); } - // exp(-x*x) for coul/long styles + /*! Fast implementation of exp(-x*x) for little endian CPUs for coul/long styles + * + * This function implements an optimized version of exp(-x*x) based on exp2_x86() + * for use with little endian CPUs. If little endian cannot be safely detected, + * the result of calling the exp(-x*x) implementation in the standard math + * library will be returned. + * + * \param x argument + * \return value of e^(-x*x) as double precision number */ static inline double expmsq(double x) { x *= x; x *= 1.4426950408889634074; // log_2(e) -#if defined(__BYTE_ORDER__) && __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ +#if defined(__BYTE_ORDER__) && __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ return (x < 1023.0) ? exp2_x86(-x) : 0.0; #else return (x < 1023.0) ? exp2(-x) : 0.0; #endif } - // x**2, use instead of pow(x,2.0) - KOKKOS_INLINE_FUNCTION - static double square(const double &x) { return x*x; } + /*! Fast inline version of pow(x, 2.0) + * + * \param x argument + * \return x*x */ - // x**3, use instead of pow(x,3.0) KOKKOS_INLINE_FUNCTION - static double cube(const double &x) { return x*x*x; } + static double square(const double &x) { return x * x; } + + /*! Fast inline version of pow(x, 3.0) + * + * \param x argument + * \return x*x */ + + KOKKOS_INLINE_FUNCTION + static double cube(const double &x) { return x * x * x; } + + /* Fast inline version of pow(-1.0, n) + * + * \param n argument (integer) + * \return -1 if n is odd, 1.0 if n is even */ - // return -1.0 for odd n, 1.0 for even n, like pow(-1.0,n) KOKKOS_INLINE_FUNCTION static double powsign(const int n) { return (n & 1) ? -1.0 : 1.0; } - // optimized version of pow(x,n) with n being integer - // up to 10x faster than pow(x,y) + /* Fast inline version of pow(x,n) for integer n + * + * This is a version of pow(x,n) optimized for n being integer. + * Speedups of up to 10x faster than pow(x,y) have been measured. + * + * \param n argument (integer) + * \return value of x^n */ KOKKOS_INLINE_FUNCTION - static double powint(const double &x, const int n) { - double yy,ww; + static double powint(const double &x, const int n) + { + double yy, ww; if (x == 0.0) return 0.0; int nn = (n > 0) ? n : -n; ww = x; - for (yy = 1.0; nn != 0; nn >>= 1, ww *=ww) + for (yy = 1.0; nn != 0; nn >>= 1, ww *= ww) if (nn & 1) yy *= ww; - return (n > 0) ? yy : 1.0/yy; + return (n > 0) ? yy : 1.0 / yy; } - // optimized version of (sin(x)/x)**n with n being a _positive_ integer + /* Fast inline version of (sin(x)/x)^n as used by PPPM kspace styles + * + * This is an optimized function to compute (sin(x)/x)^n as frequently used by PPPM. + * + * \param n argument (integer). Expected to be positive. + * \return value of (sin(x)/x)^n */ KOKKOS_INLINE_FUNCTION - static double powsinxx(const double &x, int n) { - double yy,ww; + static double powsinxx(const double &x, int n) + { + double yy, ww; if (x == 0.0) return 1.0; - ww = sin(x)/x; + ww = sin(x) / x; - for (yy = 1.0; n != 0; n >>= 1, ww *=ww) + for (yy = 1.0; n != 0; n >>= 1, ww *= ww) if (n & 1) yy *= ww; return yy; } -} -} +} // namespace MathSpecialKokkos +} // namespace LAMMPS_NS #endif diff --git a/src/KOKKOS/meam_dens_final_kokkos.h b/src/KOKKOS/meam_dens_final_kokkos.h new file mode 100644 index 0000000000..a3b95e837d --- /dev/null +++ b/src/KOKKOS/meam_dens_final_kokkos.h @@ -0,0 +1,164 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "meam_kokkos.h" +#include "math_special.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +void +MEAMKokkos::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, + typename ArrayTypes::t_efloat_1d eatom, int ntype, typename AT::t_int_1d type, typename AT::t_int_1d d_map, typename AT::t_int_2d d_scale, int& errorflag, EV_FLOAT &ev_all) +{ + EV_FLOAT ev; + this->eflag_either = eflag_either; + this->eflag_global = eflag_global; + this->eflag_atom = eflag_atom; + this->d_eatom = eatom; + this->ntype = ntype; + this->type = type; + this->d_map = d_map; + this->d_scale = d_scale; + + Kokkos::deep_copy(d_errorflag,0); + + // Complete the calculation of density + + copymode = 1; + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,nlocal),*this,ev); + ev_all.evdwl += ev.evdwl; + copymode = 0; + + auto h_errorflag = Kokkos::create_mirror_view_and_copy(LMPHostType(),d_errorflag); + errorflag = h_errorflag(); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MEAMKokkos::operator()(TagMEAMDensFinal, const int &i, EV_FLOAT& ev) const { + + F_FLOAT rhob, G, dG, Gbar, dGbar, gam, shp[3], Z; + F_FLOAT denom, rho_bkgd, Fl; + double scaleii; + + int elti = d_map[type[i]]; + if (elti >= 0) { + scaleii = d_scale(type[i],type[i]); + d_rho1[i] = 0.0; + d_rho2[i] = -1.0 / 3.0 * d_arho2b[i] * d_arho2b[i]; + d_rho3[i] = 0.0; + for (int m = 0; m < 3; m++) { + d_rho1[i] += d_arho1(i,m) * d_arho1(i,m); + d_rho3[i] -= 3.0 / 5.0 * d_arho3b(i,m) * d_arho3b(i,m); + } + for (int m = 0; m < 6; m++) + d_rho2[i] += v2D[m] * d_arho2(i,m) * d_arho2(i,m); + for (int m = 0; m < 10; m++) + d_rho3[i] += v3D[m] * d_arho3(i,m) * d_arho3(i,m); + + if (d_rho0[i] > 0.0) { + if (ialloy == 1) { + d_t_ave(i,0) = fdiv_zero_kk(d_t_ave(i,0), d_tsq_ave(i,0)); + d_t_ave(i,1) = fdiv_zero_kk(d_t_ave(i,1), d_tsq_ave(i,1)); + d_t_ave(i,2) = fdiv_zero_kk(d_t_ave(i,2), d_tsq_ave(i,2)); + } else if (ialloy == 2) { + d_t_ave(i,0) = t1_meam[elti]; + d_t_ave(i,1) = t2_meam[elti]; + d_t_ave(i,2) = t3_meam[elti]; + } else { + d_t_ave(i,0) /= d_rho0[i]; + d_t_ave(i,1) /= d_rho0[i]; + d_t_ave(i,2) /= d_rho0[i]; + } + } + + d_gamma[i] = d_t_ave(i,0) * d_rho1[i] + d_t_ave(i,1) * d_rho2[i] + d_t_ave(i,2) * d_rho3[i]; + + if (d_rho0[i] > 0.0) + d_gamma[i] /= (d_rho0[i] * d_rho0[i]); + + Z = get_Zij(lattce_meam[elti][elti]); + + G = G_gam(d_gamma[i], ibar_meam[elti], d_errorflag()); + if (d_errorflag() != 0) + return; + + get_shpfcn(lattce_meam[elti][elti], stheta_meam[elti][elti], ctheta_meam[elti][elti], shp); + if (ibar_meam[elti] <= 0) { + Gbar = 1.0; + dGbar = 0.0; + } else { + if (mix_ref_t == 1) + gam = (d_t_ave(i,0) * shp[0] + d_t_ave(i,1) * shp[1] + d_t_ave(i,2) * shp[2]) / (Z * Z); + else + gam = (t1_meam[elti] * shp[0] + t2_meam[elti] * shp[1] + t3_meam[elti] * shp[2]) / + (Z * Z); + Gbar = G_gam(gam, ibar_meam[elti], d_errorflag()); + } + d_rho[i] = d_rho0[i] * G; + + if (mix_ref_t == 1) { + if (ibar_meam[elti] <= 0) { + Gbar = 1.0; + dGbar = 0.0; + } else { + gam = (d_t_ave(i,0) * shp[0] + d_t_ave(i,1) * shp[1] + d_t_ave(i,2) * shp[2]) / (Z * Z); + Gbar = dG_gam(gam, ibar_meam[elti], dGbar); + } + rho_bkgd = rho0_meam[elti] * Z * Gbar; + } else { + if (bkgd_dyn == 1) + rho_bkgd = rho0_meam[elti] * Z; + else + rho_bkgd = rho_ref_meam[elti]; + } + rhob = d_rho[i] / rho_bkgd; + denom = 1.0 / rho_bkgd; + + G = dG_gam(d_gamma[i], ibar_meam[elti], dG); + + d_dgamma1[i] = (G - 2 * dG * d_gamma[i]) * denom; + + if (!iszero_kk(d_rho0[i])) + d_dgamma2[i] = (dG / d_rho0[i]) * denom; + else + d_dgamma2[i] = 0.0; + + // dgamma3 is nonzero only if we are using the "mixed" rule for + // computing t in the reference system (which is not correct, but + // included for backward compatibility + if (mix_ref_t == 1) + d_dgamma3[i] = d_rho0[i] * G * dGbar / (Gbar * Z * Z) * denom; + else + d_dgamma3[i] = 0.0; + + Fl = embedding(A_meam[elti], Ec_meam[elti][elti], rhob, d_frhop[i]); + + if (eflag_either) { + Fl *= scaleii; + if (eflag_global) { + ev.evdwl += Fl; + } + if (eflag_atom) { + d_eatom[i] += Fl; + } + } + } +} + diff --git a/src/KOKKOS/meam_dens_init_kokkos.h b/src/KOKKOS/meam_dens_init_kokkos.h new file mode 100644 index 0000000000..4342cc1ba1 --- /dev/null +++ b/src/KOKKOS/meam_dens_init_kokkos.h @@ -0,0 +1,602 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "meam_kokkos.h" +#include "math_special_kokkos.h" + +using namespace LAMMPS_NS; +using namespace MathSpecialKokkos; + +/* ---------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION +void MEAMKokkos::operator()(TagMEAMDensInit, const int &i) const { + int ii, offsetval; + ii = d_ilist_half[i]; + offsetval = d_offset[i]; + // compute screening function and derivatives + this->template getscreen(ii, offsetval, x, d_numneigh_half, + d_numneigh_full, ntype, type, d_map); + + // calculate intermediate density terms to be communicated + this->template calc_rho1(ii, ntype, type, d_map, x, d_numneigh_half, offsetval); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MEAMKokkos::operator()(TagMEAMZero, const int &i) const { + d_rho0[i] = 0.0; + d_arho2b[i] = 0.0; + d_arho1(i,0) = d_arho1(i,1) = d_arho1(i,2) = 0.0; + for (int j = 0; j < 6; j++) + d_arho2(i,j) = 0.0; + for (int j = 0; j < 10; j++) + d_arho3(i,j) = 0.0; + d_arho3b(i,0) = d_arho3b(i,1) = d_arho3b(i,2) = 0.0; + d_t_ave(i,0) = d_t_ave(i,1) = d_t_ave(i,2) = 0.0; + d_tsq_ave(i,0) = d_tsq_ave(i,1) = d_tsq_ave(i,2) = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +template +void +MEAMKokkos::meam_dens_setup(int atom_nmax, int nall, int n_neigh) +{ + MemoryKokkos *memoryKK = (MemoryKokkos *)memory; + + // grow local arrays if necessary + + if (atom_nmax > nmax) { + memoryKK->destroy_kokkos(k_rho,rho); + memoryKK->destroy_kokkos(k_rho0,rho0); + memoryKK->destroy_kokkos(k_rho1,rho1); + memoryKK->destroy_kokkos(k_rho2,rho2); + memoryKK->destroy_kokkos(k_rho3,rho3); + memoryKK->destroy_kokkos(k_frhop,frhop); + memoryKK->destroy_kokkos(k_gamma,gamma); + memoryKK->destroy_kokkos(k_dgamma1,dgamma1); + memoryKK->destroy_kokkos(k_dgamma2,dgamma2); + memoryKK->destroy_kokkos(k_dgamma3,dgamma3); + memoryKK->destroy_kokkos(k_arho2b,arho2b); + memoryKK->destroy_kokkos(k_arho1,arho1); + memoryKK->destroy_kokkos(k_arho2,arho2); + memoryKK->destroy_kokkos(k_arho3,arho3); + memoryKK->destroy_kokkos(k_arho3b,arho3b); + memoryKK->destroy_kokkos(k_t_ave,t_ave); + memoryKK->destroy_kokkos(k_tsq_ave,tsq_ave); + + nmax = atom_nmax; +// memory->create(rho, nmax, "pair:rho"); + k_rho = DAT::tdual_ffloat_1d("pair:rho",nmax); + d_rho = k_rho.template view(); + h_rho = k_rho.h_view; + // memory->create(rho0, nmax, "pair:rho0"); + k_rho0 = DAT::tdual_ffloat_1d("pair:rho0",nmax); + d_rho0 = k_rho0.template view(); + h_rho0 = k_rho0.h_view; + //memory->create(rho1, nmax, "pair:rho1"); + k_rho1 = DAT::tdual_ffloat_1d("pair:rho1",nmax); + d_rho1 = k_rho1.template view(); + h_rho1 = k_rho1.h_view; + //memory->create(rho2, nmax, "pair:rho2"); + k_rho2 = DAT::tdual_ffloat_1d("pair:rho2",nmax); + d_rho2 = k_rho2.template view(); + h_rho2 = k_rho2.h_view; + //memory->create(rho3, nmax, "pair:rho3"); + k_rho3 = DAT::tdual_ffloat_1d("pair:rho3",nmax); + d_rho3 = k_rho3.template view(); + h_rho3 = k_rho3.h_view; + //memory->create(frhop, nmax, "pair:frhop"); + k_frhop = DAT::tdual_ffloat_1d("pair:frhop",nmax); + d_frhop = k_frhop.template view(); + h_frhop = k_frhop.h_view; + //memory->create(gamma, nmax, "pair:gamma"); + k_gamma = DAT::tdual_ffloat_1d("pair:gamma",nmax); + d_gamma = k_gamma.template view(); + h_gamma = k_gamma.h_view; + //memory->create(dgamma1, nmax, "pair:dgamma1"); + k_dgamma1 = DAT::tdual_ffloat_1d("pair:dgamma1",nmax); + d_dgamma1 = k_dgamma1.template view(); + h_dgamma1 = k_dgamma1.h_view; + //memory->create(dgamma2, nmax, "pair:dgamma2"); + k_dgamma2 = DAT::tdual_ffloat_1d("pair:dgamma2",nmax); + d_dgamma2 = k_dgamma2.template view(); + h_dgamma2 = k_dgamma2.h_view; + //memory->create(dgamma3, nmax, "pair:dgamma3"); + k_dgamma3 = DAT::tdual_ffloat_1d("pair:dgamma3",nmax); + d_dgamma3 = k_dgamma3.template view(); + h_dgamma3 = k_dgamma3.h_view; + //memory->create(arho2b, nmax, "pair:arho2b"); + k_arho2b = DAT::tdual_ffloat_1d("pair:arho2b",nmax); + d_arho2b = k_arho2b.template view(); + h_arho2b = k_arho2b.h_view; + //memory->create(arho1, nmax, 3, "pair:arho1"); + k_arho1 = DAT::tdual_ffloat_2d("pair:arho1",nmax, 3); + d_arho1 = k_arho1.template view(); + h_arho1 = k_arho1.h_view; + //memory->create(arho2, nmax, 6, "pair:arho2"); + k_arho2 = DAT::tdual_ffloat_2d("pair:arho2",nmax, 6); + d_arho2 = k_arho2.template view(); + h_arho2 = k_arho2.h_view; + //memory->create(arho3, nmax, 10, "pair:arho3"); + k_arho3 = DAT::tdual_ffloat_2d("pair:arho3",nmax, 10); + d_arho3 = k_arho3.template view(); + h_arho3 = k_arho3.h_view; + //memory->create(arho3b, nmax, 3, "pair:arho3b"); + k_arho3b = DAT::tdual_ffloat_2d("pair:arho3b",nmax, 3); + d_arho3b = k_arho3b.template view(); + h_arho3b = k_arho3b.h_view; + //memory->create(t_ave, nmax, 3, "pair:t_ave"); + k_t_ave = DAT::tdual_ffloat_2d("pair:t_ave",nmax, 3); + d_t_ave = k_t_ave.template view(); + h_t_ave = k_t_ave.h_view; + //memory->create(tsq_ave, nmax, 3, "pair:tsq_ave"); + k_tsq_ave = DAT::tdual_ffloat_2d("pair:tsq_ave",nmax, 3); + d_tsq_ave = k_tsq_ave.template view(); + h_tsq_ave = k_tsq_ave.h_view; + } + + if (n_neigh > maxneigh) { + memoryKK->destroy_kokkos(k_scrfcn,scrfcn); + memoryKK->destroy_kokkos(k_dscrfcn,dscrfcn); + memoryKK->destroy_kokkos(k_fcpair,fcpair); + maxneigh = n_neigh; + // memory->create(scrfcn, maxneigh, "pair:scrfcn"); + k_scrfcn = DAT::tdual_ffloat_1d("pair:scrfcn", maxneigh); + d_scrfcn = k_scrfcn.template view(); + h_scrfcn = k_scrfcn.h_view; + //memory->create(dscrfcn, maxneigh, "pair:dscrfcn"); + k_dscrfcn = DAT::tdual_ffloat_1d("pair:dscrfcn", maxneigh); + d_dscrfcn = k_dscrfcn.template view(); + h_dscrfcn = k_dscrfcn.h_view; + //memory->create(fcpair, maxneigh, "pair:fcpair"); + k_fcpair = DAT::tdual_ffloat_1d("pair:fcpair", maxneigh); + d_fcpair = k_fcpair.template view(); + h_fcpair = k_fcpair.h_view; + } + + // zero out local arrays + + copymode = 1; + Kokkos::parallel_for(Kokkos::RangePolicy(0, nall),*this); + copymode = 0; +} + +/* ---------------------------------------------------------------------- */ + +template +void +MEAMKokkos::meam_dens_init(int inum_half, int ntype, typename AT::t_int_1d type, typename AT::t_int_1d d_map, typename AT::t_x_array x, typename AT::t_int_1d d_numneigh_half, typename AT::t_int_1d d_numneigh_full, + typename AT::t_int_1d d_ilist_half, typename AT::t_neighbors_2d d_neighbors_half, typename AT::t_neighbors_2d d_neighbors_full, typename AT::t_int_1d d_offset, int neighflag, int need_dup) +{ + this->ntype = ntype; + this->type = type; + this->d_map = d_map; + this->x = x; + this->d_numneigh_half = d_numneigh_half; + this->d_numneigh_full = d_numneigh_full; + this->d_ilist_half = d_ilist_half; + this->d_neighbors_half = d_neighbors_half; + this->d_neighbors_full = d_neighbors_full; + this->d_offset = d_offset; + this->nlocal = nlocal; + + if (need_dup) { + dup_rho0 = Kokkos::Experimental::create_scatter_view(d_rho0); + dup_arho2b = Kokkos::Experimental::create_scatter_view(d_arho2b); + dup_arho1 = Kokkos::Experimental::create_scatter_view(d_arho1); + dup_arho2 = Kokkos::Experimental::create_scatter_view(d_arho2); + dup_arho3 = Kokkos::Experimental::create_scatter_view(d_arho3); + dup_arho3b = Kokkos::Experimental::create_scatter_view(d_arho3b); + dup_t_ave = Kokkos::Experimental::create_scatter_view(d_t_ave); + dup_tsq_ave = Kokkos::Experimental::create_scatter_view(d_tsq_ave); + } else { + ndup_rho0 = Kokkos::Experimental::create_scatter_view(d_rho0); + ndup_arho2b = Kokkos::Experimental::create_scatter_view(d_arho2b); + ndup_arho1 = Kokkos::Experimental::create_scatter_view(d_arho1); + ndup_arho2 = Kokkos::Experimental::create_scatter_view(d_arho2); + ndup_arho3 = Kokkos::Experimental::create_scatter_view(d_arho3); + ndup_arho3b = Kokkos::Experimental::create_scatter_view(d_arho3b); + ndup_t_ave = Kokkos::Experimental::create_scatter_view(d_t_ave); + ndup_tsq_ave = Kokkos::Experimental::create_scatter_view(d_tsq_ave); + } + + copymode = 1; + if (neighflag == HALF) + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum_half),*this); + else if (neighflag == HALFTHREAD) + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum_half),*this); + copymode = 0; + + if (need_dup) { + Kokkos::Experimental::contribute(d_rho0, dup_rho0); + Kokkos::Experimental::contribute(d_arho2b, dup_arho2b); + Kokkos::Experimental::contribute(d_arho1, dup_arho1); + Kokkos::Experimental::contribute(d_arho2, dup_arho2); + Kokkos::Experimental::contribute(d_arho3, dup_arho3); + Kokkos::Experimental::contribute(d_arho3b, dup_arho3b); + Kokkos::Experimental::contribute(d_t_ave, dup_t_ave); + Kokkos::Experimental::contribute(d_tsq_ave, dup_tsq_ave); + + // free duplicated memory + dup_rho0 = decltype(dup_rho0)(); + dup_arho2b = decltype(dup_arho2b)(); + dup_arho1 = decltype(dup_arho1)(); + dup_arho2 = decltype(dup_arho2)(); + dup_arho3 = decltype(dup_arho3)(); + dup_arho3b = decltype(dup_arho3b)(); + dup_t_ave = decltype(dup_t_ave)(); + dup_tsq_ave = decltype(dup_tsq_ave)(); + } +} + +/* ---------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION +void +MEAMKokkos::getscreen(int i, int offset, typename AT::t_x_array x, typename AT::t_int_1d d_numneigh_half, + typename AT::t_int_1d d_numneigh_full, int /*ntype*/, typename AT::t_int_1d type, typename AT::t_int_1d d_map) +const { + const double drinv = 1.0 / delr_meam; + const int elti = d_map[type[i]]; + if (elti < 0) return; + + const double xitmp = x(i,0); + const double yitmp = x(i,1); + const double zitmp = x(i,2); + + for (int jn = 0; jn < d_numneigh_half[i]; jn++) { + const int j = d_neighbors_half(i,jn); + + const int eltj = d_map[type[j]]; + if (eltj < 0) continue; + + // First compute screening function itself, sij + const double xjtmp = x(j,0); + const double yjtmp = x(j,1); + const double zjtmp = x(j,2); + const double delxij = xjtmp - xitmp; + const double delyij = yjtmp - yitmp; + const double delzij = zjtmp - zitmp; + + const double rij2 = delxij * delxij + delyij * delyij + delzij * delzij; + + if (rij2 > cutforcesq) { + d_dscrfcn[offset+jn] = 0.0; + d_scrfcn[offset+jn] = 0.0; + d_fcpair[offset+jn] = 0.0; + continue; + } + + // Now compute derivatives + const double rbound = ebound_meam[elti][eltj] * rij2; + const double rij = sqrt(rij2); + const double rnorm = (cutforce - rij) * drinv; + double sij = 1.0; + + // if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse + for (int kn = 0; kn < d_numneigh_full[i]; kn++) { + int k = d_neighbors_full(i,kn); + if (k == j) continue; + int eltk = d_map[type[k]]; + if (eltk < 0) continue; + + const double xktmp = x(k,0); + const double yktmp = x(k,1); + const double zktmp = x(k,2); + + const double delxjk = xktmp - xjtmp; + const double delyjk = yktmp - yjtmp; + const double delzjk = zktmp - zjtmp; + const double rjk2 = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk; + if (rjk2 > rbound) continue; + + const double delxik = xktmp - xitmp; + const double delyik = yktmp - yitmp; + const double delzik = zktmp - zitmp; + const double rik2 = delxik * delxik + delyik * delyik + delzik * delzik; + if (rik2 > rbound) continue; + + const double xik = rik2 / rij2; + const double xjk = rjk2 / rij2; + const double a = 1 - (xik - xjk) * (xik - xjk); + // if a < 0, then ellipse equation doesn't describe this case and + // atom k can't possibly screen i-j + if (a <= 0.0) continue; + + double cikj = (2.0 * (xik + xjk) + a - 2.0) / a; + const double Cmax = Cmax_meam[elti][eltj][eltk]; + const double Cmin = Cmin_meam[elti][eltj][eltk]; + double sikj; + if (cikj >= Cmax) continue; + // note that cikj may be slightly negative (within numerical + // tolerance) if atoms are colinear, so don't reject that case here + // (other negative cikj cases were handled by the test on "a" above) + else if (cikj <= Cmin) { + sij = 0.0; + break; + } else { + const double delc = Cmax - Cmin; + cikj = (cikj - Cmin) / delc; + sikj = fcut(cikj); + } + sij *= sikj; + } + + double dfc; + const double fc = dfcut(rnorm, dfc); + const double fcij = fc; + const double dfcij = dfc * drinv; + + // Now compute derivatives + d_dscrfcn[offset+jn] = 0.0; + const double sfcij = sij * fcij; + if (!iszero_kk(sfcij) && !isone_kk(sfcij)) { + for (int kn = 0; kn < d_numneigh_full[i]; kn++) { + const int k = d_neighbors_full(i,kn); + if (k == j) continue; + const int eltk = d_map[type[k]]; + if (eltk < 0) continue; + + const double delxjk = x(k,0) - xjtmp; + const double delyjk = x(k,1) - yjtmp; + const double delzjk = x(k,2) - zjtmp; + const double rjk2 = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk; + if (rjk2 > rbound) continue; + + const double delxik = x(k,0) - xitmp; + const double delyik = x(k,1) - yitmp; + const double delzik = x(k,2) - zitmp; + const double rik2 = delxik * delxik + delyik * delyik + delzik * delzik; + if (rik2 > rbound) continue; + + const double xik = rik2 / rij2; + const double xjk = rjk2 / rij2; + const double a = 1 - (xik - xjk) * (xik - xjk); + // if a < 0, then ellipse equation doesn't describe this case and + // atom k can't possibly screen i-j + if (a <= 0.0) continue; + + double cikj = (2.0 * (xik + xjk) + a - 2.0) / a; + const double Cmax = Cmax_meam[elti][eltj][eltk]; + const double Cmin = Cmin_meam[elti][eltj][eltk]; + if (cikj >= Cmax) { + continue; + // Note that cikj may be slightly negative (within numerical + // tolerance) if atoms are colinear, so don't reject that case + // here + // (other negative cikj cases were handled by the test on "a" + // above) + // Note that we never have 0 +template +KOKKOS_INLINE_FUNCTION +void +MEAMKokkos::calc_rho1(int i, int /*ntype*/, typename AT::t_int_1d type, typename AT::t_int_1d d_map, typename AT::t_x_array x, typename AT::t_int_1d d_numneigh, + int offset) const +{ + // The rho0, etc. arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho0 = ScatterViewHelper,decltype(dup_rho0),decltype(ndup_rho0)>::get(dup_rho0,ndup_rho0); + auto a_rho0 = v_rho0.template access>(); + auto v_arho2b = ScatterViewHelper,decltype(dup_arho2b),decltype(ndup_arho2b)>::get(dup_arho2b,ndup_arho2b); + auto a_arho2b = v_arho2b.template access>(); + auto v_arho1 = ScatterViewHelper,decltype(dup_arho1),decltype(ndup_arho1)>::get(dup_arho1,ndup_arho1); + auto a_arho1 = v_arho1.template access>(); + auto v_arho2 = ScatterViewHelper,decltype(dup_arho2),decltype(ndup_arho2)>::get(dup_arho2,ndup_arho2); + auto a_arho2 = v_arho2.template access>(); + auto v_arho3 = ScatterViewHelper,decltype(dup_arho3),decltype(ndup_arho3)>::get(dup_arho3,ndup_arho3); + auto a_arho3 = v_arho3.template access>(); + auto v_arho3b = ScatterViewHelper,decltype(dup_arho3b),decltype(ndup_arho3b)>::get(dup_arho3b,ndup_arho3b); + auto a_arho3b = v_arho3b.template access>(); + auto v_t_ave = ScatterViewHelper,decltype(dup_t_ave),decltype(ndup_t_ave)>::get(dup_t_ave,ndup_t_ave); + auto a_t_ave = v_t_ave.template access>(); + auto v_tsq_ave = ScatterViewHelper,decltype(dup_tsq_ave),decltype(ndup_tsq_ave)>::get(dup_tsq_ave,ndup_tsq_ave); + auto a_tsq_ave = v_tsq_ave.template access>(); + + const int elti = d_map[type[i]]; + const double xtmp = x(i,0); + const double ytmp = x(i,1); + const double ztmp = x(i,2); + for (int jn = 0; jn < d_numneigh[i]; jn++) { + if (!iszero_kk(d_scrfcn[offset+jn])) { + const int j = d_neighbors_half(i,jn); + const double sij = d_scrfcn[offset+jn] * d_fcpair[offset+jn]; + double delij[3]; + delij[0] = x(j,0) - xtmp; + delij[1] = x(j,1) - ytmp; + delij[2] = x(j,2) - ztmp; + const double rij2 = delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2]; + if (rij2 < cutforcesq) { + const int eltj = d_map[type[j]]; + const double rij = sqrt(rij2); + const double ai = rij / re_meam[elti][elti] - 1.0; + const double aj = rij / re_meam[eltj][eltj] - 1.0; + const double ro0i = rho0_meam[elti]; + const double ro0j = rho0_meam[eltj]; + const double rhoa0j = ro0j * MathSpecialKokkos::fm_exp(-beta0_meam[eltj] * aj) * sij; + double rhoa1j = ro0j * MathSpecialKokkos::fm_exp(-beta1_meam[eltj] * aj) * sij; + double rhoa2j = ro0j * MathSpecialKokkos::fm_exp(-beta2_meam[eltj] * aj) * sij; + double rhoa3j = ro0j * MathSpecialKokkos::fm_exp(-beta3_meam[eltj] * aj) * sij; + const double rhoa0i = ro0i * MathSpecialKokkos::fm_exp(-beta0_meam[elti] * ai) * sij; + double rhoa1i = ro0i * MathSpecialKokkos::fm_exp(-beta1_meam[elti] * ai) * sij; + double rhoa2i = ro0i * MathSpecialKokkos::fm_exp(-beta2_meam[elti] * ai) * sij; + double rhoa3i = ro0i * MathSpecialKokkos::fm_exp(-beta3_meam[elti] * ai) * sij; + if (ialloy == 1) { + rhoa1j *= t1_meam[eltj]; + rhoa2j *= t2_meam[eltj]; + rhoa3j *= t3_meam[eltj]; + rhoa1i *= t1_meam[elti]; + rhoa2i *= t2_meam[elti]; + rhoa3i *= t3_meam[elti]; + } + a_rho0[i] += rhoa0j; + a_rho0[j] += rhoa0i; + // For ialloy = 2, use single-element value (not average) + if (ialloy != 2) { + a_t_ave(i,0) += t1_meam[eltj] * rhoa0j; + a_t_ave(i,1) += t2_meam[eltj] * rhoa0j; + a_t_ave(i,2) += t3_meam[eltj] * rhoa0j; + a_t_ave(j,0) += t1_meam[elti] * rhoa0i; + a_t_ave(j,1) += t2_meam[elti] * rhoa0i; + a_t_ave(j,2) += t3_meam[elti] * rhoa0i; + } + if (ialloy == 1) { + a_tsq_ave(i,0) += t1_meam[eltj] * t1_meam[eltj] * rhoa0j; + a_tsq_ave(i,1) += t2_meam[eltj] * t2_meam[eltj] * rhoa0j; + a_tsq_ave(i,2) += t3_meam[eltj] * t3_meam[eltj] * rhoa0j; + a_tsq_ave(j,0) += t1_meam[elti] * t1_meam[elti] * rhoa0i; + a_tsq_ave(j,1) += t2_meam[elti] * t2_meam[elti] * rhoa0i; + a_tsq_ave(j,2) += t3_meam[elti] * t3_meam[elti] * rhoa0i; + } + a_arho2b[i] += rhoa2j; + a_arho2b[j] += rhoa2i; + + const double A1j = rhoa1j / rij; + const double A2j = rhoa2j / rij2; + const double A3j = rhoa3j / (rij2 * rij); + const double A1i = rhoa1i / rij; + const double A2i = rhoa2i / rij2; + const double A3i = rhoa3i / (rij2 * rij); + int nv2 = 0; + int nv3 = 0; + for (int m = 0; m < 3; m++) { + a_arho1(i,m) += A1j * delij[m]; + a_arho1(j,m) += -A1i * delij[m]; + a_arho3b(i,m) += rhoa3j * delij[m] / rij; + a_arho3b(j,m) += -rhoa3i * delij[m] / rij; + for (int n = m; n < 3; n++) { + a_arho2(i,nv2) += A2j * delij[m] * delij[n]; + a_arho2(j,nv2) += A2i * delij[m] * delij[n]; + nv2++; + for (int p = n; p < 3; p++) { + a_arho3(i,nv3) += A3j * delij[m] * delij[n] * delij[p]; + a_arho3(j,nv3) += -A3i * delij[m] * delij[n] * delij[p]; + nv3++; + } + } + } + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +//Cutoff function and derivative + +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::dfcut(const double xi, double& dfc) const +{ + if (xi >= 1.0) { + dfc = 0.0; + return 1.0; + } else if (xi <= 0.0) { + dfc = 0.0; + return 0.0; + } else { + const double a = 1.0 - xi; + const double a3 = a * a * a; + const double a4 = a * a3; + const double a1m4 = 1.0 - a4; + + dfc = 8 * a1m4 * a3; + return a1m4*a1m4; + } +} + + //----------------------------------------------------------------------------- + // Derivative of Cikj w.r.t. rij + // Inputs: rij,rij2,rik2,rjk2 + +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::dCfunc(const double rij2, const double rik2, const double rjk2) const +{ + const double rij4 = rij2 * rij2; + const double a = rik2 - rjk2; + const double b = rik2 + rjk2; + const double asq = a*a; + double denom = rij4 - asq; + denom = denom * denom; + return -4 * (-2 * rij2 * asq + rij4 * b + asq * b) / denom; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MEAMKokkos::dCfunc2(const double rij2, const double rik2, const double rjk2, double& dCikj1, double& dCikj2) const +{ + const double rij4 = rij2 * rij2; + const double rik4 = rik2 * rik2; + const double rjk4 = rjk2 * rjk2; + const double a = rik2 - rjk2; + double denom = rij4 - a * a; + denom = denom * denom; + dCikj1 = 4 * rij2 * (rij4 + rik4 + 2 * rik2 * rjk2 - 3 * rjk4 - 2 * rij2 * a) / denom; + dCikj2 = 4 * rij2 * (rij4 - 3 * rik4 + 2 * rik2 * rjk2 + rjk4 + 2 * rij2 * a) / denom; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::fcut(const double xi) const +{ + double a; + if (xi >= 1.0) + return 1.0; + else if (xi <= 0.0) + return 0.0; + else { + // ( 1.d0 - (1.d0 - xi)**4 )**2, but with better codegen + a = 1.0 - xi; + a *= a; a *= a; + a = 1.0 - a; + return a * a; + } +} + diff --git a/src/KOKKOS/meam_force_kokkos.h b/src/KOKKOS/meam_force_kokkos.h new file mode 100644 index 0000000000..e7e6c64231 --- /dev/null +++ b/src/KOKKOS/meam_force_kokkos.h @@ -0,0 +1,613 @@ +#include "math_special_kokkos.h" +#include "meam_kokkos.h" +#include + +using namespace LAMMPS_NS; +using namespace MathSpecialKokkos; + +template +void MEAMKokkos::meam_force( + int inum_half, int eflag_global, int eflag_atom, int vflag_global, int vflag_atom, + typename ArrayTypes::t_efloat_1d eatom, int ntype, typename AT::t_int_1d type, + typename AT::t_int_1d d_map, typename AT::t_x_array x, typename AT::t_int_1d numneigh, + typename AT::t_int_1d numneigh_full, typename AT::t_f_array f, + typename ArrayTypes::t_virial_array vatom, typename AT::t_int_1d d_ilist_half, + typename AT::t_int_1d d_offset, typename AT::t_neighbors_2d d_neighbors_half, + typename AT::t_neighbors_2d d_neighbors_full, int neighflag, int need_dup, EV_FLOAT &ev_all) +{ + EV_FLOAT ev; + + this->eflag_either = eflag_either; + this->eflag_global = eflag_global; + this->eflag_atom = eflag_atom; + this->vflag_global = vflag_global; + this->vflag_atom = vflag_atom; + eflag_either = eflag_atom || eflag_global; + vflag_either = vflag_atom || vflag_global; + this->d_eatom = eatom; + this->ntype = ntype; + this->type = type; + this->d_map = d_map; + this->x = x; + this->d_numneigh_half = numneigh; + this->d_numneigh_full = numneigh_full; + this->d_neighbors_half = d_neighbors_half; + this->d_neighbors_full = d_neighbors_full; + this->f = f; + this->d_vatom = vatom; + this->d_ilist_half = d_ilist_half; + this->d_offset = d_offset; + + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + if (eflag_atom) + dup_eatom = Kokkos::Experimental::create_scatter_view< + Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom); + if (vflag_atom) + dup_vatom = Kokkos::Experimental::create_scatter_view< + Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom); + } else { + ndup_f = + Kokkos::Experimental::create_scatter_view(f); + if (eflag_atom) + ndup_eatom = Kokkos::Experimental::create_scatter_view< + Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom); + if (vflag_atom) + ndup_vatom = Kokkos::Experimental::create_scatter_view< + Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom); + } + + copymode = 1; + if (neighflag == HALF) + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0, inum_half), + *this, ev); + else if (neighflag == HALFTHREAD) + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0, inum_half), + *this, ev); + ev_all += ev; + copymode = 0; + + if (need_dup) { + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_atom) Kokkos::Experimental::contribute(d_eatom, dup_eatom); + if (vflag_atom) Kokkos::Experimental::contribute(d_vatom, dup_vatom); + + // free duplicated memory + dup_f = decltype(dup_f)(); + if (eflag_atom) dup_eatom = decltype(dup_eatom)(); + if (vflag_atom) dup_vatom = decltype(dup_vatom)(); + } +} + +template +template +KOKKOS_INLINE_FUNCTION void MEAMKokkos::operator()(TagMEAMForce, + const int &ii, EV_FLOAT &ev) const +{ + int i, j, jn, k, kn, kk, m, n, p, q; + int nv2, nv3, elti, eltj, eltk, ind; + X_FLOAT xitmp, yitmp, zitmp, delij[3]; + double rij2, rij, rij3; + double v[6], fi[3], fj[3]; + double third, sixth; + double pp, dUdrij, dUdsij, dUdrijm[3], force, forcem; + double recip, phi, phip; + double sij; + double a1, a1i, a1j, a2, a2i, a2j; + double a3i, a3j; + double shpi[3], shpj[3]; + double ai, aj, ro0i, ro0j, invrei, invrej; + double rhoa0j, drhoa0j, rhoa0i, drhoa0i; + double rhoa1j, drhoa1j, rhoa1i, drhoa1i; + double rhoa2j, drhoa2j, rhoa2i, drhoa2i; + double a3, a3a, rhoa3j, drhoa3j, rhoa3i, drhoa3i; + double drho0dr1, drho0dr2, drho0ds1, drho0ds2; + double drho1dr1, drho1dr2, drho1ds1, drho1ds2; + double drho1drm1[3], drho1drm2[3]; + double drho2dr1, drho2dr2, drho2ds1, drho2ds2; + double drho2drm1[3], drho2drm2[3]; + double drho3dr1, drho3dr2, drho3ds1, drho3ds2; + double drho3drm1[3], drho3drm2[3]; + double dt1dr1, dt1dr2, dt1ds1, dt1ds2; + double dt2dr1, dt2dr2, dt2ds1, dt2ds2; + double dt3dr1, dt3dr2, dt3ds1, dt3ds2; + double drhodr1, drhodr2, drhods1, drhods2, drhodrm1[3], drhodrm2[3]; + double arg; + double arg1i1, arg1j1, arg1i2, arg1j2, arg1i3, arg1j3, arg3i3, arg3j3; + double dsij1, dsij2, force1, force2; + double t1i, t2i, t3i, t1j, t2j, t3j; + int fnoffset; + + // The f, etc. arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = + ScatterViewHelper, decltype(dup_f), decltype(ndup_f)>::get( + dup_f, ndup_f); + auto a_f = v_f.template access>(); + auto v_eatom = ScatterViewHelper, decltype(dup_eatom), + decltype(ndup_eatom)>::get(dup_eatom, ndup_eatom); + auto a_eatom = v_eatom.template access>(); + auto v_vatom = ScatterViewHelper, decltype(dup_vatom), + decltype(ndup_vatom)>::get(dup_vatom, ndup_vatom); + auto a_vatom = v_vatom.template access>(); + + i = d_ilist_half[ii]; + fnoffset = d_offset[i]; + third = 1.0 / 3.0; + sixth = 1.0 / 6.0; + + elti = d_map[type[i]]; + if (elti < 0) return; + + xitmp = x(i, 0); + yitmp = x(i, 1); + zitmp = x(i, 2); + + // Treat each pair + for (jn = 0; jn < d_numneigh_half[i]; jn++) { + j = d_neighbors_half(i, jn); + eltj = d_map[type[j]]; + + if (!iszero_kk(d_scrfcn[fnoffset + jn]) && eltj >= 0) { + + sij = d_scrfcn[fnoffset + jn] * d_fcpair[fnoffset + jn]; + delij[0] = x(j, 0) - xitmp; + delij[1] = x(j, 1) - yitmp; + delij[2] = x(j, 2) - zitmp; + rij2 = delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2]; + if (rij2 < cutforcesq) { + rij = sqrt(rij2); + recip = 1.0 / rij; + + // Compute phi and phip + ind = eltind[elti][eltj]; + pp = rij * rdrar; + kk = (int) pp; + kk = (kk <= (nrar - 2)) ? kk : nrar - 2; + pp = pp - kk; + pp = (pp <= 1.0) ? pp : 1.0; + phi = ((d_phirar3(ind, kk) * pp + d_phirar2(ind, kk)) * pp + d_phirar1(ind, kk)) * pp + + d_phirar(ind, kk); + phip = (d_phirar6(ind, kk) * pp + d_phirar5(ind, kk)) * pp + d_phirar4(ind, kk); + + if (eflag_either) { + double scaleij = d_scale(type[i], type[i]); + double phi_sc = phi * scaleij; + if (eflag_global) ev.evdwl += phi_sc * sij; + if (eflag_atom) { + a_eatom[i] += 0.5 * phi * sij; + a_eatom[j] += 0.5 * phi * sij; + } + } + + // write(1,*) "force_meamf: phi: ",phi + // write(1,*) "force_meamf: phip: ",phip + + // Compute pair densities and derivatives + invrei = 1.0 / re_meam[elti][elti]; + ai = rij * invrei - 1.0; + ro0i = rho0_meam[elti]; + rhoa0i = ro0i * MathSpecialKokkos::fm_exp(-beta0_meam[elti] * ai); + drhoa0i = -beta0_meam[elti] * invrei * rhoa0i; + rhoa1i = ro0i * MathSpecialKokkos::fm_exp(-beta1_meam[elti] * ai); + drhoa1i = -beta1_meam[elti] * invrei * rhoa1i; + rhoa2i = ro0i * MathSpecialKokkos::fm_exp(-beta2_meam[elti] * ai); + drhoa2i = -beta2_meam[elti] * invrei * rhoa2i; + rhoa3i = ro0i * MathSpecialKokkos::fm_exp(-beta3_meam[elti] * ai); + drhoa3i = -beta3_meam[elti] * invrei * rhoa3i; + + if (elti != eltj) { + invrej = 1.0 / re_meam[eltj][eltj]; + aj = rij * invrej - 1.0; + ro0j = rho0_meam[eltj]; + rhoa0j = ro0j * MathSpecialKokkos::fm_exp(-beta0_meam[eltj] * aj); + drhoa0j = -beta0_meam[eltj] * invrej * rhoa0j; + rhoa1j = ro0j * MathSpecialKokkos::fm_exp(-beta1_meam[eltj] * aj); + drhoa1j = -beta1_meam[eltj] * invrej * rhoa1j; + rhoa2j = ro0j * MathSpecialKokkos::fm_exp(-beta2_meam[eltj] * aj); + drhoa2j = -beta2_meam[eltj] * invrej * rhoa2j; + rhoa3j = ro0j * MathSpecialKokkos::fm_exp(-beta3_meam[eltj] * aj); + drhoa3j = -beta3_meam[eltj] * invrej * rhoa3j; + } else { + rhoa0j = rhoa0i; + drhoa0j = drhoa0i; + rhoa1j = rhoa1i; + drhoa1j = drhoa1i; + rhoa2j = rhoa2i; + drhoa2j = drhoa2i; + rhoa3j = rhoa3i; + drhoa3j = drhoa3i; + } + + const double t1mi = t1_meam[elti]; + const double t2mi = t2_meam[elti]; + const double t3mi = t3_meam[elti]; + const double t1mj = t1_meam[eltj]; + const double t2mj = t2_meam[eltj]; + const double t3mj = t3_meam[eltj]; + + if (ialloy == 1) { + rhoa1j *= t1mj; + rhoa2j *= t2mj; + rhoa3j *= t3mj; + rhoa1i *= t1mi; + rhoa2i *= t2mi; + rhoa3i *= t3mi; + drhoa1j *= t1mj; + drhoa2j *= t2mj; + drhoa3j *= t3mj; + drhoa1i *= t1mi; + drhoa2i *= t2mi; + drhoa3i *= t3mi; + } + + nv2 = 0; + nv3 = 0; + arg1i1 = 0.0; + arg1j1 = 0.0; + arg1i2 = 0.0; + arg1j2 = 0.0; + arg1i3 = 0.0; + arg1j3 = 0.0; + arg3i3 = 0.0; + arg3j3 = 0.0; + for (n = 0; n < 3; n++) { + for (p = n; p < 3; p++) { + for (q = p; q < 3; q++) { + arg = delij[n] * delij[p] * delij[q] * v3D[nv3]; + arg1i3 = arg1i3 + d_arho3(i, nv3) * arg; + arg1j3 = arg1j3 - d_arho3(j, nv3) * arg; + nv3 = nv3 + 1; + } + arg = delij[n] * delij[p] * v2D[nv2]; + arg1i2 = arg1i2 + d_arho2(i, nv2) * arg; + arg1j2 = arg1j2 + d_arho2(j, nv2) * arg; + nv2 = nv2 + 1; + } + arg1i1 = arg1i1 + d_arho1(i, n) * delij[n]; + arg1j1 = arg1j1 - d_arho1(j, n) * delij[n]; + arg3i3 = arg3i3 + d_arho3b(i, n) * delij[n]; + arg3j3 = arg3j3 - d_arho3b(j, n) * delij[n]; + } + + // rho0 terms + drho0dr1 = drhoa0j * sij; + drho0dr2 = drhoa0i * sij; + + // rho1 terms + a1 = 2 * sij / rij; + drho1dr1 = a1 * (drhoa1j - rhoa1j / rij) * arg1i1; + drho1dr2 = a1 * (drhoa1i - rhoa1i / rij) * arg1j1; + a1 = 2.0 * sij / rij; + for (m = 0; m < 3; m++) { + drho1drm1[m] = a1 * rhoa1j * d_arho1(i, m); + drho1drm2[m] = -a1 * rhoa1i * d_arho1(j, m); + } + + // rho2 terms + a2 = 2 * sij / rij2; + drho2dr1 = + a2 * (drhoa2j - 2 * rhoa2j / rij) * arg1i2 - 2.0 / 3.0 * d_arho2b[i] * drhoa2j * sij; + drho2dr2 = + a2 * (drhoa2i - 2 * rhoa2i / rij) * arg1j2 - 2.0 / 3.0 * d_arho2b[j] * drhoa2i * sij; + a2 = 4 * sij / rij2; + for (m = 0; m < 3; m++) { + drho2drm1[m] = 0.0; + drho2drm2[m] = 0.0; + for (n = 0; n < 3; n++) { + drho2drm1[m] = drho2drm1[m] + d_arho2(i, vind2D[m][n]) * delij[n]; + drho2drm2[m] = drho2drm2[m] - d_arho2(j, vind2D[m][n]) * delij[n]; + } + drho2drm1[m] = a2 * rhoa2j * drho2drm1[m]; + drho2drm2[m] = -a2 * rhoa2i * drho2drm2[m]; + } + + // rho3 terms + rij3 = rij * rij2; + a3 = 2 * sij / rij3; + a3a = 6.0 / 5.0 * sij / rij; + drho3dr1 = + a3 * (drhoa3j - 3 * rhoa3j / rij) * arg1i3 - a3a * (drhoa3j - rhoa3j / rij) * arg3i3; + drho3dr2 = + a3 * (drhoa3i - 3 * rhoa3i / rij) * arg1j3 - a3a * (drhoa3i - rhoa3i / rij) * arg3j3; + a3 = 6 * sij / rij3; + a3a = 6 * sij / (5 * rij); + for (m = 0; m < 3; m++) { + drho3drm1[m] = 0.0; + drho3drm2[m] = 0.0; + nv2 = 0; + for (n = 0; n < 3; n++) { + for (p = n; p < 3; p++) { + arg = delij[n] * delij[p] * v2D[nv2]; + drho3drm1[m] = drho3drm1[m] + d_arho3(i, vind3D[m][n][p]) * arg; + drho3drm2[m] = drho3drm2[m] + d_arho3(j, vind3D[m][n][p]) * arg; + nv2 = nv2 + 1; + } + } + drho3drm1[m] = (a3 * drho3drm1[m] - a3a * d_arho3b(i, m)) * rhoa3j; + drho3drm2[m] = (-a3 * drho3drm2[m] + a3a * d_arho3b(j, m)) * rhoa3i; + } + + // Compute derivatives of weighting functions t wrt rij + t1i = d_t_ave(i, 0); + t2i = d_t_ave(i, 1); + t3i = d_t_ave(i, 2); + t1j = d_t_ave(j, 0); + t2j = d_t_ave(j, 1); + t3j = d_t_ave(j, 2); + + if (ialloy == 1) { + + a1i = fdiv_zero_kk(drhoa0j * sij, d_tsq_ave(i, 0)); + a1j = fdiv_zero_kk(drhoa0i * sij, d_tsq_ave(j, 0)); + a2i = fdiv_zero_kk(drhoa0j * sij, d_tsq_ave(i, 1)); + a2j = fdiv_zero_kk(drhoa0i * sij, d_tsq_ave(j, 1)); + a3i = fdiv_zero_kk(drhoa0j * sij, d_tsq_ave(i, 2)); + a3j = fdiv_zero_kk(drhoa0i * sij, d_tsq_ave(j, 2)); + + dt1dr1 = a1i * (t1mj - t1i * MathSpecialKokkos::square(t1mj)); + dt1dr2 = a1j * (t1mi - t1j * MathSpecialKokkos::square(t1mi)); + dt2dr1 = a2i * (t2mj - t2i * MathSpecialKokkos::square(t2mj)); + dt2dr2 = a2j * (t2mi - t2j * MathSpecialKokkos::square(t2mi)); + dt3dr1 = a3i * (t3mj - t3i * MathSpecialKokkos::square(t3mj)); + dt3dr2 = a3j * (t3mi - t3j * MathSpecialKokkos::square(t3mi)); + + } else if (ialloy == 2) { + + dt1dr1 = 0.0; + dt1dr2 = 0.0; + dt2dr1 = 0.0; + dt2dr2 = 0.0; + dt3dr1 = 0.0; + dt3dr2 = 0.0; + + } else { + + ai = 0.0; + if (!iszero_kk(d_rho0[i])) ai = drhoa0j * sij / d_rho0[i]; + aj = 0.0; + if (!iszero_kk(d_rho0[j])) aj = drhoa0i * sij / d_rho0[j]; + + dt1dr1 = ai * (t1mj - t1i); + dt1dr2 = aj * (t1mi - t1j); + dt2dr1 = ai * (t2mj - t2i); + dt2dr2 = aj * (t2mi - t2j); + dt3dr1 = ai * (t3mj - t3i); + dt3dr2 = aj * (t3mi - t3j); + } + + // Compute derivatives of total density wrt rij, sij and rij(3) + get_shpfcn(lattce_meam[elti][elti], stheta_meam[elti][elti], ctheta_meam[elti][elti], shpi); + get_shpfcn(lattce_meam[eltj][eltj], stheta_meam[elti][elti], ctheta_meam[elti][elti], shpj); + + drhodr1 = d_dgamma1[i] * drho0dr1 + + d_dgamma2[i] * + (dt1dr1 * d_rho1[i] + t1i * drho1dr1 + dt2dr1 * d_rho2[i] + t2i * drho2dr1 + + dt3dr1 * d_rho3[i] + t3i * drho3dr1) - + d_dgamma3[i] * (shpi[0] * dt1dr1 + shpi[1] * dt2dr1 + shpi[2] * dt3dr1); + drhodr2 = d_dgamma1[j] * drho0dr2 + + d_dgamma2[j] * + (dt1dr2 * d_rho1[j] + t1j * drho1dr2 + dt2dr2 * d_rho2[j] + t2j * drho2dr2 + + dt3dr2 * d_rho3[j] + t3j * drho3dr2) - + d_dgamma3[j] * (shpj[0] * dt1dr2 + shpj[1] * dt2dr2 + shpj[2] * dt3dr2); + for (m = 0; m < 3; m++) { + drhodrm1[m] = 0.0; + drhodrm2[m] = 0.0; + drhodrm1[m] = + d_dgamma2[i] * (t1i * drho1drm1[m] + t2i * drho2drm1[m] + t3i * drho3drm1[m]); + drhodrm2[m] = + d_dgamma2[j] * (t1j * drho1drm2[m] + t2j * drho2drm2[m] + t3j * drho3drm2[m]); + } + + // Compute derivatives wrt sij, but only if necessary + if (!iszero_kk(d_dscrfcn[fnoffset + jn])) { + drho0ds1 = rhoa0j; + drho0ds2 = rhoa0i; + a1 = 2.0 / rij; + drho1ds1 = a1 * rhoa1j * arg1i1; + drho1ds2 = a1 * rhoa1i * arg1j1; + a2 = 2.0 / rij2; + drho2ds1 = a2 * rhoa2j * arg1i2 - 2.0 / 3.0 * d_arho2b[i] * rhoa2j; + drho2ds2 = a2 * rhoa2i * arg1j2 - 2.0 / 3.0 * d_arho2b[j] * rhoa2i; + a3 = 2.0 / rij3; + a3a = 6.0 / (5.0 * rij); + drho3ds1 = a3 * rhoa3j * arg1i3 - a3a * rhoa3j * arg3i3; + drho3ds2 = a3 * rhoa3i * arg1j3 - a3a * rhoa3i * arg3j3; + + if (ialloy == 1) { + a1i = fdiv_zero_kk(rhoa0j, d_tsq_ave(i, 0)); + a1j = fdiv_zero_kk(rhoa0i, d_tsq_ave(j, 0)); + a2i = fdiv_zero_kk(rhoa0j, d_tsq_ave(i, 1)); + a2j = fdiv_zero_kk(rhoa0i, d_tsq_ave(j, 1)); + a3i = fdiv_zero_kk(rhoa0j, d_tsq_ave(i, 2)); + a3j = fdiv_zero_kk(rhoa0i, d_tsq_ave(j, 2)); + + dt1ds1 = a1i * (t1mj - t1i * MathSpecialKokkos::square(t1mj)); + dt1ds2 = a1j * (t1mi - t1j * MathSpecialKokkos::square(t1mi)); + dt2ds1 = a2i * (t2mj - t2i * MathSpecialKokkos::square(t2mj)); + dt2ds2 = a2j * (t2mi - t2j * MathSpecialKokkos::square(t2mi)); + dt3ds1 = a3i * (t3mj - t3i * MathSpecialKokkos::square(t3mj)); + dt3ds2 = a3j * (t3mi - t3j * MathSpecialKokkos::square(t3mi)); + + } else if (ialloy == 2) { + + dt1ds1 = 0.0; + dt1ds2 = 0.0; + dt2ds1 = 0.0; + dt2ds2 = 0.0; + dt3ds1 = 0.0; + dt3ds2 = 0.0; + + } else { + + ai = 0.0; + if (!iszero_kk(d_rho0[i])) ai = rhoa0j / d_rho0[i]; + aj = 0.0; + if (!iszero_kk(d_rho0[j])) aj = rhoa0i / d_rho0[j]; + + dt1ds1 = ai * (t1mj - t1i); + dt1ds2 = aj * (t1mi - t1j); + dt2ds1 = ai * (t2mj - t2i); + dt2ds2 = aj * (t2mi - t2j); + dt3ds1 = ai * (t3mj - t3i); + dt3ds2 = aj * (t3mi - t3j); + } + + drhods1 = d_dgamma1[i] * drho0ds1 + + d_dgamma2[i] * + (dt1ds1 * d_rho1[i] + t1i * drho1ds1 + dt2ds1 * d_rho2[i] + t2i * drho2ds1 + + dt3ds1 * d_rho3[i] + t3i * drho3ds1) - + d_dgamma3[i] * (shpi[0] * dt1ds1 + shpi[1] * dt2ds1 + shpi[2] * dt3ds1); + drhods2 = d_dgamma1[j] * drho0ds2 + + d_dgamma2[j] * + (dt1ds2 * d_rho1[j] + t1j * drho1ds2 + dt2ds2 * d_rho2[j] + t2j * drho2ds2 + + dt3ds2 * d_rho3[j] + t3j * drho3ds2) - + d_dgamma3[j] * (shpj[0] * dt1ds2 + shpj[1] * dt2ds2 + shpj[2] * dt3ds2); + } + + // Compute derivatives of energy wrt rij, sij and rij[3] + dUdrij = phip * sij + d_frhop[i] * drhodr1 + d_frhop[j] * drhodr2; + dUdsij = 0.0; + if (!iszero_kk(d_dscrfcn[fnoffset + jn])) { + dUdsij = phi + d_frhop[i] * drhods1 + d_frhop[j] * drhods2; + } + for (m = 0; m < 3; m++) { + dUdrijm[m] = d_frhop[i] * drhodrm1[m] + d_frhop[j] * drhodrm2[m]; + } + + // Add the part of the force due to dUdrij and dUdsij + force = dUdrij * recip + dUdsij * d_dscrfcn[fnoffset + jn]; + for (m = 0; m < 3; m++) { + forcem = delij[m] * force + dUdrijm[m]; + a_f(i, m) += forcem; + a_f(j, m) -= forcem; + } + + // Tabulate per-atom virial as symmetrized stress tensor + + if (vflag_either) { + fi[0] = delij[0] * force + dUdrijm[0]; + fi[1] = delij[1] * force + dUdrijm[1]; + fi[2] = delij[2] * force + dUdrijm[2]; + v[0] = -0.5 * (delij[0] * fi[0]); + v[1] = -0.5 * (delij[1] * fi[1]); + v[2] = -0.5 * (delij[2] * fi[2]); + v[3] = -0.25 * (delij[0] * fi[1] + delij[1] * fi[0]); + v[4] = -0.25 * (delij[0] * fi[2] + delij[2] * fi[0]); + v[5] = -0.25 * (delij[1] * fi[2] + delij[2] * fi[1]); + + if (vflag_global) + for (m = 0; m < 6; m++) ev.v[m] += 2.0 * v[m]; + + if (vflag_atom) { + for (m = 0; m < 6; m++) { + a_vatom(i, m) += v[m]; + a_vatom(j, m) += v[m]; + } + } + } + + // Now compute forces on other atoms k due to change in sij + + if (iszero_kk(sij) || isone_kk(sij)) continue; //: cont jn loop + + double dxik(0), dyik(0), dzik(0); + double dxjk(0), dyjk(0), dzjk(0); + + for (kn = 0; kn < d_numneigh_full[i]; kn++) { + k = d_neighbors_full(i, kn); + eltk = d_map[type[k]]; + if (k != j && eltk >= 0) { + double xik, xjk, cikj, sikj, dfc, a; + double dCikj1, dCikj2; + double delc, rik2, rjk2; + + sij = d_scrfcn[jn + fnoffset] * d_fcpair[jn + fnoffset]; + const double Cmax = Cmax_meam[elti][eltj][eltk]; + const double Cmin = Cmin_meam[elti][eltj][eltk]; + + dsij1 = 0.0; + dsij2 = 0.0; + if (!iszero_kk(sij) && !isone_kk(sij)) { + const double rbound = rij2 * ebound_meam[elti][eltj]; + delc = Cmax - Cmin; + dxjk = x(k, 0) - x(j, 0); + dyjk = x(k, 1) - x(j, 1); + dzjk = x(k, 2) - x(j, 2); + rjk2 = dxjk * dxjk + dyjk * dyjk + dzjk * dzjk; + if (rjk2 <= rbound) { + dxik = x(k, 0) - x(i, 0); + dyik = x(k, 1) - x(i, 1); + dzik = x(k, 2) - x(i, 2); + rik2 = dxik * dxik + dyik * dyik + dzik * dzik; + if (rik2 <= rbound) { + xik = rik2 / rij2; + xjk = rjk2 / rij2; + a = 1 - (xik - xjk) * (xik - xjk); + if (!iszero_kk(a)) { + cikj = (2.0 * (xik + xjk) + a - 2.0) / a; + if (cikj >= Cmin && cikj <= Cmax) { + cikj = (cikj - Cmin) / delc; + sikj = dfcut(cikj, dfc); + dCfunc2(rij2, rik2, rjk2, dCikj1, dCikj2); + a = sij / delc * dfc / sikj; + dsij1 = a * dCikj1; + dsij2 = a * dCikj2; + } + } + } + } + } + + if (!iszero_kk(dsij1) || !iszero_kk(dsij2)) { + force1 = dUdsij * dsij1; + force2 = dUdsij * dsij2; + + a_f(i, 0) += force1 * dxik; + a_f(i, 1) += force1 * dyik; + a_f(i, 2) += force1 * dzik; + a_f(j, 0) += force2 * dxjk; + a_f(j, 1) += force2 * dyjk; + a_f(j, 2) += force2 * dzjk; + a_f(k, 0) -= force1 * dxik + force2 * dxjk; + a_f(k, 1) -= force1 * dyik + force2 * dyjk; + a_f(k, 2) -= force1 * dzik + force2 * dzjk; + + // Tabulate per-atom virial as symmetrized stress tensor + + if (vflag_either) { + fi[0] = force1 * dxik; + fi[1] = force1 * dyik; + fi[2] = force1 * dzik; + fj[0] = force2 * dxjk; + fj[1] = force2 * dyjk; + fj[2] = force2 * dzjk; + v[0] = -third * (dxik * fi[0] + dxjk * fj[0]); + v[1] = -third * (dyik * fi[1] + dyjk * fj[1]); + v[2] = -third * (dzik * fi[2] + dzjk * fj[2]); + v[3] = -sixth * (dxik * fi[1] + dxjk * fj[1] + dyik * fi[0] + dyjk * fj[0]); + v[4] = -sixth * (dxik * fi[2] + dxjk * fj[2] + dzik * fi[0] + dzjk * fj[0]); + v[5] = -sixth * (dyik * fi[2] + dyjk * fj[2] + dzik * fi[1] + dzjk * fj[1]); + + if (vflag_global) + for (m = 0; m < 6; m++) ev.v[m] += 3.0 * v[m]; + + if (vflag_atom) { + for (m = 0; m < 6; m++) { + a_vatom(i, m) += v[m]; + a_vatom(j, m) += v[m]; + a_vatom(k, m) += v[m]; + } + } + } + } + } + // end of k loop + } + } + } + // end of j loop + } +} diff --git a/src/KOKKOS/meam_funcs_kokkos.h b/src/KOKKOS/meam_funcs_kokkos.h new file mode 100644 index 0000000000..a20f0c9182 --- /dev/null +++ b/src/KOKKOS/meam_funcs_kokkos.h @@ -0,0 +1,289 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Naga Vydyanathan (NVIDIA) +------------------------------------------------------------------------- */ + +#include "math_special_kokkos.h" +#include +#include "meam_kokkos.h" +using namespace MathSpecialKokkos; + +//----------------------------------------------------------------------------- +// Compute G(gamma) based on selection flag ibar: +// 0 => G = sqrt(1+gamma) +// 1 => G = exp(gamma/2) +// 2 => not implemented +// 3 => G = 2/(1+exp(-gamma)) +// 4 => G = sqrt(1+gamma) +// -5 => G = +-sqrt(abs(1+gamma)) +// +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::G_gam(const double gamma, const int ibar, int &errorflag) const +{ + double gsmooth_switchpoint; + + switch (ibar) { + case 0: + case 4: + gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor + 1); + if (gamma < gsmooth_switchpoint) { + // e.g. gsmooth_factor is 99, {: + // gsmooth_switchpoint = -0.99 + // G = 0.01*(-0.99/gamma)**99 + double G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor); + return sqrt(G); + } else { + return sqrt(1.0 + gamma); + } + case 1: + return MathSpecialKokkos::fm_exp(gamma / 2.0); + case 3: + return 2.0 / (1.0 + MathSpecialKokkos::fm_exp(-gamma)); + case -5: + if ((1.0 + gamma) >= 0) { + return sqrt(1.0 + gamma); + } else { + return -sqrt(-1.0 - gamma); + } + } + errorflag = 1; + return 0.0; +} + +//----------------------------------------------------------------------------- +// Compute G(gamma and dG(gamma) based on selection flag ibar: +// 0 => G = sqrt(1+gamma) +// 1 => G = exp(gamma/2) +// 2 => not implemented +// 3 => G = 2/(1+exp(-gamma)) +// 4 => G = sqrt(1+gamma) +// -5 => G = +-sqrt(abs(1+gamma)) +// +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::dG_gam(const double gamma, const int ibar, double& dG) const +{ + double gsmooth_switchpoint; + double G; + + switch (ibar) { + case 0: + case 4: + gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor + 1); + if (gamma < gsmooth_switchpoint) { + // e.g. gsmooth_factor is 99, {: + // gsmooth_switchpoint = -0.99 + // G = 0.01*(-0.99/gamma)**99 + G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor); + G = sqrt(G); + dG = -gsmooth_factor * G / (2.0 * gamma); + return G; + } else { + G = sqrt(1.0 + gamma); + dG = 1.0 / (2.0 * G); + return G; + } + case 1: + G = MathSpecialKokkos::fm_exp(gamma / 2.0); + dG = G / 2.0; + return G; + case 3: + G = 2.0 / (1.0 + MathSpecialKokkos::fm_exp(-gamma)); + dG = G * (2.0 - G) / 2; + return G; + case -5: + if ((1.0 + gamma) >= 0) { + G = sqrt(1.0 + gamma); + dG = 1.0 / (2.0 * G); + return G; + } else { + G = -sqrt(-1.0 - gamma); + dG = -1.0 / (2.0 * G); + return G; + } + } + dG = 1.0; + return 0.0; +} + +//----------------------------------------------------------------------------- +// Compute ZBL potential +// +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::zbl(const double r, const int z1, const int z2) const +{ + int i; + const double c[] = { 0.028171, 0.28022, 0.50986, 0.18175 }; + const double d[] = { 0.20162, 0.40290, 0.94229, 3.1998 }; + const double azero = 0.4685; + const double cc = 14.3997; + double a, x; + // azero = (9pi^2/128)^1/3 (0.529) Angstroms + a = azero / (pow(z1, 0.23) + pow(z2, 0.23)); + double result = 0.0; + x = r / a; + for (i = 0; i <= 3; i++) { + result = result + c[i] * MathSpecialKokkos::fm_exp(-d[i] * x); + } + if (r > 0.0) + result = result * z1 * z2 / r * cc; + return result; +} + +//----------------------------------------------------------------------------- +// Compute embedding function F(rhobar) and derivative F'(rhobar), eqn I.5 +// +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::embedding(const double A, const double Ec, const double rhobar, double& dF) const +{ + const double AEc = A * Ec; + + if (rhobar > 0.0) { + const double lrb = log(rhobar); + dF = AEc * (1.0 + lrb); + return AEc * rhobar * lrb; + } else { + if (emb_lin_neg == 0) { + dF = 0.0; + return 0.0; + } else { + dF = - AEc; + return - AEc * rhobar; + } + } +} + +//----------------------------------------------------------------------------- +// Compute Rose energy function, I.16 +// +template +KOKKOS_INLINE_FUNCTION +double MEAMKokkos::erose(const double r, const double re, const double alpha, const double Ec, const double repuls, + const double attrac, const int form) const +{ + double astar, a3; + double result = 0.0; + + if (r > 0.0) { + astar = alpha * (r / re - 1.0); + a3 = 0.0; + if (astar >= 0) + a3 = attrac; + else if (astar < 0) + a3 = repuls; + + if (form == 1) + result = -Ec * (1 + astar + (-attrac + repuls / r) * MathSpecialKokkos::cube(astar)) * MathSpecialKokkos::fm_exp(-astar); + else if (form == 2) + result = -Ec * (1 + astar + a3 * MathSpecialKokkos::cube(astar)) * MathSpecialKokkos::fm_exp(-astar); + else + result = -Ec * (1 + astar + a3 * MathSpecialKokkos::cube(astar) / (r / re)) * MathSpecialKokkos::fm_exp(-astar); + } + return result; +} + +//----------------------------------------------------------------------------- +// Shape factors for various configurations +// +template +KOKKOS_INLINE_FUNCTION +void MEAMKokkos::get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3]) const +{ + switch (latt) { + case FCC: + case BCC: + case B1: + case B2: + s[0] = 0.0; + s[1] = 0.0; + s[2] = 0.0; + break; + case HCP: + s[0] = 0.0; + s[1] = 0.0; + s[2] = 1.0 / 3.0; + break; + case CH4: // CH4 actually needs shape factor for diamond for C, dimer for H + case DIA: + case DIA3: + s[0] = 0.0; + s[1] = 0.0; + s[2] = 32.0 / 9.0; + break; + case DIM: + s[0] = 1.0; + s[1] = 2.0 / 3.0; + // s(4) = 1.d0 // this should be 0.4 unless (1-legendre) is multiplied in the density calc. + s[2] = 0.40; // this is (1-legendre) where legendre = 0.6 in dynamo is accounted. + break; + case LIN: // linear, theta being 180 + s[0] = 0.0; + s[1] = 8.0 / 3.0; // 4*(co**4 + si**4 - 1.0/3.0) in zig become 4*(1-1/3) + s[2] = 0.0; + break; + case ZIG: //zig-zag + case TRI: //trimer e.g. H2O + s[0] = 4.0*pow(cthe,2); + s[1] = 4.0*(pow(cthe,4) + pow(sthe,4) - 1.0/3.0); + s[2] = 4.0*(pow(cthe,2) * (3*pow(sthe,4) + pow(cthe,4))); + s[2] = s[2] - 0.6*s[0]; //legend in dyn, 0.6 is default value. + break; + default: + s[0] = 0.0; + // call error('Lattice not defined in get_shpfcn.') + } +} + +//----------------------------------------------------------------------------- +// Number of neighbors for the reference structure +// +template +KOKKOS_INLINE_FUNCTION +int MEAMKokkos::get_Zij(const lattice_t latt) const +{ + switch (latt) { + case FCC: + return 12; + case BCC: + return 8; + case HCP: + return 12; + case DIA: + case DIA3: + return 4; + case DIM: + return 1; + case B1: + return 6; + case C11: + return 10; + case L12: + return 12; + case B2: + return 8; + case CH4: // DYNAMO currently implemented this way while it needs two Z values, 4 and 1 + return 4; + case LIN: + case ZIG: + case TRI: + return 2; + // call error('Lattice not defined in get_Zij.') + } + return 0; +} diff --git a/src/KOKKOS/meam_impl_kokkos.h b/src/KOKKOS/meam_impl_kokkos.h new file mode 100644 index 0000000000..be69f247be --- /dev/null +++ b/src/KOKKOS/meam_impl_kokkos.h @@ -0,0 +1,68 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Naga Vydyanathan (NVIDIA), Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include "memory_kokkos.h" +#include "meam_kokkos.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +MEAMKokkos::MEAMKokkos(Memory *mem) : MEAM(mem) +{ + d_errorflag = typename AT::t_int_scalar("meam:errorflag"); +} + +template +MEAMKokkos::~MEAMKokkos() +{ + if (copymode) return; + + MemoryKokkos *memoryKK = (MemoryKokkos *)memory; + + memoryKK->destroy_kokkos(k_rho,rho); + memoryKK->destroy_kokkos(k_rho0,rho0); + memoryKK->destroy_kokkos(k_rho1,rho1); + memoryKK->destroy_kokkos(k_rho2,rho2); + memoryKK->destroy_kokkos(k_rho3,rho3); + memoryKK->destroy_kokkos(k_frhop,frhop); + memoryKK->destroy_kokkos(k_gamma,gamma); + memoryKK->destroy_kokkos(k_dgamma1,dgamma1); + memoryKK->destroy_kokkos(k_dgamma2,dgamma2); + memoryKK->destroy_kokkos(k_dgamma3,dgamma3); + memoryKK->destroy_kokkos(k_arho2b,arho2b); + + memoryKK->destroy_kokkos(k_arho1,arho1); + memoryKK->destroy_kokkos(k_arho2,arho2); + memoryKK->destroy_kokkos(k_arho3,arho3); + memoryKK->destroy_kokkos(k_arho3b,arho3b); + memoryKK->destroy_kokkos(k_t_ave,t_ave); + memoryKK->destroy_kokkos(k_tsq_ave,tsq_ave); + + memoryKK->destroy_kokkos(k_scrfcn,scrfcn); + memoryKK->destroy_kokkos(k_dscrfcn,dscrfcn); + memoryKK->destroy_kokkos(k_fcpair,fcpair); +} + +#include "meam_setup_done_kokkos.h" +#include "meam_funcs_kokkos.h" +#include "meam_dens_init_kokkos.h" +#include "meam_dens_final_kokkos.h" +#include "meam_force_kokkos.h" + diff --git a/src/KOKKOS/meam_kokkos.h b/src/KOKKOS/meam_kokkos.h new file mode 100644 index 0000000000..1f289d6a4f --- /dev/null +++ b/src/KOKKOS/meam_kokkos.h @@ -0,0 +1,224 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MEAMKOKKOS_H +#define LMP_MEAMKOKKOS_H + +#include "kokkos.h" +#include "meam.h" +#include "memory_kokkos.h" +#include "neigh_request.h" +#include "neighbor_kokkos.h" +#include +#include + +namespace LAMMPS_NS { + +struct TagMEAMDensFinal {}; +template struct TagMEAMDensInit { +}; +struct TagMEAMZero {}; +template struct TagMEAMForce { +}; + +template class MEAMKokkos : public MEAM { + public: + typedef ArrayTypes AT; + typedef EV_FLOAT value_type; + MEAMKokkos(Memory *mem); + ~MEAMKokkos() override; + + KOKKOS_INLINE_FUNCTION + void operator()(TagMEAMDensFinal, const int &, EV_FLOAT &) const; + + template + KOKKOS_INLINE_FUNCTION void operator()(TagMEAMDensInit, const int &) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagMEAMZero, const int &) const; + + template + KOKKOS_INLINE_FUNCTION void operator()(TagMEAMForce, const int &, EV_FLOAT &) const; + + private: + // parameters to meam_dens_init + + int ntype, nlocal; + typename AT::t_int_1d type; + typename AT::t_int_1d d_offset; + typename AT::t_int_1d d_map; + typename AT::t_int_2d d_scale; + typename AT::t_x_array x; + typename AT::t_int_1d d_numneigh_half; + typename AT::t_int_1d d_numneigh_full; + typename AT::t_neighbors_2d d_neighbors_half; + typename AT::t_neighbors_2d d_neighbors_full; + typename AT::t_int_1d d_ilist_half; + typename AT::t_f_array f; + typename ArrayTypes::t_virial_array d_vatom; + + // parameters to meam_dens_final + + typename AT::t_int_scalar d_errorflag; + int eflag_either, eflag_global, eflag_atom, vflag_either, vflag_global, vflag_atom; + typename ArrayTypes::t_efloat_1d d_eatom; + + public: + void meam_dens_setup(int, int, int) override; + void meam_setup_done(double *) override; + void meam_dens_init(int, int, typename AT::t_int_1d, typename AT::t_int_1d, + typename AT::t_x_array, typename AT::t_int_1d, typename AT::t_int_1d, + typename AT::t_int_1d, typename AT::t_neighbors_2d, + typename AT::t_neighbors_2d, typename AT::t_int_1d, int, int); + void meam_dens_final(int, int, int, int, typename ArrayTypes::t_efloat_1d, int, + typename AT::t_int_1d, typename AT::t_int_1d, typename AT::t_int_2d, int &, + EV_FLOAT &); + void meam_force(int, int, int, int, int, typename ArrayTypes::t_efloat_1d, int, + typename AT::t_int_1d, typename AT::t_int_1d, typename AT::t_x_array, + typename AT::t_int_1d, typename AT::t_int_1d, typename AT::t_f_array, + typename ArrayTypes::t_virial_array, typename AT::t_int_1d, + typename AT::t_int_1d, typename AT::t_neighbors_2d, typename AT::t_neighbors_2d, + int, int, EV_FLOAT &); + template + KOKKOS_INLINE_FUNCTION void getscreen(int, int, typename AT::t_x_array, typename AT::t_int_1d, + typename AT::t_int_1d, int, typename AT::t_int_1d, + typename AT::t_int_1d) const; + template + KOKKOS_INLINE_FUNCTION void calc_rho1(int, int, typename AT::t_int_1d, typename AT::t_int_1d, + typename AT::t_x_array, typename AT::t_int_1d, int) const; + KOKKOS_INLINE_FUNCTION + double fcut(const double xi) const; + KOKKOS_INLINE_FUNCTION + double dfcut(const double xi, double &dfc) const; + KOKKOS_INLINE_FUNCTION + double dCfunc(const double, const double, const double) const; + KOKKOS_INLINE_FUNCTION + void dCfunc2(const double, const double, const double, double &, double &) const; + KOKKOS_INLINE_FUNCTION + double G_gam(const double, const int, int &) const; + KOKKOS_INLINE_FUNCTION + double dG_gam(const double, const int, double &) const; + KOKKOS_INLINE_FUNCTION + double zbl(const double, const int, const int) const; + KOKKOS_INLINE_FUNCTION + double embedding(const double, const double, const double, double &) const; + KOKKOS_INLINE_FUNCTION + double erose(const double, const double, const double, const double, const double, const double, + const int) const; + KOKKOS_INLINE_FUNCTION + void get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3]) const; + KOKKOS_INLINE_FUNCTION + int get_Zij(const lattice_t) const; + + public: + DAT::tdual_ffloat_1d k_rho, k_rho0, k_rho1, k_rho2, k_rho3, k_frhop; + typename ArrayTypes::t_ffloat_1d d_rho, d_rho0, d_rho1, d_rho2, d_rho3, d_frhop; + HAT::t_ffloat_1d h_rho, h_rho0, h_rho1, h_rho2, h_rho3, h_frhop; + DAT::tdual_ffloat_1d k_gamma, k_dgamma1, k_dgamma2, k_dgamma3, k_arho2b; + typename ArrayTypes::t_ffloat_1d d_gamma, d_dgamma1, d_dgamma2, d_dgamma3, d_arho2b; + HAT::t_ffloat_1d h_gamma, h_dgamma1, h_dgamma2, h_dgamma3, h_arho2b; + DAT::tdual_ffloat_2d k_arho1, k_arho2, k_arho3, k_arho3b, k_t_ave, k_tsq_ave; + typename ArrayTypes::t_ffloat_2d d_arho1, d_arho2, d_arho3, d_arho3b, d_t_ave, + d_tsq_ave; + HAT::t_ffloat_2d h_arho1, h_arho2, h_arho3, h_arho3b, h_t_ave, h_tsq_ave; + typename ArrayTypes::t_ffloat_2d d_phir, d_phirar, d_phirar1, d_phirar2, d_phirar3, + d_phirar4, d_phirar5, d_phirar6; + DAT::tdual_ffloat_1d k_scrfcn, k_dscrfcn, k_fcpair; + typename ArrayTypes::t_ffloat_1d d_scrfcn, d_dscrfcn, d_fcpair; + HAT::t_ffloat_1d h_scrfcn, h_dscrfcn, h_fcpair; + + protected: + int need_dup; + using KKDeviceType = typename KKDevice::value; + + template + using DupScatterView = + KKScatterView; + + template + using NonDupScatterView = + KKScatterView; + + DupScatterView + dup_rho0; + NonDupScatterView + ndup_rho0; + DupScatterView + dup_arho2b; + NonDupScatterView + ndup_arho2b; + DupScatterView + dup_arho1; + NonDupScatterView + ndup_arho1; + DupScatterView + dup_arho2; + NonDupScatterView + ndup_arho2; + DupScatterView + dup_arho3; + NonDupScatterView + ndup_arho3; + DupScatterView + dup_arho3b; + NonDupScatterView + ndup_arho3b; + DupScatterView + dup_t_ave; + NonDupScatterView + ndup_t_ave; + DupScatterView + dup_tsq_ave; + NonDupScatterView + ndup_tsq_ave; + DupScatterView dup_f; + NonDupScatterView ndup_f; + DupScatterView + dup_eatom; + NonDupScatterView + ndup_eatom; + DupScatterView + dup_vatom; + NonDupScatterView + ndup_vatom; +}; + +KOKKOS_INLINE_FUNCTION +static bool iszero_kk(const double f) +{ + return fabs(f) < 1e-20; +} + +KOKKOS_INLINE_FUNCTION +static bool isone_kk(const double f) +{ + return fabs(f - 1.0) < 1e-20; +} + +KOKKOS_INLINE_FUNCTION +static double fdiv_zero_kk(const double n, const double d) +{ + if (iszero_kk(d)) return 0.0; + return n / d; +} + +// Functions we need for compat + +} // namespace LAMMPS_NS +#include "meam_impl_kokkos.h" + +#endif diff --git a/src/KOKKOS/meam_setup_done_kokkos.h b/src/KOKKOS/meam_setup_done_kokkos.h new file mode 100644 index 0000000000..8b705217b0 --- /dev/null +++ b/src/KOKKOS/meam_setup_done_kokkos.h @@ -0,0 +1,60 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "meam_kokkos.h" + +template +void MEAMKokkos::meam_setup_done(double* cutmax) +{ + MEAM::meam_setup_done(cutmax); + + MemKK::realloc_kokkos(d_phir, "pair:phir", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar, "pair:phirar", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar1, "pair:phirar1", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar2, "pair:phirar2", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar3, "pair:phirar3", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar4, "pair:phirar4", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar5, "pair:phirar5", (neltypes * (neltypes + 1)) / 2, nr); + MemKK::realloc_kokkos(d_phirar6, "pair:phirar6", (neltypes * (neltypes + 1)) / 2, nr); + + auto h_phir = Kokkos::create_mirror_view(d_phir); + auto h_phirar = Kokkos::create_mirror_view(d_phirar); + auto h_phirar1 = Kokkos::create_mirror_view(d_phirar1); + auto h_phirar2 = Kokkos::create_mirror_view(d_phirar2); + auto h_phirar3 = Kokkos::create_mirror_view(d_phirar3); + auto h_phirar4 = Kokkos::create_mirror_view(d_phirar4); + auto h_phirar5 = Kokkos::create_mirror_view(d_phirar5); + auto h_phirar6 = Kokkos::create_mirror_view(d_phirar6); + + for (int i = 0; i <(neltypes * (neltypes + 1)) / 2; i++) + for(int j = 0; j < nr; j++) { + h_phir(i,j) = phir[i][j]; + h_phirar(i,j) = phirar[i][j]; + h_phirar1(i,j) = phirar1[i][j]; + h_phirar2(i,j) = phirar2[i][j]; + h_phirar3(i,j) = phirar3[i][j]; + h_phirar4(i,j) = phirar4[i][j]; + h_phirar5(i,j) = phirar5[i][j]; + h_phirar6(i,j) = phirar6[i][j]; + } + + Kokkos::deep_copy(d_phir,h_phir); + Kokkos::deep_copy(d_phirar,h_phirar); + Kokkos::deep_copy(d_phirar1,h_phirar1); + Kokkos::deep_copy(d_phirar2,h_phirar2); + Kokkos::deep_copy(d_phirar3,h_phirar3); + Kokkos::deep_copy(d_phirar4,h_phirar4); + Kokkos::deep_copy(d_phirar5,h_phirar5); + Kokkos::deep_copy(d_phirar6,h_phirar6); +} diff --git a/src/KOKKOS/min_cg_kokkos.cpp b/src/KOKKOS/min_cg_kokkos.cpp index 32f97437c7..53c4031f9b 100644 --- a/src/KOKKOS/min_cg_kokkos.cpp +++ b/src/KOKKOS/min_cg_kokkos.cpp @@ -49,6 +49,8 @@ int MinCGKokkos::iterate(int maxiter) fix_minimize_kk->k_vectors.sync(); fix_minimize_kk->k_vectors.modify(); + atomKK->sync(Device,F_MASK); + // nlimit = max # of CG iterations before restarting // set to ndoftotal unless too big diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index 8dc7b68287..a590409c49 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -79,6 +79,8 @@ void MinKokkos::setup(int flag) } update->setupflag = 1; + lmp->kokkos->auto_sync = 1; + // setup extra global dof due to fixes // cannot be done in init() b/c update init() is before modify init() @@ -170,7 +172,7 @@ void MinKokkos::setup(int flag) } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { + if (atom->molecular != Atom::ATOMIC) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); force->bond->compute(eflag,vflag); @@ -242,6 +244,8 @@ void MinKokkos::setup_minimal(int flag) // acquire ghosts // build neighbor lists + lmp->kokkos->auto_sync = 1; + if (flag) { modify->setup_pre_exchange(); if (triclinic) domain->x2lamda(atom->nlocal); @@ -277,7 +281,7 @@ void MinKokkos::setup_minimal(int flag) } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { + if (atom->molecular != Atom::ATOMIC) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); force->bond->compute(eflag,vflag); @@ -495,6 +499,7 @@ double MinKokkos::energy_force(int resetflag) if (force->newton) { comm->reverse_comm(); timer->stamp(Timer::COMM); + atomKK->sync(Device,F_MASK); } // update per-atom minimization variables stored by pair styles @@ -567,7 +572,7 @@ void MinKokkos::force_clear() } }); } - atomKK->modified(Device,F_MASK); + atomKK->modified(Device,F_MASK|TORQUE_MASK); } /* ---------------------------------------------------------------------- @@ -576,6 +581,7 @@ void MinKokkos::force_clear() double MinKokkos::fnorm_sqr() { + atomKK->sync(Device,F_MASK); double local_norm2_sqr = 0.0; { @@ -604,6 +610,7 @@ double MinKokkos::fnorm_sqr() double MinKokkos::fnorm_inf() { + atomKK->sync(Device,F_MASK); double local_norm_inf = 0.0; { @@ -632,6 +639,7 @@ double MinKokkos::fnorm_inf() double MinKokkos::fnorm_max() { + atomKK->sync(Device,F_MASK); double local_norm_max = 0.0; { diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index 2fad14f3b4..76ea522fa8 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -111,9 +111,6 @@ void MinLineSearchKokkos::reset_vectors() x0 = fix_minimize_kk->request_vector_kokkos(0); g = fix_minimize_kk->request_vector_kokkos(1); h = fix_minimize_kk->request_vector_kokkos(2); - - auto h_fvec = Kokkos::create_mirror_view(fvec); - Kokkos::deep_copy(h_fvec,fvec); } /* ---------------------------------------------------------------------- @@ -181,6 +178,8 @@ int MinLineSearchKokkos::linemin_quadratic(double eoriginal, double &alpha) fix_minimize_kk->k_vectors.sync(); fix_minimize_kk->k_vectors.modify(); + atomKK->sync(Device,X_MASK|F_MASK); + // fdothall = projection of search dir along downhill gradient // if search direction is not downhill, exit with error @@ -364,8 +363,8 @@ double MinLineSearchKokkos::alpha_step(double alpha, int resetflag) // reset to starting point if (nextra_global) modify->min_step(0.0,hextra); - atomKK->k_x.clear_sync_state(); // ignore if host positions since device - // positions will be reset below + atomKK->k_x.clear_sync_state(); // ignore if host positions modified since + // device positions will be reset below { // local variables for lambda capture @@ -409,6 +408,8 @@ double MinLineSearchKokkos::compute_dir_deriv(double &ff) double dot[2],dotall[2]; double fh; + atomKK->sync(Device,F_MASK); + // compute new fh, alpha, delfh s_double2 sdot; diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 5be91fed4a..a1f8fcbf48 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -153,6 +153,9 @@ void NPairKokkos::build(NeighList *list_) int nall = nlocal; if (GHOST) nall += atom->nghost; + + if (nall == 0) return; + list->grow(nall); NeighborKokkosExecute diff --git a/src/KOKKOS/pair_meam_kokkos.cpp b/src/KOKKOS/pair_meam_kokkos.cpp new file mode 100644 index 0000000000..c0f18a2969 --- /dev/null +++ b/src/KOKKOS/pair_meam_kokkos.cpp @@ -0,0 +1,753 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Naga Vydyanathan (NVIDIA), Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include "pair_meam_kokkos.h" +#include "meam_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +PairMEAMKokkos::PairMEAMKokkos(LAMMPS *lmp) : PairMEAM(lmp) +{ + respa_enable = 0; + + kokkosable = 1; + reverse_comm_device = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; + + delete meam_inst; + meam_inst_kk = new MEAMKokkos(memory); + meam_inst = meam_inst_kk; +} + +/* ---------------------------------------------------------------------- */ + +template +PairMEAMKokkos::~PairMEAMKokkos() +{ + if (copymode) return; + + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + delete meam_inst_kk; + meam_inst = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMEAMKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom"); + d_vatom = k_vatom.view(); + } + + // neighbor list info + + int inum_half = listhalf->inum; + NeighListKokkos* k_halflist = static_cast*>(listhalf); + d_ilist_half = k_halflist->d_ilist; + d_numneigh_half = k_halflist->d_numneigh; + d_neighbors_half = k_halflist->d_neighbors; + + NeighListKokkos* k_fulllist = static_cast*>(listfull); + d_numneigh_full = k_fulllist->d_numneigh; + d_neighbors_full = k_fulllist->d_neighbors; + + EV_FLOAT ev; + + copymode = 1; + meam_inst_kk->copymode = 1; + + // strip neighbor lists of any special bond flags before using with MEAM + // necessary before doing neigh_f2c and neigh_c2f conversions each step + + if (neighbor->ago == 0) + Kokkos::parallel_for(Kokkos::RangePolicy(0,inum_half),*this); + + // check size of scrfcn based on half neighbor list + + nlocal = atom->nlocal; + nall = nlocal + atom->nghost; + + int n = 0; + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,inum_half),*this,n); + + meam_inst_kk->meam_dens_setup(atom->nmax, nall, n); + + x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + type = atomKK->k_type.view(); + + atomKK->sync(execution_space,datamask_read); + + int ntype = atom->ntypes; + + // 3 stages of MEAM calculation + // loop over my atoms followed by communication + + int errorflag = 0; + + d_offset = typename AT::t_int_1d("pair:offset",inum_half+1); + { + // local variables for lambda capture + + auto l_ilist_half = d_ilist_half; + auto l_numneigh_half = d_numneigh_half; + auto l_offset = d_offset; + + Kokkos::parallel_scan(inum_half, LAMMPS_LAMBDA(int ii, int &m_fill, bool final) { + int i = l_ilist_half[ii]; + m_fill += l_numneigh_half[i]; + if (final) + l_offset[ii+1] = m_fill; + }); + } + + int need_dup = lmp->kokkos->need_dup(); + + meam_inst_kk->meam_dens_init(inum_half,ntype,type,d_map,x,d_numneigh_half,d_numneigh_full,d_ilist_half,d_neighbors_half, d_neighbors_full, d_offset, neighflag, need_dup); + + meam_inst_kk->k_rho0.template modify(); + meam_inst_kk->k_arho2b.template modify(); + meam_inst_kk->k_arho1.template modify(); + meam_inst_kk->k_arho2.template modify(); + meam_inst_kk->k_arho3.template modify(); + meam_inst_kk->k_arho3b.template modify(); + meam_inst_kk->k_t_ave.template modify(); + meam_inst_kk->k_tsq_ave.template modify(); + + comm->reverse_comm(this); + + meam_inst_kk->k_rho0.template sync(); + meam_inst_kk->k_arho2b.template sync(); + meam_inst_kk->k_arho1.template sync(); + meam_inst_kk->k_arho2.template sync(); + meam_inst_kk->k_arho3.template sync(); + meam_inst_kk->k_arho3b.template sync(); + meam_inst_kk->k_t_ave.template sync(); + meam_inst_kk->k_tsq_ave.template sync(); + + meam_inst_kk->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom, + d_eatom,ntype,type,d_map,d_scale,errorflag,ev); + + if (errorflag) + error->one(FLERR,"MEAM library error {}",errorflag); + + meam_inst_kk->k_rho0.template modify(); + meam_inst_kk->k_rho1.template modify(); + meam_inst_kk->k_rho2.template modify(); + meam_inst_kk->k_rho3.template modify(); + meam_inst_kk->k_frhop.template modify(); + meam_inst_kk->k_gamma.template modify(); + meam_inst_kk->k_dgamma1.template modify(); + meam_inst_kk->k_dgamma2.template modify(); + meam_inst_kk->k_dgamma3.template modify(); + meam_inst_kk->k_arho2b.template modify(); + meam_inst_kk->k_arho1.template modify(); + meam_inst_kk->k_arho2.template modify(); + meam_inst_kk->k_arho3.template modify(); + meam_inst_kk->k_arho3b.template modify(); + meam_inst_kk->k_t_ave.template modify(); + meam_inst_kk->k_tsq_ave.template modify(); + + comm->forward_comm(this); + + meam_inst_kk->k_rho0.template sync(); + meam_inst_kk->k_rho1.template sync(); + meam_inst_kk->k_rho2.template sync(); + meam_inst_kk->k_rho3.template sync(); + meam_inst_kk->k_frhop.template sync(); + meam_inst_kk->k_gamma.template sync(); + meam_inst_kk->k_dgamma1.template sync(); + meam_inst_kk->k_dgamma2.template sync(); + meam_inst_kk->k_dgamma3.template sync(); + meam_inst_kk->k_arho2b.template sync(); + meam_inst_kk->k_arho1.template sync(); + meam_inst_kk->k_arho2.template sync(); + meam_inst_kk->k_arho3.template sync(); + meam_inst_kk->k_arho3b.template sync(); + meam_inst_kk->k_t_ave.template sync(); + meam_inst_kk->k_tsq_ave.template sync(); + + meam_inst_kk->meam_force(inum_half,eflag_global,eflag_atom,vflag_global, + vflag_atom,d_eatom,ntype,type,d_map,x, + d_numneigh_half, d_numneigh_full,f,d_vatom, + d_ilist_half, d_offset, d_neighbors_half, d_neighbors_full, + neighflag, need_dup, ev); + + if (eflag_global) eng_vdwl += ev.evdwl; + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.sync_host(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.sync_host(); + } + + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK); + + copymode = 0; + meam_inst_kk->copymode = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ +template +void PairMEAMKokkos::coeff(int narg, char **arg) +{ + PairMEAM::coeff(narg,arg); + + // sync map and scale + + int n = atom->ntypes; + MemKK::realloc_kokkos(d_map,"pair:map",n+1); + MemKK::realloc_kokkos(d_scale,"pair:scale",n+1,n+1); + auto h_map = Kokkos::create_mirror_view(d_map); + auto h_scale = Kokkos::create_mirror_view(d_scale); + + for (int i = 1; i <= n; i++) { + h_map[i] = map[i]; + for (int j = 1; j <= n; j++) + h_scale(i,j) = scale[i][j]; + } + + Kokkos::deep_copy(d_map,h_map); + Kokkos::deep_copy(d_scale,h_scale); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ +template +void PairMEAMKokkos::init_style() +{ + PairMEAM::init_style(); + + // adjust neighbor list request for KOKKOS + + neighflag = lmp->kokkos->neighflag; + auto request = neighbor->find_request(this,1); + request->set_kokkos_host(std::is_same::value && + !std::is_same::value); + request->set_kokkos_device(std::is_same::value); + + request = neighbor->find_request(this,2); + request->set_kokkos_host(std::is_same::value && + !std::is_same::value); + request->set_kokkos_device(std::is_same::value); + + if (neighflag == FULL) + error->all(FLERR,"Must use half neighbor list style with pair meam/kk"); +} + +/* ---------------------------------------------------------------------- */ + +template +int PairMEAMKokkos::pack_forward_comm_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &buf, + int /*pbc_flag*/, int * /*pbc*/) +{ + d_sendlist = k_sendlist.view(); + iswap = iswap_in; + v_buf = buf.view(); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); + return n*38; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMPackForwardComm, const int &i) const { + int j = d_sendlist(iswap, i); + int m = i*38; + v_buf[m++] = meam_inst_kk->d_rho0[j]; + v_buf[m++] = meam_inst_kk->d_rho1[j]; + v_buf[m++] = meam_inst_kk->d_rho2[j]; + v_buf[m++] = meam_inst_kk->d_rho3[j]; + v_buf[m++] = meam_inst_kk->d_frhop[j]; + v_buf[m++] = meam_inst_kk->d_gamma[j]; + v_buf[m++] = meam_inst_kk->d_dgamma1[j]; + v_buf[m++] = meam_inst_kk->d_dgamma2[j]; + v_buf[m++] = meam_inst_kk->d_dgamma3[j]; + v_buf[m++] = meam_inst_kk->d_arho2b[j]; + v_buf[m++] = meam_inst_kk->d_arho1(j,0); + v_buf[m++] = meam_inst_kk->d_arho1(j,1); + v_buf[m++] = meam_inst_kk->d_arho1(j,2); + v_buf[m++] = meam_inst_kk->d_arho2(j,0); + v_buf[m++] = meam_inst_kk->d_arho2(j,1); + v_buf[m++] = meam_inst_kk->d_arho2(j,2); + v_buf[m++] = meam_inst_kk->d_arho2(j,3); + v_buf[m++] = meam_inst_kk->d_arho2(j,4); + v_buf[m++] = meam_inst_kk->d_arho2(j,5); + for (int k = 0; k < 10; k++) v_buf[m++] = meam_inst_kk->d_arho3(j,k); + v_buf[m++] = meam_inst_kk->d_arho3b(j,0); + v_buf[m++] = meam_inst_kk->d_arho3b(j,1); + v_buf[m++] = meam_inst_kk->d_arho3b(j,2); + v_buf[m++] = meam_inst_kk->d_t_ave(j,0); + v_buf[m++] = meam_inst_kk->d_t_ave(j,1); + v_buf[m++] = meam_inst_kk->d_t_ave(j,2); + v_buf[m++] = meam_inst_kk->d_tsq_ave(j,0); + v_buf[m++] = meam_inst_kk->d_tsq_ave(j,1); + v_buf[m++] = meam_inst_kk->d_tsq_ave(j,2); +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMEAMKokkos::unpack_forward_comm_kokkos(int n, int first_in, DAT::tdual_xfloat_1d &buf) +{ + first = first_in; + v_buf = buf.view(); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMUnpackForwardComm, const int &i) const{ + int m = i*38; + + meam_inst_kk->d_rho0[i+first] = v_buf[m++]; + meam_inst_kk->d_rho1[i+first] = v_buf[m++]; + meam_inst_kk->d_rho2[i+first] = v_buf[m++]; + meam_inst_kk->d_rho3[i+first] = v_buf[m++]; + meam_inst_kk->d_frhop[i+first] = v_buf[m++]; + meam_inst_kk->d_gamma[i+first] = v_buf[m++]; + meam_inst_kk->d_dgamma1[i+first] = v_buf[m++]; + meam_inst_kk->d_dgamma2[i+first] = v_buf[m++]; + meam_inst_kk->d_dgamma3[i+first] = v_buf[m++]; + meam_inst_kk->d_arho2b[i+first] = v_buf[m++]; + meam_inst_kk->d_arho1(i+first,0) = v_buf[m++]; + meam_inst_kk->d_arho1(i+first,1) = v_buf[m++]; + meam_inst_kk->d_arho1(i+first,2) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,0) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,1) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,2) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,3) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,4) = v_buf[m++]; + meam_inst_kk->d_arho2(i+first,5) = v_buf[m++]; + for (int k = 0; k < 10; k++) meam_inst_kk->d_arho3(i+first,k) = v_buf[m++]; + meam_inst_kk->d_arho3b(i+first,0) = v_buf[m++]; + meam_inst_kk->d_arho3b(i+first,1) = v_buf[m++]; + meam_inst_kk->d_arho3b(i+first,2) = v_buf[m++]; + meam_inst_kk->d_t_ave(i+first,0) = v_buf[m++]; + meam_inst_kk->d_t_ave(i+first,1) = v_buf[m++]; + meam_inst_kk->d_t_ave(i+first,2) = v_buf[m++]; + meam_inst_kk->d_tsq_ave(i+first,0) = v_buf[m++]; + meam_inst_kk->d_tsq_ave(i+first,1) = v_buf[m++]; + meam_inst_kk->d_tsq_ave(i+first,2) = v_buf[m++]; + } + +/* ---------------------------------------------------------------------- */ + +template +int PairMEAMKokkos::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + meam_inst_kk->k_rho0.sync_host(); + meam_inst_kk->k_rho1.sync_host(); + meam_inst_kk->k_rho2.sync_host(); + meam_inst_kk->k_rho3.sync_host(); + meam_inst_kk->k_frhop.sync_host(); + meam_inst_kk->k_gamma.sync_host(); + meam_inst_kk->k_dgamma1.sync_host(); + meam_inst_kk->k_dgamma2.sync_host(); + meam_inst_kk->k_dgamma3.sync_host(); + meam_inst_kk->k_arho2b.sync_host(); + meam_inst_kk->k_arho1.sync_host(); + meam_inst_kk->k_arho2.sync_host(); + meam_inst_kk->k_arho3.sync_host(); + meam_inst_kk->k_arho3b.sync_host(); + meam_inst_kk->k_t_ave.sync_host(); + meam_inst_kk->k_tsq_ave.sync_host(); + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + buf[m++] = meam_inst_kk->h_rho0[j]; + buf[m++] = meam_inst_kk->h_rho1[j]; + buf[m++] = meam_inst_kk->h_rho2[j]; + buf[m++] = meam_inst_kk->h_rho3[j]; + buf[m++] = meam_inst_kk->h_frhop[j]; + buf[m++] = meam_inst_kk->h_gamma[j]; + buf[m++] = meam_inst_kk->h_dgamma1[j]; + buf[m++] = meam_inst_kk->h_dgamma2[j]; + buf[m++] = meam_inst_kk->h_dgamma3[j]; + buf[m++] = meam_inst_kk->h_arho2b[j]; + buf[m++] = meam_inst_kk->h_arho1(j,0); + buf[m++] = meam_inst_kk->h_arho1(j,1); + buf[m++] = meam_inst_kk->h_arho1(j,2); + buf[m++] = meam_inst_kk->h_arho2(j,0); + buf[m++] = meam_inst_kk->h_arho2(j,1); + buf[m++] = meam_inst_kk->h_arho2(j,2); + buf[m++] = meam_inst_kk->h_arho2(j,3); + buf[m++] = meam_inst_kk->h_arho2(j,4); + buf[m++] = meam_inst_kk->h_arho2(j,5); + for (int k = 0; k < 10; k++) buf[m++] = meam_inst_kk->h_arho3(j,k); + buf[m++] = meam_inst_kk->h_arho3b(j,0); + buf[m++] = meam_inst_kk->h_arho3b(j,1); + buf[m++] = meam_inst_kk->h_arho3b(j,2); + buf[m++] = meam_inst_kk->h_t_ave(j,0); + buf[m++] = meam_inst_kk->h_t_ave(j,1); + buf[m++] = meam_inst_kk->h_t_ave(j,2); + buf[m++] = meam_inst_kk->h_tsq_ave(j,0); + buf[m++] = meam_inst_kk->h_tsq_ave(j,1); + buf[m++] = meam_inst_kk->h_tsq_ave(j,2); + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMEAMKokkos::unpack_forward_comm(int n, int first, double *buf) +{ + meam_inst_kk->k_rho0.sync_host(); + meam_inst_kk->k_rho1.sync_host(); + meam_inst_kk->k_rho2.sync_host(); + meam_inst_kk->k_rho3.sync_host(); + meam_inst_kk->k_frhop.sync_host(); + meam_inst_kk->k_gamma.sync_host(); + meam_inst_kk->k_dgamma1.sync_host(); + meam_inst_kk->k_dgamma2.sync_host(); + meam_inst_kk->k_dgamma3.sync_host(); + meam_inst_kk->k_arho2b.sync_host(); + meam_inst_kk->k_arho1.sync_host(); + meam_inst_kk->k_arho2.sync_host(); + meam_inst_kk->k_arho3.sync_host(); + meam_inst_kk->k_arho3b.sync_host(); + meam_inst_kk->k_t_ave.sync_host(); + meam_inst_kk->k_tsq_ave.sync_host(); + + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + meam_inst_kk->h_rho0[i] = buf[m++]; + meam_inst_kk->h_rho1[i] = buf[m++]; + meam_inst_kk->h_rho2[i] = buf[m++]; + meam_inst_kk->h_rho3[i] = buf[m++]; + meam_inst_kk->h_frhop[i] = buf[m++]; + meam_inst_kk->h_gamma[i] = buf[m++]; + meam_inst_kk->h_dgamma1[i] = buf[m++]; + meam_inst_kk->h_dgamma2[i] = buf[m++]; + meam_inst_kk->h_dgamma3[i] = buf[m++]; + meam_inst_kk->h_arho2b[i] = buf[m++]; + meam_inst_kk->h_arho1(i,0) = buf[m++]; + meam_inst_kk->h_arho1(i,1) = buf[m++]; + meam_inst_kk->h_arho1(i,2) = buf[m++]; + meam_inst_kk->h_arho2(i,0) = buf[m++]; + meam_inst_kk->h_arho2(i,1) = buf[m++]; + meam_inst_kk->h_arho2(i,2) = buf[m++]; + meam_inst_kk->h_arho2(i,3) = buf[m++]; + meam_inst_kk->h_arho2(i,4) = buf[m++]; + meam_inst_kk->h_arho2(i,5) = buf[m++]; + for (int k = 0; k < 10; k++) meam_inst_kk->h_arho3(i,k) = buf[m++]; + meam_inst_kk->h_arho3b(i,0) = buf[m++]; + meam_inst_kk->h_arho3b(i,1) = buf[m++]; + meam_inst_kk->h_arho3b(i,2) = buf[m++]; + meam_inst_kk->h_t_ave(i,0) = buf[m++]; + meam_inst_kk->h_t_ave(i,1) = buf[m++]; + meam_inst_kk->h_t_ave(i,2) = buf[m++]; + meam_inst_kk->h_tsq_ave(i,0) = buf[m++]; + meam_inst_kk->h_tsq_ave(i,1) = buf[m++]; + meam_inst_kk->h_tsq_ave(i,2) = buf[m++]; + } + + meam_inst_kk->k_rho0.modify_host(); + meam_inst_kk->k_rho1.modify_host(); + meam_inst_kk->k_rho2.modify_host(); + meam_inst_kk->k_rho3.modify_host(); + meam_inst_kk->k_frhop.modify_host(); + meam_inst_kk->k_gamma.modify_host(); + meam_inst_kk->k_dgamma1.modify_host(); + meam_inst_kk->k_dgamma2.modify_host(); + meam_inst_kk->k_dgamma3.modify_host(); + meam_inst_kk->k_arho2b.modify_host(); + meam_inst_kk->k_arho1.modify_host(); + meam_inst_kk->k_arho2.modify_host(); + meam_inst_kk->k_arho3.modify_host(); + meam_inst_kk->k_arho3b.modify_host(); + meam_inst_kk->k_t_ave.modify_host(); + meam_inst_kk->k_tsq_ave.modify_host(); +} + +/* ---------------------------------------------------------------------- */ + +template +int PairMEAMKokkos::pack_reverse_comm_kokkos(int n, int first_in, DAT::tdual_xfloat_1d &buf) +{ + first = first_in; + v_buf = buf.view(); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); + return n*30; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMPackReverseComm, const int &i) const { + int m = i*30; + + v_buf[m++] = meam_inst_kk->d_rho0[i+first]; + v_buf[m++] = meam_inst_kk->d_arho2b[i+first]; + v_buf[m++] = meam_inst_kk->d_arho1(i+first,0); + v_buf[m++] = meam_inst_kk->d_arho1(i+first,1); + v_buf[m++] = meam_inst_kk->d_arho1(i+first,2); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,0); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,1); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,2); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,3); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,4); + v_buf[m++] = meam_inst_kk->d_arho2(i+first,5); + for (int k = 0; k < 10; k++) v_buf[m++] = meam_inst_kk->d_arho3(i+first,k); + v_buf[m++] = meam_inst_kk->d_arho3b(i+first,0); + v_buf[m++] = meam_inst_kk->d_arho3b(i+first,1); + v_buf[m++] = meam_inst_kk->d_arho3b(i+first,2); + v_buf[m++] = meam_inst_kk->d_t_ave(i+first,0); + v_buf[m++] = meam_inst_kk->d_t_ave(i+first,1); + v_buf[m++] = meam_inst_kk->d_t_ave(i+first,2); + v_buf[m++] = meam_inst_kk->d_tsq_ave(i+first,0); + v_buf[m++] = meam_inst_kk->d_tsq_ave(i+first,1); + v_buf[m++] = meam_inst_kk->d_tsq_ave(i+first,2); +} + +/* ---------------------------------------------------------------------- */ + +template +int PairMEAMKokkos::pack_reverse_comm(int n, int first, double *buf) +{ + meam_inst_kk->k_rho0.sync_host(); + meam_inst_kk->k_arho2b.sync_host(); + meam_inst_kk->k_arho1.sync_host(); + meam_inst_kk->k_arho2.sync_host(); + meam_inst_kk->k_arho3.sync_host(); + meam_inst_kk->k_arho3b.sync_host(); + meam_inst_kk->k_t_ave.sync_host(); + meam_inst_kk->k_tsq_ave.sync_host(); + + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + buf[m++] = meam_inst_kk->h_rho0[i]; + buf[m++] = meam_inst_kk->h_arho2b[i]; + buf[m++] = meam_inst_kk->h_arho1(i,0); + buf[m++] = meam_inst_kk->h_arho1(i,1); + buf[m++] = meam_inst_kk->h_arho1(i,2); + buf[m++] = meam_inst_kk->h_arho2(i,0); + buf[m++] = meam_inst_kk->h_arho2(i,1); + buf[m++] = meam_inst_kk->h_arho2(i,2); + buf[m++] = meam_inst_kk->h_arho2(i,3); + buf[m++] = meam_inst_kk->h_arho2(i,4); + buf[m++] = meam_inst_kk->h_arho2(i,5); + for (int k = 0; k < 10; k++) buf[m++] = meam_inst_kk->h_arho3(i,k); + buf[m++] = meam_inst_kk->h_arho3b(i,0); + buf[m++] = meam_inst_kk->h_arho3b(i,1); + buf[m++] = meam_inst_kk->h_arho3b(i,2); + buf[m++] = meam_inst_kk->h_t_ave(i,0); + buf[m++] = meam_inst_kk->h_t_ave(i,1); + buf[m++] = meam_inst_kk->h_t_ave(i,2); + buf[m++] = meam_inst_kk->h_tsq_ave(i,0); + buf[m++] = meam_inst_kk->h_tsq_ave(i,1); + buf[m++] = meam_inst_kk->h_tsq_ave(i,2); + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMEAMKokkos::unpack_reverse_comm_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &buf) +{ + d_sendlist = k_sendlist.view(); + iswap = iswap_in; + v_buf = buf.view(); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMUnpackReverseComm, const int &i) const { + int j = d_sendlist(iswap, i); + int m = i*30; + + meam_inst_kk->d_rho0[j] += v_buf[m++]; + meam_inst_kk->d_arho2b[j] += v_buf[m++]; + meam_inst_kk->d_arho1(j,0) += v_buf[m++]; + meam_inst_kk->d_arho1(j,1) += v_buf[m++]; + meam_inst_kk->d_arho1(j,2) += v_buf[m++]; + meam_inst_kk->d_arho2(j,0) += v_buf[m++]; + meam_inst_kk->d_arho2(j,1) += v_buf[m++]; + meam_inst_kk->d_arho2(j,2) += v_buf[m++]; + meam_inst_kk->d_arho2(j,3) += v_buf[m++]; + meam_inst_kk->d_arho2(j,4) += v_buf[m++]; + meam_inst_kk->d_arho2(j,5) += v_buf[m++]; + for (int k = 0; k < 10; k++) meam_inst_kk->d_arho3(j,k) += v_buf[m++]; + meam_inst_kk->d_arho3b(j,0) += v_buf[m++]; + meam_inst_kk->d_arho3b(j,1) += v_buf[m++]; + meam_inst_kk->d_arho3b(j,2) += v_buf[m++]; + meam_inst_kk->d_t_ave(j,0) += v_buf[m++]; + meam_inst_kk->d_t_ave(j,1) += v_buf[m++]; + meam_inst_kk->d_t_ave(j,2) += v_buf[m++]; + meam_inst_kk->d_tsq_ave(j,0) += v_buf[m++]; + meam_inst_kk->d_tsq_ave(j,1) += v_buf[m++]; + meam_inst_kk->d_tsq_ave(j,2) += v_buf[m++]; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMEAMKokkos::unpack_reverse_comm(int n, int *list, double *buf) +{ + meam_inst_kk->k_rho0.sync_host(); + meam_inst_kk->k_arho2b.sync_host(); + meam_inst_kk->k_arho1.sync_host(); + meam_inst_kk->k_arho2.sync_host(); + meam_inst_kk->k_arho3.sync_host(); + meam_inst_kk->k_arho3b.sync_host(); + meam_inst_kk->k_t_ave.sync_host(); + meam_inst_kk->k_tsq_ave.sync_host(); + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + meam_inst_kk->h_rho0[j] += buf[m++]; + meam_inst_kk->h_arho2b[j] += buf[m++]; + meam_inst_kk->h_arho1(j,0) += buf[m++]; + meam_inst_kk->h_arho1(j,1) += buf[m++]; + meam_inst_kk->h_arho1(j,2) += buf[m++]; + meam_inst_kk->h_arho2(j,0) += buf[m++]; + meam_inst_kk->h_arho2(j,1) += buf[m++]; + meam_inst_kk->h_arho2(j,2) += buf[m++]; + meam_inst_kk->h_arho2(j,3) += buf[m++]; + meam_inst_kk->h_arho2(j,4) += buf[m++]; + meam_inst_kk->h_arho2(j,5) += buf[m++]; + for (int k = 0; k < 10; k++) meam_inst_kk->h_arho3(j,k) += buf[m++]; + meam_inst_kk->h_arho3b(j,0) += buf[m++]; + meam_inst_kk->h_arho3b(j,1) += buf[m++]; + meam_inst_kk->h_arho3b(j,2) += buf[m++]; + meam_inst_kk->h_t_ave(j,0) += buf[m++]; + meam_inst_kk->h_t_ave(j,1) += buf[m++]; + meam_inst_kk->h_t_ave(j,2) += buf[m++]; + meam_inst_kk->h_tsq_ave(j,0) += buf[m++]; + meam_inst_kk->h_tsq_ave(j,1) += buf[m++]; + meam_inst_kk->h_tsq_ave(j,2) += buf[m++]; + } + + meam_inst_kk->k_rho0.modify_host(); + meam_inst_kk->k_arho2b.modify_host(); + meam_inst_kk->k_arho1.modify_host(); + meam_inst_kk->k_arho2.modify_host(); + meam_inst_kk->k_arho3.modify_host(); + meam_inst_kk->k_arho3b.modify_host(); + meam_inst_kk->k_t_ave.modify_host(); + meam_inst_kk->k_tsq_ave.modify_host(); +} + +/* ---------------------------------------------------------------------- + strip special bond flags from neighbor list entries + are not used with MEAM + need to do here so Fortran lib doesn't see them + done once per reneighbor so that neigh_f2c and neigh_c2f don't see them +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMNeighStrip, const int &ii) const { + + const int i = d_ilist_half[ii]; + const int jnum_half = d_numneigh_half[i]; + const int jnum_full = d_numneigh_full[i]; + for (int jj = 0; jj < jnum_half; jj++) + d_neighbors_half(i,jj) &= NEIGHMASK; + for (int jj = 0; jj < jnum_full; jj++) + d_neighbors_full(i,jj) &= NEIGHMASK; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairMEAMKokkos::operator()(TagPairMEAMOffsets, const int ii, int &n) const { + const int i = d_ilist_half[ii]; + n += d_numneigh_half[i]; +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class PairMEAMKokkos; +#ifdef KOKKOS_ENABLE_CUDA +template class PairMEAMKokkos; +#endif +} + diff --git a/src/KOKKOS/pair_meam_kokkos.h b/src/KOKKOS/pair_meam_kokkos.h new file mode 100644 index 0000000000..fef4266b8a --- /dev/null +++ b/src/KOKKOS/pair_meam_kokkos.h @@ -0,0 +1,123 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(meam/c/kk,PairMEAMKokkos) +PairStyle(meam/c/kk/device,PairMEAMKokkos) +PairStyle(meam/c/kk/host,PairMEAMKokkos) +PairStyle(meam/kk,PairMEAMKokkos) +PairStyle(meam/kk/device,PairMEAMKokkos) +PairStyle(meam/kk/host,PairMEAMKokkos) +// clang-format on +#else + +// clang-format off +#ifndef LMP_PAIR_MEAM_KOKKOS_H +#define LMP_PAIR_MEAM_KOKKOS_H + +#include "kokkos_base.h" +#include "pair_kokkos.h" +#include "pair_meam.h" +#include "meam_kokkos.h" + +namespace LAMMPS_NS { + +struct TagPairMEAMNeighStrip{}; +struct TagPairMEAMOffsets{}; +struct TagPairMEAMPackForwardComm{}; +struct TagPairMEAMUnpackForwardComm{}; +struct TagPairMEAMPackReverseComm{}; +struct TagPairMEAMUnpackReverseComm{}; + +template +class MEAMKokkos; + +template +class PairMEAMKokkos : public PairMEAM, public KokkosBase { + public: + enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF}; + enum {COUL_FLAG=0}; + typedef DeviceType device_type; + typedef ArrayTypes AT; + typedef int value_type; + + PairMEAMKokkos(class LAMMPS *); + ~PairMEAMKokkos() override; + void compute(int, int) override; + void coeff(int, char **) override; + void init_style() override; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMPackForwardComm, const int&) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMUnpackForwardComm, const int&) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMPackReverseComm, const int&) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMUnpackReverseComm, const int&) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMNeighStrip, const int&) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairMEAMOffsets, const int, int&) const; + + int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&, + int, int *) override; + int pack_forward_comm(int, int *, double *, int, int *) override; + void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&) override; + void unpack_forward_comm(int, int, double *) override; + int pack_reverse_comm_kokkos(int, int, DAT::tdual_xfloat_1d&) override; + int pack_reverse_comm(int, int, double *) override; + void unpack_reverse_comm_kokkos(int, DAT::tdual_int_2d, + int, DAT::tdual_xfloat_1d&) override; + void unpack_reverse_comm(int, int *, double *) override; + + protected: + class MEAMKokkos *meam_inst_kk; + typename AT::t_x_array x; + typename AT::t_f_array f; + typename AT::t_int_1d type; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + + typename AT::t_int_1d d_offset; + + DAT::tdual_int_1d k_map; + typename AT::t_int_1d d_map; + typename AT::t_int_2d d_scale; + typename AT::t_int_1d d_ilist_half; + typename AT::t_int_1d d_numneigh_half; + typename AT::t_neighbors_2d d_neighbors_half; + typename AT::t_int_1d d_numneigh_full; + typename AT::t_neighbors_2d d_neighbors_full; + typename AT::t_int_2d d_sendlist; + typename AT::t_xfloat_1d_um v_buf; + + int iswap,first; + int neighflag,nlocal,nall,eflag,vflag; + + friend void pair_virial_fdotr_compute(PairMEAMKokkos*); +}; + +} +#endif +#endif + diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 0656a1f9ee..d36497964e 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -139,7 +139,7 @@ template void PairSNAPKokkos::compute(int eflag_in, int vflag_in) { if (host_flag) { - atomKK->sync(Host,X_MASK|TYPE_MASK); + atomKK->sync(Host,X_MASK|F_MASK|TYPE_MASK); PairSNAP::compute(eflag_in,vflag_in); atomKK->modified(Host,F_MASK); return; diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 316c583717..e881196e5e 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -126,8 +126,6 @@ void PairZBLKokkos::compute(int eflag_in, int vflag_in) } atomKK->sync(execution_space,datamask_read); - if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); - else atomKK->modified(execution_space,F_MASK); x = atomKK->k_x.view(); f = atomKK->k_f.view(); @@ -177,6 +175,9 @@ void PairZBLKokkos::compute(int eflag_in, int vflag_in) } if (vflag_fdotr) pair_virial_fdotr_compute(this); + + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK); } template diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 1816415b47..573a6118b9 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -282,8 +282,6 @@ void VerletKokkos::run(int n) f_merge_copy = DAT::t_f_array("VerletKokkos::f_merge_copy",atomKK->k_f.extent(0)); atomKK->sync(Device,ALL_MASK); - //static double time = 0.0; - //Kokkos::Timer ktimer; timer->init_timeout(); for (int i = 0; i < n; i++) { @@ -297,10 +295,8 @@ void VerletKokkos::run(int n) // initial time integration - //ktimer.reset(); timer->stamp(); modify->initial_integrate(vflag); - //time += ktimer.seconds(); if (n_post_integrate) modify->post_integrate(); timer->stamp(Timer::MODIFY); @@ -445,7 +441,6 @@ void VerletKokkos::run(int n) if (pair_compute_flag) { atomKK->sync(force->pair->execution_space,force->pair->datamask_read); atomKK->sync(force->pair->execution_space,~(~force->pair->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK))); - Kokkos::Timer ktimer; force->pair->compute(eflag,vflag); atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); atomKK->modified(force->pair->execution_space,~(~force->pair->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK))); diff --git a/src/MDI/fix_mdi_aimd.cpp b/src/MDI/fix_mdi_aimd.cpp deleted file mode 100644 index c878d183d3..0000000000 --- a/src/MDI/fix_mdi_aimd.cpp +++ /dev/null @@ -1,379 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "fix_mdi_aimd.h" -#include "atom.h" -#include "comm.h" -#include "domain.h" -#include "error.h" -#include "force.h" -#include "memory.h" -#include "update.h" - -using namespace LAMMPS_NS; -using namespace FixConst; - -enum { NATIVE, REAL, METAL }; // LAMMPS units which MDI supports - -/* ---------------------------------------------------------------------- */ - -FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) -{ - if (narg != 3) error->all(FLERR, "Illegal fix mdi/aimd command"); - - scalar_flag = 1; - global_freq = 1; - extscalar = 1; - energy_global_flag = 1; - virial_global_flag = 1; - thermo_energy = thermo_virial = 1; - - // check requirements for LAMMPS to work with MDI as an engine - - if (atom->tag_enable == 0) error->all(FLERR, "Cannot use MDI engine without atom IDs"); - - if (atom->natoms && atom->tag_consecutive() == 0) - error->all(FLERR, "MDI engine requires consecutive atom IDs"); - - // confirm LAMMPS is being run as a driver - - int role; - MDI_Get_role(&role); - if (role != MDI_DRIVER) - error->all(FLERR, "Must invoke LAMMPS as an MDI driver to use fix mdi/aimd"); - - // mdicomm will be one-time initialized in init() - // cannot be done here for a plugin library, b/c mdi plugin command is later - - mdicomm = MDI_COMM_NULL; - - // storage for all atoms - - buf3 = buf3all = nullptr; - maxbuf = 0; - - // set unit conversion factors - - if (strcmp(update->unit_style, "real") == 0) - lmpunits = REAL; - else if (strcmp(update->unit_style, "metal") == 0) - lmpunits = METAL; - else - lmpunits = NATIVE; - - unit_conversions(); - - nprocs = comm->nprocs; -} - -/* ---------------------------------------------------------------------- */ - -FixMDIAimd::~FixMDIAimd() -{ - // send exit command to engine if it is a stand-alone code - // for plugin, this happens in MDIPlugin::plugin_wrapper() - - if (!plugin) { - int ierr = MDI_Send_command("EXIT", mdicomm); - if (ierr) error->all(FLERR, "MDI: EXIT command"); - } - - // clean up - - memory->destroy(buf3); - memory->destroy(buf3all); -} - -/* ---------------------------------------------------------------------- */ - -int FixMDIAimd::setmask() -{ - int mask = 0; - mask |= PRE_REVERSE; - mask |= POST_FORCE; - mask |= MIN_POST_FORCE; - return mask; -} - -/* ---------------------------------------------------------------------- */ - -void FixMDIAimd::init() -{ - if (mdicomm != MDI_COMM_NULL) return; - - // one-time auto-detect whether engine is stand-alone code or plugin library - // also initializes mdicomm - // plugin = 0/1 for engine = stand-alone code vs plugin library - - MDI_Get_communicator(&mdicomm, 0); - - if (mdicomm == MDI_COMM_NULL) { - plugin = 0; - MDI_Accept_communicator(&mdicomm); - if (mdicomm == MDI_COMM_NULL) error->all(FLERR, "MDI unable to connect to stand-alone engine"); - } else { - plugin = 1; - int method; - MDI_Get_method(&method, mdicomm); - if (method != MDI_PLUGIN) error->all(FLERR, "MDI internal error for plugin engine"); - } -} - -/* ---------------------------------------------------------------------- */ - -void FixMDIAimd::setup(int vflag) -{ - post_force(vflag); -} - -/* ---------------------------------------------------------------------- */ - -void FixMDIAimd::setup_pre_reverse(int eflag, int vflag) -{ - pre_reverse(eflag, vflag); -} - -/* ---------------------------------------------------------------------- - store eflag, so can use it in post_force to request energy -------------------------------------------------------------------------- */ - -void FixMDIAimd::pre_reverse(int eflag, int /*vflag*/) -{ - eflag_caller = eflag; -} - -/* ---------------------------------------------------------------------- */ - -void FixMDIAimd::post_force(int vflag) -{ - int ilocal, ierr; - double cell[9]; - - int eflag = eflag_caller; - ev_init(eflag, vflag); - - // if simulation box dynamically changes, send current box to MDI engine - - if (domain->box_change_size || domain->box_change_shape) { - ierr = MDI_Send_command(">CELL_DISPL", mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); - cell[0] = domain->boxlo[0] * lmp2mdi_length; - cell[1] = domain->boxlo[1] * lmp2mdi_length; - cell[2] = domain->boxlo[2] * lmp2mdi_length; - ierr = MDI_Send(cell, 3, MDI_DOUBLE, mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL_DISPL data"); - - ierr = MDI_Send_command(">CELL", mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL command"); - cell[0] = domain->boxhi[0] - domain->boxlo[0]; - cell[1] = 0.0; - cell[2] = 0.0; - cell[3] = domain->xy; - cell[4] = domain->boxhi[1] - domain->boxlo[1]; - cell[5] = 0.0; - cell[6] = domain->xz; - cell[7] = domain->yz; - cell[8] = domain->boxhi[2] - domain->boxlo[2]; - ierr = MDI_Send(cell, 9, MDI_DOUBLE, mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL data"); - } - - // gather all coords, ordered by atomID - - reallocate(); - memset(buf3, 0, 3 * atom->natoms * sizeof(double)); - - double **x = atom->x; - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - - for (int i = 0; i < nlocal; i++) { - ilocal = static_cast(tag[i]) - 1; - buf3[3 * ilocal + 0] = x[i][0] * lmp2mdi_length; - buf3[3 * ilocal + 1] = x[i][1] * lmp2mdi_length; - buf3[3 * ilocal + 2] = x[i][2] * lmp2mdi_length; - } - - MPI_Reduce(buf3, buf3all, 3 * atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world); - - // send current coords to MDI engine - - ierr = MDI_Send_command(">COORDS", mdicomm); - if (ierr) error->all(FLERR, "MDI: >COORDS command"); - ierr = MDI_Send(buf3all, 3 * atom->natoms, MDI_DOUBLE, mdicomm); - if (ierr) error->all(FLERR, "MDI: >COORDS data"); - - // request forces from MDI engine - // this triggers engine to evaluate forces,energy,stress for current system - - ierr = MDI_Send_command("all(FLERR, "MDI: natoms, MDI_DOUBLE, mdicomm); - if (ierr) error->all(FLERR, "MDI: natoms, MPI_DOUBLE, 0, world); - - // add forces to owned atoms - // use atomID to index into ordered buf3 - - double **f = atom->f; - - for (int i = 0; i < nlocal; i++) { - ilocal = static_cast(tag[i]) - 1; - f[i][0] += buf3[3 * ilocal + 0] * mdi2lmp_force; - f[i][1] += buf3[3 * ilocal + 1] * mdi2lmp_force; - f[i][2] += buf3[3 * ilocal + 2] * mdi2lmp_force; - } - - // optionally request potential energy from MDI engine - - if (eflag_global) { - ierr = MDI_Send_command("all(FLERR, "MDI: all(FLERR, "MDI: all(FLERR, "MDI: all(FLERR, "MDI: xprd * domain->yprd * domain->zprd; - for (int i = 0; i < 6; i++) { - ptensor[i] *= mdi2lmp_pressure; - virial[i] = ptensor[i] * volume / force->nktv2p / nprocs; - } - } -} - -/* ---------------------------------------------------------------------- */ - -void FixMDIAimd::min_post_force(int vflag) -{ - post_force(vflag); -} - -/* ---------------------------------------------------------------------- - energy from MDI engine -------------------------------------------------------------------------- */ - -double FixMDIAimd::compute_scalar() -{ - return engine_energy; -} - -/* ---------------------------------------------------------------------- - reallocate storage for all atoms if necessary -------------------------------------------------------------------------- */ - -void FixMDIAimd::reallocate() -{ - if (atom->natoms <= maxbuf) return; - - if (3 * atom->natoms > MAXSMALLINT) - error->all(FLERR, "Natoms too large to use with fix mdi/aimd"); - - maxbuf = atom->natoms; - - memory->destroy(buf3); - memory->destroy(buf3all); - - memory->create(buf3, 3 * maxbuf, "mdi:buf3"); - memory->create(buf3all, 3 * maxbuf, "mdi:buf3all"); -} - -/* ---------------------------------------------------------------------- - MDI to/from LAMMPS conversion factors -------------------------------------------------------------------------- */ - -void FixMDIAimd::unit_conversions() -{ - double angstrom_to_bohr, kelvin_to_hartree, ev_to_hartree, second_to_aut; - - MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr); - MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree); - MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree); - MDI_Conversion_Factor("second", "atomic_unit_of_time", &second_to_aut); - - // length units - - mdi2lmp_length = 1.0; - lmp2mdi_length = 1.0; - - if (lmpunits == REAL || lmpunits == METAL) { - lmp2mdi_length = angstrom_to_bohr; - mdi2lmp_length = 1.0 / angstrom_to_bohr; - } - - // energy units - - mdi2lmp_energy = 1.0; - lmp2mdi_energy = 1.0; - - if (lmpunits == REAL) { - lmp2mdi_energy = kelvin_to_hartree / force->boltz; - mdi2lmp_energy = force->boltz / kelvin_to_hartree; - } else if (lmpunits == METAL) { - lmp2mdi_energy = ev_to_hartree; - mdi2lmp_energy = 1.0 / ev_to_hartree; - } - - // force units = energy/length - - mdi2lmp_force = 1.0; - lmp2mdi_force = 1.0; - - if (lmpunits == REAL) { - lmp2mdi_force = (kelvin_to_hartree / force->boltz) / angstrom_to_bohr; - mdi2lmp_force = 1.0 / lmp2mdi_force; - } else if (lmpunits == METAL) { - lmp2mdi_force = ev_to_hartree / angstrom_to_bohr; - mdi2lmp_force = angstrom_to_bohr / ev_to_hartree; - } - - // pressure or stress units = force/area = energy/volume - - mdi2lmp_pressure = 1.0; - lmp2mdi_pressure = 1.0; - - if (lmpunits == REAL) { - lmp2mdi_pressure = (kelvin_to_hartree / force->boltz) / - (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p; - mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; - } else if (lmpunits == METAL) { - lmp2mdi_pressure = - ev_to_hartree / (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p; - mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; - } - - // velocity units = distance/time - - mdi2lmp_velocity = 1.0; - lmp2mdi_velocity = 1.0; - - if (lmpunits == REAL) { - lmp2mdi_velocity = angstrom_to_bohr / (1.0e-15 * second_to_aut); - mdi2lmp_velocity = 1.0 / lmp2mdi_velocity; - } else if (lmpunits == METAL) { - lmp2mdi_velocity = angstrom_to_bohr / (1.0e-12 * second_to_aut); - mdi2lmp_velocity = 1.0 / lmp2mdi_velocity; - } -} diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp new file mode 100644 index 0000000000..db1c59ada9 --- /dev/null +++ b/src/MDI/fix_mdi_qm.cpp @@ -0,0 +1,591 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_mdi_qm.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum { NATIVE, REAL, METAL }; // LAMMPS units which MDI supports + +#define MAXELEMENT 103 // used elsewhere in MDI package + +/* ---------------------------------------------------------------------- */ + +FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +{ + // check requirements for LAMMPS to work with MDI as an engine + + if (atom->tag_enable == 0) + error->all(FLERR, "Cannot use MDI engine without atom IDs"); + if (atom->natoms && atom->tag_consecutive() == 0) + error->all(FLERR, "MDI engine requires consecutive atom IDs"); + + // confirm LAMMPS is being run as a driver + + int role; + MDI_Get_role(&role); + if (role != MDI_DRIVER) + error->all(FLERR, "Must invoke LAMMPS as an MDI driver to use fix mdi/qm"); + + // optional args + + virialflag = 0; + addflag = 1; + every = 1; + connectflag = 1; + elements = nullptr; + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"virial") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); + if (strcmp(arg[iarg+1],"yes") == 0) virialflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) virialflag = 0; + else error->all(FLERR,"Illegal fix mdi/qm command"); + iarg += 2; + } else if (strcmp(arg[iarg],"add") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); + if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0; + else error->all(FLERR,"Illegal fix mdi/qm command"); + iarg += 2; + } else if (strcmp(arg[iarg],"every") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); + every = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command"); + iarg += 2; + } else if (strcmp(arg[iarg],"connect") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); + if (strcmp(arg[iarg+1],"yes") == 0) connectflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0; + else error->all(FLERR,"Illegal fix mdi/qm command"); + iarg += 2; + } else if (strcmp(arg[iarg],"elements") == 0) { + int ntypes = atom->ntypes; + if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); + delete [] elements; + elements = new int[ntypes+1]; + for (int i = 1; i <= ntypes; i++) { + elements[i] = utils::inumeric(FLERR,arg[iarg+i],false,lmp); + if (elements[i] < 1 || elements[i] > MAXELEMENT) + error->all(FLERR,"Illegal fix mdi/qm command"); + } + iarg += ntypes+1; + } else error->all(FLERR,"Illegal fix mdi/qm command"); + } + + // fix output settings are based on optional keywords + + scalar_flag = 1; + global_freq = every; + extscalar = 1; + + peratom_flag = 1; + size_peratom_cols = 3; + peratom_freq = every; + extvector = 0; + + if (virialflag) { + vector_flag = 1; + size_vector = 6; + } + + if (addflag) { + energy_global_flag = 1; + virial_global_flag = 1; + thermo_energy = thermo_virial = 1; + } + + // mdicomm will be initialized in init() + // cannot do here for a plugin library, b/c mdi plugin command comes later + + mdicomm = MDI_COMM_NULL; + + // peratom storage, both for nlocal and global natoms + + fqm = nullptr; + maxlocal = 0; + + ibuf1 = ibuf1all = nullptr; + buf3 = buf3all = nullptr; + maxbuf = 0; + + // set unit conversion factors + + if (strcmp(update->unit_style, "real") == 0) + lmpunits = REAL; + else if (strcmp(update->unit_style, "metal") == 0) + lmpunits = METAL; + else + lmpunits = NATIVE; + + unit_conversions(); + + nprocs = comm->nprocs; + + // initialize outputs + + qm_energy = 0.0; + if (virialflag) { + for (int i = 0; i < 6; i++) { + qm_virial[i] = 0.0; + virial[i] = 0.0; + } + sumflag = 0; + } +} + +/* ---------------------------------------------------------------------- */ + +FixMDIQM::~FixMDIQM() +{ + // send exit command to stand-alone engine code + // for connnectflag = 0, this is done via "mdi exit" command + // for plugin, this is done in MDIPlugin::plugin_wrapper() + + if (mdicomm != MDI_COMM_NULL && connectflag && !plugin) { + int ierr = MDI_Send_command("EXIT", mdicomm); + if (ierr) error->all(FLERR, "MDI: EXIT command"); + } + + // clean up + + delete[] elements; + + memory->destroy(fqm); + + memory->destroy(ibuf1); + memory->destroy(ibuf1all); + memory->destroy(buf3); + memory->destroy(buf3all); +} + +/* ---------------------------------------------------------------------- */ + +int FixMDIQM::setmask() +{ + int mask = 0; + mask |= PRE_REVERSE; + mask |= POST_FORCE; + mask |= MIN_POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMDIQM::init() +{ + // set local mdicomm one-time only + // also set plugin = 0/1 for engine = stand-alone code vs plugin library + + if (mdicomm == MDI_COMM_NULL) { + + // this fix makes one-time connection to engine + + if (connectflag) { + + // if MDI's mdicomm not set, need to Accept_comm() with stand-alone engine + // othewise are already connected to plugin engine + + MDI_Get_communicator(&mdicomm, 0); + + if (mdicomm == MDI_COMM_NULL) { + plugin = 0; + MDI_Accept_communicator(&mdicomm); + if (mdicomm == MDI_COMM_NULL) + error->all(FLERR, "MDI unable to connect to stand-alone engine"); + + } else { + plugin = 1; + int method; + MDI_Get_method(&method, mdicomm); + if (method != MDI_PLUGIN) + error->all(FLERR, "MDI internal error for plugin engine"); + } + + // connection should have been already made by "mdi connect" command + // only works for stand-alone engines + + } else { + plugin = 0; + + if (lmp->mdicomm == nullptr) + error->all(FLERR,"Fix mdi/qm is not connected to engine via mdi connect"); + + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) lmp->mdicomm; + memcpy(&mdicomm,ptrcomm,nbytes); + } + } + + // send natoms, atom types or elements, and simulation box to engine + // this will trigger setup of a new system + // subsequent calls in post_force() will be for same system until new init() + + reallocate(); + + int ierr = MDI_Send_command(">NATOMS", mdicomm); + if (ierr) error->all(FLERR, "MDI: >NATOMS command"); + int n = static_cast (atom->natoms); + ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); + if (ierr) error->all(FLERR, "MDI: >NATOMS data"); + + if (elements) send_elements(); + else send_types(); + send_box(); +} + +/* ---------------------------------------------------------------------- */ + +void FixMDIQM::setup(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMDIQM::post_force(int vflag) +{ + int index, ierr; + + // skip if timestep is not a multiple of every + + if (update->ntimestep % every) return; + + // reallocate peratom storage if necessary, both natoms and nlocal + + reallocate(); + + // if simulation box dynamically changes, send current box to MDI engine + + if (domain->box_change_size || domain->box_change_shape) + send_box(); + + // gather all coords, ordered by atomID + + memset(buf3, 0, 3 * atom->natoms * sizeof(double)); + + double **x = atom->x; + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + index = static_cast(tag[i]) - 1; + buf3[3 * index + 0] = x[i][0] * lmp2mdi_length; + buf3[3 * index + 1] = x[i][1] * lmp2mdi_length; + buf3[3 * index + 2] = x[i][2] * lmp2mdi_length; + } + + int n = static_cast (atom->natoms); + MPI_Reduce(buf3, buf3all, 3 * n, MPI_DOUBLE, MPI_SUM, 0, world); + + // send current coords to MDI engine + + ierr = MDI_Send_command(">COORDS", mdicomm); + if (ierr) error->all(FLERR, "MDI: >COORDS command"); + ierr = MDI_Send(buf3all, 3 * atom->natoms, MDI_DOUBLE, mdicomm); + if (ierr) error->all(FLERR, "MDI: >COORDS data"); + + // request potential energy from MDI engine + // this triggers engine to perform QM calculation + // qm_energy = fix output for global QM energy + + ierr = MDI_Send_command("all(FLERR, "MDI: all(FLERR, "MDI: all(FLERR, "MDI: natoms, MDI_DOUBLE, mdicomm); + if (ierr) error->all(FLERR, "MDI: (tag[i]) - 1; + fqm[i][0] = buf3[3 * index + 0] * mdi2lmp_force; + fqm[i][1] = buf3[3 * index + 1] * mdi2lmp_force; + fqm[i][2] = buf3[3 * index + 2] * mdi2lmp_force; + } + + + // optionally add forces to owned atoms + // use atomID of local atoms to index into ordered buf3 + + if (addflag) { + double **f = atom->f; + for (int i = 0; i < nlocal; i++) { + index = static_cast(tag[i]) - 1; + f[i][0] += buf3[3 * index + 0] * mdi2lmp_force; + f[i][1] += buf3[3 * index + 1] * mdi2lmp_force; + f[i][2] += buf3[3 * index + 2] * mdi2lmp_force; + } + } + + // optionally request stress tensor from MDI engine, convert to virial + // qm_virial = fix output for global QM virial + + if (virialflag) { + ierr = MDI_Send_command("all(FLERR, "MDI: all(FLERR, "MDI: virial + // multiply by volume to make it extensive + // divide by nprocs so each proc stores a portion + // this is b/c ComputePressure expects that as input from a fix + // it will do an MPI_Allreduce and divide by volume + + if (virialflag && addflag) { + double volume; + if (domain->dimension == 2) + volume = domain->xprd * domain->yprd; + else if (domain->dimension == 3) + volume = domain->xprd * domain->yprd * domain->zprd; + for (int i = 0; i < 6; i++) + virial[i] = qm_virial_symmetric[i]*volume/nprocs; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMDIQM::min_post_force(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- + energy from MDI engine +------------------------------------------------------------------------- */ + +double FixMDIQM::compute_scalar() +{ + return qm_energy; +} + +/* ---------------------------------------------------------------------- + virial from MDI engine +------------------------------------------------------------------------- */ + +double FixMDIQM::compute_vector(int n) +{ + return qm_virial_symmetric[n]; +} + +/* ---------------------------------------------------------------------- + reallocate storage for local and global and atoms if needed +------------------------------------------------------------------------- */ + +void FixMDIQM::reallocate() +{ + if (atom->nlocal > maxlocal) { + maxlocal = atom->nmax; + memory->destroy(fqm); + memory->create(fqm, maxlocal, 3, "mdi:fqm"); + array_atom = fqm; + } + + if (atom->natoms > maxbuf) { + bigint nsize = atom->natoms * 3; + if (nsize > MAXSMALLINT) + error->all(FLERR, "Natoms too large to use with fix mdi/qm"); + + maxbuf = static_cast (atom->natoms); + memory->destroy(ibuf1); + memory->destroy(buf3); + memory->destroy(buf3all); + memory->create(ibuf1, maxbuf, "mdi:ibuf1"); + memory->create(ibuf1all, maxbuf, "mdi:ibuf1all"); + memory->create(buf3, 3 * maxbuf, "mdi:buf3"); + memory->create(buf3all, 3 * maxbuf, "mdi:buf3all"); + } +} + +/* ---------------------------------------------------------------------- + send LAMMPS atom types to MDI engine +------------------------------------------------------------------------- */ + +void FixMDIQM::send_types() +{ + int n = static_cast (atom->natoms); + memset(ibuf1, 0, n * sizeof(int)); + + // use local atomID to index into ordered ibuf1 + + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + + int index; + for (int i = 0; i < nlocal; i++) { + index = static_cast(tag[i]) - 1; + ibuf1[index] = type[i]; + } + + MPI_Reduce(ibuf1, ibuf1all, n, MPI_INT, MPI_SUM, 0, world); + + int ierr = MDI_Send_command(">TYPES", mdicomm); + if (ierr) error->all(FLERR, "MDI: >TYPES command"); + ierr = MDI_Send(ibuf1all, n, MDI_INT, mdicomm); + if (ierr) error->all(FLERR, "MDI: >TYPES data"); +} + +/* ---------------------------------------------------------------------- + send elements to MDI engine = atomic numbers for each type +------------------------------------------------------------------------- */ + +void FixMDIQM::send_elements() +{ + int n = static_cast (atom->natoms); + memset(ibuf1, 0, n * sizeof(int)); + + // use local atomID to index into ordered ibuf1 + + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + + int index; + for (int i = 0; i < nlocal; i++) { + index = static_cast(tag[i]) - 1; + ibuf1[index] = elements[type[i]]; + } + + MPI_Reduce(ibuf1, ibuf1all, n, MPI_INT, MPI_SUM, 0, world); + + int ierr = MDI_Send_command(">ELEMENTS", mdicomm); + if (ierr) error->all(FLERR, "MDI: >ELEMENTS command"); + ierr = MDI_Send(ibuf1all, n, MDI_INT, mdicomm); + if (ierr) error->all(FLERR, "MDI: >ELEMETNS data"); +} + +/* ---------------------------------------------------------------------- + send simulation box size and shape to MDI engine +------------------------------------------------------------------------- */ + +void FixMDIQM::send_box() +{ + double cell[9]; + + int ierr = MDI_Send_command(">CELL_DISPL", mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); + cell[0] = domain->boxlo[0] * lmp2mdi_length; + cell[1] = domain->boxlo[1] * lmp2mdi_length; + cell[2] = domain->boxlo[2] * lmp2mdi_length; + ierr = MDI_Send(cell, 3, MDI_DOUBLE, mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL_DISPL data"); + + ierr = MDI_Send_command(">CELL", mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL command"); + cell[0] = domain->boxhi[0] - domain->boxlo[0]; + cell[1] = 0.0; + cell[2] = 0.0; + cell[3] = domain->xy; + cell[4] = domain->boxhi[1] - domain->boxlo[1]; + cell[5] = 0.0; + cell[6] = domain->xz; + cell[7] = domain->yz; + cell[8] = domain->boxhi[2] - domain->boxlo[2]; + ierr = MDI_Send(cell, 9, MDI_DOUBLE, mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL data"); +} + +/* ---------------------------------------------------------------------- + MDI to/from LAMMPS conversion factors +------------------------------------------------------------------------- */ + +void FixMDIQM::unit_conversions() +{ + double angstrom_to_bohr, kelvin_to_hartree, ev_to_hartree, second_to_aut; + + MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr); + MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree); + MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree); + MDI_Conversion_Factor("second", "atomic_unit_of_time", &second_to_aut); + + // length units + + mdi2lmp_length = 1.0; + lmp2mdi_length = 1.0; + + if (lmpunits == REAL || lmpunits == METAL) { + lmp2mdi_length = angstrom_to_bohr; + mdi2lmp_length = 1.0 / angstrom_to_bohr; + } + + // energy units + + mdi2lmp_energy = 1.0; + lmp2mdi_energy = 1.0; + + if (lmpunits == REAL) { + lmp2mdi_energy = kelvin_to_hartree / force->boltz; + mdi2lmp_energy = force->boltz / kelvin_to_hartree; + } else if (lmpunits == METAL) { + lmp2mdi_energy = ev_to_hartree; + mdi2lmp_energy = 1.0 / ev_to_hartree; + } + + // force units = energy/length + + mdi2lmp_force = 1.0; + lmp2mdi_force = 1.0; + + if (lmpunits == REAL) { + lmp2mdi_force = (kelvin_to_hartree / force->boltz) / angstrom_to_bohr; + mdi2lmp_force = 1.0 / lmp2mdi_force; + } else if (lmpunits == METAL) { + lmp2mdi_force = ev_to_hartree / angstrom_to_bohr; + mdi2lmp_force = angstrom_to_bohr / ev_to_hartree; + } + + // pressure or stress units = force/area = energy/volume + + mdi2lmp_pressure = 1.0; + lmp2mdi_pressure = 1.0; + + if (lmpunits == REAL) { + lmp2mdi_pressure = (kelvin_to_hartree / force->boltz) / + (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p; + mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; + } else if (lmpunits == METAL) { + lmp2mdi_pressure = + ev_to_hartree / (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p; + mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; + } +} diff --git a/src/MDI/fix_mdi_aimd.h b/src/MDI/fix_mdi_qm.h similarity index 75% rename from src/MDI/fix_mdi_aimd.h rename to src/MDI/fix_mdi_qm.h index cdb7977c37..11180925b1 100644 --- a/src/MDI/fix_mdi_aimd.h +++ b/src/MDI/fix_mdi_qm.h @@ -13,42 +13,46 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(mdi/aimd,FixMDIAimd); +FixStyle(mdi/qm,FixMDIQM); // clang-format on #else -#ifndef LMP_FIX_MDI_AIMD_H -#define LMP_FIX_MDI_AIMD_H +#ifndef LMP_FIX_MDI_QM_H +#define LMP_FIX_MDI_QM_H #include "fix.h" #include namespace LAMMPS_NS { -class FixMDIAimd : public Fix { +class FixMDIQM : public Fix { public: - FixMDIAimd(class LAMMPS *, int, char **); - ~FixMDIAimd(); + FixMDIQM(class LAMMPS *, int, char **); + ~FixMDIQM(); int setmask(); void init(); void setup(int); - void setup_pre_reverse(int, int); - void pre_reverse(int, int); void post_force(int); void min_post_force(int); double compute_scalar(); + double compute_vector(int); private: int nprocs; + int every,virialflag,addflag,connectflag; int plugin; + int maxlocal; + int sumflag; + int *elements; + + double qm_energy; + int lmpunits; + double qm_virial[9],qm_virial_symmetric[6]; + double **fqm; MDI_Comm mdicomm; - int eflag_caller; - double engine_energy; - int lmpunits; - // unit conversion factors double lmp2mdi_length, mdi2lmp_length; @@ -60,11 +64,15 @@ class FixMDIAimd : public Fix { // buffers for MDI comm int maxbuf; + int *ibuf1, *ibuf1all; double *buf3, *buf3all; // methods void reallocate(); + void send_types(); + void send_elements(); + void send_box(); void unit_conversions(); }; diff --git a/src/MDI/mdi_command.cpp b/src/MDI/mdi_command.cpp index 65e47e197a..42d8b2691a 100644 --- a/src/MDI/mdi_command.cpp +++ b/src/MDI/mdi_command.cpp @@ -16,13 +16,19 @@ #include "error.h" #include "mdi_engine.h" #include "mdi_plugin.h" +#include "memory.h" #include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- - mdi command: engine or plugin + mdi command: engine or plugin or connect or exit + engine is used when LAMMPS is an MDI engine, to start listening for requests + plugin is used when LAMMPS is an MDI driver to load a plugin library + connect and exit are used when LAMMPS is an MDI driver to + (a) connect = setup comm with a stand-alone MDI engine + (b) exit = terminate comm with a stand-alone MDI engine ---------------------------------------------------------------------- */ void MDICommand::command(int narg, char **arg) @@ -31,8 +37,45 @@ void MDICommand::command(int narg, char **arg) if (strcmp(arg[0], "engine") == 0) { MDIEngine(lmp, narg - 1, &arg[1]); + } else if (strcmp(arg[0], "plugin") == 0) { MDIPlugin(lmp, narg - 1, &arg[1]); - } else - error->all(FLERR, "Illegal mdi command"); + + } else if (strcmp(arg[0], "connect") == 0) { + + if (lmp->mdicomm != nullptr) + error->all(FLERR,"MDI cannot connect to already connected engine"); + + MDI_Comm mdicomm; + MDI_Get_communicator(&mdicomm, 0); + + if (mdicomm == MDI_COMM_NULL) { + MDI_Accept_communicator(&mdicomm); + if (mdicomm == MDI_COMM_NULL) + error->all(FLERR, "MDI unable to connect to stand-alone engine"); + } else error->all(FLERR, "Cannot use mdi connect with plugin engine"); + + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) memory->smalloc(nbytes,"mdi:mdicomm"); + memcpy(ptrcomm,&mdicomm,nbytes); + + lmp->mdicomm = (void *) ptrcomm; + + } else if (strcmp(arg[0], "exit") == 0) { + + if (lmp->mdicomm == nullptr) + error->all(FLERR,"MDI cannot send exit to unconnected engine"); + + MDI_Comm mdicomm; + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) lmp->mdicomm; + memcpy(&mdicomm,ptrcomm,nbytes); + + int ierr = MDI_Send_command("EXIT", mdicomm); + if (ierr) error->all(FLERR, "MDI: EXIT command"); + + memory->sfree(ptrcomm); + lmp->mdicomm = nullptr; + + } else error->all(FLERR, "Illegal mdi command"); } diff --git a/src/MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp index f2b96cb69a..91774659ff 100644 --- a/src/MDI/mdi_engine.cpp +++ b/src/MDI/mdi_engine.cpp @@ -54,6 +54,8 @@ enum { DEFAULT, MD, OPT }; // top-level MDI engine modes enum { TYPE, CHARGE, MASS, COORD, VELOCITY, FORCE, ADDFORCE }; +#define MAXELEMENT 103 // used elsewhere in MDI package + /* ---------------------------------------------------------------------- trigger LAMMPS to start acting as an MDI engine either in standalone mode or plugin mode @@ -63,17 +65,47 @@ enum { TYPE, CHARGE, MASS, COORD, VELOCITY, FORCE, ADDFORCE }; when EXIT command is received, mdi engine command exits ---------------------------------------------------------------------- */ -MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** /*arg*/) : Pointers(_lmp) +MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** arg) : Pointers(_lmp) { - if (narg) error->all(FLERR, "Illegal mdi engine command"); - // check requirements for LAMMPS to work with MDI as an engine - if (atom->tag_enable == 0) error->all(FLERR, "Cannot use MDI engine without atom IDs"); + if (atom->tag_enable == 0) error->all(FLERR, "MDI engine requires atom IDs"); if (atom->natoms && atom->tag_consecutive() == 0) error->all(FLERR, "MDI engine requires consecutive atom IDs"); + // optional args + + elements = nullptr; + + int iarg = 0; + while (iarg < narg) { + if (strcmp(arg[iarg],"elements") == 0) { + int ntypes = atom->ntypes; + delete [] elements; + elements = new int[ntypes+1]; + if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal mdi engine command"); + for (int i = 1; i <= ntypes; i++) { + elements[i] = utils::inumeric(FLERR,arg[iarg+i],false,lmp); + if (elements[i] < 0 || elements[i] > MAXELEMENT) + error->all(FLERR,"Illegal mdi engine command"); + } + iarg += ntypes+1; + } else error->all(FLERR,"Illegal mdi engine command"); + } + + // error check an MDI element does not map to multiple atom types + + if (elements) { + int ntypes = atom->ntypes; + for (int i = 1; i < ntypes; i++) + for (int j = i+1; j <= ntypes; j++) { + if (elements[i] == 0 || elements[j] == 0) continue; + if (elements[i] == elements[j]) + error->all(FLERR,"MDI engine element cannot map to multiple types"); + } + } + // confirm LAMMPS is being run as an engine int role; @@ -135,7 +167,7 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** /*arg*/) : Pointers(_lmp) ibuf1 = ibuf1all = nullptr; maxatom = 0; - sys_natoms = atom->natoms; + sys_natoms = static_cast (atom->natoms); reallocate(); nsteps = 0; @@ -194,6 +226,8 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** /*arg*/) : Pointers(_lmp) // clean up + delete[] elements; + delete[] mdicmd; delete[] node_engine; delete[] node_driver; @@ -299,6 +333,11 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) } else if (strcmp(command, ">COORDS") == 0) { receive_coords(); + } else if (strcmp(command, ">ELEMENTS") == 0) { + if (!elements) + error->all(FLERR,"MDI engine command did not define element list"); + receive_elements(); + } else if (strcmp(command, ">FORCES") == 0) { receive_double3(FORCE); @@ -323,7 +362,7 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) else receive_double3(VELOCITY); - // ----------------------------------------------- + // ----------------------------------------------- } else if (strcmp(command, "<@") == 0) { ierr = MDI_Send(node_engine, MDI_NAME_LENGTH, MDI_CHAR, mdicomm); @@ -372,9 +411,9 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) } else if (strcmp(command, "all(FLERR, "MDI: MDI engine is already performing a simulation"); @@ -419,14 +458,14 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) strncpy(node_driver, command, MDI_COMMAND_LENGTH); node_match = false; - // exit command + // exit command } else if (strcmp(command, "EXIT") == 0) { exit_command = true; - // ------------------------------------------------------- - // custom LAMMPS commands - // ------------------------------------------------------- + // ------------------------------------------------------- + // custom LAMMPS commands + // ------------------------------------------------------- } else if (strcmp(command, "NBYTES") == 0) { nbytes_command(); @@ -439,9 +478,9 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) } else if (strcmp(command, "all(FLERR, "MDI: Unknown command {} received from driver", command); @@ -479,6 +518,7 @@ void MDIEngine::mdi_commands() MDI_Register_command("@DEFAULT", ">CELL_DISPL"); MDI_Register_command("@DEFAULT", ">CHARGES"); MDI_Register_command("@DEFAULT", ">COORDS"); + MDI_Register_command("@DEFAULT", ">ELEMENTS"); MDI_Register_command("@DEFAULT", ">NATOMS"); MDI_Register_command("@DEFAULT", ">NSTEPS"); MDI_Register_command("@DEFAULT", ">TOLERANCE"); @@ -914,7 +954,7 @@ void MDIEngine::evaluate() /* ---------------------------------------------------------------------- create a new system - >CELL, >NATOMS, >TYPES, >COORDS commands are required + >CELL, >NATOMS, >TYPES or >ELEMENTS, >COORDS commands are required >CELL_DISPL, >CHARGES, >VELOCITIES commands are optional ---------------------------------------------------------------------- */ @@ -924,8 +964,8 @@ void MDIEngine::create_system() if (flag_cell == 0 || flag_natoms == 0 || flag_types == 0 || flag_coords == 0) error->all(FLERR, - "MDI create_system requires >CELL, >NATOMS, >TYPES, >COORDS " - "MDI commands"); + "MDI create_system requires >CELL, >NATOMS, " + ">TYPES or >ELEMENTS, >COORDS MDI commands"); // remove all existing atoms via delete_atoms command @@ -955,16 +995,23 @@ void MDIEngine::create_system() lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz); // invoke lib->create_atoms() + // create list of 1 to sys_natoms IDs // optionally set charges if specified by ">CHARGES" + tagint* sys_ids; + memory->create(sys_ids, sys_natoms, "mdi:sys_ids"); + for (int i = 0; i < sys_natoms; i++) sys_ids[i] = i+1; + if (flag_velocities) - lammps_create_atoms(lmp, sys_natoms, nullptr, sys_types, sys_coords, sys_velocities, nullptr, + lammps_create_atoms(lmp, sys_natoms, sys_ids, sys_types, sys_coords, sys_velocities, nullptr, 1); else - lammps_create_atoms(lmp, sys_natoms, nullptr, sys_types, sys_coords, nullptr, nullptr, 1); + lammps_create_atoms(lmp, sys_natoms, sys_ids, sys_types, sys_coords, nullptr, nullptr, 1); if (flag_charges) lammps_scatter_atoms(lmp, (char *) "q", 1, 1, sys_charges); + memory->destroy(sys_ids); + // new system update->ntimestep = 0; @@ -1153,6 +1200,38 @@ void MDIEngine::receive_coords() for (int i = 0; i < n; i++) sys_coords[i] *= mdi2lmp_length; } +/* ---------------------------------------------------------------------- + >ELEMENTS command + receive elements for each atom = atomic numbers + convert to LAMMPS atom types and store in sys_types +---------------------------------------------------------------------- */ + +void MDIEngine::receive_elements() +{ + actionflag = 0; + flag_types = 1; + int ierr = MDI_Recv(sys_types, sys_natoms, MDI_INT, mdicomm); + if (ierr) error->all(FLERR, "MDI: >ELEMENTS data"); + MPI_Bcast(sys_types, sys_natoms, MPI_INT, 0, world); + + // convert from element atomic numbers to LAMMPS atom types + // use maping provided by mdi engine command + + int ntypes = atom->ntypes; + int itype; + + for (int i = 0; i < sys_natoms; i++) { + for (itype = 1; itype <= ntypes; itype++) { + if (sys_types[i] == elements[itype]) { + sys_types[i] = itype; + break; + } + } + if (itype > ntypes) + error->all(FLERR,"MDI element not found in element list"); + } +} + /* ---------------------------------------------------------------------- >NATOMS command natoms cannot exceed 32-bit int for use with MDI @@ -1239,7 +1318,7 @@ void MDIEngine::receive_velocities() void MDIEngine::receive_double3(int which) { - int n = 3 * atom->natoms; + int n = 3 * sys_natoms; int ierr = MDI_Recv(buf3, n, MDI_DOUBLE, mdicomm); if (ierr) error->all(FLERR, "MDI: natoms * MDI_LABEL_LENGTH]; - memset(labels, ' ', atom->natoms * MDI_LABEL_LENGTH); + auto labels = new char[sys_natoms * MDI_LABEL_LENGTH]; + memset(labels, ' ', sys_natoms * MDI_LABEL_LENGTH); - memset(ibuf1, 0, atom->natoms * sizeof(int)); + memset(ibuf1, 0, sys_natoms * sizeof(int)); // use atomID to index into ordered ibuf1 @@ -1370,17 +1449,17 @@ void MDIEngine::send_labels() ibuf1[ilocal] = type[i]; } - MPI_Reduce(ibuf1, ibuf1all, atom->natoms, MPI_INT, MPI_SUM, 0, world); + MPI_Reduce(ibuf1, ibuf1all, sys_natoms, MPI_INT, MPI_SUM, 0, world); if (comm->me == 0) { - for (int iatom = 0; iatom < atom->natoms; iatom++) { + for (int iatom = 0; iatom < sys_natoms; iatom++) { std::string label = std::to_string(ibuf1all[iatom]); int label_len = std::min(int(label.length()), MDI_LABEL_LENGTH); strncpy(&labels[iatom * MDI_LABEL_LENGTH], label.c_str(), label_len); } } - int ierr = MDI_Send(labels, atom->natoms * MDI_LABEL_LENGTH, MDI_CHAR, mdicomm); + int ierr = MDI_Send(labels, sys_natoms * MDI_LABEL_LENGTH, MDI_CHAR, mdicomm); if (ierr) error->all(FLERR, "MDI: (atom->natoms); - int ierr = MDI_Send(&natoms, 1, MDI_INT, mdicomm); + int ierr = MDI_Send(&sys_natoms, 1, MDI_INT, mdicomm); if (ierr != 0) error->all(FLERR, "MDI: compute_vector(); - for (int i = 0; i < 6; i++) vtensor[i] = press->vector[i] * lmp2mdi_pressure; + vtensor_full[0] = press->vector[0] * lmp2mdi_pressure; + vtensor_full[4] = press->vector[1] * lmp2mdi_pressure; + vtensor_full[8] = press->vector[2] * lmp2mdi_pressure; + vtensor_full[1] = vtensor_full[3] = press->vector[3] * lmp2mdi_pressure; + vtensor_full[2] = vtensor_full[6] = press->vector[4] * lmp2mdi_pressure; + vtensor_full[5] = vtensor_full[7] = press->vector[5] * lmp2mdi_pressure; - int ierr = MDI_Send(vtensor, 6, MDI_DOUBLE, mdicomm); + int ierr = MDI_Send(vtensor_full, 9, MDI_DOUBLE, mdicomm); if (ierr) error->all(FLERR, "MDI: natoms * sizeof(double)); + memset(buf1, 0, sys_natoms * sizeof(double)); // use atomID to index into ordered buf1 @@ -1467,9 +1550,9 @@ void MDIEngine::send_double1(int which) } } - MPI_Reduce(buf1, buf1all, atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world); + MPI_Reduce(buf1, buf1all, sys_natoms, MPI_DOUBLE, MPI_SUM, 0, world); - int ierr = MDI_Send(buf1all, atom->natoms, MDI_DOUBLE, mdicomm); + int ierr = MDI_Send(buf1all, sys_natoms, MDI_DOUBLE, mdicomm); if (ierr) error->all(FLERR, "MDI: natoms * sizeof(int)); + memset(ibuf1, 0, sys_natoms * sizeof(int)); // use atomID to index into ordered ibuf1 @@ -1498,9 +1581,9 @@ void MDIEngine::send_int1(int which) } } - MPI_Reduce(ibuf1, ibuf1all, atom->natoms, MPI_INT, MPI_SUM, 0, world); + MPI_Reduce(ibuf1, ibuf1all, sys_natoms, MPI_INT, MPI_SUM, 0, world); - int ierr = MDI_Send(ibuf1all, atom->natoms, MDI_INT, mdicomm); + int ierr = MDI_Send(ibuf1all, sys_natoms, MDI_INT, mdicomm); if (ierr) error->all(FLERR, "MDI: natoms * sizeof(double)); + memset(buf3, 0, 3 * sys_natoms * sizeof(double)); // use atomID to index into ordered buf3 @@ -1547,9 +1630,9 @@ void MDIEngine::send_double3(int which) } } - MPI_Reduce(buf3, buf3all, 3 * atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world); + MPI_Reduce(buf3, buf3all, 3 * sys_natoms, MPI_DOUBLE, MPI_SUM, 0, world); - int ierr = MDI_Send(buf3all, 3 * atom->natoms, MDI_DOUBLE, mdicomm); + int ierr = MDI_Send(buf3all, 3 * sys_natoms, MDI_DOUBLE, mdicomm); if (ierr) error->all(FLERR, "MDI: MAXSMALLINT) error->all(FLERR, "Natoms too large to use with mdi engine"); + bigint nsize = (bigint) sys_natoms * 3; + if (nsize > MAXSMALLINT) error->all(FLERR, "Natoms too large to use with mdi engine"); maxatom = sys_natoms; diff --git a/src/MDI/mdi_engine.h b/src/MDI/mdi_engine.h index ea840fba02..242755e3b7 100644 --- a/src/MDI/mdi_engine.h +++ b/src/MDI/mdi_engine.h @@ -70,6 +70,8 @@ class MDIEngine : protected Pointers { int actionflag; // 1 if MD or OPTG just completed, else 0 + int *elements; + // buffers for MDI comm int maxatom; @@ -106,6 +108,7 @@ class MDIEngine : protected Pointers { void receive_cell_displ(); void receive_charges(); void receive_coords(); + void receive_elements(); void receive_natoms(); void receive_nsteps(); void receive_tolerance(); diff --git a/src/MDI/mdi_plugin.cpp b/src/MDI/mdi_plugin.cpp index 3c8e38481d..c2add38266 100644 --- a/src/MDI/mdi_plugin.cpp +++ b/src/MDI/mdi_plugin.cpp @@ -19,7 +19,6 @@ #include "mdi_plugin.h" #include "error.h" -#include "fix_mdi_aimd.h" #include "input.h" #include "modify.h" diff --git a/src/MEAM/meam.h b/src/MEAM/meam.h index 237ffed8aa..8a2f43e354 100644 --- a/src/MEAM/meam.h +++ b/src/MEAM/meam.h @@ -27,9 +27,11 @@ typedef enum { FCC, BCC, HCP, DIM, DIA, DIA3, B1, C11, L12, B2, CH4, LIN, ZIG, T class MEAM { public: MEAM(Memory *mem); - ~MEAM(); + virtual ~MEAM(); - private: + int copymode; + + protected: Memory *memory; // cutforce = force cutoff @@ -285,8 +287,8 @@ class MEAM { double *rozero, int *ibar); void meam_setup_param(int which, double value, int nindex, int *index /*index(3)*/, int *errorflag); - void meam_setup_done(double *cutmax); - void meam_dens_setup(int atom_nmax, int nall, int n_neigh); + virtual void meam_setup_done(double *cutmax); + virtual void meam_dens_setup(int atom_nmax, int nall, int n_neigh); void meam_dens_init(int i, int ntype, int *type, int *fmap, double **x, int numneigh, int *firstneigh, int numneigh_full, int *firstneigh_full, int fnoffset); void meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, diff --git a/src/MEAM/meam_impl.cpp b/src/MEAM/meam_impl.cpp index 499a2b1520..d0d81cee88 100644 --- a/src/MEAM/meam_impl.cpp +++ b/src/MEAM/meam_impl.cpp @@ -36,6 +36,7 @@ MEAM::MEAM(Memory* mem) maxneigh = 0; scrfcn = dscrfcn = fcpair = nullptr; + copymode = 0; neltypes = 0; for (int i = 0; i < maxelt; i++) { @@ -53,6 +54,8 @@ MEAM::MEAM(Memory* mem) MEAM::~MEAM() { + if (copymode) return; + memory->destroy(this->phirar6); memory->destroy(this->phirar5); memory->destroy(this->phirar4); diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index 7dcb16d3f6..6cbe5c69b9 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -73,7 +73,10 @@ PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) PairMEAM::~PairMEAM() { - delete meam_inst; + if (copymode) return; + + if (meam_inst) + delete meam_inst; if (allocated) { memory->destroy(setflag); diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h index eea3893309..304e7eb41f 100644 --- a/src/MEAM/pair_meam.h +++ b/src/MEAM/pair_meam.h @@ -43,7 +43,7 @@ class PairMEAM : public Pair { void unpack_reverse_comm(int, int *, double *) override; double memory_usage() override; - private: + protected: class MEAM *meam_inst; double cutmax; // max cutoff for all elements int nlibelements; // # of library elements diff --git a/src/ML-SNAP/compute_grid.cpp b/src/ML-SNAP/compute_grid.cpp new file mode 100644 index 0000000000..7a5ffe1e24 --- /dev/null +++ b/src/ML-SNAP/compute_grid.cpp @@ -0,0 +1,242 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_grid.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeGrid::ComputeGrid(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), grid(nullptr), gridall(nullptr), gridlocal(nullptr) +{ + if (narg < 6) error->all(FLERR, "Illegal compute grid command"); + + array_flag = 1; + size_array_cols = 0; + size_array_rows = 0; + extarray = 0; + + int iarg0 = 3; + int iarg = iarg0; + if (strcmp(arg[iarg], "grid") == 0) { + if (iarg + 4 > narg) error->all(FLERR, "Illegal compute grid command"); + nx = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + ny = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); + nz = utils::inumeric(FLERR, arg[iarg + 3], false, lmp); + if (nx <= 0 || ny <= 0 || nz <= 0) error->all(FLERR, "All grid dimensions must be positive"); + iarg += 4; + } else + error->all(FLERR, "Illegal compute grid command"); + + nargbase = iarg - iarg0; + + size_array_rows = nx * ny * nz; + size_array_cols_base = 3; + gridlocal_allocated = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeGrid::~ComputeGrid() +{ + deallocate(); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeGrid::setup() +{ + deallocate(); + set_grid_global(); + set_grid_local(); + allocate(); +} + +/* ---------------------------------------------------------------------- + convert global array index to box coords +------------------------------------------------------------------------- */ + +void ComputeGrid::grid2x(int igrid, double *x) +{ + int iz = igrid / (nx * ny); + igrid -= iz * (nx * ny); + int iy = igrid / nx; + igrid -= iy * nx; + int ix = igrid; + + x[0] = ix * delx; + x[1] = iy * dely; + x[2] = iz * delz; + + if (triclinic) domain->lamda2x(x, x); +} + +/* ---------------------------------------------------------------------- + copy coords to global array +------------------------------------------------------------------------- */ + +void ComputeGrid::assign_coords_all() +{ + double x[3]; + for (int igrid = 0; igrid < size_array_rows; igrid++) { + grid2x(igrid, x); + gridall[igrid][0] = x[0]; + gridall[igrid][1] = x[1]; + gridall[igrid][2] = x[2]; + } +} + +/* ---------------------------------------------------------------------- + create arrays +------------------------------------------------------------------------- */ + +void ComputeGrid::allocate() +{ + // allocate arrays + + memory->create(grid, size_array_rows, size_array_cols, "grid:grid"); + memory->create(gridall, size_array_rows, size_array_cols, "grid:gridall"); + if (nxlo <= nxhi && nylo <= nyhi && nzlo <= nzhi) { + gridlocal_allocated = 1; + memory->create4d_offset(gridlocal, size_array_cols, nzlo, nzhi, nylo, nyhi, nxlo, nxhi, + "grid:gridlocal"); + } + array = gridall; +} + +/* ---------------------------------------------------------------------- + free arrays +------------------------------------------------------------------------- */ + +void ComputeGrid::deallocate() +{ + memory->destroy(grid); + memory->destroy(gridall); + if (gridlocal_allocated) { + gridlocal_allocated = 0; + memory->destroy4d_offset(gridlocal, nzlo, nylo, nxlo); + } + array = nullptr; +} + +/* ---------------------------------------------------------------------- + set global grid +------------------------------------------------------------------------- */ + +void ComputeGrid::set_grid_global() +{ + // calculate grid layout + + triclinic = domain->triclinic; + + if (triclinic == 0) { + prd = domain->prd; + boxlo = domain->boxlo; + sublo = domain->sublo; + subhi = domain->subhi; + } else { + prd = domain->prd_lamda; + boxlo = domain->boxlo_lamda; + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } + + double xprd = prd[0]; + double yprd = prd[1]; + double zprd = prd[2]; + + delxinv = nx / xprd; + delyinv = ny / yprd; + delzinv = nz / zprd; + + delx = 1.0 / delxinv; + dely = 1.0 / delyinv; + delz = 1.0 / delzinv; +} + +/* ---------------------------------------------------------------------- + set local subset of grid that I own + n xyz lo/hi = 3d brick that I own (inclusive) +------------------------------------------------------------------------- */ + +void ComputeGrid::set_grid_local() +{ + // nx,ny,nz = extent of global grid + // indices into the global grid range from 0 to N-1 in each dim + // if grid point is inside my sub-domain I own it, + // this includes sub-domain lo boundary but excludes hi boundary + // ixyz lo/hi = inclusive lo/hi bounds of global grid sub-brick I own + // if proc owns no grid cells in a dim, then ilo > ihi + // if 2 procs share a boundary a grid point is exactly on, + // the 2 equality if tests insure a consistent decision + // as to which proc owns it + + double xfraclo, xfrachi, yfraclo, yfrachi, zfraclo, zfrachi; + + if (comm->layout != Comm::LAYOUT_TILED) { + xfraclo = comm->xsplit[comm->myloc[0]]; + xfrachi = comm->xsplit[comm->myloc[0] + 1]; + yfraclo = comm->ysplit[comm->myloc[1]]; + yfrachi = comm->ysplit[comm->myloc[1] + 1]; + zfraclo = comm->zsplit[comm->myloc[2]]; + zfrachi = comm->zsplit[comm->myloc[2] + 1]; + } else { + xfraclo = comm->mysplit[0][0]; + xfrachi = comm->mysplit[0][1]; + yfraclo = comm->mysplit[1][0]; + yfrachi = comm->mysplit[1][1]; + zfraclo = comm->mysplit[2][0]; + zfrachi = comm->mysplit[2][1]; + } + + nxlo = static_cast(xfraclo * nx); + if (1.0 * nxlo != xfraclo * nx) nxlo++; + nxhi = static_cast(xfrachi * nx); + if (1.0 * nxhi == xfrachi * nx) nxhi--; + + nylo = static_cast(yfraclo * ny); + if (1.0 * nylo != yfraclo * ny) nylo++; + nyhi = static_cast(yfrachi * ny); + if (1.0 * nyhi == yfrachi * ny) nyhi--; + + nzlo = static_cast(zfraclo * nz); + if (1.0 * nzlo != zfraclo * nz) nzlo++; + nzhi = static_cast(zfrachi * nz); + if (1.0 * nzhi == zfrachi * nz) nzhi--; + + ngridlocal = (nxhi - nxlo + 1) * (nyhi - nylo + 1) * (nzhi - nzlo + 1); +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double ComputeGrid::memory_usage() +{ + double nbytes = size_array_rows * size_array_cols * sizeof(double); // grid + nbytes += size_array_rows * size_array_cols * sizeof(double); // gridall + nbytes += size_array_cols * ngridlocal * sizeof(double); // gridlocal + return nbytes; +} diff --git a/src/ML-SNAP/compute_grid.h b/src/ML-SNAP/compute_grid.h new file mode 100644 index 0000000000..84b3bc4e98 --- /dev/null +++ b/src/ML-SNAP/compute_grid.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_COMPUTE_GRID_H +#define LMP_COMPUTE_GRID_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeGrid : public Compute { + public: + ComputeGrid(class LAMMPS *, int, char **); + ~ComputeGrid() override; + void setup() override; + void compute_array() override = 0; + + double memory_usage() override; + + protected: + int nx, ny, nz; // global grid dimensions + int nxlo, nxhi, nylo, nyhi, nzlo, nzhi; // local grid bounds, inclusive + int ngridlocal; // number of local grid points + int nvalues; // number of values per grid point + double **grid; // global grid + double **gridall; // global grid summed over procs + double ****gridlocal; // local grid + int triclinic; // triclinic flag + double *boxlo, *prd; // box info (units real/ortho or reduced/tri) + double *sublo, *subhi; // subdomain info (units real/ortho or reduced/tri) + double delxinv, delyinv, delzinv; // inverse grid spacing + double delx, dely, delz; // grid spacing + int nargbase; // number of base class args + double cutmax; // largest cutoff distance + int size_array_cols_base; // number of columns used for coords, etc. + int gridlocal_allocated; // shows if gridlocal allocated + + void allocate(); // create arrays + void deallocate(); // free arrays + void grid2x(int, double *); // convert grid point to coord + void assign_coords_all(); // assign coords for global grid + void set_grid_global(); // set global grid + void set_grid_local(); // set bounds for local grid +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-SNAP/compute_grid_local.cpp b/src/ML-SNAP/compute_grid_local.cpp new file mode 100644 index 0000000000..48714962ac --- /dev/null +++ b/src/ML-SNAP/compute_grid_local.cpp @@ -0,0 +1,270 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_grid_local.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include + +// For the subdomain test below; grid-points and subdomain boundaries +// sometimes differ by minimal amounts (in the order of 2e-17). +static constexpr double EPSILON = 1.0e-10; + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeGridLocal::ComputeGridLocal(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), alocal(nullptr) +{ + if (narg < 6) error->all(FLERR, "Illegal compute grid/local command"); + + local_flag = 1; + size_local_cols = 0; + size_local_rows = 0; + extarray = 0; + + int iarg0 = 3; + int iarg = iarg0; + if (strcmp(arg[iarg], "grid") == 0) { + if (iarg + 4 > narg) error->all(FLERR, "Illegal compute grid/local command"); + nx = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + ny = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); + nz = utils::inumeric(FLERR, arg[iarg + 3], false, lmp); + if (nx <= 0 || ny <= 0 || nz <= 0) + error->all(FLERR, "All grid/local dimensions must be positive"); + iarg += 4; + } else + error->all(FLERR, "Illegal compute grid/local command"); + + nargbase = iarg - iarg0; + + size_local_cols_base = 6; + gridlocal_allocated = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeGridLocal::~ComputeGridLocal() +{ + deallocate(); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeGridLocal::setup() +{ + deallocate(); + set_grid_global(); + set_grid_local(); + allocate(); + assign_coords(); +} + +/* ---------------------------------------------------------------------- + convert global array indexes to box coords +------------------------------------------------------------------------- */ + +void ComputeGridLocal::grid2x(int ix, int iy, int iz, double *x) +{ + x[0] = ix * delx; + x[1] = iy * dely; + x[2] = iz * delz; + + if (triclinic) domain->lamda2x(x, x); +} + +/* ---------------------------------------------------------------------- + convert global array indexes to lamda coords; for orthorombic + cells defaults to grid2x. +------------------------------------------------------------------------- */ + +void ComputeGridLocal::grid2lamda(int ix, int iy, int iz, double *x) +{ + x[0] = ix * delx; + x[1] = iy * dely; + x[2] = iz * delz; +} + +/* ---------------------------------------------------------------------- + create arrays +------------------------------------------------------------------------- */ + +void ComputeGridLocal::allocate() +{ + if (nxlo <= nxhi && nylo <= nyhi && nzlo <= nzhi) { + gridlocal_allocated = 1; + memory->create(alocal, size_local_rows, size_local_cols, "compute/grid/local:alocal"); + array_local = alocal; + } +} + +/* ---------------------------------------------------------------------- + free arrays +------------------------------------------------------------------------- */ + +void ComputeGridLocal::deallocate() +{ + if (gridlocal_allocated) { + gridlocal_allocated = 0; + memory->destroy(alocal); + } + array_local = nullptr; +} + +/* ---------------------------------------------------------------------- + set global grid +------------------------------------------------------------------------- */ + +void ComputeGridLocal::set_grid_global() +{ + // calculate grid layout + + triclinic = domain->triclinic; + + if (triclinic == 0) { + prd = domain->prd; + boxlo = domain->boxlo; + sublo = domain->sublo; + subhi = domain->subhi; + } else { + prd = domain->prd_lamda; + boxlo = domain->boxlo_lamda; + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } + + double xprd = prd[0]; + double yprd = prd[1]; + double zprd = prd[2]; + + delxinv = nx / xprd; + delyinv = ny / yprd; + delzinv = nz / zprd; + + delx = 1.0 / delxinv; + dely = 1.0 / delyinv; + delz = 1.0 / delzinv; +} + +/* ---------------------------------------------------------------------- + set local subset of grid that I own + n xyz lo/hi = 3d brick that I own (inclusive) +------------------------------------------------------------------------- */ + +void ComputeGridLocal::set_grid_local() +{ + // nx,ny,nz = extent of global grid + // indices into the global grid range from 0 to N-1 in each dim + // if grid point is inside my sub-domain I own it, + // this includes sub-domain lo boundary but excludes hi boundary + // ixyz lo/hi = inclusive lo/hi bounds of global grid sub-brick I own + // if proc owns no grid cells in a dim, then ilo > ihi + // if 2 procs share a boundary a grid point is exactly on, + // the 2 equality if tests insure a consistent decision + // as to which proc owns it + + double xfraclo, xfrachi, yfraclo, yfrachi, zfraclo, zfrachi; + + if (comm->layout != Comm::LAYOUT_TILED) { + xfraclo = comm->xsplit[comm->myloc[0]]; + xfrachi = comm->xsplit[comm->myloc[0] + 1]; + yfraclo = comm->ysplit[comm->myloc[1]]; + yfrachi = comm->ysplit[comm->myloc[1] + 1]; + zfraclo = comm->zsplit[comm->myloc[2]]; + zfrachi = comm->zsplit[comm->myloc[2] + 1]; + } else { + xfraclo = comm->mysplit[0][0]; + xfrachi = comm->mysplit[0][1]; + yfraclo = comm->mysplit[1][0]; + yfrachi = comm->mysplit[1][1]; + zfraclo = comm->mysplit[2][0]; + zfrachi = comm->mysplit[2][1]; + } + + nxlo = static_cast(xfraclo * nx); + if (1.0 * nxlo != xfraclo * nx) nxlo++; + nxhi = static_cast(xfrachi * nx); + if (1.0 * nxhi == xfrachi * nx) nxhi--; + + nylo = static_cast(yfraclo * ny); + if (1.0 * nylo != yfraclo * ny) nylo++; + nyhi = static_cast(yfrachi * ny); + if (1.0 * nyhi == yfrachi * ny) nyhi--; + + nzlo = static_cast(zfraclo * nz); + if (1.0 * nzlo != zfraclo * nz) nzlo++; + nzhi = static_cast(zfrachi * nz); + if (1.0 * nzhi == zfrachi * nz) nzhi--; + + size_local_rows = (nxhi - nxlo + 1) * (nyhi - nylo + 1) * (nzhi - nzlo + 1); +} + +/* ---------------------------------------------------------------------- + copy coords to local array +------------------------------------------------------------------------- */ + +void ComputeGridLocal::assign_coords() +{ + int igrid = 0; + for (int iz = nzlo; iz <= nzhi; iz++) + for (int iy = nylo; iy <= nyhi; iy++) + for (int ix = nxlo; ix <= nxhi; ix++) { + alocal[igrid][0] = ix; + alocal[igrid][1] = iy; + alocal[igrid][2] = iz; + double xgrid[3]; + + // for triclinic: create gridpoint in lamda coordinates and transform after check. + // for orthorombic: create gridpoint in box coordinates. + + if (triclinic) + grid2lamda(ix, iy, iz, xgrid); + else + grid2x(ix, iy, iz, xgrid); + + // ensure gridpoint is not strictly outside subdomain + + if ((sublo[0] - xgrid[0]) > EPSILON || (xgrid[0] - subhi[0]) > EPSILON || + (sublo[1] - xgrid[1]) > EPSILON || (xgrid[1] - subhi[1]) > EPSILON || + (sublo[2] - xgrid[2]) > EPSILON || (xgrid[2] - subhi[2]) > EPSILON) + error->one(FLERR, "Invalid gridpoint position in compute grid/local"); + + // convert lamda to x, y, z, after sudomain check + + if (triclinic) domain->lamda2x(xgrid, xgrid); + + alocal[igrid][3] = xgrid[0]; + alocal[igrid][4] = xgrid[1]; + alocal[igrid][5] = xgrid[2]; + igrid++; + } +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double ComputeGridLocal::memory_usage() +{ + int nbytes = size_local_rows * size_local_cols * sizeof(double); // gridlocal + return nbytes; +} diff --git a/src/ML-SNAP/compute_grid_local.h b/src/ML-SNAP/compute_grid_local.h new file mode 100644 index 0000000000..5bc6f2082a --- /dev/null +++ b/src/ML-SNAP/compute_grid_local.h @@ -0,0 +1,56 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_COMPUTE_GRID_LOCAL_H +#define LMP_COMPUTE_GRID_LOCAL_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeGridLocal : public Compute { + public: + ComputeGridLocal(class LAMMPS *, int, char **); + ~ComputeGridLocal() override; + void setup() override; + void compute_local() override = 0; + + double memory_usage() override; + + protected: + int nx, ny, nz; // global grid dimensions + int nxlo, nxhi, nylo, nyhi, nzlo, nzhi; // local grid bounds, inclusive + int nvalues; // number of values per grid point + double **alocal; // pointer to Compute::array_local + int triclinic; // triclinic flag + double *boxlo, *prd; // box info (units real/ortho or reduced/tri) + double *sublo, *subhi; // subdomain info (units real/ortho or reduced/tri) + double delxinv, delyinv, delzinv; // inverse grid spacing + double delx, dely, delz; // grid spacing + int nargbase; // number of base class args + double cutmax; // largest cutoff distance + int size_local_cols_base; // number of columns used for coords, etc. + int gridlocal_allocated; // shows if gridlocal allocated + + void allocate(); // create arrays + void deallocate(); // free arrays + void grid2x(int, int, int, double *); // convert global indices to coordinates + void grid2lamda(int, int, int, double *); // convert global indices to lamda coordinates + void set_grid_global(); // set global grid + void set_grid_local(); // set bounds for local grid + void assign_coords(); // assign coords for grid +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp index 5f24ebeaa6..1d2190d50d 100644 --- a/src/ML-SNAP/compute_sna_atom.cpp +++ b/src/ML-SNAP/compute_sna_atom.cpp @@ -35,20 +35,21 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { - double rmin0, rfac0; + // begin code common to all SNAP computes + + double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; int ntypes = atom->ntypes; - int nargmin = 6+2*ntypes; + int nargmin = 6 + 2 * ntypes; - if (narg < nargmin) error->all(FLERR,"Illegal compute sna/atom command"); + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); // default values rmin0 = 0.0; switchflag = 1; bzeroflag = 1; - bnormflag = 0; quadraticflag = 0; chemflag = 0; bnormflag = 0; @@ -56,32 +57,34 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : switchinnerflag = 0; nelements = 1; - // offset by 1 to match up with types + // process required arguments - memory->create(radelem,ntypes+1,"sna/atom:radelem"); - memory->create(wjelem,ntypes+1,"sna/atom:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); - rcutfac = atof(arg[3]); - rfac0 = atof(arg[4]); - twojmax = atoi(arg[5]); + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); for (int i = 0; i < ntypes; i++) - radelem[i+1] = atof(arg[6+i]); + radelem[i + 1] = + utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i+1] = atof(arg[6+ntypes+i]); + wjelem[i + 1] = + utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); // construct cutsq double cut; cutmax = 0.0; - memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { - cut = 2.0*radelem[i]*rcutfac; + cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; - cutsq[i][i] = cut*cut; - for (int j = i+1; j <= ntypes; j++) { - cut = (radelem[i]+radelem[j])*rcutfac; - cutsq[i][j] = cutsq[j][i] = cut*cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; } } @@ -95,89 +98,87 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = nargmin; while (iarg < narg) { - if (strcmp(arg[iarg],"rmin0") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - rmin0 = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - switchflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"bzeroflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - bzeroflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"quadraticflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - quadraticflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"chem") == 0) { - if (iarg+2+ntypes > narg) - error->all(FLERR,"Illegal compute sna/atom command"); + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); chemflag = 1; - memory->create(map,ntypes+1,"compute_sna_atom:map"); - nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); for (int i = 0; i < ntypes; i++) { - int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp); - if (jelem < 0 || jelem >= nelements) - error->all(FLERR,"Illegal compute sna/atom command"); - map[i+1] = jelem; + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; } - iarg += 2+ntypes; - } else if (strcmp(arg[iarg],"bnormflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - bnormflag = atoi(arg[iarg+1]); + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"wselfallflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - wselfallflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - switchinnerflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchinnerflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"sinner") == 0) { + } else if (strcmp(arg[iarg], "sinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - memory->create(sinnerelem,ntypes+1,"sna/atom:sinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); for (int i = 0; i < ntypes; i++) - sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); sinnerflag = 1; iarg += ntypes; - } else if (strcmp(arg[iarg],"dinner") == 0) { + } else if (strcmp(arg[iarg], "dinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute sna/atom command"); - memory->create(dinnerelem,ntypes+1,"sna/atom:dinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); for (int i = 0; i < ntypes; i++) - dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); dinnerflag = 1; iarg += ntypes; - } else error->all(FLERR,"Illegal compute sna/atom command"); + } else + error->all(FLERR, "Illegal compute {} command", style); } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR,"Illegal compute sna/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR,"Illegal compute sna/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); - snaptr = new SNA(lmp, rfac0, twojmax, - rmin0, switchflag, bzeroflag, - chemflag, bnormflag, wselfallflag, - nelements, switchinnerflag); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, + wselfallflag, nelements, switchinnerflag); ncoeff = snaptr->ncoeff; - size_peratom_cols = ncoeff; - if (quadraticflag) size_peratom_cols += (ncoeff*(ncoeff+1))/2; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + + size_peratom_cols = nvalues; peratom_flag = 1; nmax = 0; diff --git a/src/ML-SNAP/compute_sna_atom.h b/src/ML-SNAP/compute_sna_atom.h index 7d1ebfa2f8..059062670f 100644 --- a/src/ML-SNAP/compute_sna_atom.h +++ b/src/ML-SNAP/compute_sna_atom.h @@ -50,6 +50,7 @@ class ComputeSNAAtom : public Compute { class SNA *snaptr; double cutmax; int quadraticflag; + int nvalues; }; } // namespace LAMMPS_NS diff --git a/src/ML-SNAP/compute_sna_grid.cpp b/src/ML-SNAP/compute_sna_grid.cpp new file mode 100644 index 0000000000..497390f99a --- /dev/null +++ b/src/ML-SNAP/compute_sna_grid.cpp @@ -0,0 +1,320 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_sna_grid.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "sna.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) : + ComputeGrid(lmp, narg, arg), cutsq(nullptr), radelem(nullptr), wjelem(nullptr) +{ + // skip over arguments used by base class + // so that argument positions are identical to + // regular per-atom compute + + arg += nargbase; + narg -= nargbase; + + // begin code common to all SNAP computes + + double rfac0, rmin0; + int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; + + int ntypes = atom->ntypes; + int nargmin = 6 + 2 * ntypes; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + + // default values + + rmin0 = 0.0; + switchflag = 1; + bzeroflag = 1; + quadraticflag = 0; + chemflag = 0; + bnormflag = 0; + wselfallflag = 0; + switchinnerflag = 0; + nelements = 1; + + // process required arguments + + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); + + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); + + for (int i = 0; i < ntypes; i++) radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp); + for (int i = 0; i < ntypes; i++) + wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); + + // construct cutsq + + double cut; + cutmax = 0.0; + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); + for (int i = 1; i <= ntypes; i++) { + cut = 2.0 * radelem[i] * rcutfac; + if (cut > cutmax) cutmax = cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; + } + } + + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + + // process optional args + + int iarg = nargmin; + + while (iarg < narg) { + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + chemflag = 1; + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + for (int i = 0; i < ntypes; i++) { + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; + } + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "switchinnerflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "sinner") == 0) { + iarg++; + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); + for (int i = 0; i < ntypes; i++) + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); + sinnerflag = 1; + iarg += ntypes; + } else if (strcmp(arg[iarg], "dinner") == 0) { + iarg++; + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); + for (int i = 0; i < ntypes; i++) + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); + dinnerflag = 1; + iarg += ntypes; + } else + error->all(FLERR, "Illegal compute {} command", style); + } + + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, + wselfallflag, nelements, switchinnerflag); + + ncoeff = snaptr->ncoeff; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + + size_array_cols = size_array_cols_base + nvalues; + array_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSNAGrid::~ComputeSNAGrid() +{ + memory->destroy(radelem); + memory->destroy(wjelem); + memory->destroy(cutsq); + delete snaptr; + + if (chemflag) memory->destroy(map); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSNAGrid::init() +{ + if ((modify->get_compute_by_style("^sna/grid$").size() > 1) && (comm->me == 0)) + error->warning(FLERR, "More than one instance of compute sna/grid"); + snaptr->init(); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSNAGrid::compute_array() +{ + invoked_array = update->ntimestep; + + // compute sna for each gridpoint + + double **const x = atom->x; + const int *const mask = atom->mask; + int *const type = atom->type; + const int ntotal = atom->nlocal + atom->nghost; + + // insure rij, inside, and typej are of size jnum + + snaptr->grow_rij(ntotal); + + for (int iz = nzlo; iz <= nzhi; iz++) + for (int iy = nylo; iy <= nyhi; iy++) + for (int ix = nxlo; ix <= nxhi; ix++) { + double xgrid[3]; + const int igrid = iz * (nx * ny) + iy * nx + ix; + grid2x(igrid, xgrid); + const double xtmp = xgrid[0]; + const double ytmp = xgrid[1]; + const double ztmp = xgrid[2]; + + // currently, all grid points are type 1 + // not clear what a better choice would be + + const int itype = 1; + int ielem = 0; + if (chemflag) ielem = map[itype]; + + // rij[][3] = displacements between atom I and those neighbors + // inside = indices of neighbors of I within cutoff + // typej = types of neighbors of I within cutoff + + int ninside = 0; + for (int j = 0; j < ntotal; j++) { + + // check that j is in compute group + + if (!(mask[j] & groupbit)) continue; + + const double delx = xtmp - x[j][0]; + const double dely = ytmp - x[j][1]; + const double delz = ztmp - x[j][2]; + const double rsq = delx * delx + dely * dely + delz * delz; + int jtype = type[j]; + int jelem = 0; + if (chemflag) jelem = map[jtype]; + + if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) { + snaptr->rij[ninside][0] = delx; + snaptr->rij[ninside][1] = dely; + snaptr->rij[ninside][2] = delz; + snaptr->inside[ninside] = j; + snaptr->wj[ninside] = wjelem[jtype]; + snaptr->rcutij[ninside] = 2.0 * radelem[jtype] * rcutfac; + if (switchinnerflag) { + snaptr->sinnerij[ninside] = sinnerelem[jelem]; + snaptr->dinnerij[ninside] = dinnerelem[jelem]; + } + if (chemflag) snaptr->element[ninside] = jelem; + ninside++; + } + } + + snaptr->compute_ui(ninside, ielem); + snaptr->compute_zi(); + snaptr->compute_bi(ielem); + + // linear contributions + + for (int icoeff = 0; icoeff < ncoeff; icoeff++) + gridlocal[size_array_cols_base + icoeff][iz][iy][ix] = snaptr->blist[icoeff]; + + // quadratic contributions + + if (quadraticflag) { + int ncount = ncoeff; + for (int icoeff = 0; icoeff < ncoeff; icoeff++) { + double bveci = snaptr->blist[icoeff]; + gridlocal[size_array_cols_base + ncount++][iz][iy][ix] = 0.5 * bveci * bveci; + for (int jcoeff = icoeff + 1; jcoeff < ncoeff; jcoeff++) + gridlocal[size_array_cols_base + ncount++][iz][iy][ix] = + bveci * snaptr->blist[jcoeff]; + } + } + } + + memset(&grid[0][0], 0, size_array_rows * size_array_cols * sizeof(double)); + + for (int iz = nzlo; iz <= nzhi; iz++) + for (int iy = nylo; iy <= nyhi; iy++) + for (int ix = nxlo; ix <= nxhi; ix++) { + const int igrid = iz * (nx * ny) + iy * nx + ix; + for (int j = 0; j < nvalues; j++) + grid[igrid][size_array_cols_base + j] = gridlocal[size_array_cols_base + j][iz][iy][ix]; + } + MPI_Allreduce(&grid[0][0], &gridall[0][0], size_array_rows * size_array_cols, MPI_DOUBLE, MPI_SUM, + world); + assign_coords_all(); +} + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double ComputeSNAGrid::memory_usage() +{ + double nbytes = snaptr->memory_usage(); // SNA object + int n = atom->ntypes + 1; + nbytes += (double) n * sizeof(int); // map + + return nbytes; +} diff --git a/src/ML-SNAP/compute_sna_grid.h b/src/ML-SNAP/compute_sna_grid.h new file mode 100644 index 0000000000..839003dc2e --- /dev/null +++ b/src/ML-SNAP/compute_sna_grid.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(sna/grid,ComputeSNAGrid); +// clang-format on +#else + +#ifndef LMP_COMPUTE_SNA_GRID_H +#define LMP_COMPUTE_SNA_GRID_H + +#include "compute_grid.h" + +namespace LAMMPS_NS { + +class ComputeSNAGrid : public ComputeGrid { + public: + ComputeSNAGrid(class LAMMPS *, int, char **); + ~ComputeSNAGrid() override; + void init() override; + void compute_array() override; + double memory_usage() override; + + private: + int ncoeff; + double **cutsq; + double rcutfac; + double *radelem; + double *wjelem; + int *map; // map types to [0,nelements) + int nelements, chemflag; + int switchinnerflag; + double *sinnerelem; + double *dinnerelem; + class SNA *snaptr; + double cutmax; + int quadraticflag; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-SNAP/compute_sna_grid_local.cpp b/src/ML-SNAP/compute_sna_grid_local.cpp new file mode 100644 index 0000000000..76fe03a03b --- /dev/null +++ b/src/ML-SNAP/compute_sna_grid_local.cpp @@ -0,0 +1,306 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_sna_grid_local.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "sna.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) : + ComputeGridLocal(lmp, narg, arg), cutsq(nullptr), radelem(nullptr), wjelem(nullptr) +{ + // skip over arguments used by base class + // so that argument positions are identical to + // regular per-atom compute + + arg += nargbase; + narg -= nargbase; + + // begin code common to all SNAP computes + + double rfac0, rmin0; + int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; + + int ntypes = atom->ntypes; + int nargmin = 6 + 2 * ntypes; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + + // default values + + rmin0 = 0.0; + switchflag = 1; + bzeroflag = 1; + quadraticflag = 0; + chemflag = 0; + bnormflag = 0; + wselfallflag = 0; + switchinnerflag = 0; + nelements = 1; + + // process required arguments + + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); + + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); + + for (int i = 0; i < ntypes; i++) radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp); + for (int i = 0; i < ntypes; i++) + wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); + + // construct cutsq + + double cut; + cutmax = 0.0; + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); + for (int i = 1; i <= ntypes; i++) { + cut = 2.0 * radelem[i] * rcutfac; + if (cut > cutmax) cutmax = cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; + } + } + + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + + // process optional args + + int iarg = nargmin; + + while (iarg < narg) { + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + chemflag = 1; + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + for (int i = 0; i < ntypes; i++) { + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; + } + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "switchinnerflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "sinner") == 0) { + iarg++; + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); + for (int i = 0; i < ntypes; i++) + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); + sinnerflag = 1; + iarg += ntypes; + } else if (strcmp(arg[iarg], "dinner") == 0) { + iarg++; + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); + for (int i = 0; i < ntypes; i++) + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); + dinnerflag = 1; + iarg += ntypes; + } else + error->all(FLERR, "Illegal compute {} command", style); + } + + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, + wselfallflag, nelements, switchinnerflag); + + ncoeff = snaptr->ncoeff; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + + size_local_cols = size_local_cols_base + nvalues; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSNAGridLocal::~ComputeSNAGridLocal() +{ + memory->destroy(radelem); + memory->destroy(wjelem); + memory->destroy(cutsq); + delete snaptr; + + if (chemflag) memory->destroy(map); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSNAGridLocal::init() +{ + if ((modify->get_compute_by_style("^sna/grid/local$").size() > 1) && (comm->me == 0)) + error->warning(FLERR, "More than one instance of compute sna/grid/local"); + snaptr->init(); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSNAGridLocal::compute_local() +{ + invoked_local = update->ntimestep; + + // compute sna for each gridpoint + + double **const x = atom->x; + const int *const mask = atom->mask; + int *const type = atom->type; + const int ntotal = atom->nlocal + atom->nghost; + + // insure rij, inside, and typej are of size jnum + + snaptr->grow_rij(ntotal); + + int igrid = 0; + for (int iz = nzlo; iz <= nzhi; iz++) + for (int iy = nylo; iy <= nyhi; iy++) + for (int ix = nxlo; ix <= nxhi; ix++) { + double xgrid[3]; + grid2x(ix, iy, iz, xgrid); + const double xtmp = xgrid[0]; + const double ytmp = xgrid[1]; + const double ztmp = xgrid[2]; + + // currently, all grid points are type 1 + // not clear what a better choice would be + + const int itype = 1; + int ielem = 0; + if (chemflag) ielem = map[itype]; + + // rij[][3] = displacements between atom I and those neighbors + // inside = indices of neighbors of I within cutoff + // typej = types of neighbors of I within cutoff + + int ninside = 0; + for (int j = 0; j < ntotal; j++) { + + // check that j is in compute group + + if (!(mask[j] & groupbit)) continue; + + const double delx = xtmp - x[j][0]; + const double dely = ytmp - x[j][1]; + const double delz = ztmp - x[j][2]; + const double rsq = delx * delx + dely * dely + delz * delz; + int jtype = type[j]; + int jelem = 0; + if (chemflag) jelem = map[jtype]; + if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) { + snaptr->rij[ninside][0] = delx; + snaptr->rij[ninside][1] = dely; + snaptr->rij[ninside][2] = delz; + snaptr->inside[ninside] = j; + snaptr->wj[ninside] = wjelem[jtype]; + snaptr->rcutij[ninside] = 2.0 * radelem[jtype] * rcutfac; + if (switchinnerflag) { + snaptr->sinnerij[ninside] = sinnerelem[jelem]; + snaptr->dinnerij[ninside] = dinnerelem[jelem]; + } + if (chemflag) + snaptr->element[ninside] = jelem; // element index for multi-element snap + ninside++; + } + } + + snaptr->compute_ui(ninside, ielem); + snaptr->compute_zi(); + snaptr->compute_bi(ielem); + + // linear contributions + + for (int icoeff = 0; icoeff < ncoeff; icoeff++) + alocal[igrid][size_local_cols_base + icoeff] = snaptr->blist[icoeff]; + + // quadratic contributions + + if (quadraticflag) { + int ncount = ncoeff; + for (int icoeff = 0; icoeff < ncoeff; icoeff++) { + double bveci = snaptr->blist[icoeff]; + alocal[igrid][size_local_cols_base + ncount++] = 0.5 * bveci * bveci; + for (int jcoeff = icoeff + 1; jcoeff < ncoeff; jcoeff++) + alocal[igrid][size_local_cols_base + ncount++] = bveci * snaptr->blist[jcoeff]; + } + } + igrid++; + } +} + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double ComputeSNAGridLocal::memory_usage() +{ + double nbytes = snaptr->memory_usage(); // SNA object + int n = atom->ntypes + 1; + nbytes += (double) n * sizeof(int); // map + + return nbytes; +} diff --git a/src/ML-SNAP/compute_sna_grid_local.h b/src/ML-SNAP/compute_sna_grid_local.h new file mode 100644 index 0000000000..60f93b92b0 --- /dev/null +++ b/src/ML-SNAP/compute_sna_grid_local.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(sna/grid/local,ComputeSNAGridLocal); +// clang-format on +#else + +#ifndef LMP_COMPUTE_SNA_GRID_LOCAL_H +#define LMP_COMPUTE_SNA_GRID_LOCAL_H + +#include "compute_grid_local.h" + +namespace LAMMPS_NS { + +class ComputeSNAGridLocal : public ComputeGridLocal { + public: + ComputeSNAGridLocal(class LAMMPS *, int, char **); + ~ComputeSNAGridLocal() override; + void init() override; + void compute_local() override; + double memory_usage() override; + + private: + int ncoeff; + double **cutsq; + double rcutfac; + double *radelem; + double *wjelem; + int *map; // map types to [0,nelements) + int nelements, chemflag; + int switchinnerflag; + double *sinnerelem; + double *dinnerelem; + class SNA *snaptr; + double cutmax; + int quadraticflag; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp index 838d8a85c9..12839629a9 100644 --- a/src/ML-SNAP/compute_snad_atom.cpp +++ b/src/ML-SNAP/compute_snad_atom.cpp @@ -34,20 +34,22 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snad(nullptr), radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { + + // begin code common to all SNAP computes + double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; int ntypes = atom->ntypes; - int nargmin = 6+2*ntypes; + int nargmin = 6 + 2 * ntypes; - if (narg < nargmin) error->all(FLERR,"Illegal compute snad/atom command"); + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); // default values rmin0 = 0.0; switchflag = 1; bzeroflag = 1; - bnormflag = 0; quadraticflag = 0; chemflag = 0; bnormflag = 0; @@ -57,28 +59,32 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem,ntypes+1,"snad/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem,ntypes+1,"snad/atom:wjelem"); - rcutfac = atof(arg[3]); - rfac0 = atof(arg[4]); - twojmax = atoi(arg[5]); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); + + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); + for (int i = 0; i < ntypes; i++) - radelem[i+1] = atof(arg[6+i]); + radelem[i + 1] = + utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i+1] = atof(arg[6+ntypes+i]); + wjelem[i + 1] = + utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); // construct cutsq double cut; cutmax = 0.0; - memory->create(cutsq,ntypes+1,ntypes+1,"snad/atom:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { - cut = 2.0*radelem[i]*rcutfac; + cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; - cutsq[i][i] = cut*cut; - for (int j = i+1; j <= ntypes; j++) { - cut = (radelem[i]+radelem[j])*rcutfac; - cutsq[i][j] = cutsq[j][i] = cut*cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; } } @@ -92,93 +98,89 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = nargmin; while (iarg < narg) { - if (strcmp(arg[iarg],"rmin0") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - rmin0 = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"bzeroflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - bzeroflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - switchflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"quadraticflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - quadraticflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"chem") == 0) { - if (iarg+2+ntypes > narg) - error->all(FLERR,"Illegal compute snad/atom command"); + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); chemflag = 1; - memory->create(map,ntypes+1,"compute_snad_atom:map"); - nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); for (int i = 0; i < ntypes; i++) { - int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp); - if (jelem < 0 || jelem >= nelements) - error->all(FLERR,"Illegal compute snad/atom command"); - map[i+1] = jelem; + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; } - iarg += 2+ntypes; - } else if (strcmp(arg[iarg],"bnormflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - bnormflag = atoi(arg[iarg+1]); + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"wselfallflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - wselfallflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - switchinnerflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchinnerflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"sinner") == 0) { + } else if (strcmp(arg[iarg], "sinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - memory->create(sinnerelem,ntypes+1,"snad/atom:sinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); for (int i = 0; i < ntypes; i++) - sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); sinnerflag = 1; iarg += ntypes; - } else if (strcmp(arg[iarg],"dinner") == 0) { + } else if (strcmp(arg[iarg], "dinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snad/atom command"); - memory->create(dinnerelem,ntypes+1,"snad/atom:dinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); for (int i = 0; i < ntypes; i++) - dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); dinnerflag = 1; iarg += ntypes; - } else error->all(FLERR,"Illegal compute snad/atom command"); + } else + error->all(FLERR, "Illegal compute {} command", style); } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR,"Illegal compute snad/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR,"Illegal compute snad/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); - - snaptr = new SNA(lmp, rfac0, twojmax, - rmin0, switchflag, bzeroflag, - chemflag, bnormflag, wselfallflag, - nelements, switchinnerflag); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, + wselfallflag, nelements, switchinnerflag); ncoeff = snaptr->ncoeff; - nperdim = ncoeff; - if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; - yoffset = nperdim; - zoffset = 2*nperdim; - size_peratom_cols = 3*nperdim*atom->ntypes; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + + yoffset = nvalues; + zoffset = 2*nvalues; + size_peratom_cols = 3*nvalues*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -289,7 +291,7 @@ void ComputeSNADAtom::compute_peratom() // const int typeoffset = threencoeff*(atom->type[i]-1); // const int quadraticoffset = threencoeff*atom->ntypes + // threencoeffq*(atom->type[i]-1); - const int typeoffset = 3*nperdim*(atom->type[i]-1); + const int typeoffset = 3*nvalues*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum diff --git a/src/ML-SNAP/compute_snad_atom.h b/src/ML-SNAP/compute_snad_atom.h index 0cdb075daf..ac27e10769 100644 --- a/src/ML-SNAP/compute_snad_atom.h +++ b/src/ML-SNAP/compute_snad_atom.h @@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute { private: int nmax; - int ncoeff, nperdim, yoffset, zoffset; + int ncoeff, nvalues, yoffset, zoffset; double **cutsq; class NeighList *list; double **snad; diff --git a/src/ML-SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp index 25c5c488fa..5b935320ee 100644 --- a/src/ML-SNAP/compute_snap.cpp +++ b/src/ML-SNAP/compute_snap.cpp @@ -41,13 +41,15 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : array_flag = 1; extarray = 0; + // begin code common to all SNAP computes + double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; int ntypes = atom->ntypes; - int nargmin = 6+2*ntypes; + int nargmin = 6 + 2 * ntypes; - if (narg < nargmin) error->all(FLERR,"Illegal compute snap command"); + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); // default values @@ -65,28 +67,30 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types - memory->create(wjelem,ntypes+1,"snap:wjelem"); - rcutfac = atof(arg[3]); - rfac0 = atof(arg[4]); - twojmax = atoi(arg[5]); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); + + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); + for (int i = 0; i < ntypes; i++) - radelem[i+1] = atof(arg[6+i]); + radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i+1] = atof(arg[6+ntypes+i]); + wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); // construct cutsq double cut; cutmax = 0.0; - memory->create(cutsq,ntypes+1,ntypes+1,"snap:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { - cut = 2.0*radelem[i]*rcutfac; + cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; - cutsq[i][i] = cut*cut; - for (int j = i+1; j <= ntypes; j++) { - cut = (radelem[i]+radelem[j])*rcutfac; - cutsq[i][j] = cutsq[j][i] = cut*cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; } } @@ -100,53 +104,44 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : int iarg = nargmin; while (iarg < narg) { - if (strcmp(arg[iarg],"rmin0") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - rmin0 = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"bzeroflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - bzeroflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - switchflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"quadraticflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - quadraticflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"chem") == 0) { - if (iarg+2+ntypes > narg) - error->all(FLERR,"Illegal compute snap command"); + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); chemflag = 1; - memory->create(map,ntypes+1,"compute_snap:map"); - nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); for (int i = 0; i < ntypes; i++) { - int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp); - if (jelem < 0 || jelem >= nelements) - error->all(FLERR,"Illegal compute snap command"); - map[i+1] = jelem; + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; } - iarg += 2+ntypes; - } else if (strcmp(arg[iarg],"bnormflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - bnormflag = atoi(arg[iarg+1]); + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"wselfallflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - wselfallflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"bikflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snap command"); - bikflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "bikflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bikflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg],"dgradflag") == 0) { if (iarg+2 > narg) @@ -158,32 +153,37 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal compute snap command"); switchinnerflag = atoi(arg[iarg+1]); iarg += 2; - } else if (strcmp(arg[iarg],"sinner") == 0) { + } else if (strcmp(arg[iarg], "sinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snap command"); - memory->create(sinnerelem,ntypes+1,"snap:sinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); for (int i = 0; i < ntypes; i++) - sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); sinnerflag = 1; iarg += ntypes; - } else if (strcmp(arg[iarg],"dinner") == 0) { + } else if (strcmp(arg[iarg], "dinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snap command"); - memory->create(dinnerelem,ntypes+1,"snap:dinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); for (int i = 0; i < ntypes; i++) - dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); dinnerflag = 1; iarg += ntypes; - } else error->all(FLERR,"Illegal compute snap command"); + } else + error->all(FLERR, "Illegal compute {} command", style); } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR,"Illegal compute snap command: switchinnerflag = 1, missing sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR,"Illegal compute snap command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); if (dgradflag && !bikflag) error->all(FLERR,"Illegal compute snap command: dgradflag=1 requires bikflag=1"); @@ -197,12 +197,15 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : nelements, switchinnerflag); ncoeff = snaptr->ncoeff; - nperdim = ncoeff; - if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + ndims_force = 3; ndims_virial = 6; - yoffset = nperdim; - zoffset = 2 * nperdim; + yoffset = nvalues; + zoffset = 2 * nvalues; natoms = atom->natoms; bik_rows = 1; if (bikflag) bik_rows = natoms; @@ -210,14 +213,14 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : size_array_rows = bik_rows+dgrad_rows + ndims_virial; if (dgradflag){ size_array_rows = bik_rows + 3*natoms*natoms + 1; - size_array_cols = nperdim + 3; + size_array_cols = nvalues + 3; error->warning(FLERR,"dgradflag=1 creates a N^2 array, beware of large systems."); } - else size_array_cols = nperdim*atom->ntypes + 1; + else size_array_cols = nvalues*atom->ntypes + 1; lastcol = size_array_cols-1; ndims_peratom = ndims_force; - size_peratom = ndims_peratom * nperdim * atom->ntypes; + size_peratom = ndims_peratom*nvalues*atom->ntypes; nmax = 0; } @@ -364,8 +367,8 @@ void ComputeSnap::compute_array() const double radi = radelem[itype]; const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset_local = ndims_peratom*nperdim*(itype-1); - const int typeoffset_global = nperdim*(itype-1); + const int typeoffset_local = ndims_peratom*nvalues*(itype-1); + const int typeoffset_global = nvalues*(itype-1); if (dgradflag){ // dBi/dRi tags @@ -573,9 +576,9 @@ void ComputeSnap::compute_array() if (!dgradflag) { for (int itype = 0; itype < atom->ntypes; itype++) { - const int typeoffset_local = ndims_peratom*nperdim*itype; - const int typeoffset_global = nperdim*itype; - for (int icoeff = 0; icoeff < nperdim; icoeff++) { + const int typeoffset_local = ndims_peratom*nvalues*itype; + const int typeoffset_global = nvalues*itype; + for (int icoeff = 0; icoeff < nvalues; icoeff++) { for (int i = 0; i < ntotal; i++) { double *snadi = snap_peratom[i]+typeoffset_local; int iglobal = atom->tag[i]; @@ -675,10 +678,10 @@ void ComputeSnap::dbdotr_compute() int nall = atom->nlocal + atom->nghost; for (int i = 0; i < nall; i++) for (int itype = 0; itype < atom->ntypes; itype++) { - const int typeoffset_local = ndims_peratom*nperdim*itype; - const int typeoffset_global = nperdim*itype; + const int typeoffset_local = ndims_peratom*nvalues*itype; + const int typeoffset_global = nvalues*itype; double *snadi = snap_peratom[i]+typeoffset_local; - for (int icoeff = 0; icoeff < nperdim; icoeff++) { + for (int icoeff = 0; icoeff < nvalues; icoeff++) { double dbdx = snadi[icoeff]; double dbdy = snadi[icoeff+yoffset]; double dbdz = snadi[icoeff+zoffset]; diff --git a/src/ML-SNAP/compute_snap.h b/src/ML-SNAP/compute_snap.h index a89a870fe8..7f7252eaa8 100644 --- a/src/ML-SNAP/compute_snap.h +++ b/src/ML-SNAP/compute_snap.h @@ -35,7 +35,7 @@ class ComputeSnap : public Compute { private: int natoms, nmax, size_peratom, lastcol; - int ncoeff, nperdim, yoffset, zoffset; + int ncoeff, nvalues, yoffset, zoffset; int ndims_peratom, ndims_force, ndims_virial; double **cutsq; class NeighList *list; diff --git a/src/ML-SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp index 0baa4bc110..949dda8e5c 100644 --- a/src/ML-SNAP/compute_snav_atom.cpp +++ b/src/ML-SNAP/compute_snav_atom.cpp @@ -21,6 +21,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "force.h" +#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" @@ -33,20 +34,22 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snav(nullptr), radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { + + // begin code common to all SNAP computes + double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; int ntypes = atom->ntypes; - int nargmin = 6+2*ntypes; + int nargmin = 6 + 2 * ntypes; - if (narg < nargmin) error->all(FLERR,"Illegal compute snav/atom command"); + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); // default values rmin0 = 0.0; switchflag = 1; bzeroflag = 1; - bnormflag = 0; quadraticflag = 0; chemflag = 0; bnormflag = 0; @@ -56,24 +59,32 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem,ntypes+1,"snav/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem,ntypes+1,"snav/atom:wjelem"); - rcutfac = atof(arg[3]); - rfac0 = atof(arg[4]); - twojmax = atoi(arg[5]); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); + + rcutfac = utils::numeric(FLERR, arg[3], false, lmp); + rfac0 = utils::numeric(FLERR, arg[4], false, lmp); + twojmax = utils::inumeric(FLERR, arg[5], false, lmp); + for (int i = 0; i < ntypes; i++) - radelem[i+1] = atof(arg[6+i]); + radelem[i + 1] = + utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i+1] = atof(arg[6+ntypes+i]); + wjelem[i + 1] = + utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); + // construct cutsq + double cut; - memory->create(cutsq,ntypes+1,ntypes+1,"snav/atom:cutsq"); + cutmax = 0.0; + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { - cut = 2.0*radelem[i]*rcutfac; - cutsq[i][i] = cut*cut; - for (int j = i+1; j <= ntypes; j++) { - cut = (radelem[i]+radelem[j])*rcutfac; - cutsq[i][j] = cutsq[j][i] = cut*cut; + cut = 2.0 * radelem[i] * rcutfac; + if (cut > cutmax) cutmax = cut; + cutsq[i][i] = cut * cut; + for (int j = i + 1; j <= ntypes; j++) { + cut = (radelem[i] + radelem[j]) * rcutfac; + cutsq[i][j] = cutsq[j][i] = cut * cut; } } @@ -87,90 +98,87 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = nargmin; while (iarg < narg) { - if (strcmp(arg[iarg],"rmin0") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - rmin0 = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "rmin0") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - switchflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"bzeroflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - bzeroflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "bzeroflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"quadraticflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - quadraticflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "quadraticflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"chem") == 0) { - if (iarg+2+ntypes > narg) - error->all(FLERR,"Illegal compute snav/atom command"); + } else if (strcmp(arg[iarg], "chem") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); chemflag = 1; - memory->create(map,ntypes+1,"compute_sna_atom:map"); - nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + memory->create(map, ntypes + 1, "compute_sna_grid:map"); + nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); for (int i = 0; i < ntypes; i++) { - int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp); - if (jelem < 0 || jelem >= nelements) - error->all(FLERR,"Illegal compute snav/atom command"); - map[i+1] = jelem; + int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp); + if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style); + map[i + 1] = jelem; } - iarg += 2+ntypes; - } else if (strcmp(arg[iarg],"bnormflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - bnormflag = atoi(arg[iarg+1]); + iarg += 2 + ntypes; + } else if (strcmp(arg[iarg], "bnormflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"wselfallflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - wselfallflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "wselfallflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - switchinnerflag = atoi(arg[iarg+1]); + } else if (strcmp(arg[iarg], "switchinnerflag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style); + switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"sinner") == 0) { + } else if (strcmp(arg[iarg], "sinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - memory->create(sinnerelem,ntypes+1,"snav/atom:sinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem"); for (int i = 0; i < ntypes; i++) - sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); sinnerflag = 1; iarg += ntypes; - } else if (strcmp(arg[iarg],"dinner") == 0) { + } else if (strcmp(arg[iarg], "dinner") == 0) { iarg++; - if (iarg+ntypes > narg) - error->all(FLERR,"Illegal compute snav/atom command"); - memory->create(dinnerelem,ntypes+1,"snav/atom:dinnerelem"); + if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style); + memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem"); for (int i = 0; i < ntypes; i++) - dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp); dinnerflag = 1; iarg += ntypes; - } else error->all(FLERR,"Illegal compute snav/atom command"); + } else + error->all(FLERR, "Illegal compute {} command", style); } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR,"Illegal compute snav/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR,"Illegal compute snav/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + error->all( + FLERR, + "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", + style); - snaptr = new SNA(lmp, rfac0, twojmax, - rmin0, switchflag, bzeroflag, - chemflag, bnormflag, wselfallflag, - nelements, switchinnerflag); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, + wselfallflag, nelements, switchinnerflag); ncoeff = snaptr->ncoeff; - nperdim = ncoeff; - if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; - size_peratom_cols = 6*nperdim*atom->ntypes; + nvalues = ncoeff; + if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; + + // end code common to all SNAP computes + + size_peratom_cols = 6*nvalues*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -203,10 +211,9 @@ void ComputeSNAVAtom::init() { if (force->pair == nullptr) error->all(FLERR,"Compute snav/atom requires a pair style be defined"); - // TODO: Not sure what to do with this error check since cutoff radius is not - // a single number - //if (sqrt(cutsq) > force->pair->cutforce) - // error->all(FLERR,"Compute snav/atom cutoff is longer than pairwise cutoff"); + + if (cutmax > force->pair->cutforce) + error->all(FLERR,"Compute snav/atom cutoff is longer than pairwise cutoff"); // need an occasional full neighbor list @@ -280,7 +287,7 @@ void ComputeSNAVAtom::compute_peratom() const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset = 6*nperdim*(atom->type[i]-1); + const int typeoffset = 6*nvalues*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum @@ -339,17 +346,17 @@ void ComputeSNAVAtom::compute_peratom() for (int icoeff = 0; icoeff < ncoeff; icoeff++) { snavi[icoeff] += snaptr->dblist[icoeff][0]*xtmp; - snavi[icoeff+nperdim] += snaptr->dblist[icoeff][1]*ytmp; - snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp; - snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp; - snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp; - snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp; + snavi[icoeff+nvalues] += snaptr->dblist[icoeff][1]*ytmp; + snavi[icoeff+2*nvalues] += snaptr->dblist[icoeff][2]*ztmp; + snavi[icoeff+3*nvalues] += snaptr->dblist[icoeff][1]*ztmp; + snavi[icoeff+4*nvalues] += snaptr->dblist[icoeff][0]*ztmp; + snavi[icoeff+5*nvalues] += snaptr->dblist[icoeff][0]*ytmp; snavj[icoeff] -= snaptr->dblist[icoeff][0]*x[j][0]; - snavj[icoeff+nperdim] -= snaptr->dblist[icoeff][1]*x[j][1]; - snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2]; - snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2]; - snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2]; - snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1]; + snavj[icoeff+nvalues] -= snaptr->dblist[icoeff][1]*x[j][1]; + snavj[icoeff+2*nvalues] -= snaptr->dblist[icoeff][2]*x[j][2]; + snavj[icoeff+3*nvalues] -= snaptr->dblist[icoeff][1]*x[j][2]; + snavj[icoeff+4*nvalues] -= snaptr->dblist[icoeff][0]*x[j][2]; + snavj[icoeff+5*nvalues] -= snaptr->dblist[icoeff][0]*x[j][1]; } if (quadraticflag) { @@ -369,17 +376,17 @@ void ComputeSNAVAtom::compute_peratom() double dbytmp = bi*biy; double dbztmp = bi*biz; snavi[ncount] += dbxtmp*xtmp; - snavi[ncount+nperdim] += dbytmp*ytmp; - snavi[ncount+2*nperdim] += dbztmp*ztmp; - snavi[ncount+3*nperdim] += dbytmp*ztmp; - snavi[ncount+4*nperdim] += dbxtmp*ztmp; - snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavi[ncount+nvalues] += dbytmp*ytmp; + snavi[ncount+2*nvalues] += dbztmp*ztmp; + snavi[ncount+3*nvalues] += dbytmp*ztmp; + snavi[ncount+4*nvalues] += dbxtmp*ztmp; + snavi[ncount+5*nvalues] += dbxtmp*ytmp; snavj[ncount] -= dbxtmp*x[j][0]; - snavj[ncount+nperdim] -= dbytmp*x[j][1]; - snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; - snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; - snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; - snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; + snavj[ncount+nvalues] -= dbytmp*x[j][1]; + snavj[ncount+2*nvalues] -= dbztmp*x[j][2]; + snavj[ncount+3*nvalues] -= dbytmp*x[j][2]; + snavj[ncount+4*nvalues] -= dbxtmp*x[j][2]; + snavj[ncount+5*nvalues] -= dbxtmp*x[j][1]; ncount++; // upper-triangular elements of quadratic matrix @@ -392,17 +399,17 @@ void ComputeSNAVAtom::compute_peratom() double dbztmp = bi*snaptr->dblist[jcoeff][2] + biz*snaptr->blist[jcoeff]; snavi[ncount] += dbxtmp*xtmp; - snavi[ncount+nperdim] += dbytmp*ytmp; - snavi[ncount+2*nperdim] += dbztmp*ztmp; - snavi[ncount+3*nperdim] += dbytmp*ztmp; - snavi[ncount+4*nperdim] += dbxtmp*ztmp; - snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavi[ncount+nvalues] += dbytmp*ytmp; + snavi[ncount+2*nvalues] += dbztmp*ztmp; + snavi[ncount+3*nvalues] += dbytmp*ztmp; + snavi[ncount+4*nvalues] += dbxtmp*ztmp; + snavi[ncount+5*nvalues] += dbxtmp*ytmp; snavj[ncount] -= dbxtmp*x[j][0]; - snavj[ncount+nperdim] -= dbytmp*x[j][1]; - snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; - snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; - snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; - snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; + snavj[ncount+nvalues] -= dbytmp*x[j][1]; + snavj[ncount+2*nvalues] -= dbztmp*x[j][2]; + snavj[ncount+3*nvalues] -= dbytmp*x[j][2]; + snavj[ncount+4*nvalues] -= dbxtmp*x[j][2]; + snavj[ncount+5*nvalues] -= dbxtmp*x[j][1]; ncount++; } } diff --git a/src/ML-SNAP/compute_snav_atom.h b/src/ML-SNAP/compute_snav_atom.h index 1eb84d8df7..2eac0b7b28 100644 --- a/src/ML-SNAP/compute_snav_atom.h +++ b/src/ML-SNAP/compute_snav_atom.h @@ -37,7 +37,7 @@ class ComputeSNAVAtom : public Compute { private: int nmax; - int ncoeff, nperdim; + int ncoeff, nvalues; double **cutsq; class NeighList *list; double **snav; @@ -50,6 +50,7 @@ class ComputeSNAVAtom : public Compute { double *sinnerelem; double *dinnerelem; class SNA *snaptr; + double cutmax; int quadraticflag; }; diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 07a8237ab5..7c6e0a8b5d 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -63,11 +63,8 @@ PairSNAP::~PairSNAP() memory->destroy(radelem); memory->destroy(wjelem); memory->destroy(coeffelem); - - if (switchinnerflag) { - memory->destroy(sinnerelem); - memory->destroy(dinnerelem); - } + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); memory->destroy(beta); memory->destroy(bispectrum); diff --git a/src/atom.cpp b/src/atom.cpp index 8b3ab8c75d..9aa9e00bce 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -2659,10 +2659,18 @@ void *Atom::extract(const char *name) if (strcmp(name,"body") == 0) return (void *) body; if (strcmp(name,"quat") == 0) return (void *) quat; + // PERI PACKAGE + if (strcmp(name,"vfrac") == 0) return (void *) vfrac; if (strcmp(name,"s0") == 0) return (void *) s0; if (strcmp(name,"x0") == 0) return (void *) x0; + // SPIN PACKAGE + + if (strcmp(name,"sp") == 0) return (void *) sp; + + // EFF and AWPMD packages + if (strcmp(name,"spin") == 0) return (void *) spin; if (strcmp(name,"eradius") == 0) return (void *) eradius; if (strcmp(name,"ervel") == 0) return (void *) ervel; @@ -2673,6 +2681,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"vforce") == 0) return (void *) vforce; if (strcmp(name,"etag") == 0) return (void *) etag; + // SPH package if (strcmp(name,"rho") == 0) return (void *) rho; if (strcmp(name,"drho") == 0) return (void *) drho; if (strcmp(name,"esph") == 0) return (void *) esph; diff --git a/src/dump.cpp b/src/dump.cpp index a354be4f04..22750ed05c 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -332,6 +332,7 @@ void Dump::write() // if file per timestep, open new file if (multifile) openfile(); + if (fp) clearerr(fp); // simulation box bounds @@ -519,6 +520,8 @@ void Dump::write() if (filewriter && fp != nullptr) write_footer(); + if (fp && ferror(fp)) error->one(FLERR,"Error writing dump {}: {}", id, utils::getsyserror()); + // if file per timestep, close file if I am filewriter if (multifile) { diff --git a/src/lammps.cpp b/src/lammps.cpp index c74983be43..3ddfafeb5d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -129,9 +129,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : version = (const char *) LAMMPS_VERSION; num_ver = utils::date2num(version); - clientserver = 0; - cslib = nullptr; - cscomm = 0; + external_comm = 0; + mdicomm = nullptr; skiprunflag = 0; @@ -155,19 +154,16 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : #endif // check if -mpicolor is first arg - // if so, then 2 apps were launched with one mpirun command + // if so, then 2 or more apps were launched with one mpirun command // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS - // e.g. for client/server coupling with another code - // in the future LAMMPS might leverage this in other ways // universe communicator needs to shrink to be just LAMMPS // syntax: -mpicolor color - // color = integer for this app, different than other app(s) + // color = integer for this app, different than any other app(s) // do the following: // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm - // NOTE: this assumes other app(s) does same thing, else will hang! + // NOTE: this assumes other app(s) make same call, else will hang! // re-create universe with subcomm - // store full multi-app comm in cscomm - // cscomm is used by CSLIB package to exchange messages w/ other app + // store comm that all apps belong to in external_comm int iarg = 1; if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpicolor") == 0 || @@ -178,7 +174,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : int color = atoi(arg[iarg+1]); MPI_Comm subcomm; MPI_Comm_split(communicator,color,me,&subcomm); - cscomm = communicator; + external_comm = communicator; communicator = subcomm; delete universe; universe = new Universe(this,communicator); @@ -290,7 +286,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : logflag = iarg + 1; iarg += 2; - } else if (strcmp(arg[iarg],"-mpi") == 0 || + } else if (strcmp(arg[iarg],"-mpicolor") == 0 || strcmp(arg[iarg],"-m") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); @@ -762,13 +758,13 @@ LAMMPS::~LAMMPS() delete [] suffix2; delete [] suffixp; - // free the MPI comm created by -mpi command-line arg processed in constructor + // free the MPI comm created by -mpicolor cmdline arg processed in constructor // it was passed to universe as if original universe world // may have been split later by partitions, universe will free the splits // free a copy of uorig here, so check in universe destructor will still work MPI_Comm copy = universe->uorig; - if (cscomm) MPI_Comm_free(©); + if (external_comm) MPI_Comm_free(©); delete input; delete universe; diff --git a/src/lammps.h b/src/lammps.h index 4f3e9cf110..4cdb873db9 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -61,13 +61,15 @@ class LAMMPS { char *suffix, *suffix2, *suffixp; // suffixes to add to input script style names int suffix_enable; // 1 if suffixes are enabled, 0 if disabled char *exename; // pointer to argv[0] - // + char ***packargs; // arguments for cmdline package commands int num_package; // number of cmdline package commands - // - int clientserver; // 0 = neither, 1 = client, 2 = server - void *cslib; // client/server messaging via CSlib - MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode + + MPI_Comm external_comm; // MPI comm encompassing external programs + // when multiple programs launched by mpirun + // set by -mpicolor command line arg + + void *mdicomm; // for use with MDI code coupling library const char *match_style(const char *style, const char *name); static const char *installed_packages[]; diff --git a/src/pair.cpp b/src/pair.cpp index 44f23745d9..5ce4dc2d32 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -126,6 +126,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) datamask_modify = ALL_MASK; kokkosable = 0; + reverse_comm_device = 0; copymode = 0; } diff --git a/src/pair.h b/src/pair.h index 4763a225d2..5bad9e14a3 100644 --- a/src/pair.h +++ b/src/pair.h @@ -123,6 +123,7 @@ class Pair : protected Pointers { ExecutionSpace execution_space; unsigned int datamask_read, datamask_modify; int kokkosable; // 1 if Kokkos pair + int reverse_comm_device; // 1 if reverse comm on Device Pair(class LAMMPS *); ~Pair() override; diff --git a/src/variable.cpp b/src/variable.cpp index 7392379017..878066f466 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -4770,12 +4770,14 @@ double Variable::evaluate_boolean(char *str) } if (opprevious == NOT) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag2) + error->all(FLERR,"If command boolean not cannot operate on string"); if (value2 == 0.0) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; + } else if (opprevious == EQ) { if (flag1 != flag2) - error->all(FLERR,"Invalid Boolean syntax in if command"); + error->all(FLERR,"If command boolean is comparing string to number"); if (flag2 == 0) { if (value1 == value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; @@ -4787,7 +4789,7 @@ double Variable::evaluate_boolean(char *str) } } else if (opprevious == NE) { if (flag1 != flag2) - error->all(FLERR,"Invalid Boolean syntax in if command"); + error->all(FLERR,"If command boolean is comparing string to number"); if (flag2 == 0) { if (value1 != value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; @@ -4797,32 +4799,41 @@ double Variable::evaluate_boolean(char *str) delete[] str1; delete[] str2; } + } else if (opprevious == LT) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 < value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; } else if (opprevious == LE) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 <= value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; } else if (opprevious == GT) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 > value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; } else if (opprevious == GE) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 >= value2) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; + } else if (opprevious == AND) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 != 0.0 && value2 != 0.0) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; } else if (opprevious == OR) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if (value1 != 0.0 || value2 != 0.0) argstack[nargstack].value = 1.0; else argstack[nargstack].value = 0.0; } else if (opprevious == XOR) { - if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command"); + if (flag1 || flag2) + error->all(FLERR,"If command boolean can only operate on numbers"); if ((value1 == 0.0 && value2 != 0.0) || (value1 != 0.0 && value2 == 0.0)) argstack[nargstack].value = 1.0; @@ -4845,6 +4856,13 @@ double Variable::evaluate_boolean(char *str) if (nopstack) error->all(FLERR,"Invalid Boolean syntax in if command"); if (nargstack != 1) error->all(FLERR,"Invalid Boolean syntax in if command"); + + // if flag == 1, Boolean expression was a single string with no operator + // error b/c invalid, only single number with no operator is allowed + + if (argstack[0].flag == 1) + error->all(FLERR,"If command boolean cannot be single string"); + return argstack[0].value; } diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index a015ee6856..28b3e1c1cd 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -5,8 +5,8 @@ ######################################## # download and build googletest framework message(STATUS "Downloading and building googletest framework") -set(GTEST_URL "https://github.com/google/googletest/archive/8d51dc50eb7e7698427fed81b85edad0e032112e.tar.gz" CACHE STRING "URL of googletest source") -set(GTEST_MD5 "bc33f94adf48a91051dc195077f7e8dc" CACHE STRING "MD5 sum for googletest source") +set(GTEST_URL "https://github.com/google/googletest/archive/release-1.12.1.tar.gz" CACHE STRING "URL of googletest source") +set(GTEST_MD5 "e82199374acdfda3f425331028eb4e2a" CACHE STRING "MD5 sum for googletest source") mark_as_advanced(GTEST_URL) mark_as_advanced(GTEST_MD5) set(gtest_force_shared_crt ON CACHE BOOL "" FORCE) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 0533de7329..29b985927d 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -389,6 +389,8 @@ TEST_F(VariableTest, IfCommand) { BEGIN_HIDE_OUTPUT(); command("variable one index 1"); + command("variable two string xx"); + command("variable three equal 1"); END_HIDE_OUTPUT(); BEGIN_CAPTURE_OUTPUT(); @@ -401,11 +403,36 @@ TEST_F(VariableTest, IfCommand) text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, ContainsRegex(".*nope\?.*")); + BEGIN_CAPTURE_OUTPUT(); + command("if 0<1 then 'print \"bingo!\"'"); + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*bingo!.*")); + + BEGIN_CAPTURE_OUTPUT(); + command("if 2<1 then 'print \"bingo!\"' else 'print \"nope?\"'"); + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*nope\?.*")); + BEGIN_CAPTURE_OUTPUT(); command("if (1<=0) then 'print \"bingo!\"' else 'print \"nope?\"'"); text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, ContainsRegex(".*nope\?.*")); + BEGIN_CAPTURE_OUTPUT(); + command("if (0<=0) then 'print \"bingo!\"' else 'print \"nope?\"'"); + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*bingo!.*")); + + BEGIN_CAPTURE_OUTPUT(); + command("if (0>=1) then 'print \"bingo!\"' else 'print \"nope?\"'"); + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*nope\?.*")); + + BEGIN_CAPTURE_OUTPUT(); + command("if (1>=1) then 'print \"bingo!\"' else 'print \"nope?\"'"); + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*bingo!.*")); + BEGIN_CAPTURE_OUTPUT(); command("if (-1.0e-1<0.0E+0)|^(1<0) then 'print \"bingo!\"'"); text = END_CAPTURE_OUTPUT(); @@ -444,7 +471,11 @@ TEST_F(VariableTest, IfCommand) BEGIN_CAPTURE_OUTPUT(); command("if x!=x|^a!=b then 'print \"bingo!\"'"); text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, ContainsRegex(".*bingo!.*")); + BEGIN_CAPTURE_OUTPUT(); + command("if (${three}) then 'print \"bingo!\"'"); + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, ContainsRegex(".*bingo!.*")); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", @@ -455,8 +486,16 @@ TEST_F(VariableTest, IfCommand) command("if 1a then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if 1=<2 then 'print \"bingo!\"'");); - TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + TEST_FAILURE(".*ERROR: If command boolean is comparing string to number.*", command("if 1!=a then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean can only operate on numbers.*", + command("if ab then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean can only operate on numbers.*", + command("if a<=b then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean can only operate on numbers.*", + command("if a<=b then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if 1&<2 then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", @@ -465,8 +504,14 @@ TEST_F(VariableTest, IfCommand) command("if (1)( then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if (1)1 then 'print \"bingo!\"'");); - TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + TEST_FAILURE(".*ERROR: If command boolean is comparing string to number.*", command("if (v_one==1.0)&&(2>=1) then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean cannot be single string.*", + command("if (something) then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean cannot be single string.*", + command("if (v_one) then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: If command boolean cannot be single string.*", + command("if (${two}) then 'print \"bingo!\"'");); } TEST_F(VariableTest, NextCommand) diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index d25bf43656..64ce1eefb1 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -83,8 +83,8 @@ TEST_F(LAMMPS_plain, InitMembers) EXPECT_STREQ(lmp->exename, "LAMMPS_test"); EXPECT_EQ(lmp->num_package, 0); - EXPECT_EQ(lmp->clientserver, 0); + EXPECT_EQ(lmp->mdicomm, nullptr); EXPECT_EQ(lmp->kokkos, nullptr); EXPECT_EQ(lmp->atomKK, nullptr); EXPECT_EQ(lmp->memoryKK, nullptr); @@ -218,8 +218,8 @@ TEST_F(LAMMPS_omp, InitMembers) EXPECT_STREQ(lmp->exename, "LAMMPS_test"); EXPECT_EQ(lmp->num_package, 1); - EXPECT_EQ(lmp->clientserver, 0); + EXPECT_EQ(lmp->mdicomm, nullptr); EXPECT_EQ(lmp->kokkos, nullptr); EXPECT_EQ(lmp->atomKK, nullptr); EXPECT_EQ(lmp->memoryKK, nullptr); @@ -302,12 +302,12 @@ TEST_F(LAMMPS_kokkos, InitMembers) EXPECT_STREQ(lmp->exename, "LAMMPS_test"); EXPECT_EQ(lmp->num_package, 0); - EXPECT_EQ(lmp->clientserver, 0); if (Info::has_accelerator_feature("KOKKOS", "api", "openmp")) EXPECT_EQ(lmp->comm->nthreads, 2); else EXPECT_EQ(lmp->comm->nthreads, 1); + EXPECT_EQ(lmp->mdicomm, nullptr); EXPECT_NE(lmp->kokkos, nullptr); EXPECT_NE(lmp->atomKK, nullptr); EXPECT_NE(lmp->memoryKK, nullptr); diff --git a/unittest/fortran/CMakeLists.txt b/unittest/fortran/CMakeLists.txt index 94672a58d8..047dcf3207 100644 --- a/unittest/fortran/CMakeLists.txt +++ b/unittest/fortran/CMakeLists.txt @@ -10,11 +10,6 @@ if(NOT CMAKE_Fortran_COMPILER_ID) message(STATUS "Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler") return() endif() -find_package(MPI QUIET) -if(BUILD_MPI AND NOT MPI_Fortran) - message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no MPI support for Fortran") - return() -endif() if(CMAKE_Fortran_COMPILER) enable_language(C) @@ -22,6 +17,10 @@ if(CMAKE_Fortran_COMPILER) get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE) if(BUILD_MPI) find_package(MPI REQUIRED) + if((NOT MPI_Fortran) OR (NOT MPI_Fortran_HAVE_F77_HEADER) OR (NOT MPI_Fortran_HAVE_F90_MODULE)) + message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no MPI support for Fortran") + return() + endif() else() add_library(fmpi_stubs STATIC mpi_stubs.f90) add_library(MPI::MPI_Fortran ALIAS fmpi_stubs)