diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a9a4bd861f8..1254ee9f126 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -306,6 +306,7 @@ set(STANDARD_PACKAGES MACHDYN MANIFOLD MANYBODY + MBX MC MDI MEAM @@ -561,7 +562,7 @@ else() endif() foreach(PKG_WITH_INCL GRAPHICS KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF - PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND) + PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND MBX) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake index 418396fa4dc..765c3a51977 100644 --- a/cmake/Modules/LAMMPSInterfacePlugin.cmake +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -65,6 +65,10 @@ set(CMAKE_POSITION_INDEPENDENT_CODE TRUE) # skip over obsolete MPI-2 C++ bindings set(MPI_CXX_SKIP_MPICXX TRUE) +# compile external libraries for linking to shared objects +set(CONFIGURE_REQUEST_PIC "--with-pic") +set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}") + ####### # helper functions from LAMMPSUtils.cmake function(validate_option name values) diff --git a/cmake/Modules/Packages/MBX.cmake b/cmake/Modules/Packages/MBX.cmake new file mode 100644 index 00000000000..247991b546b --- /dev/null +++ b/cmake/Modules/Packages/MBX.cmake @@ -0,0 +1,107 @@ +# MBX v1.3.0+ support for MBX package +# Based off of PLUMED.cmake + +# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW +if(POLICY CMP0135) + cmake_policy(SET CMP0135 OLD) +endif() + +if(CMAKE_SYSTEM_NAME STREQUAL "Windows") + message(FATAL_ERROR "Compiling the MBX package for Windows is currently not supported") +endif() + +# for supporting multiple concurrent mbx installations for debugging and testing +set(MBX_SUFFIX "" CACHE STRING "Suffix for MBX library") +mark_as_advanced(MBX_SUFFIX) + +set(MBX_CONFIG_CC ${CMAKE_C_COMPILER}) +set(MBX_CONFIG_CXX ${CMAKE_CXX_COMPILER}) +if(BUILD_MPI) + set(MBX_CONFIG_FLAGS "--enable-mpi") + set(MBX_CONFIG_CC ${MPI_C_COMPILER}) + set(MBX_CONFIG_CXX ${MPI_CXX_COMPILER}) +else() + set(MBX_CONFIG_FLAGS "--disable-mpi") +endif() + +if(BUILD_OMP) + list(APPEND MBX_CONFIG_FLAGS --enable-openmp) +else() + list(APPEND MBX_CONFIG_FLAGS --disable-openmp) +endif() + +if(CONFIGURE_REQUEST_PIC) + list(APPEND MBX_CONFIG_FLAGS ${CONFIGURE_REQUEST_PIC}) +endif() + +set(MBXLIB_URL "https://github.com/paesanilab/MBX/releases/download/v1.3.3/mbx-1.3.3.tar.gz" CACHE STRING "URL for MBX tarball") +set(MBXLIB_MD5 "78abbf597e8077e5e0b18e86fc3248c1" CACHE STRING "MD5 checksum of MBX tarball") + +mark_as_advanced(MBXLIB_URL) +mark_as_advanced(MBXLIB_MD5) + +set(MBX_LINK_LIBS) +find_package(FFTW3 REQUIRED) +if(FFTW3_FOUND) + list(APPEND MBX_LINK_LIBS FFTW3::FFTW3) +endif() + +find_package(PkgConfig QUIET) +set(DOWNLOAD_MBX_DEFAULT ON) +if(PKG_CONFIG_FOUND) + pkg_check_modules(MBX QUIET mbx) + if(MBX_FOUND) + set(DOWNLOAD_MBX_DEFAULT OFF) + endif() +endif() + +option(DOWNLOAD_MBX "Download MBX package instead of using an already installed one" ${DOWNLOAD_MBX_DEFAULT}) +if(DOWNLOAD_MBX) + message(STATUS "MBX download requested - we will build our own") + set(MBX_BUILD_BYPRODUCTS "/lib/${CMAKE_STATIC_LIBRARY_PREFIX}mbx${CMAKE_STATIC_LIBRARY_SUFFIX}") + + message(STATUS "MBX_CONFIG_CC: ${MBX_CONFIG_CC}") + message(STATUS "MBX_CONFIG_CXX: ${MBX_CONFIG_CXX}") + message(STATUS "MBX_CONFIG_FLAGS: ${MBX_CONFIG_FLAGS}") + + include(ExternalProject) + ExternalProject_Add(mbx_build + URL ${MBXLIB_URL} + URL_HASH MD5=${MBXLIB_MD5} + CONFIGURE_COMMAND /configure + --prefix= + ${MBX_CONFIG_FLAGS} + CXX=${MBX_CONFIG_CXX} + CC=${MBX_CONFIG_CC} + CPPFLAGS=-I${FFTW3_INCLUDE_DIRS} + BUILD_BYPRODUCTS ${MBX_BUILD_BYPRODUCTS} + ) + ExternalProject_get_property(mbx_build INSTALL_DIR) + add_library(LAMMPS::MBX UNKNOWN IMPORTED) + add_dependencies(LAMMPS::MBX mbx_build) + set_target_properties(LAMMPS::MBX PROPERTIES + IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}mbx${CMAKE_STATIC_LIBRARY_SUFFIX} + INTERFACE_LINK_LIBRARIES "${MBX_LINK_LIBS};${CMAKE_DL_LIBS}" + ) + + set_target_properties(LAMMPS::MBX PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include) + file(MAKE_DIRECTORY ${INSTALL_DIR}/include) + if(CMAKE_PROJECT_NAME STREQUAL "lammps") + target_link_libraries(lammps PRIVATE LAMMPS::MBX) + endif() +else() + find_package(PkgConfig REQUIRED) + pkg_check_modules(MBX REQUIRED mbx${MBX_SUFFIX}) + add_library(LAMMPS::MBX INTERFACE IMPORTED) + + file(MAKE_DIRECTORY ${MBX_INCLUDE_DIRS}) + + target_include_directories(LAMMPS::MBX INTERFACE ${MBX_INCLUDE_DIRS}) + target_link_directories(LAMMPS::MBX INTERFACE ${MBX_LIBRARY_DIRS}) + target_link_libraries(LAMMPS::MBX INTERFACE "${MBX_LINK_LIBS};${MBX_LIBRARIES};${CMAKE_DL_LIBS}") + + if(CMAKE_PROJECT_NAME STREQUAL "lammps") + target_link_libraries(lammps PUBLIC LAMMPS::MBX) + endif() +endif() + diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index b32539c1e7a..684155eee8d 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -48,6 +48,7 @@ set(ALL_PACKAGES MACHDYN MANIFOLD MANYBODY + MBX MC MDI MEAM diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 7c81327317c..8548edeb59b 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -50,6 +50,7 @@ set(ALL_PACKAGES MACHDYN MANIFOLD MANYBODY + MBX MC MDI MEAM diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index a853bef649e..4efd7e1e13b 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -49,6 +49,7 @@ This is the list of packages that may require additional steps. * :ref:`KOKKOS ` * :ref:`LEPTON ` * :ref:`MACHDYN ` + * :ref:`MBX ` * :ref:`MDI ` * :ref:`MISC ` * :ref:`ML-HDNNP ` @@ -106,7 +107,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile. .. versionchanged:: 10Sep2025 - The COMPRESS package no longer supports the the traditional make build. + The COMPRESS package no longer supports the traditional make build. You need to build LAMMPS with CMake. ---------- @@ -440,7 +441,7 @@ minutes to hours) to build. Of course you only need to do that once.) .. versionchanged:: 10Sep2025 - The KIM package no longer supports the the traditional make build. + The KIM package no longer supports the traditional make build. You need to build LAMMPS with CMake. Debugging OpenKIM web queries in LAMMPS @@ -915,7 +916,7 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder. .. versionchanged:: 10Sep2025 - The LEPTON package no longer supports the the traditional make build. + The LEPTON package no longer supports the traditional make build. You need to build LAMMPS with CMake. ---------- @@ -948,7 +949,7 @@ Eigen3 is a template library, so you do not need to build it. .. versionchanged:: 10Sep2025 - The MACHDYN package no longer supports the the traditional make build. + The MACHDYN package no longer supports the traditional make build. You need to build LAMMPS with CMake. ---------- @@ -1053,7 +1054,7 @@ for additional details. .. versionchanged:: 10Sep2025 - The PYTHON package no longer supports the the traditional make build. + The PYTHON package no longer supports the traditional make build. You need to build LAMMPS with CMake. ---------- @@ -1092,7 +1093,7 @@ binary package provided by your operating system. .. versionchanged:: 10Sep2025 - The VORONOI package no longer supports the the traditional make build. + The VORONOI package no longer supports the traditional make build. You need to build LAMMPS with CMake. ---------- @@ -1162,7 +1163,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ `_ + +Instead of including the MBX package directly into LAMMPS, it is also +possible to skip this step and build the MBX package as a plugin using +the CMake script files in the ``examples/PACKAGE/mbx/plugin`` folder and +then load this plugin at runtime with the :doc:`plugin command +`. + +.. tabs:: + + .. tab:: CMake build + + By default the MBX library will be downloaded from the git repository + and built automatically when the MBX package is enabled with + ``-D PKG_MBX=yes``. The location for the sources may be + customized by setting the variable ``MBXLIB_URL`` when + configuring with CMake (e.g. to use a local archive on machines + without internet access). Since CMake checks the validity of the + archive with ``md5sum`` you may also need to set ``MBXLIB_MD5`` + if you provide a different library version than what is downloaded + automatically. + + + .. tab:: Traditional make + + The MBX package does not support the traditional make + build. You need to build LAMMPS with CMake to use it. + +---------- + .. _ml-pace: ML-PACE package @@ -1267,7 +1309,7 @@ folder and then load this plugin at runtime with the :doc:`plugin command ` * :doc:`lubricateU ` * :doc:`lubricateU/poly ` + * :doc:`mbx ` * :doc:`mdpd (g) ` * :doc:`mdpd/rhosum ` * :doc:`meam (k) ` diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 97205f0af31..6594f8ec5ba 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -293,6 +293,11 @@ whether an extra library is needed to build and use the package: - :doc:`pair_style tersoff ` - shear - no + * - :ref:`MBX ` + - `MBX MB-nrg potential library `_ + - :doc:`pair_mbx ` + - ``PACKAGES/mbx`` + - no * - :ref:`MC ` - Monte Carlo options - :doc:`fix gcmc ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 3d5cb232e24..861ee2a751c 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -72,6 +72,7 @@ gives those details. * :ref:`MACHDYN ` * :ref:`MANIFOLD ` * :ref:`MANYBODY ` + * :ref:`MBX ` * :ref:`MC ` * :ref:`MDI ` * :ref:`MEAM ` @@ -364,7 +365,7 @@ fix brownian/asphere ` as well as Dynamics time integration of point, spherical and aspherical particles and also support self-propelled particles. -**Authors:** Sam Cameron (University of Bristol), +**Authors:** Sam Cameron (University of Bristol), Arthur Straube (Zuse Institute Berlin), Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) .. versionadded:: 14May2021 @@ -1537,6 +1538,38 @@ A variety of many-body and bond-order potentials. These include ---------- +.. _PKG-MBX: + +MBX Package +----------- + +**Contents** + +The pair_style mbx command implements the MBX library for +MB-pol and MB-nrg data-driven many-body potential energy functions. MBX +is called using :doc:`pair_style mbx ` command, which +allow for MB-nrg potentials such as MB-pol to be used in LAMMPS. +For more information on MBX, see the `MBX library `_ website. + +**Authors:** The `MBX library `_ is developed +by the Paesani group at the University of California, San Diego. Major contributors +include: Marc Riera, Christopher Knight, Ethan Bull-Vulpe, and Henry Agnew. + +.. versionadded:: TBD + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* ``src/MBX``: filenames -> commands +* :doc:`pair_style mbx ` +* https://mbxsimulations.com/ + +---------- + .. _PKG-MC: MC package diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst index cf3f7735508..0e04b1bc44c 100644 --- a/doc/src/fix_brownian.rst +++ b/doc/src/fix_brownian.rst @@ -23,7 +23,7 @@ Syntax * temp = temperature * seed = random number generator seed * one or more keyword/value pairs may be appended -* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t* or *rotation_temp* or *planar_rotation* +* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t* or *rotation_style* or *rotation_temp* or *planar_rotation* .. parsed-literal:: @@ -41,8 +41,11 @@ Syntax *gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor *gamma_t* values = *gt* for *brownian* and *brownian/sphere* *gt* = magnitude of the (isotropic) translational friction tensor + *rotation_style* values = *geometric* or *projection* for *brownian/sphere* + *geometric* = geometric, rotation-based integration scheme + *projection* = projection-based integration scheme *rotation_temp* values = *T* for *brownian/sphere* and *brownian/asphere* - *T* = rotation temperature, which can be different then *temp* when out of equilibrium + *T* = rotation temperature, which can be different than *temp* when out of equilibrium *planar_rotation* values = none (constrains rotational diffusion to be in xy plane if in 3D) Examples @@ -53,7 +56,8 @@ Examples fix 1 all brownian 1.0 12908410 gamma_t 1.0 fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0 - fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none + fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none + fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng gaussian rotation_style projection fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0 @@ -77,10 +81,11 @@ positions is in the lab-frame (i.e., :math:`\boldsymbol{\gamma}_t` is not diagonal, but only depends on orientation and so the noise is still additive). -The rotational motion for the spherical and ellipsoidal particles is not -as simple an expression, but is chosen to replicate the Boltzmann -distribution for the case of conservative torques (see :ref:`(Ilie) -` or :ref:`(Delong) `). +The overdamped rotational motion for the spherical and ellipsoidal particles +results from random rotations instead of translations, which are chosen in such +a way that the motion reproduces the equilibrium Boltzmann distribution for the +case of conservative torques (see :ref:`(Hoefling) `, :ref:`(Ilie) +`, and :ref:`(Delong) `). For the style *brownian*, only the positions of the particles are updated. This is therefore suitable for point particle simulations. @@ -93,18 +98,34 @@ updated. This style therefore requires the hybrid atom style .. math:: - \boldsymbol{\mu}(t+dt) = \frac{\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}dt - }{|\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}|} + \boldsymbol{\mu}(t+dt) = \mathrm{R}(\boldsymbol{\omega} dt) \, \boldsymbol{\mu}(t) \,, -which correctly reproduces a Boltzmann distribution of orientations and -rotational diffusion moments (see :ref:`(Ilie) `) when +where :math:`\mathrm{R}(\boldsymbol{\omega} dt)` is a rotation matrix with axis +:math:`\boldsymbol{n} = \boldsymbol{\omega} / |\boldsymbol{\omega}|` +and angle :math:`\theta = |\boldsymbol{\omega}| dt` (see :ref:`(Hoefling) `). +For small angles, the action of the rotation matrix can be cast into a +tangential increment :math:`\boldsymbol{\omega} \times \boldsymbol{\mu}dt` and +subsequent projection to preserve the magnitude :math:`|\boldsymbol{\mu}(t)|` of +the dipole (see :ref:`(Ilie) `): + +.. math:: + + \boldsymbol{\mu}(t+dt) = |\boldsymbol{\mu}(t)| \, + \frac{\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}dt + }{|\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}dt|}\,. + +For suitable time step :math:`dt`, both expressions were shown to correctly +reproduce the Boltzmann distribution of orientations and rotational diffusion +moments when .. math:: \boldsymbol{\omega} = \frac{\mathbf{T}}{\gamma_r} + \sqrt{\frac{2 k_B T_{rot}}{\gamma_r}\frac{d\mathbf{W}}{dt}}, -with :math:`d\mathbf{W}` being a random number with zero mean and variance :math:`dt` -and :math:`T_{rot}` is *rotation_temp*. +with :math:`d\mathbf{W}` being a random number with zero mean and variance +:math:`dt` and :math:`T_{rot}` is *rotation_temp*. The geometric integration +scheme, however, accepts time steps that can be an order of magnitude larger +(see :ref:`(Hoefling) `). For the style *brownian/asphere*, the center of mass positions and the quaternions of ellipsoidal particles are updated. This fix style is @@ -160,7 +181,6 @@ a similar algorithm. --------- - If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see :ref:`(Dunweg) ` for why this works). This is the same method @@ -193,8 +213,18 @@ If the *dipole* keyword is used, then the dipole moments of the particles are updated as described above. Only compatible with *brownian/asphere* (as *brownian/sphere* updates dipoles automatically). +.. versionadded:: TBD + +If the *rotation_style* keyword is used with the *geometric* value, then the +geometric, rotation-based integration scheme (:ref:`(Hoefling) `) +is used. If the keyword is used with the *projection* value, the linearized, +projection-based scheme (:ref:`(Ilie) `) is used. Only +compatible with *brownian/sphere*. + +Note: *rotation_style projection* reproduces the legacy behavior (the former default). + If the *rotation_temp* keyword is used, then the rotational diffusion -will be occur at this prescribed temperature instead of *temp*. Only +will occur at this prescribed temperature instead of *temp*. Only compatible with *brownian/sphere* and *brownian/asphere*. If the *planar_rotation* keyword is used, then rotation is constrained @@ -245,18 +275,25 @@ Related commands Default """"""" -The default for *rng* is *uniform*. The default for the rotational and -translational friction tensors are the identity tensor. +.. versionchanged:: TBD + +The default for *rng* is *uniform*. The default for *rotation_style* is *geometric*. +The default for the rotational and translational friction tensors are the identity +tensor. ---------- +.. _Hoefling1: + +**(Hoefling)** :math:`\mathrm{H\ddot{o}fling}` and Straube, Physical Review Research, 7, 043034 (2025). + .. _Ilie1: **(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015). .. _Delong1: -**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015) +**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015). .. _Dunweg7: diff --git a/doc/src/pair_mbx.rst b/doc/src/pair_mbx.rst new file mode 100644 index 00000000000..ba02f0b32a1 --- /dev/null +++ b/doc/src/pair_mbx.rst @@ -0,0 +1,214 @@ +.. index:: pair_style mbx + +pair_style mbx command +====================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style mbx cutoff + +* cutoff = real-space cutoff for MBX in Angstroms + + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style mbx 9.0 + pair_coeff * * 1 h2o 1 2 2 json mbx.json + compute mbx all pair mbx + + # For a system involving ch4 (atom types C=1, H=2) and + # water (atom types O=3, H=4) + pair_style mbx 9.0 + pair_coeff * * 2 ch4 1 2 2 2 2 h2o 3 4 4 json mbx.json + compute mbx all pair mbx + + # For a system involving water (atom types O=12, H=13) in a hybrid simulation + pair_style hybrid/overlay mbx 9.0 lj/cut 9.0 coul/exclude 9.0 + pair_coeff * * mbx 2 dp1 1*11 h2o 12 13 13 json mbx.json + pair_coeff 1*11 1*11 coul/exclude + compute mbx all pair mbx + + # For a system involving water (atom types O=12, H=13) in a hybrid simulation + # with special_bonds and coul/exclude to exclude 1-2, 1-3, and 1-4 electrostatics + # for the charmm framework + special_bonds charmm + pair_style hybrid/overlay mbx 9.0 lj/cut 9.0 coul/exclude 9.0 + pair_coeff * * mbx 2 dp1 1*11 h2o 12 13 13 json mbx.json + pair_coeff 1*11 1*11 coul/exclude + compute mbx all pair mbx + +See ``examples/PACKAGES/mbx`` for full examples of how to use MBX in LAMMPS. + + +Description +""""""""""" + +.. versionadded:: TBD + +The MBX (Many-Body eXpansion) software is a C++ library that provides +access to many-body energy (MB-nrg) potential energy functions, such as +the MB-pol water model. Developed over the past decade, these potential +energy functions integrate physics-based and machine-learned many-body +terms trained on electronic structure data calculated at the "gold +standard" coupled-cluster level of theory. :ref:`(Gupta) ` + +This pair_style instructs LAMMPS to call the +`MBX library `_ in order to simulate +MB-nrg models such as MB-pol. The MBX library source code is available at +`https://github.com/paesanilab/MBX `_. +MBX is heavily OpenMP parallelized (OMP), and the OMP_NUM_THREADS +environment variable should be properly set to the number of threads desired. +A detailed discussion of the code structure can be found in the +manuscript :ref:`(Riera) `, while a detailed description of the +performance scaling can be found in the manuscript :ref:`(Gupta) `. + +The *cutoff* argument specifies the real-space cutoff for MBX in +Angstroms. This real-space cutoff is used for the dispersion interactions of the +MB-nrg monomers, as well as for the electrostatics of the **entire** system. +For periodic systems, a safe value for the real-space cutoff is **9.0 Angstroms**, +and all classical interactions beyond this cutoff will then be handled via particle-mesh +Ewald (PME) within MBX. For non-periodic systems, the cutoff can be set to a +large value, such as 100.0 Angstroms, to ensure that all interactions are +captured in the real-space. + +.. warning:: + + MBX must currently be used with :doc:`processors ` mapping style `xyz`. If you + do not, MBX will throw the error: + + .. code-block:: LAMMPS + + [MBX] Inconsistent proc mapping: 'processors * * * map xyz' required for PME solver + +For hybrid simulations involving MB-nrg and non-MB-nrg molecules in the +same simulation, one can use :doc:`pair_style hybrid/overlay +` to combine the MB-nrg molecules with other pair styles, +such as :doc:`lj/cut `. This has been used to simulate +MB-pol water within host frameworks such as metal-organic +frameworks (MOFs) and carbon nanotubes (CNTs). +If using MBX in a hybrid simulation involving :doc:`special_bonds `, +(such as when using the CHARMM, Amber, OPLS, or ClayFF force fields etc.), +please see the warning below for more details about +using `special_bonds` with MBX `dp1`. See ``examples/PACKAGES/mbx`` for +a complete hybrid example. + + +If you have questions not answered by this documentation, please +reference the MBX website +`mbxsimulations.com `_ or reach out to the MBX team at +`https://groups.google.com/g/mbx-users `_ + + +Pair coeff syntax +""""""""""""""""" + +MBX is many-body method, and only a single pair_coeff command is needed +to specify the mapping of LAMMPS atom IDs to MBX monomers. The syntax is as follows: + +.. code-block:: LAMMPS + + pair_coeff * * num_mon_types mon_name atom_mapping ... json mbx.json print/settings + +* num_mon_types = number of monomer types in the system +* mon_name = name of the monomer type (e.g. h2o, ch4, etc) +* atom mapping = list of LAMMPS atom IDs that correspond to the atoms in the monomer +* *json* arg = specifies the name of the MBX json configuration file, such as mbx.json +* print/settings = optionally print MBX settings to logfile + + +The *num_mon_types* argument specifies the number of different MB-nrg +monomer types in the system. + +For each monomer type, the *mon_name* argument specifies the name of +the monomer, such as `h2o` for water or `ch4` for methane. The *atom +mapping* argument specifies then the mapping of LAMMPS atom IDs to +the atoms in the monomer, such as `1 2 2` for water (O=1, H=2). +For hybrid simulations, the `dp1` (drude particle) monomer +should be used to represent the non-MB-nrg molecules. `dp1` is a +special monomer in MBX in that its *atom_mapping* can be a range of +LAMMPS atom IDs, such as `1*11` to represent atom types 1 through 11. +For a complete list of available monomers in MBX, please see the +`MBX documentation `_. + +.. warning:: + + When using MBX, **all electrostatics are handled internally by MBX.** + This is important since MB-nrg models such as MB-pol are polarizable + models that may also use geometrically dependent charges, such as + the Partridge and Schwenke charges used in MB-pol water. + + Therefore, one should **never** use a coulombic pair style in LAMMPS + such as `coul/cut` or `coul/long` when also using MBX. This + would result in double counting of electrostatic interactions. + + When performing a hybrid simulation using dp1, + note that many frameworks (Amber, CHARMM, OPLS, ClayFF etc.) require the usage of + special_bonds to exclude some bonded coulomb interactions (1-2, 1-3, and/or 1-4). + Since MBX is handling all electrostatics, this should therefore be accounted for + using the :doc:`coul/exclude ` command. + + .. code-block:: LAMMPS + + # For a system involving water (atom types O=12, H=13) in a hybrid simulation + # with special_bonds and coul/exclude to exclude 1-2, 1-3, and 1-4 electrostatics + # for the charmm framework + processors * * * map xyz + special_bonds charmm + pair_style hybrid/overlay mbx 9.0 lj/cut 9.0 coul/exclude 9.0 + pair_coeff * * mbx 2 dp1 1*11 h2o 12 13 13 json mbx.json + pair_coeff 1*11 1*11 coul/exclude + compute mbx all pair mbx + +The *json* argument specifies the name of the MBX JSON configuration +file to use, such as `mbx.json`. If this file is not provided, the pair style +will attempt to use a default configuration. See the `mbx.json documentation +`_ for more details on +how to create this file. + +The *print/settings* argument optionally will print the MBX settings to the LAMMPS +logfile at the start of the simulation. This is optionally used for debugging and +ensuring that the settings are being correctly applied. + + +Restrictions +"""""""""""" + +This pair_style is part of the MBX package. A pair style is only +enabled if LAMMPS was built with its corresponding package. +See the :doc:`Build package ` page for more info. + +MBX requires the FFTW3 library to be installed. This is needed +as part of the internal PME solver used for long-range electrostatics. + +All electrostatic interactions are calculated internally in MBX. +Therefore one should never calculate coulombic interactions in +LAMMPS such as using `coul/cut` or `coul/long` when also using MBX. +See the warning above for more details. + +MBX currently only supports :doc:`processors ` mapping style `xyz`. + +MBX is primarily tested to work with `units real` and `atom_style full`. If you encounter +issues with other unit or atom styles, please contact the MBX developers. + +Related commands +"""""""""""""""" + +:doc:`pair hybrid/overlay `, +:doc:`pair coul/exclude ` + +----------- + +.. _Riera: + +**(Riera)** M. Riera, C. Knight, E. Bull-Vulpe, X. Zhu, H. Agnew, D. Smith, A. Simmonett, F. Paesani, J. Chem. Phys. 159, 054802 (2023) + +.. _Gupta3: + +**(Gupta)** S. Gupta, E. Bull-Vulpe, H. Agnew, S. Iyer, X. Zhu, R. Zhou, C. Knight, F. Paesani, J. Chem. Theory Comput. 21, 1938 (2025) + diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index ede6a20c806..4cbe1c7d965 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -291,6 +291,7 @@ accelerated styles exist. * :doc:`lubricate/poly ` - Hydrodynamic lubrication forces with polydispersity * :doc:`lubricateU ` - Hydrodynamic lubrication forces for Fast Lubrication Dynamics * :doc:`lubricateU/poly ` - Hydrodynamic lubrication forces for Fast Lubrication with polydispersity +* :doc:`mbx ` - Many-Body eXpansion (MBX) potential * :doc:`mdpd ` - mDPD particle interactions * :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density * :doc:`meam ` - Modified embedded atom method (MEAM) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9274ebc864a..7ef975d36ef 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -917,6 +917,7 @@ doxygenclass doxygenfunction Doye Doyl +dp dpd DPD dpdTheta @@ -1169,6 +1170,7 @@ excitations excv exe executables +eXpansion extep extractable extrema @@ -1778,6 +1780,7 @@ ixz Ixz iy iycm +Iyer iyy Iyy iyz @@ -2104,6 +2107,7 @@ Likhtman limegreen linalg Lindahl +linearized lineflag lineforce linesearch @@ -2281,6 +2285,7 @@ Mayergoyz Mayoral mbt MBytes +mbx mc mcmoves McLachlan @@ -2427,6 +2432,7 @@ molindex MolPairStyle moltemplate momb +mon Monaghan Monaghans monodisperse @@ -2770,6 +2776,7 @@ Nrecent Nrecompute Nrepeat nreset +nrg Nrho Nroff nrow @@ -2928,6 +2935,7 @@ oxRNA packings padua Padua +Paesani pafi PairIJ palegoldenrod @@ -3395,6 +3403,7 @@ ri Ri Ribiere richard +Riera rigidID rigidify rij @@ -3542,6 +3551,7 @@ Schulten Schunk Schuring Schwen +Schwenke Sci scp screenshot @@ -3627,6 +3637,7 @@ Sikandar Silbert Silling Sim +Simmonett Simov Simul simulations @@ -4256,6 +4267,7 @@ vtr vtu Vu Vuilleumier +Vulpe vv vx Vx @@ -4477,6 +4489,7 @@ zstd Zstd zsu zu +Zuse zx zy Zybin diff --git a/examples/PACKAGES/mbx/256h2o/in.mbx_h2o b/examples/PACKAGES/mbx/256h2o/in.mbx_h2o new file mode 100644 index 00000000000..2c0754543e0 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o/in.mbx_h2o @@ -0,0 +1,57 @@ +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 1 h2o 1 2 2 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +#fix RIGID all shake 0.0001 20 0 b 1 a 1 +fix 1 all npt temp 298 298 100 iso 1.0 1.0 1000 + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +# write_data final.data +# write_restart restart.new diff --git a/examples/PACKAGES/mbx/256h2o/initial.data b/examples/PACKAGES/mbx/256h2o/initial.data new file mode 100644 index 00000000000..dcb55bfa2e9 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o/initial.data @@ -0,0 +1,2333 @@ +LAMMPS data file via write_data, version 2 Aug 2023, timestep = 100, units = real + +768 atoms +2 atom types +512 bonds +1 bond types +256 angles +1 angle types + +0.00033828338625596643 19.655502780867728 xlo xhi +0.00033828338625596643 19.655502780867728 ylo yhi +0.00033828338625596643 19.655502780867728 zlo zhi + +Masses + +1 15.9994 +2 1.008 + +Atoms # full + +1 1 1 -1.1128 2.6696248870790638 5.260932495840358 17.60809921420046 0 0 0 +2 1 2 0.5564 2.2427255320728574 5.934093787418942 17.063711679904596 0 0 0 +3 1 2 0.5564 2.159991697924501 5.3027213316423625 18.45965714856477 0 0 0 +4 2 1 -1.1128 1.389571720018154 4.897222580064953 0.1909144892826206 0 0 0 +5 2 2 0.5564 1.008023450378975 5.190782049871591 1.016108977687535 0 0 0 +6 2 2 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733 735 +246 1 737 736 738 +247 1 740 739 741 +248 1 743 742 744 +249 1 746 745 747 +250 1 749 748 750 +251 1 752 751 753 +252 1 755 754 756 +253 1 758 757 759 +254 1 761 760 762 +255 1 764 763 765 +256 1 767 766 768 \ No newline at end of file diff --git a/examples/PACKAGES/mbx/256h2o/log.11Dec25.256h2o.g++.1 b/examples/PACKAGES/mbx/256h2o/log.11Dec25.256h2o.g++.1 new file mode 100644 index 00000000000..ffa9a6ecc48 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o/log.11Dec25.256h2o.g++.1 @@ -0,0 +1,251 @@ +LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-714-g4ab4c2060a-modified) + using 1 OpenMP thread(s) per MPI task +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data +Reading data file ... + orthogonal box = (0.00033828339 0.00033828339 0.00033828339) to (19.655503 19.655503 19.655503) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 768 atoms + reading velocities ... + 768 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + orthogonal box = (0.00033828339 0.00033828339 0.00033828339) to (19.655503 19.655503 19.655503) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 512 bonds + reading angles ... + 256 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.014 seconds + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 1 h2o 1 2 2 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +#fix RIGID all shake 0.0001 20 0 b 1 a 1 +fix 1 all npt temp 298 298 100 iso 1.0 1.0 1000 + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair mbx command: + +@article{10.1063/5.0156036, + author = {Riera, Marc and Knight, Christopher and Bull-Vulpe, Ethan F. and Zhu, Xuanyu and Agnew, Henry and Smith, Daniel G. A. and Simmonett, Andrew C. and Paesani, Francesco}, + title = "{MBX: A many-body energy and force calculator for data-driven many-body simulations}", + journal = {The Journal of Chemical Physics}, + volume = {159}, + number = {5}, + pages = {054802}, + year = {2023}, + doi = {10.1063/5.0156036}, + version = {1.3.3} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 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 = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mbx, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes + Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press + 0 0 298 -1731.1398 681.31183 -2412.4517 -1661.3647 1.0085627 19.655164 19.655164 19.655164 7593.2911 2461.8369 -310.60207 -260.99812 630.07891 + 1 0.5 305.62775 -1731.7838 698.75101 -2430.5349 -1604.1604 1.0085626 19.655165 19.655165 19.655165 7593.2915 3142.8129 -49.500458 364.05579 1152.4561 + 2 1 307.93402 -1731.9033 704.02379 -2435.9271 -1540.1261 1.0085623 19.655167 19.655167 19.655167 7593.2936 3746.3787 260.48522 1188.4526 1731.7722 + 3 1.5 303.9937 -1731.5145 695.0151 -2426.5296 -1474.3196 1.0085617 19.65517 19.65517 19.65517 7593.298 4217.2951 581.20066 2169.0096 2322.5018 + 4 2 296.29825 -1730.8375 677.42115 -2408.2586 -1422.3017 1.0085607 19.655177 19.655177 19.655177 7593.3057 4420.3342 803.05536 3134.9506 2786.1134 + 5 2.5 289.28952 -1730.2117 661.39723 -2391.609 -1403.9703 1.0085592 19.655187 19.655187 19.655187 7593.3172 4202.1271 794.54315 3841.3086 2945.9929 + 6 3 287.0064 -1730.0104 656.17736 -2386.1878 -1433.8797 1.0085571 19.655201 19.655201 19.655201 7593.3328 3483.5568 475.4412 4063.2546 2674.0842 + 7 3.5 290.70362 -1730.3925 664.63025 -2395.0228 -1512.4048 1.0085545 19.655217 19.655217 19.655217 7593.3522 2334.38 -125.04179 3695.988 1968.4421 + 8 4 297.9483 -1731.1172 681.19364 -2412.3108 -1623.2223 1.0085516 19.655236 19.655236 19.655236 7593.3742 978.38436 -863.23287 2807.732 974.29449 + 9 4.5 304.1085 -1731.7248 695.27757 -2427.0024 -1739.5067 1.0085485 19.655256 19.655256 19.655256 7593.3976 -286.39472 -1537.5109 1613.0927 -70.270958 + 10 5 305.20311 -1731.8889 697.78017 -2429.669 -1835.2669 1.0085454 19.655277 19.655277 19.655277 7593.421 -1211.14 -1975.9958 386.63227 -933.5012 + 11 5.5 300.04419 -1731.5836 685.98543 -2417.569 -1894.9316 1.0085425 19.655296 19.655296 19.655296 7593.443 -1690.98 -2102.807 -631.28653 -1475.0245 + 12 6 290.5412 -1731.004 664.25892 -2395.2629 -1916.6676 1.0085398 19.655313 19.655313 19.655313 7593.463 -1779.9564 -1949.6549 -1299.9765 -1676.5293 + 13 6.5 280.54125 -1730.3851 641.39621 -2371.7813 -1909.4145 1.0085375 19.655328 19.655328 19.655328 7593.4807 -1629.9189 -1621.2443 -1598.6906 -1616.6179 + 14 7 274.23791 -1729.9209 626.985 -2356.9059 -1886.3696 1.0085354 19.655341 19.655341 19.655341 7593.4961 -1400.6947 -1243.4851 -1593.9631 -1412.7143 + 15 7.5 274.67265 -1729.8323 627.97895 -2357.8113 -1857.9233 1.0085336 19.655353 19.655353 19.655353 7593.5096 -1188.49 -912.5375 -1368.9065 -1156.6446 + 16 8 282.22973 -1730.2941 645.25656 -2375.5507 -1825.9123 1.0085321 19.655363 19.655363 19.655363 7593.5215 -989.39748 -649.27115 -951.58818 -863.41894 + 17 8.5 293.73139 -1731.1656 671.55259 -2402.7182 -1781.87 1.0085306 19.655373 19.655373 19.655373 7593.5323 -706.02695 -379.02781 -288.50178 -457.85218 + 18 9 303.51319 -1731.9521 693.91654 -2425.8686 -1712.3334 1.0085293 19.655381 19.655381 19.655381 7593.5423 -206.67568 29.325988 708.81014 177.15348 + 19 9.5 306.53881 -1732.1583 700.83394 -2432.9922 -1609.7256 1.0085279 19.65539 19.65539 19.65539 7593.5527 582.39119 667.35719 2066.887 1105.5451 + 20 10 301.44803 -1731.69 689.19499 -2420.885 -1481.8674 1.0085263 19.6554 19.6554 19.6554 7593.5646 1601.7277 1494.8714 3670.9486 2255.8492 + 21 10.5 291.21481 -1730.8605 665.79899 -2396.6595 -1353.0494 1.0085243 19.655413 19.655413 19.655413 7593.5796 2645.3952 2325.386 5263.8838 3411.555 + 22 11 281.28084 -1730.0673 643.08713 -2373.1545 -1255.755 1.0085217 19.65543 19.65543 19.65543 7593.5993 3422.6014 2901.1578 6525.0281 4282.9291 + 23 11.5 276.87457 -1729.6445 633.01315 -2362.6577 -1218.3897 1.0085183 19.655453 19.655453 19.655453 7593.625 3671.1482 3002.5139 7175.8231 4616.4951 + 24 12 280.63936 -1729.8338 641.62051 -2371.4544 -1254.012 1.0085141 19.65548 19.65548 19.65548 7593.657 3274.9468 2544.367 7070.2669 4296.5269 + 25 12.5 291.14418 -1730.5902 665.63751 -2396.2277 -1354.058 1.008509 19.655513 19.655513 19.655513 7593.6951 2329.0309 1627.308 6243.5232 3399.954 + 26 13 303.27158 -1731.5375 693.36414 -2424.9017 -1490.7322 1.0085033 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569.38622 -2301.2235 -1430.6305 1.0083483 19.656557 19.656557 19.656557 7594.9051 4068.0086 1734.4276 2355.6414 2719.3592 + 47 23.5 238.94858 -1731.2335 546.30368 -2277.5372 -1523.0773 1.0083337 19.656652 19.656652 19.656652 7595.0156 3318.1889 1399.9777 919.58716 1879.2513 + 48 24 220.59727 -1730.0518 504.34741 -2234.3992 -1572.4579 1.0083186 19.65675 19.65675 19.65675 7595.1287 2859.9313 1541.2101 -132.89144 1422.75 + 49 24.5 201.1818 -1728.7353 459.9582 -2188.6935 -1595.6881 1.0083034 19.656849 19.656849 19.656849 7595.2437 2525.2504 1945.092 -866.96815 1201.1247 + 50 25 188.69771 -1727.8757 431.41605 -2159.2917 -1614.9132 1.0082879 19.65695 19.65695 19.65695 7595.3604 2129.3728 2331.9662 -1401.9762 1019.7876 + 51 25.5 188.08537 -1727.8755 430.01607 -2157.8916 -1642.8614 1.0082722 19.657052 19.657052 19.657052 7595.4786 1600.1347 2496.0662 -1793.7985 767.46745 + 52 26 198.66669 -1728.6609 454.20794 -2182.8688 -1673.7841 1.0082564 19.657155 19.657155 19.657155 7595.5978 1037.6972 2413.7371 -1965.2514 495.39431 + 53 26.5 214.57057 -1729.7351 490.56868 -2220.3038 -1685.5474 1.0082405 19.657258 19.657258 19.657258 7595.7177 670.41258 2256.7055 -1730.4377 398.89347 + 54 27 227.87941 -1730.4945 520.99643 -2251.4909 -1651.8538 1.0082245 19.657362 19.657362 19.657362 7595.8381 738.37004 2292.5831 -901.26123 709.8973 + 55 27.5 232.58657 -1730.5402 531.75833 -2262.2985 -1557.7061 1.0082083 19.657467 19.657467 19.657467 7595.9596 1368.0421 2725.6086 586.84699 1560.1659 + 56 28 227.36865 -1729.8039 519.82871 -2249.6326 -1410.1549 1.0081919 19.657573 19.657573 19.657573 7596.0832 2492.3241 3566.6081 2597.3028 2885.4117 + 57 28.5 216.09215 -1728.5822 494.04743 -2222.6296 -1239.2452 1.008175 19.657683 19.657683 19.657683 7596.2109 3847.5168 4601.4675 4802.2521 4417.0788 + 58 29 205.83675 -1727.4448 470.60071 -2198.0455 -1088.4483 1.0081572 19.657799 19.657799 19.657799 7596.3446 5053.1652 5472.7452 6777.7995 5767.9033 + 59 29.5 203.16592 -1726.931 464.49445 -2191.4254 -998.26028 1.0081384 19.657921 19.657921 19.657921 7596.4864 5749.2649 5835.2972 8147.1101 6577.2241 + 60 30 210.70938 -1727.1447 481.74092 -2208.8856 -990.90331 1.0081184 19.658051 19.658051 19.658051 7596.6373 5731.743 5502.7697 8701.7707 6645.4278 + 61 30.5 226.33789 -1727.741 517.47208 -2245.213 -1064.1106 1.0080972 19.658189 19.658189 19.658189 7596.7974 5022.101 4510.7532 8436.8566 5989.9036 + 62 31 245.01053 -1728.3521 560.163 -2288.5151 -1195.6827 1.0080748 19.658335 19.658335 19.658335 7596.9658 3842.0862 3086.2017 7494.9567 4807.7482 + 63 31.5 261.08032 -1728.8173 596.90306 -2325.7204 -1353.3389 1.0080516 19.658486 19.658486 19.658486 7597.1409 2512.9725 1564.9697 6088.7617 3388.9013 + 64 32 269.79711 -1728.9251 616.83208 -2345.7572 -1504.7683 1.0080277 19.658641 19.658641 19.658641 7597.3207 1328.3209 282.92991 4458.0227 2023.0912 + 65 32.5 268.92628 -1728.3938 614.84113 -2343.235 -1627.421 1.0080035 19.658798 19.658798 19.658798 7597.5033 452.22206 -546.30276 2827.9594 911.2929 + 66 33 260.3418 -1727.2649 595.21459 -2322.4795 -1715.3672 1.0079791 19.658957 19.658957 19.658957 7597.6872 -116.26676 -909.31142 1347.7075 107.37643 + 67 33.5 249.69892 -1725.9754 570.88198 -2296.8574 -1777.9974 1.0079547 19.659116 19.659116 19.659116 7597.8713 -500.20249 -971.59181 63.347336 -469.48232 + 68 34 243.70126 -1725.066 557.16963 -2282.2356 -1830.3139 1.0079303 19.659274 19.659274 19.659274 7598.0547 -845.49773 -967.44525 -1036.4777 -949.80688 + 69 34.5 246.61269 -1724.8653 563.82599 -2288.6913 -1880.7232 1.0079062 19.659431 19.659431 19.659431 7598.2368 -1216.8263 -1060.6291 -1942.0487 -1406.5014 + 70 35 258.03713 -1725.3332 589.94546 -2315.2786 -1923.3897 1.0078823 19.659586 19.659586 19.659586 7598.417 -1541.5641 -1248.7229 -2571.5217 -1787.2695 + 71 35.5 273.16593 -1726.0585 624.53415 -2350.5927 -1939.729 1.0078587 19.65974 19.65974 19.65974 7598.5947 -1634.7071 -1365.3713 -2784.2986 -1928.1257 + 72 36 285.38157 -1726.507 652.46254 -2378.9695 -1908.5082 1.0078355 19.659891 19.659891 19.659891 7598.7698 -1292.7504 -1183.3051 -2450.8723 -1642.3093 + 73 36.5 289.74018 -1726.3141 662.42755 -2388.7417 -1819.0223 1.0078126 19.66004 19.66004 19.66004 7598.9426 -408.71466 -562.10052 -1538.8173 -836.54415 + 74 37 285.45884 -1725.4392 652.63921 -2378.0784 -1680.0975 1.0077898 19.660188 19.660188 19.660188 7599.1142 950.20913 442.59973 -165.42681 409.12735 + 75 37.5 276.25796 -1724.188 631.60341 -2355.7914 -1520.1539 1.007767 19.660336 19.660336 19.660336 7599.2864 2539.3039 1569.1695 1414.5299 1841.0011 + 76 38 268.36655 -1723.0985 613.56143 -2336.6599 -1377.8661 1.0077438 19.660487 19.660487 19.660487 7599.4612 4010.6984 2450.7556 2883.4322 3114.9621 + 77 38.5 267.07379 -1722.6216 610.60581 -2333.2274 -1287.3418 1.00772 19.660641 19.660641 19.660641 7599.6403 5035.307 2780.6312 3966.1107 3927.3496 + 78 39 273.86909 -1722.7877 626.14177 -2348.9295 -1265.4516 1.0076956 19.6608 19.6608 19.6608 7599.8249 5416.2271 2451.927 4510.6104 4126.2548 + 79 39.5 286.08161 -1723.2441 654.06303 -2377.3071 -1308.1183 1.0076703 19.660965 19.660965 19.660965 7600.0152 5141.2099 1593.738 4501.0225 3745.3234 + 80 40 298.88372 -1723.6095 683.33226 -2406.9417 -1396.1391 1.0076444 19.661133 19.661133 19.661133 7600.2107 4356.0507 497.08424 4010.0885 2954.4078 + 81 40.5 307.74794 -1723.6731 703.59837 -2427.2715 -1505.0302 1.0076179 19.661305 19.661305 19.661305 7600.4104 3285.183 -512.81885 3145.2106 1972.5249 + 82 41 310.07081 -1723.3186 708.9091 -2432.2277 -1613.7076 1.0075911 19.66148 19.66148 19.66148 7600.6128 2144.4135 -1195.4691 2017.6001 988.84817 + 83 41.5 305.97777 -1722.5854 699.55126 -2422.1367 -1710.2062 1.0075641 19.661656 19.661656 19.661656 7600.8165 1081.7243 -1466.6202 719.92101 111.67503 + 84 42 298.03815 -1721.7005 681.39904 -2403.0995 -1792.5864 1.0075371 19.661831 19.661831 19.661831 7601.0205 163.49401 -1403.4925 -678.37812 -639.45888 + 85 42.5 289.97873 -1720.8286 662.97296 -2383.8015 -1864.9065 1.0075101 19.662006 19.662006 19.662006 7601.2236 -602.96364 -1189.5588 -2106.5331 -1299.6852 + 86 43 285.42707 -1720.1321 652.56657 -2372.6987 -1931.8624 1.0074835 19.66218 19.66218 19.66218 7601.4248 -1232.8245 -1026.3028 -3470.5924 -1909.9066 + 87 43.5 286.65463 -1719.8429 655.37311 -2375.216 -1993.4772 1.0074571 19.662351 19.662351 19.662351 7601.6235 -1727.4307 -1036.8069 -4640.4971 -2468.2449 + 88 44 293.21423 -1720.0193 670.37022 -2390.3895 -2041.1683 1.0074313 19.66252 19.66252 19.66252 7601.8187 -2044.0451 -1199.1716 -5447.0768 -2896.7645 + 89 44.5 301.68913 -1720.4077 689.74621 -2410.1539 -2058.8466 1.0074059 19.662685 19.662685 19.662685 7602.0099 -2090.5154 -1357.509 -5709.903 -3052.6425 + 90 45 307.31944 -1720.5984 702.61869 -2423.2171 -2030.1879 1.0073811 19.662846 19.662846 19.662846 7602.1969 -1764.4626 -1315.8041 -5296.8072 -2792.358 + 91 45.5 306.63737 -1720.284 701.05929 -2421.3433 -1948.3884 1.0073569 19.663004 19.663004 19.663004 7602.3801 -1027.7935 -956.38563 -4187.872 -2057.3504 + 92 46 299.48972 -1719.4374 684.71774 -2404.1552 -1822.8365 1.007333 19.663159 19.663159 19.663159 7602.5604 26.751851 -313.98567 -2510.4728 -932.56888 + 93 46.5 289.23303 -1718.3493 661.26808 -2379.6174 -1678.4934 1.0073093 19.663313 19.663313 19.663313 7602.7394 1167.8941 431.33019 -520.85477 359.4565 + 94 47 280.8783 -1717.4708 642.16681 -2359.6377 -1547.5998 1.0072855 19.663468 19.663468 19.663468 7602.9189 2094.2021 1037.1223 1464.7219 1532.0154 + 95 47.5 278.23295 -1717.1077 636.1188 -2353.2265 -1457.5732 1.0072614 19.663625 19.663625 19.663625 7603.1006 2548.2421 1314.5303 3159.0476 2340.6067 + 96 48 281.92564 -1717.2059 644.56133 -2361.7672 -1421.7715 1.0072369 19.663784 19.663784 19.663784 7603.2855 2413.1905 1214.185 4365.5387 2664.3047 + 97 48.5 289.58886 -1717.4536 662.08159 -2379.5352 -1437.6426 1.0072119 19.663947 19.663947 19.663947 7603.4742 1740.0276 838.91482 4991.0957 2523.346 + 98 49 297.63541 -1717.5994 680.47828 -2398.0777 -1491.6173 1.0071865 19.664113 19.664113 19.664113 7603.6664 701.28193 384.37336 5027.9366 2037.864 + 99 49.5 302.89083 -1717.5771 692.49365 -2410.0708 -1566.0823 1.0071606 19.664281 19.664281 19.664281 7603.8614 -486.15582 46.291916 4538.2141 1366.1167 + 100 50 303.33647 -1717.3173 693.51249 -2410.8298 -1645.0949 1.0071346 19.66445 19.66445 19.66445 7604.0583 -1621.9659 -60.918905 3636.648 651.25441 +Loop time of 78.2045 on 1 procs for 100 steps with 768 atoms + +Performance: 0.055 ns/day, 434.470 hours/ns, 1.279 timesteps/s, 982.040 atom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 77.772 | 77.772 | 77.772 | 0.0 | 99.45 +Bond | 0.00018066 | 0.00018066 | 0.00018066 | 0.0 | 0.00 +Neigh | 0.012733 | 0.012733 | 0.012733 | 0.0 | 0.02 +Comm | 0.0060702 | 0.0060702 | 0.0060702 | 0.0 | 0.01 +Output | 0.26325 | 0.26325 | 0.26325 | 0.0 | 0.34 +Modify | 0.14864 | 0.14864 | 0.14864 | 0.0 | 0.19 +Other | | 0.001345 | | | 0.00 + +Nlocal: 768 ave 768 max 768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6623 ave 6623 max 6623 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 215645 ave 215645 max 215645 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 215645 +Ave neighs/atom = 280.78776 +Ave special neighs/atom = 2 +Neighbor list builds = 2 +Dangerous builds = 0 + +# write_data final.data +# write_restart restart.new +Total wall time: 0:01:19 diff --git a/examples/PACKAGES/mbx/256h2o/mbx.json b/examples/PACKAGES/mbx/256h2o/mbx.json new file mode 100644 index 00000000000..bba72b3cd19 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o/mbx.json @@ -0,0 +1,21 @@ +{ + "Note" : "This is an MBX v1.3 configuration file", + "MBX" : { + "box" : [], + "realspace_cutoff": 9.0, + "twobody_cutoff" : 6.5, + "threebody_cutoff" : 4.5, + "dipole_tolerance" : 1E-8, + "dipole_max_it" : 100, + "dipole_method" : "cg", + "alpha_ewald_elec" : 0.60, + "grid_density_elec" : 2.5, + "spline_order_elec" : 6, + "alpha_ewald_disp" : 0.60, + "grid_density_disp" : 2.5, + "spline_order_disp" : 6, + "ignore_2b_poly" : [], + "ignore_3b_poly" : [] + } +} + diff --git a/examples/PACKAGES/mbx/256h2o_dipole/in.mbx_h2o b/examples/PACKAGES/mbx/256h2o_dipole/in.mbx_h2o new file mode 100644 index 00000000000..cd933684d72 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o_dipole/in.mbx_h2o @@ -0,0 +1,74 @@ +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 1 h2o 1 2 2 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +#fix RIGID all shake 0.0001 20 0 b 1 a 1 +fix 1 all npt temp 298 298 100 iso 1.0 1.0 1000 + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + + +# Dipole moments in Debye units ## +variable dipnorm_tot atom sqrt(f__FIX_MBX_INTERNAL[7]*f__FIX_MBX_INTERNAL[7]+f__FIX_MBX_INTERNAL[8]*f__FIX_MBX_INTERNAL[8]+f__FIX_MBX_INTERNAL[9]*f__FIX_MBX_INTERNAL[9])/0.2081943 # original (total dipole) +variable dipnorm_ind atom sqrt(f__FIX_MBX_INTERNAL[4]*f__FIX_MBX_INTERNAL[4]+f__FIX_MBX_INTERNAL[5]*f__FIX_MBX_INTERNAL[5]+f__FIX_MBX_INTERNAL[6]*f__FIX_MBX_INTERNAL[6])/0.2081943 # induced +variable dipnorm_perm atom sqrt(f__FIX_MBX_INTERNAL[1]*f__FIX_MBX_INTERNAL[1]+f__FIX_MBX_INTERNAL[2]*f__FIX_MBX_INTERNAL[2]+f__FIX_MBX_INTERNAL[3]*f__FIX_MBX_INTERNAL[3])/0.2081943 # perm + +variable dipx_perm atom f__FIX_MBX_INTERNAL[1]/0.2081943 +variable dipy_perm atom f__FIX_MBX_INTERNAL[2]/0.2081943 +variable dipz_perm atom f__FIX_MBX_INTERNAL[3]/0.2081943 +variable dipx_ind atom f__FIX_MBX_INTERNAL[4]/0.2081943 +variable dipy_ind atom f__FIX_MBX_INTERNAL[5]/0.2081943 +variable dipz_ind atom f__FIX_MBX_INTERNAL[6]/0.2081943 + +# Dump details ## +dump 3 all custom 8 dump.dipoles id mol type q x y z v_dipx_perm v_dipy_perm v_dipz_perm v_dipnorm_perm v_dipx_ind v_dipy_ind v_dipz_ind v_dipnorm_ind +dump_modify 3 sort id + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +# write_data final.data +# write_restart restart.new diff --git a/examples/PACKAGES/mbx/256h2o_dipole/initial.data b/examples/PACKAGES/mbx/256h2o_dipole/initial.data new file mode 100644 index 00000000000..dcb55bfa2e9 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o_dipole/initial.data @@ -0,0 +1,2333 @@ +LAMMPS data file via write_data, version 2 Aug 2023, timestep = 100, units = real + +768 atoms +2 atom types +512 bonds +1 bond types +256 angles +1 angle types + +0.00033828338625596643 19.655502780867728 xlo xhi +0.00033828338625596643 19.655502780867728 ylo yhi +0.00033828338625596643 19.655502780867728 zlo zhi + +Masses + +1 15.9994 +2 1.008 + +Atoms # full + +1 1 1 -1.1128 2.6696248870790638 5.260932495840358 17.60809921420046 0 0 0 +2 1 2 0.5564 2.2427255320728574 5.934093787418942 17.063711679904596 0 0 0 +3 1 2 0.5564 2.159991697924501 5.3027213316423625 18.45965714856477 0 0 0 +4 2 1 -1.1128 1.389571720018154 4.897222580064953 0.1909144892826206 0 0 0 +5 2 2 0.5564 1.008023450378975 5.190782049871591 1.016108977687535 0 0 0 +6 2 2 0.5564 1.479399014421124 3.9438465336017954 0.32527591971768005 0 0 0 +7 3 1 -1.1128 8.8457943246556 5.310840562924772 0.8842110790859935 0 0 0 +8 3 2 0.5564 9.515727095293595 5.779985090038478 1.3701108097537686 0 0 0 +9 3 2 0.5564 9.486575337444252 4.70104097795048 0.45119169463407166 0 0 0 +10 4 1 -1.1128 15.041815452442309 1.5411227304596038 3.8080365668081524 0 0 0 +11 4 2 0.5564 14.367575662160878 1.8759746612135642 3.1883172534896485 0 0 0 +12 4 2 0.5564 15.834959646499327 1.9438308864285097 3.448562963546067 0 0 0 +13 5 1 -1.1128 17.325518320756224 3.1606639795692857 0.08129036843447073 0 0 0 +14 5 2 0.5564 17.36179397407105 4.1157297566878 0.09421953778870636 0 0 0 +15 5 2 0.5564 17.614844884297572 2.9808360091339545 0.9963625862748109 0 0 0 +16 6 1 -1.1128 3.8328670810789793 6.868546562799202 3.571034673265516 0 0 0 +17 6 2 0.5564 3.877353329871918 6.249294751390314 4.316906656040641 0 0 0 +18 6 2 0.5564 3.757413854871904 6.45300878862338 2.6730961297581834 0 0 0 +19 7 1 -1.1128 10.642974881728387 11.003618407599596 5.799884834950075 0 0 0 +20 7 2 0.5564 11.538788108539968 10.606820017576833 5.788274265019343 0 0 0 +21 7 2 0.5564 10.021816377499416 10.268889336734984 5.74279745910355 0 0 0 +22 8 1 -1.1128 8.394837178400177 9.2340359539736 5.289562986398152 0 0 0 +23 8 2 0.5564 7.516611464806527 9.126892405843103 4.989735929933016 0 0 0 +24 8 2 0.5564 8.579882485325838 8.40162289589208 5.790461343296388 0 0 0 +25 9 1 -1.1128 13.683435631173596 5.80471712486567 1.5904685613688943 0 0 0 +26 9 2 0.5564 13.172825412905967 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initial.data +Reading data file ... + orthogonal box = (0.00033828339 0.00033828339 0.00033828339) to (19.655503 19.655503 19.655503) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 768 atoms + reading velocities ... + 768 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + orthogonal box = (0.00033828339 0.00033828339 0.00033828339) to (19.655503 19.655503 19.655503) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 512 bonds + reading angles ... + 256 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.030 seconds + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 1 h2o 1 2 2 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +#fix RIGID all shake 0.0001 20 0 b 1 a 1 +fix 1 all npt temp 298 298 100 iso 1.0 1.0 1000 + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + + +# Dipole moments in Debye units ## +variable dipnorm_tot atom sqrt(f__FIX_MBX_INTERNAL[7]*f__FIX_MBX_INTERNAL[7]+f__FIX_MBX_INTERNAL[8]*f__FIX_MBX_INTERNAL[8]+f__FIX_MBX_INTERNAL[9]*f__FIX_MBX_INTERNAL[9])/0.2081943 # original (total dipole) +variable dipnorm_ind atom sqrt(f__FIX_MBX_INTERNAL[4]*f__FIX_MBX_INTERNAL[4]+f__FIX_MBX_INTERNAL[5]*f__FIX_MBX_INTERNAL[5]+f__FIX_MBX_INTERNAL[6]*f__FIX_MBX_INTERNAL[6])/0.2081943 # induced +variable dipnorm_perm atom sqrt(f__FIX_MBX_INTERNAL[1]*f__FIX_MBX_INTERNAL[1]+f__FIX_MBX_INTERNAL[2]*f__FIX_MBX_INTERNAL[2]+f__FIX_MBX_INTERNAL[3]*f__FIX_MBX_INTERNAL[3])/0.2081943 # perm + +variable dipx_perm atom f__FIX_MBX_INTERNAL[1]/0.2081943 +variable dipy_perm atom f__FIX_MBX_INTERNAL[2]/0.2081943 +variable dipz_perm atom f__FIX_MBX_INTERNAL[3]/0.2081943 +variable dipx_ind atom f__FIX_MBX_INTERNAL[4]/0.2081943 +variable dipy_ind atom f__FIX_MBX_INTERNAL[5]/0.2081943 +variable dipz_ind atom f__FIX_MBX_INTERNAL[6]/0.2081943 + +# Dump details ## +dump 3 all custom 8 dump.dipoles id mol type q x y z v_dipx_perm v_dipy_perm v_dipz_perm v_dipnorm_perm v_dipx_ind v_dipy_ind v_dipz_ind v_dipnorm_ind +dump_modify 3 sort id + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair mbx command: + +@article{10.1063/5.0156036, + author = {Riera, Marc and Knight, Christopher and Bull-Vulpe, Ethan F. and Zhu, Xuanyu and Agnew, Henry and Smith, Daniel G. A. and Simmonett, Andrew C. and Paesani, Francesco}, + title = "{MBX: A many-body energy and force calculator for data-driven many-body simulations}", + journal = {The Journal of Chemical Physics}, + volume = {159}, + number = {5}, + pages = {054802}, + year = {2023}, + doi = {10.1063/5.0156036}, + version = {1.3.3} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 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 = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mbx, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes + Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press + 0 0 298 -1731.1398 681.31183 -2412.4517 -1661.3647 1.0085627 19.655164 19.655164 19.655164 7593.2911 2461.8369 -310.60207 -260.99812 630.07891 + 1 0.5 305.62775 -1731.7838 698.75101 -2430.5349 -1604.1604 1.0085626 19.655165 19.655165 19.655165 7593.2915 3142.8129 -49.500458 364.05579 1152.4561 + 2 1 307.93402 -1731.9033 704.02379 -2435.9271 -1540.1261 1.0085623 19.655167 19.655167 19.655167 7593.2936 3746.3787 260.48522 1188.4526 1731.7722 + 3 1.5 303.9937 -1731.5145 695.0151 -2426.5296 -1474.3196 1.0085617 19.65517 19.65517 19.65517 7593.298 4217.2951 581.20066 2169.0096 2322.5018 + 4 2 296.29825 -1730.8375 677.42115 -2408.2586 -1422.3017 1.0085607 19.655177 19.655177 19.655177 7593.3057 4420.3342 803.05536 3134.9506 2786.1134 + 5 2.5 289.28952 -1730.2117 661.39723 -2391.609 -1403.9703 1.0085592 19.655187 19.655187 19.655187 7593.3172 4202.1271 794.54315 3841.3086 2945.9929 + 6 3 287.0064 -1730.0104 656.17736 -2386.1878 -1433.8797 1.0085571 19.655201 19.655201 19.655201 7593.3328 3483.5568 475.4412 4063.2546 2674.0842 + 7 3.5 290.70362 -1730.3925 664.63025 -2395.0228 -1512.4048 1.0085545 19.655217 19.655217 19.655217 7593.3522 2334.38 -125.04179 3695.988 1968.4421 + 8 4 297.9483 -1731.1172 681.19364 -2412.3108 -1623.2223 1.0085516 19.655236 19.655236 19.655236 7593.3742 978.38436 -863.23287 2807.732 974.29449 + 9 4.5 304.1085 -1731.7248 695.27757 -2427.0024 -1739.5067 1.0085485 19.655256 19.655256 19.655256 7593.3976 -286.39472 -1537.5109 1613.0927 -70.270958 + 10 5 305.20311 -1731.8889 697.78017 -2429.669 -1835.2669 1.0085454 19.655277 19.655277 19.655277 7593.421 -1211.14 -1975.9958 386.63227 -933.5012 + 11 5.5 300.04419 -1731.5836 685.98543 -2417.569 -1894.9316 1.0085425 19.655296 19.655296 19.655296 7593.443 -1690.98 -2102.807 -631.28653 -1475.0245 + 12 6 290.5412 -1731.004 664.25892 -2395.2629 -1916.6676 1.0085398 19.655313 19.655313 19.655313 7593.463 -1779.9564 -1949.6549 -1299.9765 -1676.5293 + 13 6.5 280.54125 -1730.3851 641.39621 -2371.7813 -1909.4145 1.0085375 19.655328 19.655328 19.655328 7593.4807 -1629.9189 -1621.2443 -1598.6906 -1616.6179 + 14 7 274.23791 -1729.9209 626.985 -2356.9059 -1886.3696 1.0085354 19.655341 19.655341 19.655341 7593.4961 -1400.6947 -1243.4851 -1593.9631 -1412.7143 + 15 7.5 274.67265 -1729.8323 627.97895 -2357.8113 -1857.9233 1.0085336 19.655353 19.655353 19.655353 7593.5096 -1188.49 -912.5375 -1368.9065 -1156.6446 + 16 8 282.22973 -1730.2941 645.25656 -2375.5507 -1825.9123 1.0085321 19.655363 19.655363 19.655363 7593.5215 -989.39748 -649.27115 -951.58818 -863.41894 + 17 8.5 293.73139 -1731.1656 671.55259 -2402.7182 -1781.87 1.0085306 19.655373 19.655373 19.655373 7593.5323 -706.02695 -379.02781 -288.50178 -457.85218 + 18 9 303.51319 -1731.9521 693.91654 -2425.8686 -1712.3334 1.0085293 19.655381 19.655381 19.655381 7593.5423 -206.67568 29.325988 708.81014 177.15348 + 19 9.5 306.53881 -1732.1583 700.83394 -2432.9922 -1609.7256 1.0085279 19.65539 19.65539 19.65539 7593.5527 582.39119 667.35719 2066.887 1105.5451 + 20 10 301.44803 -1731.69 689.19499 -2420.885 -1481.8674 1.0085263 19.6554 19.6554 19.6554 7593.5646 1601.7277 1494.8714 3670.9486 2255.8492 + 21 10.5 291.21481 -1730.8605 665.79899 -2396.6595 -1353.0494 1.0085243 19.655413 19.655413 19.655413 7593.5796 2645.3952 2325.386 5263.8838 3411.555 + 22 11 281.28084 -1730.0673 643.08713 -2373.1545 -1255.755 1.0085217 19.65543 19.65543 19.65543 7593.5993 3422.6014 2901.1578 6525.0281 4282.9291 + 23 11.5 276.87457 -1729.6445 633.01315 -2362.6577 -1218.3897 1.0085183 19.655453 19.655453 19.655453 7593.625 3671.1482 3002.5139 7175.8231 4616.4951 + 24 12 280.63936 -1729.8338 641.62051 -2371.4544 -1254.012 1.0085141 19.65548 19.65548 19.65548 7593.657 3274.9468 2544.367 7070.2669 4296.5269 + 25 12.5 291.14418 -1730.5902 665.63751 -2396.2277 -1354.058 1.008509 19.655513 19.655513 19.655513 7593.6951 2329.0309 1627.308 6243.5232 3399.954 + 26 13 303.27158 -1731.5375 693.36414 -2424.9017 -1490.7322 1.0085033 19.65555 19.65555 19.65555 7593.7378 1113.5704 511.11773 4898.4402 2174.3761 + 27 13.5 310.61407 -1732.2229 710.15113 -2442.374 -1627.75 1.0084972 19.655589 19.655589 19.655589 7593.7836 -17.710741 -486.57444 3334.3122 943.34235 + 28 14 308.4633 -1732.3517 705.23388 -2437.5856 -1733.9652 1.008491 19.65563 19.65563 19.65563 7593.8307 -781.35597 -1116.4799 1854.1273 -14.569507 + 29 14.5 295.86322 -1731.8464 676.42655 -2408.273 -1793.6016 1.0084847 19.655671 19.655671 19.655671 7593.8777 -1070.2353 -1285.9528 683.34637 -557.61391 + 30 15 276.15727 -1730.8542 631.37321 -2362.2274 -1809.6882 1.0084786 19.655711 19.655711 19.655711 7593.924 -974.88816 -1075.3604 -85.217329 -711.82197 + 31 15.5 255.89625 -1729.7656 585.05082 -2314.8165 -1799.7168 1.0084726 19.65575 19.65575 19.65575 7593.9693 -713.21572 -684.15402 -497.46606 -631.61193 + 32 16 242.15062 -1729.0942 553.62444 -2282.7186 -1784.7657 1.0084667 19.655788 19.655788 19.655788 7594.0138 -500.79186 -331.17593 -676.05284 -502.67354 + 33 16.5 239.1893 -1729.1724 546.85403 -2276.0264 -1776.8224 1.0084609 19.655826 19.655826 19.655826 7594.0576 -425.29073 -147.18828 -718.24925 -430.24275 + 34 17 246.33128 -1729.9515 563.18261 -2293.1341 -1771.1575 1.0084551 19.655863 19.655863 19.655863 7594.1007 -394.00513 -106.26895 -615.89161 -372.05523 + 35 17.5 258.24144 -1731.0399 590.41258 -2321.4525 -1748.1657 1.0084495 19.6559 19.6559 19.6559 7594.1434 -181.26587 -32.371063 -250.25697 -154.6313 + 36 18 267.47656 -1731.9227 611.52666 -2343.4493 -1683.8741 1.0084438 19.655936 19.655936 19.655936 7594.1858 453.0454 313.93963 534.51734 433.83412 + 37 18.5 267.9357 -1732.1915 612.57638 -2344.7679 -1563.9514 1.0084381 19.655974 19.655974 19.655974 7594.2289 1633.1772 1102.8046 1821.1448 1519.0422 + 38 19 257.63044 -1731.6977 589.01565 -2320.7133 -1394.3671 1.0084321 19.656013 19.656013 19.656013 7594.274 3283.7378 2322.4014 3531.0972 3045.7455 + 39 19.5 239.69151 -1730.615 548.00223 -2278.6172 -1203.7766 1.0084256 19.656055 19.656055 19.656055 7594.3234 5124.6895 3745.0405 5400.5882 4756.7727 + 40 20 221.14295 -1729.4168 505.59499 -2235.0118 -1035.8607 1.0084181 19.656104 19.656104 19.656104 7594.3794 6752.0038 4996.8546 7037.1568 6262.0051 + 41 20.5 209.69589 -1728.6881 479.42379 -2208.1119 -933.73875 1.0084095 19.656159 19.656159 19.656159 7594.4441 7781.8785 5707.3758 8042.9665 7177.4069 + 42 21 209.91575 -1728.8029 479.92646 -2208.7294 -922.95774 1.0083996 19.656224 19.656224 19.656224 7594.5187 8000.2488 5668.6097 8158.2762 7275.7116 + 43 21.5 220.76906 -1729.7025 504.74017 -2234.4426 -1001.1378 1.0083884 19.656297 19.656297 19.656297 7594.6034 7443.4993 4926.589 7363.6054 6577.8979 + 44 22 236.03186 -1730.8731 539.63522 -2270.5084 -1139.4338 1.0083759 19.656378 19.656378 19.656378 7594.6972 6369.5818 3764.2426 5885.5327 5339.7857 + 45 22.5 247.51488 -1731.6979 565.88865 -2297.5865 -1295.4642 1.0083625 19.656465 19.656465 19.656465 7594.7984 5138.9597 2582.3337 4094.1024 3938.4653 + 46 23 249.04469 -1731.8373 569.38622 -2301.2235 -1430.6305 1.0083483 19.656557 19.656557 19.656557 7594.9051 4068.0086 1734.4276 2355.6414 2719.3592 + 47 23.5 238.94858 -1731.2335 546.30368 -2277.5372 -1523.0773 1.0083337 19.656652 19.656652 19.656652 7595.0156 3318.1889 1399.9777 919.58716 1879.2513 + 48 24 220.59727 -1730.0518 504.34741 -2234.3992 -1572.4579 1.0083186 19.65675 19.65675 19.65675 7595.1287 2859.9313 1541.2101 -132.89144 1422.75 + 49 24.5 201.1818 -1728.7353 459.9582 -2188.6935 -1595.6881 1.0083034 19.656849 19.656849 19.656849 7595.2437 2525.2504 1945.092 -866.96815 1201.1247 + 50 25 188.69771 -1727.8757 431.41605 -2159.2917 -1614.9132 1.0082879 19.65695 19.65695 19.65695 7595.3604 2129.3728 2331.9662 -1401.9762 1019.7876 + 51 25.5 188.08537 -1727.8755 430.01607 -2157.8916 -1642.8614 1.0082722 19.657052 19.657052 19.657052 7595.4786 1600.1347 2496.0662 -1793.7985 767.46745 + 52 26 198.66669 -1728.6609 454.20794 -2182.8688 -1673.7841 1.0082564 19.657155 19.657155 19.657155 7595.5978 1037.6972 2413.7371 -1965.2514 495.39431 + 53 26.5 214.57057 -1729.7351 490.56868 -2220.3038 -1685.5474 1.0082405 19.657258 19.657258 19.657258 7595.7177 670.41258 2256.7055 -1730.4377 398.89347 + 54 27 227.87941 -1730.4945 520.99643 -2251.4909 -1651.8538 1.0082245 19.657362 19.657362 19.657362 7595.8381 738.37004 2292.5831 -901.26123 709.8973 + 55 27.5 232.58657 -1730.5402 531.75833 -2262.2985 -1557.7061 1.0082083 19.657467 19.657467 19.657467 7595.9596 1368.0421 2725.6086 586.84699 1560.1659 + 56 28 227.36865 -1729.8039 519.82871 -2249.6326 -1410.1549 1.0081919 19.657573 19.657573 19.657573 7596.0832 2492.3241 3566.6081 2597.3028 2885.4117 + 57 28.5 216.09215 -1728.5822 494.04743 -2222.6296 -1239.2452 1.008175 19.657683 19.657683 19.657683 7596.2109 3847.5168 4601.4675 4802.2521 4417.0788 + 58 29 205.83675 -1727.4448 470.60071 -2198.0455 -1088.4483 1.0081572 19.657799 19.657799 19.657799 7596.3446 5053.1652 5472.7452 6777.7995 5767.9033 + 59 29.5 203.16592 -1726.931 464.49445 -2191.4254 -998.26028 1.0081384 19.657921 19.657921 19.657921 7596.4864 5749.2649 5835.2972 8147.1101 6577.2241 + 60 30 210.70938 -1727.1447 481.74092 -2208.8856 -990.90331 1.0081184 19.658051 19.658051 19.658051 7596.6373 5731.743 5502.7697 8701.7707 6645.4278 + 61 30.5 226.33789 -1727.741 517.47208 -2245.213 -1064.1106 1.0080972 19.658189 19.658189 19.658189 7596.7974 5022.101 4510.7532 8436.8566 5989.9036 + 62 31 245.01053 -1728.3521 560.163 -2288.5151 -1195.6827 1.0080748 19.658335 19.658335 19.658335 7596.9658 3842.0862 3086.2017 7494.9567 4807.7482 + 63 31.5 261.08032 -1728.8173 596.90306 -2325.7204 -1353.3389 1.0080516 19.658486 19.658486 19.658486 7597.1409 2512.9725 1564.9697 6088.7617 3388.9013 + 64 32 269.79711 -1728.9251 616.83208 -2345.7572 -1504.7683 1.0080277 19.658641 19.658641 19.658641 7597.3207 1328.3209 282.92991 4458.0227 2023.0912 + 65 32.5 268.92628 -1728.3938 614.84113 -2343.235 -1627.421 1.0080035 19.658798 19.658798 19.658798 7597.5033 452.22206 -546.30276 2827.9594 911.2929 + 66 33 260.3418 -1727.2649 595.21459 -2322.4795 -1715.3672 1.0079791 19.658957 19.658957 19.658957 7597.6872 -116.26676 -909.31142 1347.7075 107.37643 + 67 33.5 249.69892 -1725.9754 570.88198 -2296.8574 -1777.9974 1.0079547 19.659116 19.659116 19.659116 7597.8713 -500.20249 -971.59181 63.347336 -469.48232 + 68 34 243.70126 -1725.066 557.16963 -2282.2356 -1830.3139 1.0079303 19.659274 19.659274 19.659274 7598.0547 -845.49773 -967.44525 -1036.4777 -949.80688 + 69 34.5 246.61269 -1724.8653 563.82599 -2288.6913 -1880.7232 1.0079062 19.659431 19.659431 19.659431 7598.2368 -1216.8263 -1060.6291 -1942.0487 -1406.5014 + 70 35 258.03713 -1725.3332 589.94546 -2315.2786 -1923.3897 1.0078823 19.659586 19.659586 19.659586 7598.417 -1541.5641 -1248.7229 -2571.5217 -1787.2695 + 71 35.5 273.16593 -1726.0585 624.53415 -2350.5927 -1939.729 1.0078587 19.65974 19.65974 19.65974 7598.5947 -1634.7071 -1365.3713 -2784.2986 -1928.1257 + 72 36 285.38157 -1726.507 652.46254 -2378.9695 -1908.5082 1.0078355 19.659891 19.659891 19.659891 7598.7698 -1292.7504 -1183.3051 -2450.8723 -1642.3093 + 73 36.5 289.74018 -1726.3141 662.42755 -2388.7417 -1819.0223 1.0078126 19.66004 19.66004 19.66004 7598.9426 -408.71466 -562.10052 -1538.8173 -836.54415 + 74 37 285.45884 -1725.4392 652.63921 -2378.0784 -1680.0975 1.0077898 19.660188 19.660188 19.660188 7599.1142 950.20913 442.59973 -165.42681 409.12735 + 75 37.5 276.25796 -1724.188 631.60341 -2355.7914 -1520.1539 1.007767 19.660336 19.660336 19.660336 7599.2864 2539.3039 1569.1695 1414.5299 1841.0011 + 76 38 268.36655 -1723.0985 613.56143 -2336.6599 -1377.8661 1.0077438 19.660487 19.660487 19.660487 7599.4612 4010.6984 2450.7556 2883.4322 3114.9621 + 77 38.5 267.07379 -1722.6216 610.60581 -2333.2274 -1287.3418 1.00772 19.660641 19.660641 19.660641 7599.6403 5035.307 2780.6312 3966.1107 3927.3496 + 78 39 273.86909 -1722.7877 626.14177 -2348.9295 -1265.4516 1.0076956 19.6608 19.6608 19.6608 7599.8249 5416.2271 2451.927 4510.6104 4126.2548 + 79 39.5 286.08161 -1723.2441 654.06303 -2377.3071 -1308.1183 1.0076703 19.660965 19.660965 19.660965 7600.0152 5141.2099 1593.738 4501.0225 3745.3234 + 80 40 298.88372 -1723.6095 683.33226 -2406.9417 -1396.1391 1.0076444 19.661133 19.661133 19.661133 7600.2107 4356.0507 497.08424 4010.0885 2954.4078 + 81 40.5 307.74794 -1723.6731 703.59837 -2427.2715 -1505.0302 1.0076179 19.661305 19.661305 19.661305 7600.4104 3285.183 -512.81885 3145.2106 1972.5249 + 82 41 310.07081 -1723.3186 708.9091 -2432.2277 -1613.7076 1.0075911 19.66148 19.66148 19.66148 7600.6128 2144.4135 -1195.4691 2017.6001 988.84817 + 83 41.5 305.97777 -1722.5854 699.55126 -2422.1367 -1710.2062 1.0075641 19.661656 19.661656 19.661656 7600.8165 1081.7243 -1466.6202 719.92101 111.67503 + 84 42 298.03815 -1721.7005 681.39904 -2403.0995 -1792.5864 1.0075371 19.661831 19.661831 19.661831 7601.0205 163.49401 -1403.4925 -678.37812 -639.45888 + 85 42.5 289.97873 -1720.8286 662.97296 -2383.8015 -1864.9065 1.0075101 19.662006 19.662006 19.662006 7601.2236 -602.96364 -1189.5588 -2106.5331 -1299.6852 + 86 43 285.42707 -1720.1321 652.56657 -2372.6987 -1931.8624 1.0074835 19.66218 19.66218 19.66218 7601.4248 -1232.8245 -1026.3028 -3470.5924 -1909.9066 + 87 43.5 286.65463 -1719.8429 655.37311 -2375.216 -1993.4772 1.0074571 19.662351 19.662351 19.662351 7601.6235 -1727.4307 -1036.8069 -4640.4971 -2468.2449 + 88 44 293.21423 -1720.0193 670.37022 -2390.3895 -2041.1683 1.0074313 19.66252 19.66252 19.66252 7601.8187 -2044.0451 -1199.1716 -5447.0768 -2896.7645 + 89 44.5 301.68913 -1720.4077 689.74621 -2410.1539 -2058.8466 1.0074059 19.662685 19.662685 19.662685 7602.0099 -2090.5154 -1357.509 -5709.903 -3052.6425 + 90 45 307.31944 -1720.5984 702.61869 -2423.2171 -2030.1879 1.0073811 19.662846 19.662846 19.662846 7602.1969 -1764.4626 -1315.8041 -5296.8072 -2792.358 + 91 45.5 306.63737 -1720.284 701.05929 -2421.3433 -1948.3884 1.0073569 19.663004 19.663004 19.663004 7602.3801 -1027.7935 -956.38563 -4187.872 -2057.3504 + 92 46 299.48972 -1719.4374 684.71774 -2404.1552 -1822.8365 1.007333 19.663159 19.663159 19.663159 7602.5604 26.751851 -313.98567 -2510.4728 -932.56888 + 93 46.5 289.23303 -1718.3493 661.26808 -2379.6174 -1678.4934 1.0073093 19.663313 19.663313 19.663313 7602.7394 1167.8941 431.33019 -520.85477 359.4565 + 94 47 280.8783 -1717.4708 642.16681 -2359.6377 -1547.5998 1.0072855 19.663468 19.663468 19.663468 7602.9189 2094.2021 1037.1223 1464.7219 1532.0154 + 95 47.5 278.23295 -1717.1077 636.1188 -2353.2265 -1457.5732 1.0072614 19.663625 19.663625 19.663625 7603.1006 2548.2421 1314.5303 3159.0476 2340.6067 + 96 48 281.92564 -1717.2059 644.56133 -2361.7672 -1421.7715 1.0072369 19.663784 19.663784 19.663784 7603.2855 2413.1905 1214.185 4365.5387 2664.3047 + 97 48.5 289.58886 -1717.4536 662.08159 -2379.5352 -1437.6426 1.0072119 19.663947 19.663947 19.663947 7603.4742 1740.0276 838.91482 4991.0957 2523.346 + 98 49 297.63541 -1717.5994 680.47828 -2398.0777 -1491.6173 1.0071865 19.664113 19.664113 19.664113 7603.6664 701.28193 384.37336 5027.9366 2037.864 + 99 49.5 302.89083 -1717.5771 692.49365 -2410.0708 -1566.0823 1.0071606 19.664281 19.664281 19.664281 7603.8614 -486.15582 46.291916 4538.2141 1366.1167 + 100 50 303.33647 -1717.3173 693.51249 -2410.8298 -1645.0949 1.0071346 19.66445 19.66445 19.66445 7604.0583 -1621.9659 -60.918905 3636.648 651.25441 +Loop time of 76.6262 on 1 procs for 100 steps with 768 atoms + +Performance: 0.056 ns/day, 425.701 hours/ns, 1.305 timesteps/s, 1.002 katom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 76.148 | 76.148 | 76.148 | 0.0 | 99.38 +Bond | 0.00012364 | 0.00012364 | 0.00012364 | 0.0 | 0.00 +Neigh | 0.011958 | 0.011958 | 0.011958 | 0.0 | 0.02 +Comm | 0.0059952 | 0.0059952 | 0.0059952 | 0.0 | 0.01 +Output | 0.32622 | 0.32622 | 0.32622 | 0.0 | 0.43 +Modify | 0.13265 | 0.13265 | 0.13265 | 0.0 | 0.17 +Other | | 0.001514 | | | 0.00 + +Nlocal: 768 ave 768 max 768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6623 ave 6623 max 6623 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 215645 ave 215645 max 215645 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 215645 +Ave neighs/atom = 280.78776 +Ave special neighs/atom = 2 +Neighbor list builds = 2 +Dangerous builds = 0 + +# write_data final.data +# write_restart restart.new +Total wall time: 0:01:17 diff --git a/examples/PACKAGES/mbx/256h2o_dipole/mbx.json b/examples/PACKAGES/mbx/256h2o_dipole/mbx.json new file mode 100644 index 00000000000..bba72b3cd19 --- /dev/null +++ b/examples/PACKAGES/mbx/256h2o_dipole/mbx.json @@ -0,0 +1,21 @@ +{ + "Note" : "This is an MBX v1.3 configuration file", + "MBX" : { + "box" : [], + "realspace_cutoff": 9.0, + "twobody_cutoff" : 6.5, + "threebody_cutoff" : 4.5, + "dipole_tolerance" : 1E-8, + "dipole_max_it" : 100, + "dipole_method" : "cg", + "alpha_ewald_elec" : 0.60, + "grid_density_elec" : 2.5, + "spline_order_elec" : 6, + "alpha_ewald_disp" : 0.60, + "grid_density_disp" : 2.5, + "spline_order_disp" : 6, + "ignore_2b_poly" : [], + "ignore_3b_poly" : [] + } +} + diff --git a/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/in.mbx_mof_1h2o b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/in.mbx_mof_1h2o new file mode 100644 index 00000000000..8bf4dc79826 --- /dev/null +++ b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/in.mbx_mof_1h2o @@ -0,0 +1,249 @@ +# Depositing TIP3P water into MOF with QeQ charges obtained with Ongari scheme + +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data + +group mof type 1 2 3 4 5 6 7 8 9 10 11 +group h2o type 12 13 + +## Bonded styles ## +bond_style harmonic +angle_style harmonic +dihedral_style harmonic +improper_style cvff + +## MOF ## +bond_coeff 1 215.077009 1.79813919 # Cr1 oc +bond_coeff 2 171.3605365 1.91925239 # Cr1 o +bond_coeff 3 30.0025985 1.70066041 # Cr2 oc +bond_coeff 4 113.3849035 1.80031867 # Cr2 o +bond_coeff 5 79.013065 2.25449382 # Cr2 Cl +bond_coeff 6 345.9 1.49100000 # c ca +bond_coeff 7 637.5 1.21800000 # c o +bond_coeff 8 461.1 1.39800000 # ca ca +bond_coeff 9 345.8 1.08600000 # ca ha +bond_coeff 10 450.2 1.40600000 # ca cp +bond_coeff 11 351.4 1.48500000 # cp cp +bond_coeff 12 321.0 1.51600000 # c3 ca +bond_coeff 13 330.6 1.09700000 # c3 hc +angle_coeff 1 57.4090405 129.511222 # Cr1-oc-Cr1 +angle_coeff 2 54.896879 115.919290 # Cr1-oc-Cr2 +angle_coeff 3 10.4928115 115.127987 # Cr1-o-c +angle_coeff 4 22.587082 94.926514 # oc-Cr1-o +angle_coeff 5 10.1522065 157.100593 # o-Cr1-o +angle_coeff 6 8.591407 133.558820 # Cr2-o-c +angle_coeff 7 27.362034 88.698347 # oc-Cr2-o +angle_coeff 8 16.499101 183.006723 # oc-Cr2-Cl +angle_coeff 9 15.7281545 182.046844 # o-Cr2-o +angle_coeff 10 18.6572345 96.972033 # o-Cr2-Cl +angle_coeff 11 64.3 120.300000 # c-ca-ca +angle_coeff 12 68.7 122.600000 # ca-c-o +angle_coeff 13 66.6 120.000000 # ca-ca-ca +angle_coeff 14 48.2 119.900000 # ca-ca-ha +angle_coeff 15 66.3 120.700000 # ca-ca-cp +angle_coeff 16 66.7 118.400000 # ca-cp-ca +angle_coeff 17 64.0 121.100000 # ca-cp-cp +angle_coeff 18 48.0 119.900000 # cp-ca-ha +angle_coeff 19 72.4 90.0000000 # cp-cp-cp +angle_coeff 20 63.5 120.800000 # c3-ca-ca +angle_coeff 21 63.6 112.200000 # ca-c3-ca +angle_coeff 22 46.8 110.500000 # ca-c3-hc +angle_coeff 23 77.9 130.200000 # o-c-o +dihedral_coeff 1 5.0040 -1 2 # Cr1-o-c-ca +dihedral_coeff 2 3.2376 1 2 # Cr1-o-c-o +dihedral_coeff 3 0.6374 1 2 # oc-Cr1-o-c +dihedral_coeff 4 4.6518 -1 2 # Cr2-o-c-ca +dihedral_coeff 5 2.6899 1 2 # Cr2-o-c-o +dihedral_coeff 6 2.1991 1 2 # oc-Cr2-o-c +dihedral_coeff 7 2.1450 -1 2 # Cl-Cr2-o-c +dihedral_coeff 8 0.0000 -1 2 # Cr1-oc-Cr1-o +dihedral_coeff 9 0.0000 -1 2 # Cr1-oc-Cr2-o +dihedral_coeff 10 0.0000 1 2 # Cr1-oc-Cr2-Cl +dihedral_coeff 11 0.0000 -1 2 # o-Cr1-o-c +dihedral_coeff 12 0.0000 -1 2 # o-Cr1-oc-Cr2 +dihedral_coeff 13 0.0000 -1 2 # o-Cr2-o-c +dihedral_coeff 14 3.6250 -1 2 # c-ca-ca-ca +dihedral_coeff 15 3.6250 -1 2 # c-ca-ca-ha +dihedral_coeff 16 3.6250 -1 2 # ca-ca-ca-cp +dihedral_coeff 17 3.6250 -1 2 # ca-ca-ca-ha +dihedral_coeff 18 3.6250 -1 2 # ca-ca-ca-ca +dihedral_coeff 19 3.6250 -1 2 # ca-ca-cp-ca +dihedral_coeff 20 3.6250 -1 2 # ca-ca-cp-cp +dihedral_coeff 21 1.0000 -1 2 # ca-cp-cp-cp +dihedral_coeff 22 1.0000 -1 2 # ca-cp-cp-ca +dihedral_coeff 23 1.0000 -1 2 # cp-cp-cp-cp +dihedral_coeff 24 3.6250 -1 2 # ha-ca-cp-cp +dihedral_coeff 25 3.6250 -1 2 # c3-ca-ca-cp +dihedral_coeff 26 3.6250 -1 2 # c3-ca-ca-ca +dihedral_coeff 27 0.0000 1 2 # ca-c3-ca-ca +dihedral_coeff 28 0.0000 1 2 # hc-c3-ca-ca +dihedral_coeff 29 3.6250 -1 2 # c3-ca-ca-c3 +dihedral_coeff 30 3.6250 -1 2 # cp-ca-ca-ha +dihedral_coeff 31 3.6250 -1 2 # ha-ca-ca-ha +dihedral_coeff 32 3.6250 -1 2 # ha-ca-cp-ca +dihedral_coeff 33 3.6250 -1 2 # c3-ca-ca-ha +dihedral_coeff 34 1.0000 -1 2 # o-c-ca-ca +improper_coeff 1 1.1000 -1 2 # c-ca-o-o +improper_coeff 2 1.1000 -1 2 # ca-c-ca-ca +improper_coeff 3 1.1000 -1 2 # ca-ca-ca-ha +improper_coeff 4 1.1000 -1 2 # ca-ca-cp-ha +improper_coeff 5 1.1000 -1 2 # cp-ca-ca-cp +improper_coeff 6 1.1000 -1 2 # cp-ca-cp-cp +improper_coeff 7 1.1000 -1 2 # ca-c3-ca-ca + +## H2O ## +#set type 3 charge -1.1128 +#set type 4 charge 0.5564 +bond_coeff 14 0.0 0.0 +angle_coeff 24 0.0 0.0 + +## LJ ## +pair_style hybrid/overlay mbx 9.0 lj/cut 9.0 coul/exclude 9.0 buck 9.0 +pair_modify tail yes + + +## MOF pair coefficients ## +pair_coeff 3 3 lj/cut 0.086000 3.399670 +pair_coeff 3 4 lj/cut 0.086000 3.399670 +pair_coeff 3 5 lj/cut 0.086000 3.399670 +pair_coeff 3 6 lj/cut 0.096997 3.399670 +pair_coeff 3 11 lj/cut 0.035917 2.999656 +pair_coeff 3 10 lj/cut 0.036745 3.024601 +pair_coeff 3 7 lj/cut 0.134387 3.179618 +pair_coeff 3 8 lj/cut 0.134387 3.179618 +pair_coeff 3 9 lj/cut 0.139721 3.458023 +pair_coeff 4 4 lj/cut 0.086000 3.399670 +pair_coeff 4 5 lj/cut 0.086000 3.399670 +pair_coeff 4 6 lj/cut 0.096997 3.399670 +pair_coeff 4 11 lj/cut 0.035917 2.999656 +pair_coeff 4 10 lj/cut 0.036745 3.024601 +pair_coeff 4 7 lj/cut 0.134387 3.179618 +pair_coeff 4 8 lj/cut 0.134387 3.179618 +pair_coeff 4 9 lj/cut 0.139721 3.458023 +pair_coeff 5 5 lj/cut 0.086000 3.399670 +pair_coeff 5 6 lj/cut 0.096997 3.399670 +pair_coeff 5 11 lj/cut 0.035917 2.999656 +pair_coeff 5 10 lj/cut 0.036745 3.024601 +pair_coeff 5 7 lj/cut 0.134387 3.179618 +pair_coeff 5 8 lj/cut 0.134387 3.179618 +pair_coeff 5 9 lj/cut 0.139721 3.458023 +pair_coeff 6 6 lj/cut 0.109400 3.399670 +pair_coeff 6 11 lj/cut 0.040509 2.999656 +pair_coeff 6 10 lj/cut 0.041444 3.024601 +pair_coeff 6 7 lj/cut 0.151572 3.179618 +pair_coeff 6 8 lj/cut 0.151572 3.179618 +pair_coeff 6 9 lj/cut 0.157587 3.458023 +pair_coeff 11 11 lj/cut 0.015000 2.599642 +pair_coeff 10 11 lj/cut 0.015346 2.624588 +pair_coeff 10 10 lj/cut 0.015700 2.649533 +pair_coeff 7 11 lj/cut 0.056125 2.779604 +pair_coeff 7 10 lj/cut 0.057420 2.804549 +pair_coeff 7 7 lj/cut 0.210000 2.959566 +pair_coeff 7 8 lj/cut 0.210000 2.959566 +pair_coeff 7 9 lj/cut 0.218335 3.237971 +pair_coeff 8 11 lj/cut 0.056125 2.779604 +pair_coeff 8 10 lj/cut 0.057420 2.804549 +pair_coeff 8 8 lj/cut 0.210000 2.959566 +pair_coeff 8 9 lj/cut 0.218335 3.237971 +pair_coeff 9 11 lj/cut 0.058352 3.058010 +pair_coeff 9 10 lj/cut 0.059698 3.082955 +pair_coeff 9 9 lj/cut 0.227000 3.516377 +pair_coeff 1 3 lj/cut 0.035917 3.046428 +pair_coeff 1 4 lj/cut 0.035917 3.046428 +pair_coeff 1 5 lj/cut 0.035917 3.046428 +pair_coeff 1 6 lj/cut 0.040509 3.046428 +pair_coeff 1 11 lj/cut 0.015000 2.646415 +pair_coeff 1 10 lj/cut 0.015346 2.671360 +pair_coeff 1 7 lj/cut 0.056125 2.826376 +pair_coeff 1 8 lj/cut 0.056125 2.826376 +pair_coeff 1 9 lj/cut 0.058352 3.104782 +pair_coeff 1 1 lj/cut 0.015000 2.693187 +pair_coeff 1 2 lj/cut 0.015000 2.693187 +pair_coeff 2 3 lj/cut 0.035917 3.046428 +pair_coeff 2 4 lj/cut 0.035917 3.046428 +pair_coeff 2 5 lj/cut 0.035917 3.046428 +pair_coeff 2 6 lj/cut 0.040509 3.046428 +pair_coeff 2 11 lj/cut 0.015000 2.646415 +pair_coeff 2 10 lj/cut 0.015346 2.671360 +pair_coeff 2 7 lj/cut 0.056125 2.826376 +pair_coeff 2 8 lj/cut 0.056125 2.826376 +pair_coeff 2 9 lj/cut 0.058352 3.104782 +pair_coeff 2 2 lj/cut 0.015000 2.693187 + + +## Mixed ## +pair_coeff 1 12 buck 168233.0 0.22 1470.0 +pair_coeff 1 13 lj/cut 0.000000 0.000000 +pair_coeff 2 12 lj/cut 0.052705 2.926043 +pair_coeff 2 13 lj/cut 0.000000 0.000000 +pair_coeff 3 12 lj/cut 0.126199 3.279285 +pair_coeff 3 13 lj/cut 0.000000 0.000000 +pair_coeff 4 12 lj/cut 0.126199 3.279285 +pair_coeff 4 13 lj/cut 0.000000 0.000000 +pair_coeff 5 12 lj/cut 0.126199 3.279285 +pair_coeff 5 13 lj/cut 0.000000 0.000000 +pair_coeff 6 12 lj/cut 0.142337 3.279285 +pair_coeff 6 13 lj/cut 0.000000 0.000000 +pair_coeff 7 12 lj/cut 0.197205 3.059233 +pair_coeff 7 13 buck 11292.0 0.296 597.0 +pair_coeff 8 12 lj/cut 0.197205 3.059233 +pair_coeff 8 13 lj/cut 0.000000 0.000000 +pair_coeff 9 12 lj/cut 0.205032 3.337639 +pair_coeff 9 13 lj/cut 0.000000 0.000000 +pair_coeff 10 12 lj/cut 0.053921 2.904216 +pair_coeff 10 13 lj/cut 0.000000 0.000000 +pair_coeff 11 12 lj/cut 0.052705 2.879271 +pair_coeff 11 13 lj/cut 0.000000 0.000000 + +#MBX-water +pair_coeff * * mbx 2 dp1 1*11 h2o 12 13 13 json mbx.json + +#coul exclude +pair_coeff 1*11 1*11 coul/exclude + +## Non-bonded k-space ## +#special_bonds amber + + +neighbor 2.0 bin +neigh_modify every 1 delay 1 check yes + +timestep 0.2 +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eele equal c_mbx[7] +variable etot equal c_mbx[8] +variable eperm equal c_mbx[9] +variable eind equal c_mbx[10] + +thermo_style custom step time temp evdwl ecoul epair ebond eangle edihed eimp emol elong etail v_e1bpip v_e2bpip v_e3bpip v_e4bpip v_edisp v_ebuck v_eele v_etot pe etotal +thermo 1 +thermo_modify flush yes + +#fix wshake water shake 1e-5 50 0 b 14 a 24 mol h2o +fix mynvt all nvt temp 298.15 298.15 $(100.0*dt) + + +velocity all create 298.15 428879 rot yes dist gaussian +#velocity all zero linear +#velocity all zero angular + +# dump 1 all custom 10 dump.lammpstrj id type x y z fx fy fz vx vy vz +# dump_modify 1 sort id + +# restart 5 restart.inter.1 restart.inter.2 + +run 100 + +# write_data final.data nocoeff +# write_restart restart.inter diff --git a/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/initial.data b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/initial.data new file mode 100644 index 00000000000..cc704b046cd --- /dev/null +++ b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/initial.data @@ -0,0 +1,7487 @@ +Created on 11/06/2021, 19:53:34 + + 891 atoms #888 MOF + 3H2O + 1058 bonds #1056 MOF + 2 H2O + 1937 angles #1936 MOF + 1H2O + 3072 dihedrals + 480 impropers + + 13 atom types #11 MOF + 2H2O + 14 bond types #13 MOF + 1H2O + 24 angle types #23 MOF + 1H2O + 34 dihedral types + 7 improper types + 0.000000 39.0060005 xlo xhi + 0.000000 33.7801873 ylo yhi + 0.000000 22.2450008 zlo zhi + -19.503000 0.0000000 0.000000 xy xz yz + +Masses + + 1 51.99610 # Cr1 + 2 51.99610 # Cr2 + 3 12.01000 # c + 4 12.01000 # ca + 5 12.01000 # cp + 6 12.01000 # c3 + 7 16.00000 # o + 8 16.00000 # oc + 9 35.45300 # Cl + 10 1.008000 # hc + 11 1.008000 # ha + 12 16.00000 # O on H2O + 13 1.008000 # H on H2O + +Atoms + +1 1 3 0.227263 9.04650500 9.69276000 2.17208600 +2 1 3 0.224305 11.33190700 5.81628200 9.76143400 +3 1 3 0.227263 9.07509700 9.72176600 9.75877000 +4 1 3 0.224305 13.58617800 9.72035700 2.19260300 +5 1 3 0.224305 13.55325600 9.76037500 9.78147000 +6 1 3 0.224305 11.32683800 5.82810400 2.19419300 +7 1 4 -0.011949 8.00111900 10.34543900 8.98189300 +8 1 4 -0.011949 11.33089200 4.57433000 8.97966500 +9 1 4 -0.011949 -4.84267600 10.34509800 2.97478900 +10 1 4 -0.011949 8.00048200 10.34218200 2.96580600 +11 1 4 -0.011949 -4.84511800 10.34290800 8.99084900 +12 1 4 -0.011949 11.32923100 4.57525300 2.96786400 +13 1 4 -0.069163 6.84156500 9.61559300 3.27692700 +14 1 4 -0.069163 -4.91588100 11.72123300 3.28965600 +15 1 4 -0.069163 12.56067800 3.94973000 8.66597100 +16 1 4 -0.069163 6.84276200 9.61544300 8.67702700 +17 1 4 -0.069163 -4.89455800 11.71348500 8.67749100 +18 1 4 -0.069163 -3.68555000 9.58495500 3.27355200 +19 1 4 -0.069163 8.07589300 11.71602200 3.28011300 +20 1 4 -0.069163 10.10114100 3.94975600 3.28765500 +21 1 4 -0.069163 -3.68989600 9.58858900 8.67097900 +22 1 4 -0.069163 8.07579200 11.71719600 8.67154900 +23 1 4 -0.069163 10.10212200 3.95224300 8.66722100 +24 1 4 -0.069163 12.55959200 3.95169700 3.28573300 +25 1 4 -0.089312 10.12469600 2.74432600 7.97066200 +26 1 4 -0.089312 12.54871200 2.73773800 3.97496700 +27 1 4 -0.089312 5.79447500 10.22430600 3.94894500 +28 1 4 -0.089312 -3.85845100 12.31572400 3.98218800 +29 1 4 -0.089312 12.55089500 2.73501600 7.97573000 +30 1 4 -0.089312 -2.64195200 10.20401500 3.96907800 +31 1 4 -0.089312 7.01326600 12.31034400 3.94606700 +32 1 4 -0.089312 10.11803300 2.73972600 3.98531100 +33 1 4 -0.089312 -2.64177700 10.20718400 7.98915900 +34 1 4 -0.089312 7.01282600 12.31121800 8.00709200 +35 1 4 -0.089312 5.79480300 10.22440600 8.00508300 +36 1 4 -0.089312 -3.84071500 12.33394300 8.01666000 +37 1 5 0.004217 5.91363600 11.54927500 4.36977800 +38 1 5 0.004217 11.33186500 2.17823300 4.39639600 +39 1 5 0.004217 -2.75693300 11.54801200 7.58535600 +40 1 5 0.004217 -2.76794700 11.53923800 4.39646500 +41 1 5 0.004217 5.91372900 11.54931600 7.58396800 +42 1 5 0.004217 11.33290600 2.17803000 7.55720900 +43 1 5 -0.00225 -1.73841500 12.13551500 6.68444600 +44 1 5 -0.00225 -1.73886800 12.13501800 5.27215900 +45 1 5 -0.00225 4.89527400 12.13589900 5.27011700 +46 1 5 -0.00225 11.32975200 0.99024200 5.27141900 +47 1 5 -0.00225 4.89530100 12.13584700 6.68367400 +48 1 5 -0.00225 11.32956200 0.99028400 6.68217600 +49 1 4 -0.089361 -0.67148600 12.75206100 4.55578600 +50 1 4 -0.089361 3.82734200 12.75235300 4.55575800 +51 1 4 -0.089361 1.57859900 16.64925600 4.55524300 +52 1 4 -0.089361 -0.67037500 12.75276700 7.39826800 +53 1 4 -0.089361 3.82736200 12.75234900 7.39792200 +54 1 4 -0.089361 1.57847800 16.64948800 7.39772300 +55 1 4 -0.008693 0.34769900 13.34003200 5.27800700 +56 1 4 -0.008693 2.80857500 13.34015400 6.67561400 +57 1 4 -0.008693 2.80853700 13.34014900 5.27803100 +58 1 4 -0.008693 1.57821600 15.47202700 5.27829300 +59 1 4 -0.008693 0.34795900 13.34020300 6.67558200 +60 1 4 -0.008693 1.57821600 15.47235700 6.67493800 +61 1 6 -0.057928 1.57819400 14.05055500 4.72826000 +62 1 6 -0.057928 1.57823700 14.05062400 7.22537600 +63 1 1 1.214625 11.33232800 10.26889900 0.42555500 +64 1 1 1.214625 9.73070000 7.48782300 0.41811400 +65 1 2 1.112858 13.03129900 7.43916600 0.41735500 +66 1 11 0.116697 13.51413100 4.41500600 8.85784900 +67 1 11 0.116697 6.78006900 8.54228700 8.85605500 +68 1 11 0.116697 -5.79239900 12.31362400 8.85610500 +69 1 11 0.116697 9.14511100 4.41373500 3.09842500 +70 1 11 0.116697 -3.62240200 8.54062700 2.94815900 +71 1 11 0.116697 -3.61180000 8.53096600 8.85739700 +72 1 11 0.116697 8.95243100 12.31578900 8.85631800 +73 1 11 0.116697 9.14512800 4.41405500 8.85557500 +74 1 11 0.116697 13.51408900 4.41515600 3.09575600 +75 1 11 0.116697 8.95210300 12.31611300 3.09795500 +76 1 11 0.116697 6.77988600 8.54243900 3.09776300 +77 1 11 0.116697 -5.79533700 12.31669000 3.09921200 +78 1 11 0.103653 7.06863800 13.39842000 7.88320600 +79 1 11 0.103653 -1.73364700 9.63544700 4.21935000 +80 1 11 0.103653 7.06887100 13.39806100 4.07048600 +81 1 11 0.103653 9.16409700 2.23973400 4.22195400 +82 1 11 0.103653 -1.74094600 9.62733800 7.73101500 +83 1 11 0.103653 9.17471000 2.24936500 7.73103200 +84 1 11 0.103653 13.50585500 2.25237500 4.22255400 +85 1 11 0.103653 4.89318600 9.65212700 4.20360100 +86 1 11 0.103653 -3.90149000 13.38905200 4.22051900 +87 1 11 0.103653 13.51087000 2.24548700 7.73376200 +88 1 11 0.103653 4.89319400 9.65228400 7.75043000 +89 1 11 0.103653 -3.90259700 13.39468400 7.73775400 +90 1 11 0.107425 3.82397100 12.75412800 3.47393300 +91 1 11 0.107425 1.57833300 16.64893000 3.46943600 +92 1 11 0.107425 -0.66687100 12.75433000 8.47972600 +93 1 11 0.107425 3.82401700 12.75410400 8.47971200 +94 1 11 0.107425 1.57840800 16.64461700 8.47989200 +95 1 11 0.107425 -0.66715800 12.75414600 3.47405200 +96 1 10 0.101268 1.58207700 14.05541300 8.34678400 +97 1 10 0.101268 1.58211800 14.05537700 3.60692500 +98 1 7 -0.397233 12.64343700 10.43367000 1.80596800 +99 1 7 -0.397233 10.17194000 6.27402200 1.84521300 +100 1 7 -0.381737 10.01344500 10.43125700 1.80631000 +101 1 7 -0.36048 13.73009700 8.55229400 1.80640900 +102 1 7 -0.397233 10.24279100 6.27549700 10.14773100 +103 1 7 -0.381737 10.01519200 10.43347000 10.14780300 +104 1 7 -0.36048 13.66709700 8.52118400 10.08751300 +105 1 7 -0.381737 8.88222700 8.47529100 1.82258200 +106 1 7 -0.36048 12.44264800 6.32588200 1.89815000 +107 1 7 -0.397233 12.57079200 10.56325100 10.14661300 +108 1 7 -0.381737 8.92886600 8.55164300 10.14770000 +109 1 7 -0.36048 12.41544800 6.27516300 10.14734600 +110 1 8 -0.693786 11.32956700 8.42007300 0.41571200 +111 1 9 -0.467782 15.06476100 6.29310300 0.40518700 +112 1 3 0.227263 9.04650500 9.69276000 13.29458642 +113 1 3 0.224305 11.33190700 5.81628200 20.88393442 +114 1 3 0.227263 9.07509700 9.72176600 20.88127042 +115 1 3 0.224305 13.58617800 9.72035700 13.31510342 +116 1 3 0.224305 13.55325600 9.76037500 20.90397042 +117 1 3 0.224305 11.32683800 5.82810400 13.31669342 +118 1 4 -0.011949 8.00111900 10.34543900 20.10439342 +119 1 4 -0.011949 11.33089200 4.57433000 20.10216542 +120 1 4 -0.011949 -4.84267600 10.34509800 14.09728942 +121 1 4 -0.011949 8.00048200 10.34218200 14.08830642 +122 1 4 -0.011949 -4.84511800 10.34290800 20.11334942 +123 1 4 -0.011949 11.32923100 4.57525300 14.09036442 +124 1 4 -0.069163 6.84156500 9.61559300 14.39942742 +125 1 4 -0.069163 -4.91588100 11.72123300 14.41215642 +126 1 4 -0.069163 12.56067800 3.94973000 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file mode 100644 index 00000000000..df632b3483b --- /dev/null +++ b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/log.22Oct525.mof.g++.1 @@ -0,0 +1,475 @@ +LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-148-gcf68ceb8e3-modified) + using 1 OpenMP thread(s) per MPI task +# Depositing TIP3P water into MOF with QeQ charges obtained with Ongari scheme + +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data +Reading data file ... + triclinic box = (0 0 0) to (39.006 33.780187 22.245001) with tilt (-19.503 0 0) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 891 atoms + scanning bonds ... + 6 = max bonds/atom + scanning angles ... + 15 = max angles/atom + scanning dihedrals ... + 20 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + triclinic box = (0 0 0) to (39.006 33.780187 22.245001) with tilt (-19.503 0 0) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 1058 bonds + reading angles ... + 1937 angles + reading dihedrals ... + 3072 dihedrals + reading impropers ... + 480 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 6 = max # of 1-2 neighbors + 13 = max # of 1-3 neighbors + 25 = max # of 1-4 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.025 seconds + +group mof type 1 2 3 4 5 6 7 8 9 10 11 +888 atoms in group mof +group h2o type 12 13 +3 atoms in group h2o + +## Bonded styles ## +bond_style harmonic +angle_style harmonic +dihedral_style harmonic +improper_style cvff + +## MOF ## +bond_coeff 1 215.077009 1.79813919 # Cr1 oc +bond_coeff 2 171.3605365 1.91925239 # Cr1 o +bond_coeff 3 30.0025985 1.70066041 # Cr2 oc +bond_coeff 4 113.3849035 1.80031867 # Cr2 o +bond_coeff 5 79.013065 2.25449382 # Cr2 Cl +bond_coeff 6 345.9 1.49100000 # c ca +bond_coeff 7 637.5 1.21800000 # c o +bond_coeff 8 461.1 1.39800000 # ca ca +bond_coeff 9 345.8 1.08600000 # ca ha +bond_coeff 10 450.2 1.40600000 # ca cp +bond_coeff 11 351.4 1.48500000 # cp cp +bond_coeff 12 321.0 1.51600000 # c3 ca +bond_coeff 13 330.6 1.09700000 # c3 hc +angle_coeff 1 57.4090405 129.511222 # Cr1-oc-Cr1 +angle_coeff 2 54.896879 115.919290 # Cr1-oc-Cr2 +angle_coeff 3 10.4928115 115.127987 # Cr1-o-c +angle_coeff 4 22.587082 94.926514 # oc-Cr1-o +angle_coeff 5 10.1522065 157.100593 # o-Cr1-o +angle_coeff 6 8.591407 133.558820 # Cr2-o-c +angle_coeff 7 27.362034 88.698347 # oc-Cr2-o +angle_coeff 8 16.499101 183.006723 # oc-Cr2-Cl +angle_coeff 9 15.7281545 182.046844 # o-Cr2-o +angle_coeff 10 18.6572345 96.972033 # o-Cr2-Cl +angle_coeff 11 64.3 120.300000 # c-ca-ca +angle_coeff 12 68.7 122.600000 # ca-c-o +angle_coeff 13 66.6 120.000000 # ca-ca-ca +angle_coeff 14 48.2 119.900000 # ca-ca-ha +angle_coeff 15 66.3 120.700000 # ca-ca-cp +angle_coeff 16 66.7 118.400000 # ca-cp-ca +angle_coeff 17 64.0 121.100000 # ca-cp-cp +angle_coeff 18 48.0 119.900000 # cp-ca-ha +angle_coeff 19 72.4 90.0000000 # cp-cp-cp +angle_coeff 20 63.5 120.800000 # c3-ca-ca +angle_coeff 21 63.6 112.200000 # ca-c3-ca +angle_coeff 22 46.8 110.500000 # ca-c3-hc +angle_coeff 23 77.9 130.200000 # o-c-o +dihedral_coeff 1 5.0040 -1 2 # Cr1-o-c-ca +dihedral_coeff 2 3.2376 1 2 # Cr1-o-c-o +dihedral_coeff 3 0.6374 1 2 # oc-Cr1-o-c +dihedral_coeff 4 4.6518 -1 2 # Cr2-o-c-ca +dihedral_coeff 5 2.6899 1 2 # Cr2-o-c-o +dihedral_coeff 6 2.1991 1 2 # oc-Cr2-o-c +dihedral_coeff 7 2.1450 -1 2 # Cl-Cr2-o-c +dihedral_coeff 8 0.0000 -1 2 # Cr1-oc-Cr1-o +dihedral_coeff 9 0.0000 -1 2 # Cr1-oc-Cr2-o +dihedral_coeff 10 0.0000 1 2 # Cr1-oc-Cr2-Cl +dihedral_coeff 11 0.0000 -1 2 # o-Cr1-o-c +dihedral_coeff 12 0.0000 -1 2 # o-Cr1-oc-Cr2 +dihedral_coeff 13 0.0000 -1 2 # o-Cr2-o-c +dihedral_coeff 14 3.6250 -1 2 # c-ca-ca-ca +dihedral_coeff 15 3.6250 -1 2 # c-ca-ca-ha +dihedral_coeff 16 3.6250 -1 2 # ca-ca-ca-cp +dihedral_coeff 17 3.6250 -1 2 # ca-ca-ca-ha +dihedral_coeff 18 3.6250 -1 2 # ca-ca-ca-ca +dihedral_coeff 19 3.6250 -1 2 # ca-ca-cp-ca +dihedral_coeff 20 3.6250 -1 2 # ca-ca-cp-cp +dihedral_coeff 21 1.0000 -1 2 # ca-cp-cp-cp +dihedral_coeff 22 1.0000 -1 2 # ca-cp-cp-ca +dihedral_coeff 23 1.0000 -1 2 # cp-cp-cp-cp +dihedral_coeff 24 3.6250 -1 2 # ha-ca-cp-cp +dihedral_coeff 25 3.6250 -1 2 # c3-ca-ca-cp +dihedral_coeff 26 3.6250 -1 2 # c3-ca-ca-ca +dihedral_coeff 27 0.0000 1 2 # ca-c3-ca-ca +dihedral_coeff 28 0.0000 1 2 # hc-c3-ca-ca +dihedral_coeff 29 3.6250 -1 2 # c3-ca-ca-c3 +dihedral_coeff 30 3.6250 -1 2 # cp-ca-ca-ha +dihedral_coeff 31 3.6250 -1 2 # ha-ca-ca-ha +dihedral_coeff 32 3.6250 -1 2 # ha-ca-cp-ca +dihedral_coeff 33 3.6250 -1 2 # c3-ca-ca-ha +dihedral_coeff 34 1.0000 -1 2 # o-c-ca-ca +improper_coeff 1 1.1000 -1 2 # c-ca-o-o +improper_coeff 2 1.1000 -1 2 # ca-c-ca-ca +improper_coeff 3 1.1000 -1 2 # ca-ca-ca-ha +improper_coeff 4 1.1000 -1 2 # ca-ca-cp-ha +improper_coeff 5 1.1000 -1 2 # cp-ca-ca-cp +improper_coeff 6 1.1000 -1 2 # cp-ca-cp-cp +improper_coeff 7 1.1000 -1 2 # ca-c3-ca-ca + +## H2O ## +#set type 3 charge -1.1128 +#set type 4 charge 0.5564 +bond_coeff 14 0.0 0.0 +angle_coeff 24 0.0 0.0 + +## LJ ## +pair_style hybrid/overlay mbx 9.0 lj/cut 9.0 coul/exclude 9.0 buck 9.0 +pair_modify tail yes + + +## MOF pair coefficients ## +pair_coeff 3 3 lj/cut 0.086000 3.399670 +pair_coeff 3 4 lj/cut 0.086000 3.399670 +pair_coeff 3 5 lj/cut 0.086000 3.399670 +pair_coeff 3 6 lj/cut 0.096997 3.399670 +pair_coeff 3 11 lj/cut 0.035917 2.999656 +pair_coeff 3 10 lj/cut 0.036745 3.024601 +pair_coeff 3 7 lj/cut 0.134387 3.179618 +pair_coeff 3 8 lj/cut 0.134387 3.179618 +pair_coeff 3 9 lj/cut 0.139721 3.458023 +pair_coeff 4 4 lj/cut 0.086000 3.399670 +pair_coeff 4 5 lj/cut 0.086000 3.399670 +pair_coeff 4 6 lj/cut 0.096997 3.399670 +pair_coeff 4 11 lj/cut 0.035917 2.999656 +pair_coeff 4 10 lj/cut 0.036745 3.024601 +pair_coeff 4 7 lj/cut 0.134387 3.179618 +pair_coeff 4 8 lj/cut 0.134387 3.179618 +pair_coeff 4 9 lj/cut 0.139721 3.458023 +pair_coeff 5 5 lj/cut 0.086000 3.399670 +pair_coeff 5 6 lj/cut 0.096997 3.399670 +pair_coeff 5 11 lj/cut 0.035917 2.999656 +pair_coeff 5 10 lj/cut 0.036745 3.024601 +pair_coeff 5 7 lj/cut 0.134387 3.179618 +pair_coeff 5 8 lj/cut 0.134387 3.179618 +pair_coeff 5 9 lj/cut 0.139721 3.458023 +pair_coeff 6 6 lj/cut 0.109400 3.399670 +pair_coeff 6 11 lj/cut 0.040509 2.999656 +pair_coeff 6 10 lj/cut 0.041444 3.024601 +pair_coeff 6 7 lj/cut 0.151572 3.179618 +pair_coeff 6 8 lj/cut 0.151572 3.179618 +pair_coeff 6 9 lj/cut 0.157587 3.458023 +pair_coeff 11 11 lj/cut 0.015000 2.599642 +pair_coeff 10 11 lj/cut 0.015346 2.624588 +pair_coeff 10 10 lj/cut 0.015700 2.649533 +pair_coeff 7 11 lj/cut 0.056125 2.779604 +pair_coeff 7 10 lj/cut 0.057420 2.804549 +pair_coeff 7 7 lj/cut 0.210000 2.959566 +pair_coeff 7 8 lj/cut 0.210000 2.959566 +pair_coeff 7 9 lj/cut 0.218335 3.237971 +pair_coeff 8 11 lj/cut 0.056125 2.779604 +pair_coeff 8 10 lj/cut 0.057420 2.804549 +pair_coeff 8 8 lj/cut 0.210000 2.959566 +pair_coeff 8 9 lj/cut 0.218335 3.237971 +pair_coeff 9 11 lj/cut 0.058352 3.058010 +pair_coeff 9 10 lj/cut 0.059698 3.082955 +pair_coeff 9 9 lj/cut 0.227000 3.516377 +pair_coeff 1 3 lj/cut 0.035917 3.046428 +pair_coeff 1 4 lj/cut 0.035917 3.046428 +pair_coeff 1 5 lj/cut 0.035917 3.046428 +pair_coeff 1 6 lj/cut 0.040509 3.046428 +pair_coeff 1 11 lj/cut 0.015000 2.646415 +pair_coeff 1 10 lj/cut 0.015346 2.671360 +pair_coeff 1 7 lj/cut 0.056125 2.826376 +pair_coeff 1 8 lj/cut 0.056125 2.826376 +pair_coeff 1 9 lj/cut 0.058352 3.104782 +pair_coeff 1 1 lj/cut 0.015000 2.693187 +pair_coeff 1 2 lj/cut 0.015000 2.693187 +pair_coeff 2 3 lj/cut 0.035917 3.046428 +pair_coeff 2 4 lj/cut 0.035917 3.046428 +pair_coeff 2 5 lj/cut 0.035917 3.046428 +pair_coeff 2 6 lj/cut 0.040509 3.046428 +pair_coeff 2 11 lj/cut 0.015000 2.646415 +pair_coeff 2 10 lj/cut 0.015346 2.671360 +pair_coeff 2 7 lj/cut 0.056125 2.826376 +pair_coeff 2 8 lj/cut 0.056125 2.826376 +pair_coeff 2 9 lj/cut 0.058352 3.104782 +pair_coeff 2 2 lj/cut 0.015000 2.693187 + + +## Mixed ## +pair_coeff 1 12 buck 168233.0 0.22 1470.0 +pair_coeff 1 13 lj/cut 0.000000 0.000000 +pair_coeff 2 12 lj/cut 0.052705 2.926043 +pair_coeff 2 13 lj/cut 0.000000 0.000000 +pair_coeff 3 12 lj/cut 0.126199 3.279285 +pair_coeff 3 13 lj/cut 0.000000 0.000000 +pair_coeff 4 12 lj/cut 0.126199 3.279285 +pair_coeff 4 13 lj/cut 0.000000 0.000000 +pair_coeff 5 12 lj/cut 0.126199 3.279285 +pair_coeff 5 13 lj/cut 0.000000 0.000000 +pair_coeff 6 12 lj/cut 0.142337 3.279285 +pair_coeff 6 13 lj/cut 0.000000 0.000000 +pair_coeff 7 12 lj/cut 0.197205 3.059233 +pair_coeff 7 13 buck 11292.0 0.296 597.0 +pair_coeff 8 12 lj/cut 0.197205 3.059233 +pair_coeff 8 13 lj/cut 0.000000 0.000000 +pair_coeff 9 12 lj/cut 0.205032 3.337639 +pair_coeff 9 13 lj/cut 0.000000 0.000000 +pair_coeff 10 12 lj/cut 0.053921 2.904216 +pair_coeff 10 13 lj/cut 0.000000 0.000000 +pair_coeff 11 12 lj/cut 0.052705 2.879271 +pair_coeff 11 13 lj/cut 0.000000 0.000000 + +#MBX-water +pair_coeff * * mbx 2 dp1 1*11 h2o 12 13 13 json mbx.json + +#coul exclude +pair_coeff 1*11 1*11 coul/exclude + +## Non-bonded k-space ## +#special_bonds amber + + +neighbor 2.0 bin +neigh_modify every 1 delay 1 check yes + +timestep 0.2 +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eele equal c_mbx[7] +variable etot equal c_mbx[8] +variable eperm equal c_mbx[9] +variable eind equal c_mbx[10] + +thermo_style custom step time temp evdwl ecoul epair ebond eangle edihed eimp emol elong etail v_e1bpip v_e2bpip v_e3bpip v_e4bpip v_edisp v_ebuck v_eele v_etot pe etotal +thermo 1 +thermo_modify flush yes + +#fix wshake water shake 1e-5 50 0 b 14 a 24 mol h2o +fix mynvt all nvt temp 298.15 298.15 $(100.0*dt) +fix mynvt all nvt temp 298.15 298.15 20 + + +velocity all create 298.15 428879 rot yes dist gaussian +#velocity all zero linear +#velocity all zero angular + +# dump 1 all custom 10 dump.lammpstrj id type x y z fx fy fz vx vy vz +# dump_modify 1 sort id + +# restart 5 restart.inter.1 restart.inter.2 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair mbx command: + +@article{10.1063/5.0156036, + author = {Riera, Marc and Knight, Christopher and Bull-Vulpe, Ethan F. and Zhu, Xuanyu and Agnew, Henry and Smith, Daniel G. A. and Simmonett, Andrew C. and Paesani, Francesco}, + title = "{MBX: A many-body energy and force calculator for data-driven many-body simulations}", + journal = {The Journal of Chemical Physics}, + volume = {159}, + number = {5}, + pages = {054802}, + year = {2023}, + doi = {10.1063/5.0156036}, +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 78 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 1 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 11 7 5 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair mbx, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) pair coul/exclude, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (4) pair buck, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (5) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard +WARNING: Inconsistent image flags +For more information see https://docs.lammps.org/err0027 (src/domain.cpp:1052) +Per MPI rank memory allocation (min/avg/max) = 21.89 | 21.89 | 21.89 Mbytes + Step Time Temp E_vdwl E_coul E_pair E_bond E_angle E_dihed E_impro E_mol E_long E_tail v_e1bpip v_e2bpip v_e3bpip v_e4bpip v_edisp v_ebuck v_eele v_etot PotEng TotEng + 0 0 298.15 -8176.5335 11692.335 3515.8017 333.85691 4108.0644 1369.7935 5.4245589 5817.1394 0 -23.891377 0.45689944 0 0 0 -2.3771962e-06 0 -7923.955 -1.1954777 9332.9411 10123.909 + 1 0.2 298.02821 -8176.4176 11692.427 3516.0089 333.6563 4108.171 1369.9997 5.4284001 5817.2554 0 -23.891377 0.47083048 0 0 0 -2.3321913e-06 0 -7923.993 -1.1939972 9333.2643 10123.91 + 2 0.4 297.6882 -8176.4177 11692.557 3516.1397 334.75222 4107.5951 1370.2305 5.4515857 5818.0294 0 -23.891377 0.47916766 0 0 0 -2.280486e-06 0 -7924.0977 -1.1919493 9334.1692 10123.912 + 3 0.6 297.15736 -8176.526 11692.725 3516.1993 337.07175 4106.3355 1370.4862 5.4941617 5819.3876 0 -23.891377 0.48297311 0 0 0 -2.2224302e-06 0 -7924.2667 -1.1893529 9335.5869 10123.922 + 4 0.8 296.48947 -8176.741 11692.927 3516.1858 340.47087 4104.3899 1370.7671 5.556231 5821.1842 0 -23.891377 0.48375375 0 0 0 -2.1583995e-06 0 -7924.4962 -1.1862088 9337.37 10123.933 + 5 1 295.76174 -8177.0515 11693.158 3516.1062 344.74255 4101.7548 1371.0745 5.6379497 5823.2098 0 -23.891377 0.48332938 0 0 0 -2.0887925e-06 0 -7924.7819 -1.1825651 9339.316 10123.948 + 6 1.2 295.07036 -8177.4469 11693.414 3515.9666 349.62842 4098.4257 1371.41 5.7395228 5825.2036 0 -23.891377 0.48367237 0 0 0 -2.0140265e-06 0 -7925.1189 -1.178426 9341.1702 10123.969 + 7 1.4 294.52509 -8177.9244 11693.689 3515.7647 354.83332 4094.3975 1371.7756 5.8611975 5826.8676 0 -23.891377 0.48672978 0 0 0 -1.9345316e-06 0 -7925.5013 -1.1738191 9342.6323 10123.984 + 8 1.6 294.24292 -8178.4583 11693.979 3515.5207 360.04204 4089.6649 1372.1738 6.0032559 5827.884 0 -23.891377 0.49423877 0 0 0 -1.8507431e-06 0 -7925.9232 -1.1687669 9343.4047 10124.008 + 9 1.8 294.34132 -8179.0432 11694.278 3515.2346 364.93727 4084.2226 1372.6075 6.1660071 5827.9334 0 -23.891377 0.5075514 0 0 0 -1.763093e-06 0 -7926.3783 -1.1632904 9343.168 10124.032 + 10 2 294.93126 -8179.6664 11694.58 3514.9136 369.21798 4078.0657 1373.0799 6.3497779 5826.7134 0 -23.891377 0.52748295 0 0 0 -1.6720022e-06 0 -7926.86 -1.1574094 9341.6269 10124.056 + 11 2.2 296.11047 -8180.3124 11694.88 3514.5679 372.61712 4071.1905 1373.5944 6.5549028 5823.9569 0 -23.891377 0.55419718 0 0 0 -1.5778741e-06 0 -7927.3622 -1.1511414 9338.5248 10124.083 + 12 2.4 297.95735 -8180.9724 11695.174 3514.2013 374.91776 4063.5946 1374.1548 6.7817146 5819.4488 0 -23.891377 0.58714035 0 0 0 -1.4810919e-06 0 -7927.8785 -1.1445029 9333.6502 10124.107 + 13 2.6 300.52562 -8181.6399 11695.456 3513.8161 375.96689 4055.2775 1374.7647 7.0305342 5813.0397 0 -23.891377 0.62503248 0 0 0 -1.3820177e-06 0 -7928.4033 -1.1375093 9326.8558 10124.127 + 14 2.8 303.84026 -8182.3113 11695.723 3513.4119 375.68603 4046.2412 1375.4281 7.3016609 5804.6569 0 -23.891377 0.66592079 0 0 0 -1.2809982e-06 0 -7928.9312 -1.1301761 9318.0688 10124.133 + 15 3 307.89473 -8182.9673 11695.972 3513.0049 374.07811 4036.4902 1376.1487 7.5953628 5794.3123 0 -23.891377 0.70729539 0 0 0 -1.1783728e-06 0 -7929.4575 -1.1225196 9307.3172 10124.138 + 16 3.2 312.64965 -8183.6105 11696.201 3512.5901 371.23031 4026.0326 1376.9302 7.9118685 5782.105 0 -23.891377 0.74626222 0 0 0 -1.0744873e-06 0 -7929.9781 -1.1145582 9294.6951 10124.13 + 17 3.4 318.03324 -8184.2357 11696.407 3512.1711 367.31255 4014.8805 1377.7762 8.2513588 5768.2206 0 -23.891377 0.77976312 0 0 0 -9.6970949e-07 0 -7930.4895 -1.1063132 9280.3916 10124.109 + 18 3.6 323.94329 -8184.8411 11696.59 3511.7487 362.57176 4003.0498 1378.6899 8.6139595 5752.9254 0 -23.891377 0.80482756 0 0 0 -8.6444861e-07 0 -7930.9891 -1.0978097 9264.6741 10124.07 + 19 3.8 330.2507 -8185.4257 11696.75 3511.324 357.32209 3990.5608 1379.6744 8.9997351 5736.557 0 -23.891377 0.81883614 0 0 0 -7.5917321e-07 0 -7931.4746 -1.0890768 9247.8811 10124.01 + 20 4 336.80437 -8185.9827 11696.887 3510.9041 351.93157 3977.4386 1380.7322 9.408683 5719.511 0 -23.891377 0.81977242 0 0 0 -6.5442882e-07 0 -7931.9446 -1.0801479 9230.4151 10123.93 + 21 4.2 343.43736 -8186.5148 11697.002 3510.4875 346.80584 3963.7124 1381.8655 9.8407288 5702.2244 0 -23.891377 0.80643785 0 0 0 -5.5085198e-07 0 -7932.3982 -1.0710601 9212.712 10123.824 + 22 4.4 349.97375 -8187.0194 11697.098 3510.0782 342.3697 3949.4162 1383.076 10.295722 5685.1576 0 -23.891377 0.77860541 0 0 0 -4.4917897e-07 0 -7932.8347 -1.0618539 9195.2358 10123.689 + 23 4.6 356.23623 -8187.4955 11697.175 3509.6793 339.04735 3934.5884 1384.3648 10.773433 5668.7739 0 -23.891377 0.7370918 0 0 0 -3.5024791e-07 0 -7933.2539 -1.052572 9178.4532 10123.52 + 24 4.8 362.05375 -8187.9418 11697.236 3509.2937 337.24233 3919.2714 1385.7324 11.273549 5653.5197 0 -23.891377 0.68373471 0 0 0 -2.5499324e-07 0 -7933.6559 -1.0432572 9162.8134 10123.313 + 25 5 367.26909 -8188.357 11697.282 3508.9252 337.31812 3903.5116 1387.1787 11.795671 5639.8042 0 -23.891377 0.62127217 0 0 0 -1.6443172e-07 0 -7934.0405 -1.0339515 9148.7293 10123.065 + 26 5.2 371.7458 -8188.7425 11697.317 3508.5741 339.58033 3887.359 1388.703 12.339315 5627.9817 0 -23.891377 0.55313241 0 0 0 -7.9640078e-08 0 -7934.408 -1.0248856 9136.5558 10122.768 + 27 5.4 375.37433 -8189.0926 11697.341 3508.2481 344.26131 3870.8666 1390.3038 12.903906 5618.3356 0 -23.891377 0.48315355 0 0 0 -1.7248112e-09 0 -7934.7583 -1.0157376 9126.5837 10122.422 + 28 5.6 378.07689 -8189.3974 11697.356 3507.9587 351.50808 3854.0903 1391.9787 13.488779 5611.0659 0 -23.891377 0.41526311 0 0 0 6.8214564e-08 0 -7935.0911 -1.006696 9119.0246 10122.033 + 29 5.8 379.81091 -8189.6617 11697.364 3507.7023 361.37399 3837.0882 1393.7247 14.093179 5606.2801 0 -23.891377 0.35314945 0 0 0 1.2912711e-07 0 -7935.406 -0.99778519 9113.9824 10121.591 + 30 6 380.57094 -8189.8844 11697.365 3507.4811 373.81466 3819.92 1395.5381 14.716258 5603.989 0 -23.891377 0.29996097 0 0 0 1.8005532e-07 0 -7935.7023 -0.98902387 9111.4701 10121.095 + 31 6.2 380.38872 -8190.0576 11697.361 3507.3033 388.68834 3802.6469 1397.4141 15.35708 5604.1064 0 -23.891377 0.25806262 0 0 0 2.2018001e-07 0 -7935.9789 -0.98042531 9111.4096 10120.551 + 32 6.4 379.33167 -8190.1907 11697.35 3507.1597 405.76068 3785.3305 1399.3472 16.014619 5606.453 0 -23.891377 0.22887169 0 0 0 2.4886395e-07 0 -7936.2347 -0.97199717 9113.6127 10119.95 + 33 6.6 377.49968 -8190.2702 11697.334 3507.0639 424.71369 3768.0328 1401.3311 16.687764 5610.7654 0 -23.891377 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3508.0384 631.00986 3595.218 1423.9784 24.73435 5674.9405 0 -23.891377 0.34831885 0 0 0 -1.7727129e-07 0 -7937.1871 -0.88148178 9182.9789 10109.584 + 45 9 349.38692 -8188.3273 11696.569 3508.2421 639.73672 3582.304 1425.8332 25.484698 5673.3586 0 -23.891377 0.333032 0 0 0 -2.3880346e-07 0 -7937.0764 -0.87441033 9181.6006 10108.497 + 46 9.2 350.18557 -8188.018 11696.478 3508.4599 646.07145 3569.9951 1427.6034 26.231331 5669.9013 0 -23.891377 0.31073231 0 0 0 -2.9623541e-07 0 -7936.9421 -0.8673323 9178.3612 10107.376 + 47 9.4 351.63069 -8187.6974 11696.392 3508.695 650.12352 3558.3065 1429.2774 26.972718 5664.6801 0 -23.891377 0.28323126 0 0 0 -3.4821694e-07 0 -7936.7868 -0.86023359 9173.3751 10106.224 + 48 9.6 353.65598 -8187.3713 11696.316 3508.9451 652.06953 3547.248 1430.8439 27.707372 5657.8689 0 -23.891377 0.25285057 0 0 0 -3.9380308e-07 0 -7936.6136 -0.85310102 9166.8139 10105.035 + 49 9.8 356.17647 -8187.0438 11696.253 3509.2096 652.13997 3536.8245 1432.2924 28.433864 5649.6907 0 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391.42875 -8183.7778 11697.117 3513.3395 601.52521 3460.9339 1438.0723 35.557589 5536.089 0 -23.891377 0.37633588 0 0 0 -5.8525039e-07 0 -7934.0148 -0.76227558 9049.4285 10087.858 + 61 12.2 394.2741 -8183.5815 11697.345 3513.7632 595.83941 3456.9547 1437.5434 36.105341 5526.4429 0 -23.891377 0.42130923 0 0 0 -6.1271289e-07 0 -7933.77 -0.75434789 9040.2061 10086.184 + 62 12.4 397.19084 -8183.4127 11697.587 3514.1746 589.78615 3453.3278 1436.8326 36.634631 5516.5812 0 -23.891377 0.45955416 0 0 0 -6.5027535e-07 0 -7933.5116 -0.7464321 9030.7558 10084.472 + 63 12.6 400.2662 -8183.2667 11697.841 3514.5739 583.16862 3450.0198 1435.9422 37.145452 5506.2761 0 -23.891377 0.48792897 0 0 0 -6.9936485e-07 0 -7933.2357 -0.7385524 9020.85 10082.725 + 64 12.8 403.59025 -8183.1463 11698.1 3514.9539 575.77875 3446.9983 1434.8757 37.637913 5495.2906 0 -23.891377 0.50402457 0 0 0 -7.6106686e-07 0 -7932.938 -0.73073358 9010.2446 10080.938 + 65 13 407.24962 -8183.0436 11698.361 3515.3175 567.41338 3444.2323 1433.6376 38.112241 5483.3955 0 -23.891377 0.50640707 0 0 0 -8.3606489e-07 0 -7932.6139 -0.72300012 8998.713 10079.114 + 66 13.2 411.32101 -8182.9515 11698.619 3515.6672 557.89046 3441.6931 1432.2333 38.568777 5470.3856 0 -23.891377 0.49477364 0 0 0 -9.2459643e-07 0 -7932.2591 -0.71537524 8986.0529 10077.255 + 67 13.4 415.86532 -8182.8736 11698.869 3515.9949 547.06451 3439.3544 1430.6693 39.007973 5456.0962 0 -23.891377 0.47000084 0 0 0 -1.0264284e-06 0 -7931.8694 -0.7078801 8972.0911 10075.349 + 68 13.6 420.92226 -8182.7914 11699.106 3516.3149 534.84038 3437.193 1428.9528 39.430388 5440.4165 0 -23.891377 0.4340771 0 0 0 -1.1408546e-06 0 -7931.4408 -0.70053305 8956.7314 10073.405 + 69 13.8 426.50612 -8182.7043 11699.328 3516.6238 521.18471 3435.189 1427.0919 39.836684 5423.3022 0 -23.891377 0.38992475 0 0 0 -1.2667166e-06 0 -7930.9701 -0.69334909 8939.9261 10071.413 + 70 14 432.60262 -8182.6079 11699.531 3516.923 506.13426 3433.3263 1425.0953 40.22762 5404.7835 0 -23.891377 0.34113083 0 0 0 -1.4024467e-06 0 -7930.4542 -0.68633948 8921.7065 10069.367 + 71 14.2 439.16729 -8182.483 11699.712 3517.2291 489.80077 3431.5927 1422.9725 40.604049 5384.97 0 -23.891377 0.29161678 0 0 0 -1.5461337e-06 0 -7929.8911 -0.67951165 8902.1991 10067.275 + 72 14.4 446.12527 -8182.3371 11699.87 3517.5325 472.37194 3429.9799 1420.7335 40.966907 5364.0522 0 -23.891377 0.24528387 0 0 0 -1.6956065e-06 0 -7929.2792 -0.67286914 8881.5847 10065.12 + 73 14.6 453.37268 -8182.1589 11700.002 3517.8435 454.10845 3428.4836 1418.3885 41.317211 5342.2977 0 -23.891377 0.20567237 0 0 0 -1.8485323e-06 0 -7928.6178 -0.66641186 8860.1412 10062.903 + 74 14.8 460.77952 -8181.9389 11700.11 3518.1709 435.33707 3427.1033 1415.9482 41.65605 5320.0447 0 -23.891377 0.17566873 0 0 0 -2.0025246e-06 0 -7927.9068 -0.66013636 8838.2156 10060.627 + 75 15 468.19391 -8181.6728 11700.192 3518.5193 416.44019 3425.8423 1413.4238 41.984579 5297.6908 0 -23.891377 0.15728722 0 0 0 -2.1552548e-06 0 -7927.147 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1383.2417 45.291618 5168.408 0 -23.891377 0.44488793 0 0 0 -3.3531719e-06 0 -7916.2834 -0.59509145 8692.0983 10029.012 + 87 17.4 500.3225 -8175.5894 11699.852 3524.2628 324.3726 3424.0923 1380.5485 45.600284 5174.6136 0 -23.891377 0.45585176 0 0 0 -3.4028862e-06 0 -7915.1544 -0.59012352 8698.8764 10026.192 + 88 17.6 495.57305 -8174.9302 11699.779 3524.8491 334.57681 3425.4239 1377.9037 45.91625 5183.8207 0 -23.891377 0.45764791 0 0 0 -3.4415204e-06 0 -7914.0165 -0.5851686 8708.6698 10023.386 + 89 17.8 489.81683 -8174.2532 11699.708 3525.4548 347.14484 3427.0061 1375.315 46.240806 5195.7067 0 -23.891377 0.45103193 0 0 0 -3.4688476e-06 0 -7912.8726 -0.58021812 8721.1615 10020.607 + 90 18 483.20611 -8173.5618 11699.64 3526.0779 361.68015 3428.8301 1372.7895 46.575189 5209.875 0 -23.891377 0.43751006 0 0 0 -3.4846938e-06 0 -7911.7257 -0.57526492 8735.9529 10017.86 + 91 18.2 475.9147 -8172.8592 11699.576 3526.7165 377.73271 3430.8828 1370.3337 46.920575 5225.8698 0 -23.891377 0.41924021 0 0 0 -3.4889784e-06 0 -7910.579 -0.57030329 8752.5863 10015.15 + 92 18.4 468.13131 -8172.1393 11699.517 3527.3782 394.81679 3433.1461 1367.9535 47.278074 5243.1945 0 -23.891377 0.39888917 0 0 0 -3.4817597e-06 0 -7909.4354 -0.56532912 8770.5726 10012.488 + 93 18.6 460.05231 -8171.4047 11699.466 3528.0617 412.42996 3435.5972 1365.6542 47.648721 5261.3301 0 -23.891377 0.37945256 0 0 0 -3.4632802e-06 0 -7908.2984 -0.56044707 8789.3918 10009.874 + 94 18.8 451.87448 -8170.6396 11699.424 3528.7846 430.07249 3438.2091 1363.4402 48.033463 5279.7553 0 -23.891377 0.36404651 0 0 0 -3.4340062e-06 0 -7907.1715 -0.55544343 8808.5399 10007.327 + 95 19 443.78788 -8169.8569 11699.393 3529.5364 447.26615 3440.9503 1361.3154 48.433158 5297.965 0 -23.891377 0.35568157 0 0 0 -3.3946623e-06 0 -7906.0585 -0.55042498 8827.5014 10004.836 + 96 19.2 435.96918 -8169.0547 11699.376 3530.3214 463.57168 3443.7856 1359.2829 48.848564 5315.4887 0 -23.891377 0.35703194 0 0 0 -3.3462592e-06 0 -7904.9637 -0.54539501 8845.8101 10002.402 + 97 19.4 428.57591 -8168.238 11699.375 3531.1375 478.6041 3446.6766 1357.345 49.280335 5331.9061 0 -23.891377 0.37021497 0 0 0 -3.2900969e-06 0 -7903.8917 -0.54035885 8863.0436 10000.022 + 98 19.6 421.74162 -8167.4074 11699.395 3531.9875 492.04515 3449.5823 1355.5035 49.729018 5346.86 0 -23.891377 0.39659715 0 0 0 -3.227711e-06 0 -7902.8475 -0.53532385 8878.8475 9997.6947 + 99 19.8 415.57236 -8166.5618 11699.438 3532.8765 503.65243 3452.4595 1353.7593 50.195047 5360.0662 0 -23.891377 0.43664364 0 0 0 -3.1607943e-06 0 -7901.8367 -0.53029933 8892.9427 9995.4233 + 100 20 410.14444 -8165.7119 11699.51 3533.7979 513.26482 3455.2638 1352.1124 50.678742 5371.3198 0 -23.891377 0.48982774 0 0 0 -3.0911162e-06 0 -7900.8651 -0.52529645 8905.1177 9993.1984 +Loop time of 32.2998 on 1 procs for 100 steps with 891 atoms + +Performance: 0.053 ns/day, 448.608 hours/ns, 3.096 timesteps/s, 2.759 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 32.195 | 32.195 | 32.195 | 0.0 | 99.68 +Bond | 0.037627 | 0.037627 | 0.037627 | 0.0 | 0.12 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0025439 | 0.0025439 | 0.0025439 | 0.0 | 0.01 +Output | 0.0077194 | 0.0077194 | 0.0077194 | 0.0 | 0.02 +Modify | 0.055351 | 0.055351 | 0.055351 | 0.0 | 0.17 +Other | | 0.001116 | | | 0.00 + +Nlocal: 891 ave 891 max 891 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4157 ave 4157 max 4157 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 +Ave special neighs/atom = 12.989899 +Neighbor list builds = 0 +Dangerous builds = 0 + +# write_data final.data nocoeff +# write_restart restart.inter +Total wall time: 0:00:32 diff --git a/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/mbx.json b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/mbx.json new file mode 100644 index 00000000000..66315f5c809 --- /dev/null +++ b/examples/PACKAGES/mbx/mof_ff_lammps+1_h2o_mbx/mbx.json @@ -0,0 +1,21 @@ +{ + "Note" : "This is an MBX v1.3 configuration file", + "MBX" : { + "box" : [], + "realspace_cutoff": 9.0, + "twobody_cutoff" : 6.5, + "threebody_cutoff" : 4.5, + "dipole_tolerance" : 1E-8, + "dipole_max_it" : 100, + "dipole_method" : "cg", + "alpha_ewald_elec" : 0.60, + "grid_density_elec" : 2.5, + "spline_order_elec" : 6, + "alpha_ewald_disp" : 0.60, + "grid_density_disp" : 2.5, + "spline_order_disp" : 6, + "ignore_2b_poly" : [], + "ignore_3b_poly" : [] + } +} + diff --git a/examples/PACKAGES/mbx/na+_slab/in.slab b/examples/PACKAGES/mbx/na+_slab/in.slab new file mode 100644 index 00000000000..020cde49876 --- /dev/null +++ b/examples/PACKAGES/mbx/na+_slab/in.slab @@ -0,0 +1,56 @@ +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 2 na+ 1 h2o 2 3 3 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +fix 1 all nvt temp 100 100 $(1000.0*dt) + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +# write_data final.data +# write_restart restart.new diff --git a/examples/PACKAGES/mbx/na+_slab/initial.data b/examples/PACKAGES/mbx/na+_slab/initial.data new file mode 100644 index 00000000000..c10b24dea25 --- /dev/null +++ b/examples/PACKAGES/mbx/na+_slab/initial.data @@ -0,0 +1,4631 @@ +LAMMPS data file via write_data, version 29 Sep 2021, timestep = 1000 + +1534 atoms +3 atom types +1022 bonds +1 bond types +511 angles +1 angle types + +-10 10 xlo xhi +-10 10 ylo yhi +-50 50 zlo zhi + +Masses + +1 22.98976967 +2 15.9949146221 +3 1.0078250321 + +Atoms # full + +609 204 3 0.5564 -4.427240961468725 -7.828950201034387 -13.128286872065173 0 1 0 +472 158 3 0.5564 -9.870431035311423 -8.665764138005247 -12.967797147982575 0 -1 0 +1492 498 3 0.5564 -3.932329958387765 -3.9586763783294248 -13.501488020935287 0 0 0 +842 282 2 -1.1128 -4.147452909115464 -8.68900171985416 -14.541728826100837 0 1 0 +843 282 3 0.5564 -3.9428811199533658 -9.532754498285692 -14.876412743423629 0 1 0 +844 282 3 0.5564 -3.9740995696489225 -8.02078074033606 -15.236550374618625 0 1 0 +74 26 2 -1.1128 -9.635128755354756 -3.9993353753197938 -16.11989011658753 0 0 0 +76 26 3 0.5564 -8.915916265035275 -3.4745458111595595 -15.703779108857225 0 0 0 +75 26 3 0.5564 -9.414234578841642 -4.1159209915873225 -17.068112346321485 0 0 0 +762 255 3 0.5564 -8.239992910577596 -3.5049292214535637 -12.763442721614613 1 0 0 +763 255 3 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1 885 884 886 diff --git a/examples/PACKAGES/mbx/na+_slab/log.11Dec25.na+_slab.g++.1 b/examples/PACKAGES/mbx/na+_slab/log.11Dec25.na+_slab.g++.1 new file mode 100644 index 00000000000..8c40bf748ac --- /dev/null +++ b/examples/PACKAGES/mbx/na+_slab/log.11Dec25.na+_slab.g++.1 @@ -0,0 +1,251 @@ +LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-714-g4ab4c2060a-modified) + using 1 OpenMP thread(s) per MPI task +processors * * * map xyz + +units real +atom_style full +boundary p p p + +read_data initial.data +Reading data file ... + orthogonal box = (-10 -10 -50) to (10 10 50) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1534 atoms + reading velocities ... + 1534 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + orthogonal box = (-10 -10 -50) to (10 10 50) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 1022 bonds + reading angles ... + 511 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.058 seconds + +pair_style mbx 9.0 + +# Define bonds and angles to use if using SHAKE constraints +bond_style zero +angle_style zero +bond_coeff 1 0.98823 # from PIMD +angle_coeff 1 105.50896 # from PIMD + +pair_coeff * * 2 na+ 1 h2o 2 3 3 json mbx.json + +neighbor 2.0 bin +neigh_modify every 1 delay 10 + +timestep 0.5 + +compute mbx all pair mbx +variable e1bpip equal c_mbx[1] +variable e2bpip equal c_mbx[2] +variable e3bpip equal c_mbx[3] +variable e4bpip equal c_mbx[4] +variable edisp equal c_mbx[5] +variable ebuck equal c_mbx[6] +variable eperm equal c_mbx[7] +variable eind equal c_mbx[8] +variable eele equal c_mbx[9] +variable etot equal c_mbx[10] + +fix 1 all nvt temp 100 100 $(1000.0*dt) +fix 1 all nvt temp 100 100 500 + +velocity all create 298 428459 rot yes dist gaussian +velocity all zero linear +velocity all zero angular + +thermo_style custom step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press +thermo 1 +thermo_modify flush yes + +# fix verbose_mbx_thermo_print all print 1 "$(step) $(0.001*time) $(temp) $(etotal) $(ke) $(pe) $(enthalpy) $(density) $(lx) $(ly) $(lz) $(vol) $(pxx) $(pyy) $(pzz) $(press) $(v_e1bpip) $(v_e2bpip) $(v_e3bpip) $(v_e4bpip) $(v_edisp) $(v_ebuck) $(v_eperm) $(v_eind) $(v_eele) $(v_etot)" file mbx_thermo.out screen no title "# step time temp etotal ke pe enthalpy density lx ly lz vol pxx pyy pzz press e1bpip e2bpip e3bpip e4bpip edisp ebuck eperm eind eele etot" + +# dump 1 all custom 1 dump.lammpstrj id mol type q x y z +# dump_modify 1 append no sort id format line "%d %d %d %8.4f %15.8f %15.8f %15.8f" + +# restart 10 restart.1 restart.2 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair mbx command: + +@article{10.1063/5.0156036, + author = {Riera, Marc and Knight, Christopher and Bull-Vulpe, Ethan F. and Zhu, Xuanyu and Agnew, Henry and Smith, Daniel G. A. and Simmonett, Andrew C. and Paesani, Francesco}, + title = "{MBX: A many-body energy and force calculator for data-driven many-body simulations}", + journal = {The Journal of Chemical Physics}, + volume = {159}, + number = {5}, + pages = {054802}, + year = {2023}, + doi = {10.1063/5.0156036}, + version = {1.3.3} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 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 = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 4 4 19 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mbx, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.784 | 8.784 | 8.784 Mbytes + Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press + 0 0 298 -3243.6847 1361.7354 -4605.4201 -3659.9061 0.38301942 20 20 100 40000 -636.3765 -547.97789 -956.11845 -713.49095 + 1 0.5 295.83833 -3243.6773 1351.8575 -4595.5348 -3647.0291 0.38301942 20 20 100 40000 -636.17689 -651.22249 -786.8903 -691.42989 + 2 1 293.01096 -3243.4325 1338.9375 -4582.37 -3600.7388 0.38301942 20 20 100 40000 -582.97141 -680.57764 -573.94515 -612.49807 + 3 1.5 290.34508 -3243.0911 1326.7556 -4569.8467 -3531.4507 0.38301942 20 20 100 40000 -477.64538 -648.98743 -356.29409 -494.30897 + 4 2 288.99207 -3242.8766 1320.5729 -4563.4495 -3454.124 0.38301942 20 20 100 40000 -335.60433 -579.06073 -171.70206 -362.12237 + 5 2.5 289.72559 -3242.9295 1323.9248 -4566.8543 -3382.5152 0.38301942 20 20 100 40000 -184.27029 -493.64682 -39.920699 -239.27927 + 6 3 292.47495 -3243.2438 1336.4882 -4579.732 -3324.7561 0.38301942 20 20 100 40000 -56.330924 -407.71865 44.862284 -139.7291 + 7 3.5 296.32159 -3243.7035 1354.0657 -4597.7692 -3282.3554 0.38301942 20 20 100 40000 20.109359 -324.91415 106.03253 -66.257423 + 8 4 299.89577 -3244.1127 1370.3982 -4614.5109 -3252.511 0.38301942 20 20 100 40000 30.580085 -240.42778 166.6581 -14.396531 + 9 4.5 302.03876 -3244.2583 1380.1908 -4624.4492 -3232.4757 0.38301942 20 20 100 40000 -23.019089 -150.10918 233.72185 20.197857 + 10 5 302.45453 -3244.0856 1382.0907 -4626.1763 -3223.5687 0.38301942 20 20 100 40000 -127.88754 -60.618459 294.01661 35.170204 + 11 5.5 301.84381 -3243.7944 1379.3 -4623.0944 -3231.7048 0.38301942 20 20 100 40000 -268.93839 7.4852999 323.62551 20.724139 + 12 6 301.29879 -3243.6595 1376.8095 -4620.469 -3263.4505 0.38301942 20 20 100 40000 -433.95086 27.665093 304.50769 -33.926023 + 13 6.5 301.48528 -3243.7583 1377.6616 -4621.4199 -3320.7606 0.38301942 20 20 100 40000 -613.59743 -19.43832 237.04157 -131.99806 + 14 7 302.36773 -3243.9536 1381.6941 -4625.6477 -3398.7312 0.38301942 20 20 100 40000 -798.99902 -137.17367 140.20858 -265.32137 + 15 7.5 303.54942 -3244.1237 1387.0939 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40000 -732.15114 3.3012181 -723.39801 -484.08264 + 84 42 295.17529 -3262.3188 1348.8276 -4611.1464 -3421.7757 0.38301942 20 20 100 40000 -535.49233 19.383459 -303.91909 -273.34266 + 85 42.5 293.92062 -3262.4932 1343.0943 -4605.5875 -3320.1178 0.38301942 20 20 100 40000 -342.4337 -15.234769 61.32647 -98.780667 + 86 43 295.94094 -3263.1591 1352.3263 -4615.4854 -3255.9847 0.38301942 20 20 100 40000 -181.49447 -96.185393 314.57504 12.298392 + 87 43.5 300.48887 -3264.2502 1373.1085 -4637.3586 -3232.4407 0.38301942 20 20 100 40000 -65.267851 -198.24202 427.09445 54.528193 + 88 44 305.47796 -3265.4101 1395.9065 -4661.3166 -3240.9851 0.38301942 20 20 100 40000 8.1028942 -287.71353 405.21898 41.869449 + 89 44.5 308.63872 -3266.2061 1410.3499 -4676.556 -3268.9122 0.38301942 20 20 100 40000 45.206117 -337.62394 278.50106 -4.6389225 + 90 45 308.84969 -3266.4883 1411.3139 -4677.8022 -3307.85 0.38301942 20 20 100 40000 46.131965 -337.82427 78.984183 -70.902707 + 91 45.5 306.61216 -3266.493 1401.0894 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-1503.5924 -1079.225 + 99 49.5 301.08075 -3270.6747 1375.8131 -4646.4878 -3878.8166 0.38301942 20 20 100 40000 -1534.157 -263.76306 -1329.5294 -1042.4832 + 100 50 298.97024 -3271.0136 1366.169 -4637.1826 -3805.2012 0.38301942 20 20 100 40000 -1456.1215 -241.98522 -1049.0228 -915.70985 +Loop time of 309.509 on 1 procs for 100 steps with 1534 atoms + +Performance: 0.014 ns/day, 1719.494 hours/ns, 0.323 timesteps/s, 495.624 atom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 309.36 | 309.36 | 309.36 | 0.0 | 99.95 +Bond | 0.00010995 | 0.00010995 | 0.00010995 | 0.0 | 0.00 +Neigh | 0.018557 | 0.018557 | 0.018557 | 0.0 | 0.01 +Comm | 0.0042462 | 0.0042462 | 0.0042462 | 0.0 | 0.00 +Output | 0.0066816 | 0.0066816 | 0.0066816 | 0.0 | 0.00 +Modify | 0.1198 | 0.1198 | 0.1198 | 0.0 | 0.04 +Other | | 0.001284 | | | 0.00 + +Nlocal: 1534 ave 1534 max 1534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5232 ave 5232 max 5232 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 378231 ave 378231 max 378231 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 378231 +Ave neighs/atom = 246.56519 +Ave special neighs/atom = 1.9986962 +Neighbor list builds = 2 +Dangerous builds = 0 + +# write_data final.data +# write_restart restart.new +Total wall time: 0:05:12 diff --git a/examples/PACKAGES/mbx/na+_slab/mbx.json b/examples/PACKAGES/mbx/na+_slab/mbx.json new file mode 100644 index 00000000000..95419edd547 --- /dev/null +++ b/examples/PACKAGES/mbx/na+_slab/mbx.json @@ -0,0 +1,21 @@ +{ + "Note" : "json file for MB-nrg Na- in a MB-pol water slab", + "MBX" : { + "box" : [], + "realspace_cutoff": 9.0, + "twobody_cutoff" : 9.0, + "threebody_cutoff" : 7.0, + "dipole_tolerance" : 1E-8, + "dipole_max_it" : 100, + "dipole_method" : "cg", + "alpha_ewald_elec" : 0.60, + "grid_density_elec" : 2.5, + "spline_order_elec" : 6, + "alpha_ewald_disp" : 0.60, + "grid_density_disp" : 2.5, + "spline_order_disp" : 6, + "ignore_2b_poly" : [], + "ignore_3b_poly" : [] + } +} + diff --git a/examples/PACKAGES/mbx/plugin/.gitignore b/examples/PACKAGES/mbx/plugin/.gitignore new file mode 100644 index 00000000000..0ec9e7f9823 --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/.gitignore @@ -0,0 +1 @@ +/build* diff --git a/examples/PACKAGES/mbx/plugin/CMakeLists.txt b/examples/PACKAGES/mbx/plugin/CMakeLists.txt new file mode 100644 index 00000000000..ebc4bdd1249 --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/CMakeLists.txt @@ -0,0 +1,61 @@ +# -*- CMake -*- build system for plugin examples. +# The is meant to be used as a template for plugins that are +# distributed independent from the LAMMPS package. +########################################## + +cmake_minimum_required(VERSION 3.20) + +project(mbxplugin VERSION 1.0 LANGUAGES CXX) + +set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}) +include(CheckIncludeFileCXX) +include(LAMMPSInterfacePlugin) +list(APPEND CMAKE_MODULE_PATH ${LAMMPS_SOURCE_DIR}/../cmake/Modules) +include(MBX) + +########################## +# building the plugins + +add_library(mbxplugin MODULE mbxplugin.cpp ${LAMMPS_SOURCE_DIR}/MBX/fix_mbx.cpp + ${LAMMPS_SOURCE_DIR}/MBX/pair_mbx.cpp) +target_link_libraries(mbxplugin PRIVATE LAMMPS::MBX) +target_link_libraries(mbxplugin PRIVATE lammps) +target_include_directories(mbxplugin PRIVATE ${LAMMPS_SOURCE_DIR}/MBX) +set_target_properties(mbxplugin PROPERTIES PREFIX "" SUFFIX ".so") + +# MacOS seems to need this +if(CMAKE_SYSTEM_NAME STREQUAL Darwin) + set_target_properties(mbxplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") +elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows") +# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers + set_target_properties(mbxplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + if(CMAKE_CROSSCOMPILING) + set_target_properties(mbxplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") + endif() + + get_lammps_version(${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}/mbxplugin.nsis + ${CMAKE_BINARY_DIR}) + if(BUILD_MPI) + if(USE_MSMPI) + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI mbxplugin.nsis + DEPENDS mbxplugin mbx_copy lammps.ico lammps-text-logo-wide.bmp mbxplugin.nsis + BYPRODUCTS LAMMPS-MBX-plugin-${LAMMPS_VERSION}-MSMPI.exe) + else() + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI mbxplugin.nsis + DEPENDS mbxplugin mbx_copy lammps.ico lammps-text-logo-wide.bmp mbxplugin.nsis + BYPRODUCTS LAMMPS-MBX-plugin-${LAMMPS_VERSION}-MPI.exe) + endif() + else() + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} mbxplugin.nsis + COMMAND ${CMAKE_COMMAND} -E echo ${PWD} + DEPENDS mbxplugin mbx_copy lammps.ico lammps-text-logo-wide.bmp mbxplugin.nsis + BYPRODUCTS LAMMPS-MBX-plugin-${LAMMPS_VERSION}.exe) + endif() + endif() +else() + set_target_properties(mbxplugin PROPERTIES LINK_FLAGS "-rdynamic") +endif() diff --git a/examples/PACKAGES/mbx/plugin/LAMMPSInterfacePlugin.cmake b/examples/PACKAGES/mbx/plugin/LAMMPSInterfacePlugin.cmake new file mode 120000 index 00000000000..2ac6d20a54b --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/LAMMPSInterfacePlugin.cmake @@ -0,0 +1 @@ +../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake \ No newline at end of file diff --git a/examples/PACKAGES/mbx/plugin/MBX.cmake b/examples/PACKAGES/mbx/plugin/MBX.cmake new file mode 120000 index 00000000000..fb01ac784f1 --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/MBX.cmake @@ -0,0 +1 @@ +../../../../cmake/Modules/Packages/MBX.cmake \ No newline at end of file diff --git a/examples/PACKAGES/mbx/plugin/README.txt b/examples/PACKAGES/mbx/plugin/README.txt new file mode 100644 index 00000000000..2faeab76fc1 --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/README.txt @@ -0,0 +1,2 @@ +This folder contains a loader and support files to build the MBX package as plugin. +For more information please see: https://docs.lammps.org/Developer_plugins.html diff --git a/examples/PACKAGES/mbx/plugin/lammps-text-logo-wide.bmp b/examples/PACKAGES/mbx/plugin/lammps-text-logo-wide.bmp new file mode 100644 index 00000000000..b9ec4c35f22 Binary files /dev/null and b/examples/PACKAGES/mbx/plugin/lammps-text-logo-wide.bmp differ diff --git a/examples/PACKAGES/mbx/plugin/lammps.ico b/examples/PACKAGES/mbx/plugin/lammps.ico new file mode 100644 index 00000000000..cce156bf799 Binary files /dev/null and b/examples/PACKAGES/mbx/plugin/lammps.ico differ diff --git a/examples/PACKAGES/mbx/plugin/mbxplugin.cpp b/examples/PACKAGES/mbx/plugin/mbxplugin.cpp new file mode 100644 index 00000000000..a8881c667da --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/mbxplugin.cpp @@ -0,0 +1,44 @@ + +#include "lammpsplugin.h" +#include "version.h" + +#include "pair_mbx.h" +#include "fix_mbx.h" + +using namespace LAMMPS_NS; + +static Fix *fix_mbx_creator(LAMMPS *lmp, int argc, char **argv) +{ + return new FixMBX(lmp, argc, argv); +} + +static Pair *pair_mbx_creator(LAMMPS *lmp) +{ + return new PairMBX(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + // register MBX pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "mbx"; + plugin.info = "MBX plugin pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_mbx_creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); + + // register MBX fix style + plugin.version = LAMMPS_VERSION; + plugin.style = "fix"; + plugin.name = "MBX"; + plugin.info = "MBX plugin fix style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_mbx_creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/PACKAGES/mbx/plugin/mbxplugin.nsis b/examples/PACKAGES/mbx/plugin/mbxplugin.nsis new file mode 100644 index 00000000000..c30ac5a86b0 --- /dev/null +++ b/examples/PACKAGES/mbx/plugin/mbxplugin.nsis @@ -0,0 +1,165 @@ +#!Nsis Installer Command Script +# +# The following external defines are recognized: +# ${VERSION} = YYYYMMDD + +!include "MUI2.nsh" +!include "FileFunc.nsh" + +!define MUI_ICON "lammps.ico" +!define MUI_UNICON "lammps.ico" +!define MUI_HEADERIMAGE +!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp" +!define MUI_HEADERIMAGE_RIGHT + +Unicode true +XPStyle on + +!include "LogicLib.nsh" +!addplugindir "envvar/Plugins/x86-unicode" +!include "x64.nsh" + +RequestExecutionLevel user + +!macro VerifyUserIsAdmin +UserInfo::GetAccountType +pop $0 +${If} $0 != "admin" + messageBox mb_iconstop "Administrator rights required!" + setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED + quit +${EndIf} +!macroend + +!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}" +OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe" + +Name "${PLUMEDPLUGIN}" +InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}" + +ShowInstDetails show +ShowUninstDetails show +SetCompressor zlib + +!define MUI_ABORTWARNING + +!insertmacro MUI_PAGE_DIRECTORY +!insertmacro MUI_PAGE_INSTFILES + +!insertmacro MUI_UNPAGE_CONFIRM +!insertmacro MUI_UNPAGE_INSTFILES + +!insertmacro MUI_LANGUAGE "English" + +function .onInit + # Determine if LAMMPS was already installed and check whether it was in 32-bit + # or 64-bit. Then look up path to uninstaller and offer to uninstall or quit + SetRegView 32 + ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits" + SetRegView LastUsed + ${If} $0 == "32" + SetRegView 32 + ${ElseIf} $0 == "64" + SetRegView 64 + ${Else} + SetRegView 64 + ${EndIf} + ClearErrors + ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" "UninstallString" + SetRegView LastUsed + ${If} ${Errors} + DetailPrint "LAMMPS MBX plugin not (yet) installed" + ${Else} + MessageBox MB_YESNO "LAMMPS MBX plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit + Pop $R1 + StrCmp $R1 2 Quit +1 + Exec $R0 + Quit: + Quit + ${EndIf} + setShellVarContext all +functionEnd + +Section "${MBXPLUGIN}" SecMbxplugin + SectionIn RO + # Write LAMMPS installation bitness marker. Always use 32-bit registry view + SetRegView 32 + IntFmt $0 "0x%08X" 64 + WriteRegDWORD HKCU "Software\LAMMPS-MBX" "Bits" $0 + + # Switch to "native" registry view + SetRegView 64 + SetShellVarContext current + + SetOutPath "$INSTDIR" + CreateDirectory "$INSTDIR\patches" + CreateDirectory "$INSTDIR\bin" + File lammps.ico + File mbxplugin.so + + # Register Application and its uninstaller + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "DisplayName" "${MBXPLUGIN}" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "Publisher" "The LAMMPS and MBX Developers" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "URLInfoAbout" "lammps.org" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "DisplayIcon" "$INSTDIR\lammps.ico" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "DisplayVersion" "${VERSION}" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "InstallLocation" "$INSTDIR" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "UninstallString" "$\"$INSTDIR\uninstall.exe$\"" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S" + + ${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2 + IntFmt $0 "0x%08X" $0 + WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" \ + "EstimatedSize" "$0" + + # update path variables + EnVar::SetHKCU + # add to LAMMPS plugin search path + EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR" + # add mbx2 patch files + EnVar::AddValue "MBX_ROOT" "$INSTDIR" + + WriteUninstaller "$INSTDIR\Uninstall.exe" +SectionEnd + +function un.onInit + SetShellVarContext current +functionEnd + +Section "Uninstall" + # remove LAMMPS bitness/installation indicator always in 32-bit registry view + SetRegView 32 + DeleteRegKey HKCU "Software\LAMMPS-MBX" + + # unregister extension, and uninstall info + SetRegView 64 + SetShellVarContext current + # unregister installation + DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-MBX" + + # update path variables + EnVar::SetHKCU + # remove entry from LAMMPS plugin search path + EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR" + # remove mbx patch environment + EnVar::Delete "MBX_ROOT" + + RMDir /r /REBOOTOK "$INSTDIR\patches" + RMDir /r /REBOOTOK "$INSTDIR\bin" + Delete /REBOOTOK "$INSTDIR\mbxplugin.so" + Delete /REBOOTOK "$INSTDIR\Uninstall.exe" + Delete /REBOOTOK "$INSTDIR\lammps.ico" + RMDir /REBOOTOK "$INSTDIR" +SectionEnd + +# Local Variables: +# mode: sh +# End: diff --git a/src/.gitignore b/src/.gitignore index df32c1da840..34f679824ca 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -247,6 +247,10 @@ /inthash.h /fix_plumed.cpp /fix_plumed.h +/fix_mbx.cpp +/fix_mbx.h +/pair_mbx.cpp +/pair_mbx.h /dump_molfile.cpp /dump_molfile.h /molfile_interface.cpp diff --git a/src/BROWNIAN/fix_brownian_base.cpp b/src/BROWNIAN/fix_brownian_base.cpp index 35a8424e747..f9330372105 100644 --- a/src/BROWNIAN/fix_brownian_base.cpp +++ b/src/BROWNIAN/fix_brownian_base.cpp @@ -14,7 +14,8 @@ /* ---------------------------------------------------------------------- Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. - Contributing author: Sam Cameron (University of Bristol) + Contributing authors: Sam Cameron (University of Bristol), + Arthur Straube (Zuse Institute Berlin) ------------------------------------------------------------------------- */ #include "fix_brownian_base.h" @@ -46,6 +47,8 @@ FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : dipole_flag = 0; rot_temp_flag = 0; planar_rot_flag = 0; + rot_style = ROT_GEOMETRIC; + if (utils::strmatch(style, "^brownian/sphere")) rot_style = ROT_PROJECTION; g2 = 0.0; std::string mystyle = fmt::format("fix {}", style); @@ -187,7 +190,21 @@ FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : planar_rot_flag = 1; if (domain->dimension == 2) error->all(FLERR, iarg, "The planar_rotation keyword is not allowed for 2D simulations"); - iarg = iarg + 1; + ++iarg; + + } else if (strcmp(arg[iarg], "rotation_style") == 0) { + + if (!utils::strmatch(style, "^brownian/sphere")) + error->all(FLERR, "Keyword rotation_style is only supported for fix brownian/sphere"); + if (narg < iarg + 2) utils::missing_cmd_args(FLERR, "fix brownian rotation_style", error); + + if (strcmp(arg[iarg + 1], "projection") == 0) + rot_style = ROT_PROJECTION; + else if (strcmp(arg[iarg + 1], "geometric") == 0) + rot_style = ROT_GEOMETRIC; + else + error->all(FLERR, iarg + 1, "Unknown fix {} rotation_style {}", style); + iarg = iarg + 2; } else { error->all(FLERR, iarg, "Unknown fix {} keyword {}", style, arg[iarg]); diff --git a/src/BROWNIAN/fix_brownian_base.h b/src/BROWNIAN/fix_brownian_base.h index 9fab2a54ce2..82553a10f23 100644 --- a/src/BROWNIAN/fix_brownian_base.h +++ b/src/BROWNIAN/fix_brownian_base.h @@ -26,6 +26,7 @@ class FixBrownianBase : public Fix { int setmask() override; void reset_dt() override; + protected: int seed; // RNG seed double dt, sqrtdt; // time step interval and its sqrt @@ -35,6 +36,8 @@ class FixBrownianBase : public Fix { int gamma_r_eigen_flag; // 0/1 if anisotropic rotational damping is unset/set int rot_temp_flag; // 0/1 if rotational temperature is unset/set int planar_rot_flag; // 0/1 if rotation is constrained to 2D (xy) plane + enum RotStyle { ROT_PROJECTION, ROT_GEOMETRIC }; + RotStyle rot_style; // set by rotation_style: projection or geometric double gamma_t, gamma_r; // translational and rotational (isotropic) damping params double *gamma_t_inv; // anisotropic damping parameter eigenvalues diff --git a/src/BROWNIAN/fix_brownian_sphere.cpp b/src/BROWNIAN/fix_brownian_sphere.cpp index 52d89091687..59a6b9ad64f 100644 --- a/src/BROWNIAN/fix_brownian_sphere.cpp +++ b/src/BROWNIAN/fix_brownian_sphere.cpp @@ -14,7 +14,8 @@ /* ---------------------------------------------------------------------- Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. - Contributing author: Sam Cameron (University of Bristol) + Contributing authors: Sam Cameron (University of Bristol) + Arthur Straube (Zuse Institute Berlin) ------------------------------------------------------------------------- */ #include "fix_brownian_sphere.h" @@ -59,36 +60,84 @@ void FixBrownianSphere::init() void FixBrownianSphere::initial_integrate(int /*vflag */) { - if (domain->dimension == 2) { - if (!noise_flag) { - initial_integrate_templated<0, 0, 1, 0>(); - } else if (gaussian_noise_flag) { - initial_integrate_templated<0, 1, 1, 0>(); - } else { - initial_integrate_templated<1, 0, 1, 0>(); - } - } else if (planar_rot_flag) { - if (!noise_flag) { - initial_integrate_templated<0, 0, 0, 1>(); - } else if (gaussian_noise_flag) { - initial_integrate_templated<0, 1, 0, 1>(); + if (rot_style == ROT_GEOMETRIC) { + + // Geometric integrator (Tp_ROTGEOM = 1) + if (domain->dimension == 2) { + + // pure 2D (2D translation + 2D rotation) + if (!noise_flag) { + initial_integrate_templated<1, 0, 0, 1, 0>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<1, 0, 1, 1, 0>(); + } else { + initial_integrate_templated<1, 1, 0, 1, 0>(); + } + + } else if (planar_rot_flag) { + + // planar rotation (3D translation + 2D rotation) + if (!noise_flag) { + initial_integrate_templated<1, 0, 0, 0, 1>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<1, 0, 1, 0, 1>(); + } else { + initial_integrate_templated<1, 1, 0, 0, 1>(); + } + } else { - initial_integrate_templated<1, 0, 0, 1>(); + + // full 3D (3D translation + 3D rotation) + if (!noise_flag) { + initial_integrate_templated<1, 0, 0, 0, 0>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<1, 0, 1, 0, 0>(); + } else { + initial_integrate_templated<1, 1, 0, 0, 0>(); + } } + } else { - if (!noise_flag) { - initial_integrate_templated<0, 0, 0, 0>(); - } else if (gaussian_noise_flag) { - initial_integrate_templated<0, 1, 0, 0>(); + + // Projection integrator (Tp_ROTGEOM = 0) + if (domain->dimension == 2) { + + if (!noise_flag) { + initial_integrate_templated<0, 0, 0, 1, 0>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<0, 0, 1, 1, 0>(); + } else { + initial_integrate_templated<0, 1, 0, 1, 0>(); + } + + } else if (planar_rot_flag) { + + if (!noise_flag) { + initial_integrate_templated<0, 0, 0, 0, 1>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<0, 0, 1, 0, 1>(); + } else { + initial_integrate_templated<0, 1, 0, 0, 1>(); + } + } else { - initial_integrate_templated<1, 0, 0, 0>(); + + if (!noise_flag) { + initial_integrate_templated<0, 0, 0, 0, 0>(); + } else if (gaussian_noise_flag) { + initial_integrate_templated<0, 0, 1, 0, 0>(); + } else { + initial_integrate_templated<0, 1, 0, 0, 0>(); + } + } + } } /* ---------------------------------------------------------------------- */ -template +template void FixBrownianSphere::initial_integrate_templated() { double **x = atom->x; @@ -180,26 +229,120 @@ void FixBrownianSphere::initial_integrate_templated() // store length of dipole as we need to convert it to a unit vector and // then back again - mulen = sqrt(mu[i][0] * mu[i][0] + mu[i][1] * mu[i][1] + mu[i][2] * mu[i][2]); + mulen = MathExtra::len3(mu[i]); + if (!(mulen > 0)) + error->one(FLERR, "Fix brownian/sphere dipole moment must have positive length"); + + // unit vector u = mu / |mu| at time t + double u[3]; + MathExtra::scale3(1 / mulen, mu[i], u); - // unit vector at time t - mux = mu[i][0] / mulen; - muy = mu[i][1] / mulen; - muz = mu[i][2] / mulen; + // effective angular velocity omega is denoted as w = (wx, wy, wz) (deterministic torque + noise) + double w[3] = {wx, wy, wz}; - // un-normalised unit vector at time t + dt - mu[i][0] = mux + (wy * muz - wz * muy) * dt; - mu[i][1] = muy + (wz * mux - wx * muz) * dt; - mu[i][2] = muz + (wx * muy - wy * mux) * dt; + if (Tp_ROTGEOM) { - // normalisation introduces the stochastic drift term due to changing from - // Stratonovich to Ito interpretation - MathExtra::norm3(mu[i]); + // --- Rotational update: Geometric integrator for overdamped rotational Brownian motion ---- + // Reference: F. Hoefling & A. V. Straube, Phys. Rev. Research 7, 043034 (2025); DOI: 10.1103/wzdn-29p4 + + if (Tp_2D || Tp_2Drot) { + + // --- Rotational update, 2D case (geometric integrator) ---- + + // ---------------------------------------------------------------------- + // Tp_2D (2D) and Tp_2Drot (planar rotation) constrain rotational dynamics to the x–y plane, + // i.e. a finite rotation about z by the angle theta = dt * wz. They differ only in translation. + // Geometric update corresponds to a 2D rotation in the x-y plane (about z) by + // the angle theta = dt * wz (wx, wy play no role and only wz matters). + // Thus: ux_new = cos(theta) ux - sin(theta) uy + // uy_new = sin(theta) ux + cos(theta) uy + // ---------------------------------------------------------------------- + + // enforce planar angular increment about z (rotation angle theta = dt * wz) + const double theta = dt * w[2]; + + const double c = cos(theta); + const double s = sin(theta); + const double ux = u[0]; + const double uy = u[1]; + + // planar rotation about z by theta = dt * wz + u[0] = c * ux - s * uy; + u[1] = s * ux + c * uy; + + // normalize to |u| = 1 and rescale to |mu| = mulen + MathExtra::snormalize3(mulen, u, mu[i]); + + } else { + + // --- Rotational update, 3D case (geometric integrator) ---- + + // ---------------------------------------------------------------------- + // Paper -> code notation: + // u : unit orientation, u = mu / |mu| + // omega : effective angular velocity (noise + deterministic torque) -> w + // omega_perp : omega - dot(omega, u) u (tangent component) -> wperp + // dOmega : omega_perp * dt -> (dt*wperp) + // theta : |dOmega| = dt * |omega_perp| -> theta + // n : dOmega / |dOmega| = omega_perp / |omega_perp| -> n + // + // Update (Rodrigues; simplified since dot(n, u) = 0 by construction): + // u_new = cos(theta) u - sin(theta) (u x n) + // Renormalize u_new to suppress roundoff drift, then restore |mu|. + // ---------------------------------------------------------------------- + + // dot product dot(omega, u) = dot(w, u) + double dot_wu = MathExtra::dot3(w, u); + + // omega_perp = omega - dot(omega, u) u + double wperp[3]; + MathExtra::scaleadd3(-dot_wu, u, w, wperp); + + // wperplen = |omega_perp| = |wperp| + double wperplen = MathExtra::len3(wperp); + + // note: if omega_perp = 0, exact map leaves u unchanged (do nothing) + if (wperplen > 0) { + + // axis n = omega_perp / |omega_perp| + double n[3]; + MathExtra::scale3(1 / wperplen, wperp, n); + + // cross-product u × n + double uxn[3]; + MathExtra::cross3(u, n, uxn); + + // rotation angle theta = |omega_perp| * dt = |dOmega| + double theta = dt * wperplen; + double c = cos(theta); + double s = sin(theta); + // new rotated orientation u <- cos(theta) u - sin(theta) (u × n) + MathExtra::scaleadd3(c, u, -s, uxn, u); + + // remove roundoff drift and restore original dipole magnitude + MathExtra::snormalize3(mulen, u, mu[i]); + } + + } + + } else { + + // --- Rotational update: Projection integrator ---- + + // cross-product wxu = w × u + double wxu[3]; + MathExtra::cross3(w, u, wxu); + + // un-normalized unit vector at time t + dt: u <- u + dt (w × u) + MathExtra::scaleadd3(dt, wxu, u, u); + + // normalize to |u| = 1 and rescale to |mu| = mulen + // original comment: "normalisation introduces the stochastic drift term due to changing from + // Stratonovich to Ito interpretation" -- the issue is clarified in the reference + MathExtra::snormalize3(mulen, u, mu[i]); + + } - // multiply by original magnitude to obtain dipole of same length - mu[i][0] = mu[i][0] * mulen; - mu[i][1] = mu[i][1] * mulen; - mu[i][2] = mu[i][2] * mulen; } } } diff --git a/src/BROWNIAN/fix_brownian_sphere.h b/src/BROWNIAN/fix_brownian_sphere.h index 712285a4e3a..9263eaf9b56 100644 --- a/src/BROWNIAN/fix_brownian_sphere.h +++ b/src/BROWNIAN/fix_brownian_sphere.h @@ -32,7 +32,7 @@ class FixBrownianSphere : public FixBrownianBase { void initial_integrate(int) override; private: - template + template void initial_integrate_templated(); double g3, g4; }; diff --git a/src/MBX/Install.sh b/src/MBX/Install.sh new file mode 100755 index 00000000000..e16da765c55 --- /dev/null +++ b/src/MBX/Install.sh @@ -0,0 +1,38 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +action () { + if (test $mode = 0) then + rm -f ../$1 + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1 || test $1 = 2) then + echo "The MBX package does not support the legacy build system. Please build LAMMPS with CMake instead." + exit 1 + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*mbx[^ \t]* //g' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^[ \t]*include.*mbx.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/MBX/README b/src/MBX/README new file mode 100644 index 00000000000..b7827f45384 --- /dev/null +++ b/src/MBX/README @@ -0,0 +1,22 @@ +This package implements the "pair_style mbx" command +for LAMMPS, which is used to perform molecular dynamics simulations +using MB-pol and MB-nrg data-driven many-body potential energy functions. + +The package uses the "MBX" library, whose source code is available +at https://github.com/paesanilab/MBX. The files in the MBX package +folder implement an interface between LAMMPS and MBX, which is written +and maintained by the Paesani Lab (https://github.com/paesanilab). +The corresponding author is Francesco Paesani (fpaesani@ucsd.edu). + +MBX can be added to LAMMPS by using ` cmake -D PKG_MBX=yes ...` as +part of the build process. LAMMPS will then automatically download +and compile the MBX library. Do note that the compilation of MBX can +take a long time and can be quite memory intensive. If MBX is already +detected on your system using PKG_CONFIG, then LAMMPS will use that +version of MBX instead of downloading and compiling it. + +Examples for MBX are located in `examples/PACKAGES/mbx`. +These examples include scripts for running simulations +with MB-pol and other MB-nrg potentials. + +For questions, please use the MBX Google group https://groups.google.com/g/mbx-users diff --git a/src/MBX/fix_mbx.cpp b/src/MBX/fix_mbx.cpp new file mode 100644 index 00000000000..f163dee0ad9 --- /dev/null +++ b/src/MBX/fix_mbx.cpp @@ -0,0 +1,2126 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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_mbx.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "pair_mbx.h" +#include "respa.h" +#include "universe.h" +#include "update.h" + +#include +#include +#include + +#include "bblock/system.h" + +#define _MAX_SIZE_MOL_NAME 16 +// Subject to further increase _MAX_SIZE_MOL_NAME +#define _MAX_ATOMS_PER_MONOMER 8 +#define SMALL 1.0e-4 + + +namespace LAMMPS_NS { +//PImpl idiom to hide MBX implementation details +struct MBXImpl { + MBXImpl() : ptr_mbx(nullptr), ptr_mbx_local(nullptr) {} + ~MBXImpl() + { + delete ptr_mbx; + delete ptr_mbx_local; + } + bblock::System *ptr_mbx; + bblock::System *ptr_mbx_local; +}; +} // namespace LAMMPS_NS + +using namespace LAMMPS_NS; +using namespace FixConst; + + +std::string FixMBX::cite_pair_mbx = std::string( + "pair mbx command:\n\n" \ + "@article{10.1063/5.0156036,\n" \ + " author = {Riera, Marc and Knight, Christopher and Bull-Vulpe, Ethan F. and Zhu, Xuanyu and " \ + "Agnew, Henry and Smith, Daniel G. A. and Simmonett, Andrew C. and Paesani, Francesco},\n" \ + " title = \"{MBX: A many-body energy and force calculator for data-driven many-body " \ + "simulations}\",\n" \ + " journal = {The Journal of Chemical Physics},\n" \ + " volume = {159},\n" \ + " number = {5},\n" \ + " pages = {054802},\n" \ + " year = {2023},\n" \ + " doi = {10.1063/5.0156036},\n" \ + " version = {") + bblock::System::get_mbx_version() + "}\n" \ + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +// Parse atom ID or range for dp1 monomer +// Input can be a single integer (e.g., "5") or a range (e.g., "1*11") +std::pair FixMBX::parse_dp1_range(const std::string &dp1_str) +{ + try { + size_t pos = 0; + int val = std::stoi(dp1_str, &pos); + if (pos == dp1_str.size()) { + // Single integer + if (val < 1) + throw std::invalid_argument("[MBX] Atom ID " + dp1_str + " in dp1 must be positive"); + return {val, val}; + } + } catch (...) { + // Not a single integer, try to parse as range + } + + // Try to parse as a range (e.g., "1*11") + size_t star = dp1_str.find('*'); + if (star == std::string::npos) + throw std::invalid_argument("[MBX] Invalid dp1 format: " + dp1_str); + + std::string start_str = dp1_str.substr(0, star); + std::string end_str = dp1_str.substr(star + 1); + int start = 0, end = 0; + try { + size_t spos = 0, epos = 0; + start = std::stoi(start_str, &spos); + end = std::stoi(end_str, &epos); + + if (spos != start_str.size() || epos != end_str.size()) + throw std::invalid_argument("Non-integer characters found in range"); + } catch (...) { + throw std::invalid_argument("[MBX] Invalid integers in dp1 range: " + dp1_str); + } + if (start < 1 || end < start) + throw std::invalid_argument("[MBX] Invalid range values for dp1: " + dp1_str); + + return {start, end}; +} + +// Validate that the input arguments to fix mbx are correct +// throws specific errors if the arguments are malformed +bool FixMBX::validateMBXFixParameters(int narg, char **arg) +{ + if (narg < 2) error->all(FLERR, ("[MBX] Input line too short")); + + int num_monomers = 0; + try { + num_monomers = std::stoi(arg[0]); + } catch (...) { + error->all(FLERR, ("[MBX] num_monomers is not a valid integer: " + std::string(arg[0]))); + } + if (num_monomers < 1) error->all(FLERR, ("[MBX] num_monomers must be positive")); + + std::map mbx_atom_id_mapping; // atom ID mapping for all monomers + + int input_validation_index = 1; // part of arg currently being validated + + // Lambda to check dp1 monomer syntax + auto check_external_dp1 = [&](int n_atoms, char **current_monomer_atoms) -> bool { + if (n_atoms != 1) + error->all( + FLERR, + ("[MBX] Wrong number of arguments for dp1: expected 1, got " + std::to_string(n_atoms))); + const std::string atom_id_str = current_monomer_atoms[0]; + + int start_index, end_index; + try { + std::tie(start_index, end_index) = parse_dp1_range(atom_id_str); + } catch (const std::exception &e) { + error->all(FLERR, e.what()); + } + if (start_index < 1 || end_index < start_index) + error->all(FLERR, ("[MBX] Invalid range values for dp1: " + atom_id_str)); + + for (int at = start_index; at <= end_index; ++at) { + if (mbx_atom_id_mapping.count(at)) + error->all(FLERR, ("[MBX] Already defined atom IDs found in dp1: " + std::to_string(at))); + mbx_atom_id_mapping[at] = "X"; + } + return true; + }; + + // Lambda to check syntax of a monomer with n_atoms and atom IDs in current_monomer + auto check_monomer_syntax = [&](int n_atoms, char **current_monomer) -> bool { + std::string current_monomer_name = current_monomer[0]; + std::vector current_monomer_atoms; + + for (int i = 1; i <= n_atoms; ++i) current_monomer_atoms.push_back(current_monomer[i]); + std::vector expected_monomer_atom_ids; + + // special handling for dp1 monomer + if (current_monomer_name == "dp1") return check_external_dp1(n_atoms, ¤t_monomer[1]); + + try { + add_monomer_atom_types(const_cast(current_monomer_name.c_str()), + expected_monomer_atom_ids); + } catch (const std::exception &e) { + error->all(FLERR, ("[MBX] Invalid monomer name " + current_monomer_name)); + } + + if (expected_monomer_atom_ids.size() != n_atoms) + error->all(FLERR, + ("[MBX] Wrong number of atoms: expected " + std::to_string(expected_monomer_atom_ids.size()) + ", got " + + std::to_string(n_atoms))); + + // validate that atom IDs are positive integers + std::vector atom_ids; + for (size_t i = 0; i < expected_monomer_atom_ids.size(); ++i) { + int at = 0; + try { + at = std::stoi(current_monomer_atoms[i]); + } catch (...) { + error->all(FLERR, + ("[MBX] Atom ID " + current_monomer_atoms[i] + " is not a valid integer")); + } + if (at < 1) + error->all(FLERR, ("[MBX] Atom ID " + current_monomer_atoms[i] + " must be positive")); + atom_ids.push_back(at); + } + + // check that number of unique atom IDs is correct + // this verifies that the monomer has the expected number of different elements + std::set unique_atom_ids(atom_ids.begin(), atom_ids.end()); + std::set unique_monomer_atom_ids(expected_monomer_atom_ids.begin(), + expected_monomer_atom_ids.end()); + if (unique_atom_ids.size() < unique_monomer_atom_ids.size()) + error->all(FLERR, + ("[MBX] Wrong number of unique atom IDs in " + current_monomer_name + + ": expected " + std::to_string(unique_monomer_atom_ids.size()) + ", got " + + std::to_string(unique_atom_ids.size()))); + std::map atom_mapping; + + // check that atom ID mapping is consistent + // atom ID mapping must match expected, such as OHH for h2o + for (size_t i = 0; i < atom_ids.size(); ++i) { + int at = atom_ids[i]; + if (!atom_mapping.count(at)) // first time seeing this atom ID + atom_mapping[at] = expected_monomer_atom_ids[i]; + else if (atom_mapping[at] != expected_monomer_atom_ids[i]) { // inconsistent mapping detected + // construct error message + std::string expected_monomer_atom_ids_string = ""; + for (const auto &mat : expected_monomer_atom_ids) { expected_monomer_atom_ids_string += mat + " "; } + std::string atom_ids_string = ""; + for (const auto &at2 : atom_ids) { atom_ids_string += std::to_string(at2) + " "; } + error->all(FLERR, + ("[MBX] Incorrect atom ID mapping in " + current_monomer_name + ". Expected " + + expected_monomer_atom_ids_string + "but got " + atom_ids_string)); + } + if (mbx_atom_id_mapping.count(at)) // atom ID already defined in another monomer + error->all(FLERR, + ("[MBX] Already defined atom IDs found in " + current_monomer_name + ": " + + std::to_string(at))); + } + + // check that atom IDs are contiguous + int minimum_index = *std::min_element(atom_ids.begin(), atom_ids.end()); + int maximum_index = *std::max_element(atom_ids.begin(), atom_ids.end()); + for (int i = minimum_index; i <= maximum_index; ++i) { + if (std::find(atom_ids.begin(), atom_ids.end(), i) == atom_ids.end()) + error->all(FLERR, + ("[MBX] Atom IDs must be contiguous in " + current_monomer_name + ". Missing " + + std::to_string(i))); + } + for (const auto &kv : atom_mapping) // transfer monomer mapping to global mapping + mbx_atom_id_mapping[kv.first] = kv.second; + return true; + }; + + // validate each monomer + for (int monomer_index = 0; monomer_index < num_monomers; ++monomer_index) { + if (input_validation_index >= narg) + error->all(FLERR, ("[MBX] Not enough arguments to read a monomer name")); + std::string monomer_name = arg[input_validation_index]; + int num_atoms = 0; + + // ensure monomer name is valid and get number of atoms + try { + bool is_ext = false; + num_atoms = get_num_atoms_per_monomer(const_cast(monomer_name.c_str()), is_ext); + } catch (const std::exception &e) { + error->all(FLERR, ("[MBX] Invalid monomer name " + monomer_name)); + } + if (input_validation_index + num_atoms >= narg) + error->all(FLERR, ("[MBX] Not enough arguments to read monomer atoms for " + monomer_name)); + + check_monomer_syntax(num_atoms, &arg[input_validation_index]); + input_validation_index += num_atoms + 1; + } + + // process remaining optional keywords + while (input_validation_index < narg) { + if (strcmp(arg[input_validation_index], "json") == 0) { + if (input_validation_index + 1 >= narg) + error->all(FLERR, ("[MBX] Not enough arguments to read json filename")); + input_validation_index += 2; + } else if (strcmp(arg[input_validation_index], "print/verbose") == 0) { + input_validation_index += 1; + } else if (strcmp(arg[input_validation_index], "print/dipoles") == + 0) { // dipoles are now always printed by default + input_validation_index += 1; + } else if (strcmp(arg[input_validation_index], "aspc/reset") == 0) { + if (input_validation_index + 1 >= narg) + error->all(FLERR, ("[MBX] Not enough arguments to read aspc/reset value")); + int aspc_reset = 0; + try { + aspc_reset = std::stoi(arg[input_validation_index + 1]); + } catch (...) { + error->all(FLERR, ("[MBX] aspc/reset value is not a valid integer")); + } + if (aspc_reset < 1) error->all(FLERR, ("[MBX] aspc/reset value must be positive")); + input_validation_index += 2; + } else { + error->all(FLERR, ("[MBX] Unknown keyword: " + std::string(arg[input_validation_index]))); + } + } + + return true; +} + +FixMBX::FixMBX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +{ + // Constructor for fix mbx, called interally by pair mbx. + // Expected arguments: + // _FIX_MBX_INTERNAL all MBX num_mol_types mon_name atom_mapping ... json mbx.json + // num_mol_types = number of monomer types in the system + // mon_name = name of the monomer type (e.g. h2o, ch4, etc) + // atom mapping = list of LAMMPS atom types that correspond to the atoms in the monomer + // json arg = specifies the name of the MBX json configuration file, such as mbx.json + + if (lmp->citeme) lmp->citeme->add(cite_pair_mbx); + + me = comm->me; + nprocs = comm->nprocs; + mbx_impl = new MBXImpl; //PImpl idiom to hide MBX implementation details + + // // validate input arguments + bool validation_result = validateMBXFixParameters(narg - 3, &arg[3]); + + if (narg < 6) error->all(FLERR, "[MBX] Illegal fix mbx command"); + + num_mol_types = utils::inumeric(FLERR, arg[3], false, lmp); + + if (num_mol_types < 1) error->all(FLERR, "[MBX] Illegal fix mbx command"); + + num_atoms_per_mol = NULL; + mol_names = NULL; + lower_atom_type_index_in_mol = NULL; + higher_atom_type_index_in_mol = NULL; + + memory->create(num_atoms_per_mol, num_mol_types, "fixmbx:num_atoms_per_mol"); + memory->create(mol_names, num_mol_types, _MAX_SIZE_MOL_NAME, "fixmbx:mol_names"); + memory->create(lower_atom_type_index_in_mol, num_mol_types, + "fixmbx:lower_atom_type_index_in_mol"); + memory->create(higher_atom_type_index_in_mol, num_mol_types, + "fixmbx:higher_atom_type_index_in_mol"); + memory->create(order_in_mol, num_mol_types, _MAX_ATOMS_PER_MONOMER, "fixmbx:order_in_mol"); + + // Extract information about min and max indexes + int iarg = 4; + bool is_ext = false; + for (int i = 0; i < num_mol_types; ++i) { + std::string current_monomer_name = arg[iarg++]; + + if (strlen(current_monomer_name.c_str()) >= _MAX_SIZE_MOL_NAME) + error->all(FLERR, + "[MBX] Monomer name too long: did developer correctly add support for monomer?"); + + strcpy(mol_names[i], current_monomer_name.c_str()); + + int current_lower_index = _MAX_ATOMS_PER_MONOMER + 1; + int current_higher_index = -1; + + int current_n_atoms = + get_num_atoms_per_monomer(const_cast(current_monomer_name.c_str()), is_ext); + + if (current_n_atoms > _MAX_ATOMS_PER_MONOMER) + error->all(FLERR, + "[MBX] num_atoms_per_mol > _MAX_ATOMS_PER_MONOMER : did developer correctly add " + "support for monomer?"); + + if (current_monomer_name == "dp1") { + // dp1 can either by a single atom ID or a range of IDs in the form "1*11" + int start, end; + try { + + std::tie(start, end) = parse_dp1_range(std::string(arg[iarg++])); + } catch (const std::exception &e) { + error->all(FLERR, e.what()); + } + + lower_atom_type_index_in_mol[i] = start; + higher_atom_type_index_in_mol[i] = end; + + order_in_mol[i][0] = start; // only one atom in dp1 + + } else { // handling all other monomers + // find min and max atom type index in the mapping + for (int j = 0; j < current_n_atoms; j++) { + int current_index = utils::inumeric(FLERR, arg[iarg + j], false, lmp); + if (current_index < current_lower_index) current_lower_index = current_index; + if (current_index > current_higher_index) current_higher_index = current_index; + + lower_atom_type_index_in_mol[i] = current_lower_index; + higher_atom_type_index_in_mol[i] = current_higher_index; + } + + for (int j = 0; j < current_n_atoms; j++) { + order_in_mol[i][j] = utils::inumeric(FLERR, arg[iarg++], false, lmp); + } + } + } + + // process remaining optional keywords + + use_json = 0; + std::string json_file; + print_verbose = 0; + print_dipoles = 1; // dipoles are now always printed by default + aspc_step_reset = 1000; + + while (iarg < narg) { + if (strcmp(arg[iarg], "json") == 0) { + json_file = std::string(arg[++iarg]); + use_json = 1; + } else if (strcmp(arg[iarg], "print/verbose") == 0) { + print_verbose = 1; + } else if (strcmp(arg[iarg], "print/dipoles") == 0) { + print_dipoles = 1; // dipoles are now always printed by default + } else if (strcmp(arg[iarg], "aspc/reset") == 0) { + aspc_step_reset = atoi(arg[++iarg]); + } else { + error->all(FLERR, "[MBX] Unknown keyword in fix mbx command: " + std::string(arg[iarg])); + } + + iarg++; + } + + mbx_aspc_enabled = false; + + // verify that this fix is not called directly + // fix mbx should only be called indirectly by pair mbx + pair_mbx = nullptr; + pair_mbx = (PairMBX *) force->pair_match("^mbx", 0); + if (!pair_mbx) error->all(FLERR, "[MBX] Pair mbx is missing"); + + array_atom = NULL; + mbx_dip = NULL; + mol_type = NULL; + mol_anchor = NULL; + mol_local = NULL; + + grow_arrays(atom->nmax); + + // MRR Call function to fill up arrays + mbx_fill_system_information_from_atom(); + + atom->add_callback(0); + atom->add_callback(1); + + mbx_num_atoms = 0; + mbx_num_ext = 0; + + + // instance of MBX with just local monomers + + mbx_num_atoms_local = 0; + mbx_num_ext_local = 0; + + // check that LAMMPS proc mapping matches PME solver + // MPI ranks must be mapped in "xyz" order for PME + if (comm->style != 0) error->all(FLERR, "[MBX] Fix mbx must be used with comm_style brick"); + + if (comm->layout != Comm::LAYOUT_UNIFORM) + error->all(FLERR, "[MBX] Fix mbx must be used with comm layout of equal-sized bricks"); + + { + // compute expected proc coordinates for this MPI rank + int proc_x = me % comm->procgrid[0]; + int proc_y = (me % (comm->procgrid[0] * comm->procgrid[1])) / comm->procgrid[0]; + int proc_z = me / (comm->procgrid[0] * comm->procgrid[1]); + + int e = 0; + // compare actual location to expected + if ((proc_x != comm->myloc[0]) || (proc_y != comm->myloc[1]) || (proc_z != comm->myloc[2])) + e = 1; + int err = 0; + MPI_Allreduce(&e, &err, 1, MPI_INT, MPI_SUM, world); + if (err) + error->all( + FLERR, + "[MBX] Inconsistent proc mapping: 'processors * * * map xyz' required for PME solver"); + } + + // setup json, if requested + + if (use_json) { + int size = 0; + if (me == 0) { + // Test if file present + FILE *fp = fopen(json_file.c_str(), "r"); + if (fp == NULL) { + error->one(FLERR, "Cannot open file " + json_file); + } else + fclose(fp); + + std::ifstream t(json_file); + t.seekg(0, std::ios::end); + size = t.tellg(); + json_settings.resize(size); + t.seekg(0); + t.read(&json_settings[0], size); + } + + MPI_Bcast(&size, 1, MPI_INT, 0, world); + if (me) json_settings.resize(size); + + MPI_Bcast(&json_settings[0], size + 1, MPI_CHAR, 0, world); + } + + memory->create(mbxt_count, FixMBX::MBXT_LABELS::NUM_TIMERS, "fixmbx:mbxt_count"); + memory->create(mbxt_time, FixMBX::MBXT_LABELS::NUM_TIMERS, "fixmbx:mbxt_time"); + memory->create(mbxt_time_start, FixMBX::MBXT_LABELS::NUM_TIMERS, "fixmbx:mbxt_time_start"); + + for (int i = 0; i < FixMBX::MBXT_LABELS::NUM_TIMERS; ++i) { + mbxt_time[i] = 0.0; + mbxt_count[i] = 0; + } + + first_step = true; + + // MBX currently requires 4-byte tags + + if (sizeof(tagint) != sizeof(int)) error->all(FLERR, "[MBX] Tagints required to be of type int."); + + aspc_dip_hist = NULL; + aspc_order = 6; // hard-coded in MBX + aspc_max_num_hist = aspc_order + 2; + aspc_per_atom_size = aspc_max_num_hist * 3; // (# of histories) * (# of dimensions) + aspc_num_hist = 0; + aspc_step = 0; + + peratom_flag = 1; + size_peratom_cols = 9; + peratom_freq = 1; + + comm_forward = aspc_per_atom_size; + + mbxt_initial_time = MPI_Wtime(); +} + +/* ---------------------------------------------------------------------- */ + +FixMBX::~FixMBX() +{ + if (mbx_aspc_enabled) memory->destroy(aspc_dip_hist); + + if (print_dipoles) memory->destroy(mbx_dip); + + memory->destroy(num_atoms_per_mol); + memory->destroy(mol_names); + + // unregister callbacks to this fix from Atom class + + atom->delete_callback(id, 0); + atom->delete_callback(id, 1); + + memory->destroy(mol_local); + memory->destroy(mol_type); + memory->destroy(mol_anchor); + memory->destroy(lower_atom_type_index_in_mol); + memory->destroy(higher_atom_type_index_in_mol); + memory->destroy(order_in_mol); + + if (mbx_impl->ptr_mbx_local) { + // accumulate timing info from pme electrostatics + + std::vector tmpi = mbx_impl->ptr_mbx_local->GetInfoElectrostaticsCounts(); + std::vector tmpd = mbx_impl->ptr_mbx_local->GetInfoElectrostaticsTimings(); + + for (int i = 0; i < tmpi.size(); ++i) { + mbxt_count[FixMBX::MBXT_LABELS::ELE_PERMDIP_REAL + i] += tmpi[i]; + mbxt_time[FixMBX::MBXT_LABELS::ELE_PERMDIP_REAL + i] += tmpd[i]; + } + + // accumulate timing info from dispersion pme + + std::vector tmpi_d = mbx_impl->ptr_mbx_local->GetInfoDispersionCounts(); + std::vector tmpd_d = mbx_impl->ptr_mbx_local->GetInfoDispersionTimings(); + + for (int i = 0; i < tmpi_d.size(); ++i) { + mbxt_count[FixMBX::MBXT_LABELS::DISP_PME_SETUP + i] += tmpi_d[i]; + mbxt_time[FixMBX::MBXT_LABELS::DISP_PME_SETUP + i] += tmpd_d[i]; + } + + } + delete mbx_impl; + + if (print_verbose) + mbxt_write_summary(); // this and collecting times should be gated by 'timer full' request + + memory->destroy(mbxt_count); + memory->destroy(mbxt_time); + memory->destroy(mbxt_time_start); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::post_constructor() {} + +/* ---------------------------------------------------------------------- */ + +int FixMBX::setmask() +{ + int mask = 0; + mask |= POST_NEIGHBOR; + mask |= MIN_POST_NEIGHBOR; + mask |= PRE_FORCE; + // mask |= PRE_FORCE_RESPA; + mask |= MIN_PRE_FORCE; + + mask |= PRE_EXCHANGE; // only needs to be set when using ASPC integrator + + mask |= POST_FORCE; // only needs to be set when printing dipoles + + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::init() +{ + if (!atom->q_flag) error->all(FLERR, "[MBX] Fix mbx requires atom attribute q"); + + ngroup = group->count(igroup); + if (ngroup == 0) error->all(FLERR, "[MBX] Fix mbx group has no atoms"); + +} + +/* ---------------------------------------------------------------------- */ + +// Fill mol_type and mol_anchor arrays from atom data +void FixMBX::mbx_fill_system_information_from_atom() +{ + const int nlocal = atom->nlocal; + const int nghost = atom->nghost; + const int nall = nlocal + nghost; + + + bigint natoms = atom->natoms; + + tagint *tag = atom->tag; + int *molecule = atom->molecule; + double **x = atom->x; + + int mtype = -1; + for (int i = 0; i < nall; ++i) { + // Assign mol_type + for (int j = 0; j < num_mol_types; ++j) + if (atom->type[i] >= lower_atom_type_index_in_mol[j] and + atom->type[i] <= higher_atom_type_index_in_mol[j]) { + mol_type[i] = j; + mtype = j; + break; + // If j is max and no type has been found, types in mbx fix do not match types in data file + } else if (j == num_mol_types - 1) { + error->all(FLERR, + "[MBX] The atom types in fix mbx do not match the atom types in the data file"); + } + } + + // Reset anchors + int * last_anchor = mol_anchor + nall; + std::fill(mol_anchor, last_anchor, 0); + + for (int i = 0; i < nall; ++i) { + // Assign anchor TODO careful, not necessarily true + // Create another peratom property -> index within molecules + tagint itag = tag[i]; + int mtype = mol_type[i]; + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + if (is_ext) { + mol_anchor[i] = 1; + continue; + } + + bool isanchor = true; + for (int j = 0; j < na; j++) { + int idx = atom->map(tag[i] + j); + if (idx < 0) { + isanchor = false; + break; + } + + isanchor = isanchor && atom->type[idx] == order_in_mol[mtype][j]; + if (!isanchor) break; + } + + if (isanchor) mol_anchor[i] = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::setup_post_neighbor() +{ + + // Figure out if there is a gcmc fix somewhere + has_gcmc = false; + int ifix = -1; + for (int i = 0; i < modify->nfix; ++i) + if (strcmp(modify->fix[i]->style, "gcmc") == 0) { + if (ifix == -1) + ifix = i; + else + error->all(FLERR, "[MBX] Only one GCMC fix instance allowed to be active"); + } + if (ifix != -1) has_gcmc = true; + + grow_arrays(atom->nmax); + + // MRR Call function to fill up arrays + mbx_fill_system_information_from_atom(); + post_neighbor(); + + first_step = false; +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::post_neighbor() +{ + // setup after neighbor build + + const int nlocal = atom->nlocal; + const int nghost = atom->nghost; + const int nall = nlocal + nghost; + + tagint *tag = atom->tag; + int *molecule = atom->molecule; + double **x = atom->x; + + mbx_fill_system_information_from_atom(); + + // tear down existing MBX objects + + if (mbx_impl->ptr_mbx) delete mbx_impl->ptr_mbx; + + if (mbx_impl->ptr_mbx_local) { + // accumulate timing info from pme electrostatics + + std::vector tmpi = mbx_impl->ptr_mbx_local->GetInfoElectrostaticsCounts(); + std::vector tmpd = mbx_impl->ptr_mbx_local->GetInfoElectrostaticsTimings(); + + for (int i = 0; i < tmpi.size(); ++i) { + mbxt_count[MBXT_LABELS::ELE_PERMDIP_REAL + i] += tmpi[i]; + mbxt_time[MBXT_LABELS::ELE_PERMDIP_REAL + i] += tmpd[i]; + } + + // accumulate timing info from dispersion pme + + std::vector tmpi_d = mbx_impl->ptr_mbx_local->GetInfoDispersionCounts(); + std::vector tmpd_d = mbx_impl->ptr_mbx_local->GetInfoDispersionTimings(); + + for (int i = 0; i < tmpi_d.size(); ++i) { + mbxt_count[MBXT_LABELS::DISP_PME_SETUP + i] += tmpi_d[i]; + mbxt_time[MBXT_LABELS::DISP_PME_SETUP + i] += tmpd_d[i]; + } + + delete mbx_impl->ptr_mbx_local; + } + + // recreate main instance of MBX object + + mbx_impl->ptr_mbx = new bblock::System(); + mbx_impl->ptr_mbx_local = new bblock::System(); + + // initialize all MBX instances + + if (aspc_step == aspc_step_reset) { + mbx_impl->ptr_mbx_local->ResetDipoleHistory(); + aspc_num_hist = 0; + aspc_step = 0; + } + + mbx_init(); + mbx_init_local(); + + if (mbx_aspc_enabled) aspc_step++; +} + +void FixMBX::min_post_neighbor() +{ + post_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::setup(int vflag) +{ + mbx_get_dipoles_local(); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::min_setup(int vflag) +{ + setup(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::setup_pre_force(int vflag) +{ + pre_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::min_setup_pre_force(int vflag) +{ + setup_pre_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::init_storage() {} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::pre_force(int vflag) +{ + // update coordinates in MBX objects + + if (has_gcmc) { post_neighbor(); } + mbx_update_xyz(); + mbx_update_xyz_local(); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::min_pre_force(int vflag) +{ + pre_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::setup_pre_exchange() +{ + pre_exchange(); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::pre_exchange() +{ + if (!mbx_aspc_enabled) return; + + // save copy of dipole history + + aspc_num_hist = mbx_impl->ptr_mbx_local->GetNumDipoleHistory(); + + // printf("# of histories= %i\n",aspc_num_hist); + + if (aspc_num_hist > aspc_max_num_hist) + error->all(FLERR, "[MBX] Inconsistent # of ASPC histories"); + + // induced dipole history does not include additional sites (e.g. water's M-site) + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + + if (mbx_num_atoms_local == 0) { return; } + + for (int h = 0; h < aspc_num_hist; ++h) { + std::vector mbx_dip_history = mbx_impl->ptr_mbx_local->GetDipoleHistory(h); + + + int indx = 0; + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i] && mol_local[i]) { + const int mtype = mol_type[i]; + + // to be replaced with integer comparison + + bool include_monomer = true; + tagint anchor = atom->tag[i]; + + // this will save history for both local and ghost particles + // comm->exchange() will sync ghost histories w/ local particles in new decomposition + + bool is_ext = false; + int na = get_include_monomer(mol_names[mtype], anchor, include_monomer, is_ext); + + // add info + + if (include_monomer) { + for (int j = 0; j < na; ++j) { + const int ii = atom->map(anchor + j); + aspc_dip_hist[ii][h * 3] = mbx_dip_history[indx++]; + aspc_dip_hist[ii][h * 3 + 1] = mbx_dip_history[indx++]; + aspc_dip_hist[ii][h * 3 + 2] = mbx_dip_history[indx++]; + } + } + } // if(anchor) + + } // for(nall) + + } // for(num_hist) + + // pack dipole history into arrays for exchange +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::post_force(int vflag) +{ + if (!print_dipoles) return; + + mbx_get_dipoles_local(); +} + +void FixMBX::min_post_force(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::mbx_get_dipoles_local() +{ + if (!print_dipoles) return; + + // only need to grab dipoles on step where output is written + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + + // conversion factor for e*Anstrom --> Debye + // const double qe_Debye = 1.0 / 0.2081943; + + // zero dipole array + + for (int i = 0; i < atom->nmax; ++i) + for (int j = 0; j < 9; ++j) mbx_dip[i][j] = 0.0; + + + { + std::vector mu_perm; + std::vector mu_ind; + std::vector mu_tot; + + mbx_impl->ptr_mbx_local->GetMolecularDipoles(mu_perm, mu_ind); + + int indx = 0; + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i] && mol_local[i]) { + const int mtype = mol_type[i]; + + // to be replaced with integer comparison + + bool include_monomer = true; + tagint anchor = atom->tag[i]; + + // this will save history for both local and ghost particles + // comm->exchange() will sync ghost histories w/ local particles in new decomposition + + bool is_ext = false; + int na = get_include_monomer(mol_names[mtype], anchor, include_monomer, is_ext); + + // add info + + if (include_monomer) { + for (int j = 0; j < 1; ++j) { + const int ii = atom->map(anchor + j); + mbx_dip[ii][0] = mu_perm[indx * 3]; + mbx_dip[ii][1] = mu_perm[indx * 3 + 1]; + mbx_dip[ii][2] = mu_perm[indx * 3 + 2]; + + mbx_dip[ii][3] = mu_ind[indx * 3]; + mbx_dip[ii][4] = mu_ind[indx * 3 + 1]; + mbx_dip[ii][5] = mu_ind[indx * 3 + 2]; + + mbx_dip[ii][6] = mbx_dip[ii][0] + mbx_dip[ii][3]; + mbx_dip[ii][7] = mbx_dip[ii][1] + mbx_dip[ii][4]; + mbx_dip[ii][8] = mbx_dip[ii][2] + mbx_dip[ii][5]; + + indx++; + } + } + } // if(anchor) + + } // for(nall) + } + + array_atom = mbx_dip; +} + +/* ---------------------------------------------------------------------- */ + +int FixMBX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) +{ + int m = 0; + for (int i = 0; i < n; ++i) { + for (int j = 0; j < aspc_per_atom_size; ++j) buf[m++] = aspc_dip_hist[list[i]][j]; + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixMBX::unpack_forward_comm(int n, int first, double *buf) +{ + int m = 0; + for (int i = first; i < first + n; ++i) { + for (int j = 0; j < aspc_per_atom_size; ++j) aspc_dip_hist[i][j] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- + allocate fictitious charge arrays +------------------------------------------------------------------------- */ + +void FixMBX::grow_arrays(int nmax) +{ + memory->grow(mol_type, nmax, "fixmbx:mol_type"); + memory->grow(mol_anchor, nmax, "fixmbx:mol_anchor"); + memory->grow(mol_local, nmax, "fixmbx:mol_local"); + + if (mbx_aspc_enabled) + memory->grow(aspc_dip_hist, nmax, aspc_per_atom_size, "fixmbx:mbx_dip_hist"); + + if (print_dipoles) memory->grow(mbx_dip, nmax, 9, "fixmbx:mbx_dip"); +} + +/* ---------------------------------------------------------------------- + copy per-atom values +------------------------------------------------------------------------- */ + +void FixMBX::copy_arrays(int i, int j, int /*delflag*/) +{ + mol_type[j] = mol_type[i]; + mol_anchor[j] = mol_anchor[i]; + mol_local[j] = mol_local[i]; + + if (mbx_aspc_enabled) + for (int k = 0; k < aspc_per_atom_size; ++k) aspc_dip_hist[j][k] = aspc_dip_hist[i][k]; +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based array for exchange with another proc +------------------------------------------------------------------------- */ + +int FixMBX::pack_exchange(int i, double *buf) +{ + int n = 0; + buf[n++] = mol_type[i]; + buf[n++] = mol_anchor[i]; + buf[n++] = mol_local[i]; + + if (mbx_aspc_enabled) + for (int j = 0; j < aspc_per_atom_size; ++j) buf[n++] = aspc_dip_hist[i][j]; + + return n; +} + +/* ---------------------------------------------------------------------- + unpack values in local atom-based array from exchange with another proc +------------------------------------------------------------------------- */ + +int FixMBX::unpack_exchange(int nlocal, double *buf) +{ + int n = 0; + mol_type[nlocal] = buf[n++]; + mol_anchor[nlocal] = buf[n++]; + mol_local[nlocal] = buf[n++]; + + if (mbx_aspc_enabled) + for (int j = 0; j < aspc_per_atom_size; ++j) aspc_dip_hist[nlocal][j] = buf[n++]; + + return n; +} + +/* ---------------------------------------------------------------------- + Initialize new MBX instance with all molecules +------------------------------------------------------------------------- */ + +void FixMBX::mbx_init() +{ + mbxt_start(MBXT_LABELS::INIT); + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + double *q = atom->q; + + mbx_num_atoms = 0; + mbx_num_ext = 0; + + std::vector molec; + + double ximage[3]; + + int nm = 0; + + const double xlo = domain->boxlo[0]; + const double ylo = domain->boxlo[1]; + const double zlo = domain->boxlo[2]; + + std::vector xyz_ext; + std::vector chg_ext; + std::vector islocal_ext; + std::vector tag_ext; + + // loop over all atoms on proc (local + ghost) + + for (int i = 0; i < nall; ++i) { + // if anchor-atom, then add to MBX (currently assume molecule is intact) + + if (mol_anchor[i]) { + std::vector names; + std::vector xyz; + + const int mtype = mol_type[i]; + + int is_local = (i < nlocal); + + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + + // ids of particles in molecule on proc + + tagint anchor = tag[i]; + + int amap[_MAX_ATOMS_PER_MONOMER]; + bool add_monomer = true; + for (int j = 1; j < na; ++j) { + amap[j] = atom->map(anchor + j); + if (amap[j] == -1) add_monomer = false; + } + + // test if external charged particle + if (strcmp("dp1", mol_names[mtype]) == 0) { + add_monomer = false; + + xyz_ext.push_back(x[i][0] - xlo); + xyz_ext.push_back(x[i][1] - ylo); + xyz_ext.push_back(x[i][2] - zlo); + chg_ext.push_back(q[i]); + islocal_ext.push_back(is_local); + tag_ext.push_back(anchor); + + mbx_num_ext++; + + // add info for monomer + + } else if (add_monomer) { + // add coordinates + + xyz.push_back(x[i][0] - xlo); + xyz.push_back(x[i][1] - ylo); + xyz.push_back(x[i][2] - zlo); + + for (int j = 1; j < na; ++j) { + domain->closest_image(x[i], x[amap[j]], ximage); + xyz.push_back(ximage[0] - xlo); + xyz.push_back(ximage[1] - ylo); + xyz.push_back(ximage[2] - zlo); + } + + // add types + add_monomer_atom_types(mol_names[mtype], names); + + // add monomer + + molec.push_back(nm); + nm++; + + mbx_impl->ptr_mbx->AddMonomer(xyz, names, mol_names[mtype], is_local, anchor); + mbx_impl->ptr_mbx->AddMolecule(molec); + + mbx_num_atoms += na; + } + + } // if(mol_anchor) + + } // for(iprocgrid; + mbx_impl->ptr_mbx->SetMPI(world, pg[0], pg[1], pg[2]); + + // set MBX solvers + + if (use_json) { + mbx_impl->ptr_mbx->SetUpFromJson(json_settings); + + // make sure cutoffs are consistent + + double mbx_cut = mbx_impl->ptr_mbx->GetRealspaceCutoff(); + double diff_sq = (mbx_cut - pair_mbx->cut_global) * (mbx_cut - pair_mbx->cut_global); + if (diff_sq > 1e-9) error->one(FLERR, "[MBX] cutoff not consistent with LAMMPS"); + double mbx_2b_cut = mbx_impl->ptr_mbx->Get2bCutoff(); + if (mbx_2b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 2-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + double mbx_3b_cut = mbx_impl->ptr_mbx->Get3bCutoff(); + if (mbx_3b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 3-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + double mbx_4b_cut = mbx_impl->ptr_mbx->Get4bCutoff(); + if (mbx_4b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 4-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + } else { + mbx_impl->ptr_mbx->SetRealspaceCutoff(pair_mbx->cut_global); + mbx_impl->ptr_mbx->SetUpFromJson(); + } + + // load external charged particles + if (mbx_num_ext > 0) { + mbx_impl->ptr_mbx->SetExternalChargesAndPositions(chg_ext, xyz_ext, islocal_ext, tag_ext); + } + + // setup MBX solver(s); need to keep pbc turned off, which currently disables electrostatic solver + + std::vector box; + mbx_impl->ptr_mbx->SetPBC(box); + + + // check for incompatible pair styles + // electrostatics should be handled entirely by MBX + Pair *pairstyles_coullong = force->pair_match(".*coul/long.*", 0); + Pair *pairstyles_coulcut = force->pair_match(".*coul/cut.*", 0); + Pair *pairstyles_coulexclude = force->pair_match("coul/exclude", 0); + + if (!pairstyles_coulexclude && mbx_num_ext > 0) + error->warning(FLERR, + "[MBX] dp1 monomers present, but coul/exclude pair style not found. If using " + "special_bonds, please include coul/exclude: "); + if (pairstyles_coulcut) { + error->all(FLERR, + "[MBX] Incompatible coul/cut pair style: coulombic interactions should be " + "handled internally by MBX: "); + } + if (pairstyles_coullong) { + error->all(FLERR, + "[MBX] Incompatible coul/long pair style: coulombic interactions should be " + "handled internally by MBX: "); + } + + mbxt_stop(MBXT_LABELS::INIT); +} + +/* ---------------------------------------------------------------------- + Initialize new MBX instance with all molecules that have local atom +------------------------------------------------------------------------- */ + +void FixMBX::mbx_init_local() +{ + mbxt_start(MBXT_LABELS::INIT_LOCAL); + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + double *q = atom->q; + + mbx_num_atoms_local = 0; + mbx_num_ext_local = 0; + + for (int i = 0; i < nall; ++i) mol_local[i] = 0; + + // add all local+ghost monomers + + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i]) mol_local[i] = 1; + } + + // remove ghost monomers that are periodic images of local monomer + // -- just an artifact for small systems and PBC + // -- should be able to remove this + + // Look for atoms that are local (0map(atom->tag[i]); + if (indx < nlocal && mol_local[indx]) mol_local[i] = 0; + } + } + + // remove ghost monomers that are periodic images of ghost monomer + // -- just an artifact for small systems and PBC + // -- should be able to remove this + + double ximage[3]; + for (int i = nlocal; i < nall - 1; ++i) { + if (mol_anchor[i] && mol_local[i]) { + for (int j = i + 1; j < nall; ++j) { + if (mol_anchor[j] && mol_local[j]) { + domain->closest_image(x[i], x[j], ximage); + double dx = x[i][0] - ximage[0]; + double dy = x[i][1] - ximage[1]; + double dz = x[i][2] - ximage[2]; + double rsq = dx * dx + dy * dy + dz * dz; + if (rsq < 0.00001) mol_local[j] = 0; + } + } + } + } + + std::vector molec; + + const double xlo = domain->boxlo[0]; + const double ylo = domain->boxlo[1]; + const double zlo = domain->boxlo[2]; + + std::vector xyz_ext; + std::vector chg_ext; + std::vector islocal_ext; + std::vector tag_ext; + + // loop over all atoms on proc + + int nm = 0; + + for (int i = 0; i < nall; ++i) { + // if anchor-atom, then add to MBX (currently assume molecule is intact) + + if (mol_anchor[i] && mol_local[i]) { + std::vector names; + std::vector xyz; + + const int mtype = mol_type[i]; + + int is_local = (i < nlocal); + + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + + // ids of particles in molecule on proc + + tagint anchor = tag[i]; + + // TODO fix this if monomer becomes too large + int amap[_MAX_ATOMS_PER_MONOMER]; + bool add_monomer = true; + for (int j = 1; j < na; ++j) { + amap[j] = atom->map(anchor + j); + if (amap[j] == -1) add_monomer = false; + } + + // test if external charged particle + if (strcmp("dp1", mol_names[mtype]) == 0) { + add_monomer = false; + + xyz_ext.push_back(x[i][0] - xlo); + xyz_ext.push_back(x[i][1] - ylo); + xyz_ext.push_back(x[i][2] - zlo); + chg_ext.push_back(q[i]); + islocal_ext.push_back(is_local); + tag_ext.push_back(anchor); + + mbx_num_ext_local++; + + // add info for monomer + + } else if (add_monomer) { + // add coordinates + + xyz.push_back(x[i][0] - xlo); + xyz.push_back(x[i][1] - ylo); + xyz.push_back(x[i][2] - zlo); + + for (int j = 1; j < na; ++j) { + domain->closest_image(x[i], x[amap[j]], ximage); + xyz.push_back(ximage[0] - xlo); + xyz.push_back(ximage[1] - ylo); + xyz.push_back(ximage[2] - zlo); + } + + add_monomer_atom_types(mol_names[mtype], names); + + molec.push_back(nm++); + + mbx_impl->ptr_mbx_local->AddMonomer(xyz, names, mol_names[mtype], is_local, anchor); + mbx_impl->ptr_mbx_local->AddMolecule(molec); + + mbx_num_atoms_local += na; + } + + } // if(mol_anchor) + + } // for(iprocgrid; + mbx_impl->ptr_mbx_local->SetMPI(world, pg[0], pg[1], pg[2]); + + // set MBX solvers + + if (use_json) { + mbx_impl->ptr_mbx_local->SetUpFromJson(json_settings); + + // make sure cutoffs are consistent + + double mbx_cut = mbx_impl->ptr_mbx_local->GetRealspaceCutoff(); + double diff_sq = (mbx_cut - pair_mbx->cut_global) * (mbx_cut - pair_mbx->cut_global); + if (diff_sq > 1e-9) error->one(FLERR, "[MBX] cutoff not consistent with LAMMPS"); + double mbx_2b_cut = mbx_impl->ptr_mbx_local->Get2bCutoff(); + if (mbx_2b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 2-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + double mbx_3b_cut = mbx_impl->ptr_mbx_local->Get3bCutoff(); + if (mbx_3b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 3-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + double mbx_4b_cut = mbx_impl->ptr_mbx_local->Get4bCutoff(); + if (mbx_4b_cut > mbx_cut) + error->one(FLERR, + "[MBX] 4-body PIP cutoff must be less than or equal to realspace cutoff. (This " + "may be changed in a future release.)"); + } else { + mbx_impl->ptr_mbx_local->SetRealspaceCutoff(pair_mbx->cut_global); + mbx_impl->ptr_mbx_local->SetUpFromJson(); + } + + // load external charged particles + if (mbx_num_ext_local > 0) { + mbx_impl->ptr_mbx_local->SetExternalChargesAndPositions(chg_ext, xyz_ext, islocal_ext, tag_ext); + } + + std::vector box; + + if (domain->nonperiodic && (domain->xperiodic || domain->yperiodic || domain->zperiodic)) + error->all(FLERR, "[MBX] System must be fully periodic or non-periodic with MBX"); + + // get ewald values from MBX and verify they make sense relative to LAMMPS periodicity + double elec_alpha, elec_grid, disp_alpha, disp_grid; + size_t elec_spline, disp_spline; + + mbx_impl->ptr_mbx_local->GetEwaldParamsElectrostatics(elec_alpha, elec_grid, elec_spline); + mbx_impl->ptr_mbx_local->GetEwaldParamsDispersion(disp_alpha, disp_grid, disp_spline); + + if ((elec_alpha > 0.0) && (!domain->xperiodic && !domain->yperiodic && !domain->zperiodic)) + error->all(FLERR, + "[MBX] Electrostatic Ewald parameters set (alpha_ewald_elec = " + + std::to_string(elec_alpha) + "), but system is not periodic"); + if ((disp_alpha > 0.0) && (!domain->xperiodic && !domain->yperiodic && !domain->zperiodic)) + error->all(FLERR, + "[MBX] Dispersion Ewald parameters set (alpha_ewald_disp = " + + std::to_string(disp_alpha) + "), but system is not periodic"); + if ((elec_alpha == 0.0 || disp_alpha == 0.0) && + (domain->xperiodic || domain->yperiodic || domain->zperiodic)) + error->warning(FLERR, "[MBX] System is periodic, but Ewald alpha parameters not set"); + + box = std::vector(9, 0.0); + + box[0] = domain->xprd; + + box[3] = domain->xy; + box[4] = domain->yprd; + + box[6] = domain->xz; + box[7] = domain->yz; + box[8] = domain->zprd; + + mbx_impl->ptr_mbx_local->SetPBC(box); + mbx_impl->ptr_mbx_local->SetBoxPMElocal(box); + + mbx_impl->ptr_mbx_local->SetPeriodicity(!domain->nonperiodic); + + std::vector egrid = mbx_impl->ptr_mbx_local->GetFFTDimensionElectrostatics(1); + std::vector dgrid = + mbx_impl->ptr_mbx_local->GetFFTDimensionDispersion(1); // will return mesh even for gas-phase + + if (print_verbose && first_step && comm->me == 0) { + std::string mbx_settings_ = mbx_impl->ptr_mbx_local->GetCurrentSystemConfig(); + if (screen) { + fprintf(screen, "\n[MBX] 'Local' Settings\n%s\n", mbx_settings_.c_str()); + fprintf(screen, "[MBX] LOCAL electrostatics FFT grid= %i %i %i\n", egrid[0], egrid[1], + egrid[2]); + fprintf(screen, "[MBX] LOCAL dispersion FFT grid= %i %i %i\n", dgrid[0], dgrid[1], dgrid[2]); + } + if (logfile) { + fprintf(logfile, "\n[MBX] 'Local' Settings\n%s\n", mbx_settings_.c_str()); + fprintf(logfile, "[MBX] LOCAL electrostatics FFT grid= %i %i %i\n", egrid[0], egrid[1], + egrid[2]); + fprintf(logfile, "[MBX] LOCAL dispersion FFT grid= %i %i %i\n", dgrid[0], dgrid[1], dgrid[2]); + } + } + + // check if using cg or aspc integrator for MBX dipoles + + if (first_step) { + std::string dip_method = mbx_impl->ptr_mbx->GetDipoleMethod(); + + if (dip_method == "aspc") { + mbx_aspc_enabled = true; + + memory->create(aspc_dip_hist, atom->nmax, aspc_per_atom_size, "fixmbx::aspc_dip_hist"); + } else if (!(dip_method == "cg")) { + error->one(FLERR, "[MBX] requested dip_method not supported with LAMMPS"); + } + } + + if (mbx_aspc_enabled) mbx_init_dipole_history_local(); + + mbxt_stop(MBXT_LABELS::INIT_LOCAL); +} + + +/* ---------------------------------------------------------------------- + Update MBX instance for all molecules +------------------------------------------------------------------------- */ + +void FixMBX::mbx_update_xyz() +{ + mbxt_start(MBXT_LABELS::UPDATE_XYZ); + + // update coordinates + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + double *q = atom->q; + + if (mbx_num_atoms + mbx_num_ext == 0) { + mbxt_stop(MBXT_LABELS::UPDATE_XYZ); + return; + } + + const double xlo = domain->boxlo[0]; + const double ylo = domain->boxlo[1]; + const double zlo = domain->boxlo[2]; + + double ximage[3]; + + std::vector xyz(mbx_num_atoms * 3); + + std::vector xyz_ext(mbx_num_ext * 3); + std::vector chg_ext(mbx_num_ext); + + int indx = 0; + int indx_ext = 0; + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i]) { + const int mtype = mol_type[i]; + + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + + // ids of particles in molecule on proc + + tagint anchor = tag[i]; + + int amap[_MAX_ATOMS_PER_MONOMER]; + bool add_monomer = true; + for (int j = 1; j < na; ++j) { + amap[j] = atom->map(anchor + j); + if (amap[j] == -1) add_monomer = false; + } + + // test if external charged particle + if (strcmp("dp1", mol_names[mtype]) == 0) { + add_monomer = false; + + xyz_ext[indx_ext * 3] = x[i][0] - xlo; + xyz_ext[indx_ext * 3 + 1] = x[i][1] - ylo; + xyz_ext[indx_ext * 3 + 2] = x[i][2] - zlo; + chg_ext[indx_ext] = q[i]; + + indx_ext++; + + // add info for monomer + + } else if (add_monomer) { + // add coordinates + + xyz[indx * 3] = x[i][0] - xlo; + xyz[indx * 3 + 1] = x[i][1] - ylo; + xyz[indx * 3 + 2] = x[i][2] - zlo; + + for (int j = 1; j < na; ++j) { + domain->closest_image(x[i], x[amap[j]], ximage); + xyz[(indx + j) * 3] = ximage[0] - xlo; + xyz[(indx + j) * 3 + 1] = ximage[1] - ylo; + xyz[(indx + j) * 3 + 2] = ximage[2] - zlo; + } + + indx += na; + } + + } // if(mol_anchor) + + } // for(ione(FLERR, "Inconsistent # of atoms"); + mbx_impl->ptr_mbx->SetRealXyz(xyz); + + if (xyz_ext.size() != indx_ext * 3) error->one(FLERR, "Inconsistent # of external charges"); + if (mbx_num_ext > 0) { mbx_impl->ptr_mbx->SetExternalChargesAndPositions(chg_ext, xyz_ext); } + + mbxt_stop(MBXT_LABELS::UPDATE_XYZ); +} + +/* ---------------------------------------------------------------------- + Update MBX instance for local molecules + plus halo +------------------------------------------------------------------------- */ + +void FixMBX::mbx_update_xyz_local() +{ + mbxt_start(MBXT_LABELS::UPDATE_XYZ_LOCAL); + + // update if box changes + // need to update box passed to PME solver + + if (domain->box_change) { + std::vector box; + + if (!domain->nonperiodic) { + box = std::vector(9, 0.0); + + box[0] = domain->xprd; + + box[3] = domain->xy; + box[4] = domain->yprd; + + box[6] = domain->xz; + box[7] = domain->yz; + box[8] = domain->zprd; + + } else if (domain->xperiodic || domain->yperiodic || domain->zperiodic) + error->all(FLERR, "[MBX] System must be fully periodic or non-periodic with MBX"); + + // get ewald values from MBX and verify they make sense relative to LAMMPS periodicity + double elec_alpha, elec_grid, disp_alpha, disp_grid; + size_t elec_spline, disp_spline; + + mbx_impl->ptr_mbx_local->GetEwaldParamsElectrostatics(elec_alpha, elec_grid, elec_spline); + mbx_impl->ptr_mbx_local->GetEwaldParamsDispersion(disp_alpha, disp_grid, disp_spline); + + if ((elec_alpha > 0.0) && (!domain->xperiodic || !domain->yperiodic || !domain->zperiodic)) + error->all(FLERR, + "[MBX] Electrostatic Ewald parameters set (alpha_ewald_elec = " + + std::to_string(elec_alpha) + "), but system is not periodic"); + if ((disp_alpha > 0.0) && (!domain->xperiodic || !domain->yperiodic || !domain->zperiodic)) + error->all(FLERR, + "[MBX] Dispersion Ewald parameters set (alpha_ewald_disp = " + + std::to_string(disp_alpha) + "), but system is not periodic"); + if ((elec_alpha == 0.0 || disp_alpha == 0.0) && + (!domain->xperiodic || !domain->yperiodic || !domain->zperiodic)) + error->warning(FLERR, "[MBX] System is periodic, but Ewald alpha parameters not set"); + + mbx_impl->ptr_mbx_local->SetPBC(box); + mbx_impl->ptr_mbx_local->SetBoxPMElocal(box); + } + + // update coordinates + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + double *q = atom->q; + + if (mbx_num_atoms_local + mbx_num_ext_local == 0) { + mbxt_stop(MBXT_LABELS::UPDATE_XYZ); + return; + } + + const double xlo = domain->boxlo[0]; + const double ylo = domain->boxlo[1]; + const double zlo = domain->boxlo[2]; + + double ximage[3]; + + std::vector xyz(mbx_num_atoms_local * 3); + + std::vector xyz_ext(mbx_num_ext_local * 3); + std::vector chg_ext(mbx_num_ext_local); + + int indx = 0; + int indx_ext = 0; + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i] && mol_local[i]) { + const int mtype = mol_type[i]; + + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + + // ids of particles in molecule on proc + + tagint anchor = tag[i]; + + int amap[_MAX_ATOMS_PER_MONOMER]; + bool add_monomer = true; + for (int j = 1; j < na; ++j) { + amap[j] = atom->map(anchor + j); + if (amap[j] == -1) add_monomer = false; + } + + // test if external charged particle + if (strcmp("dp1", mol_names[mtype]) == 0) { + add_monomer = false; + + xyz_ext[indx_ext * 3] = x[i][0] - xlo; + xyz_ext[indx_ext * 3 + 1] = x[i][1] - ylo; + xyz_ext[indx_ext * 3 + 2] = x[i][2] - zlo; + chg_ext[indx_ext] = q[i]; + + indx_ext++; + + // add info for monomer + + } else if (add_monomer) { + // add coordinates + + xyz[indx * 3] = x[i][0] - xlo; + xyz[indx * 3 + 1] = x[i][1] - ylo; + xyz[indx * 3 + 2] = x[i][2] - zlo; + + for (int j = 1; j < na; ++j) { + domain->closest_image(x[i], x[amap[j]], ximage); + xyz[(indx + j) * 3] = ximage[0] - xlo; + xyz[(indx + j) * 3 + 1] = ximage[1] - ylo; + xyz[(indx + j) * 3 + 2] = ximage[2] - zlo; + } + + indx += na; + } + + } // if(mol_anchor) + + } // for(ione(FLERR, "Inconsistent # of atoms"); + mbx_impl->ptr_mbx_local->SetRealXyz(xyz); + + if (xyz_ext.size() != indx_ext * 3) error->one(FLERR, "Inconsistent # of external charges"); + if (mbx_num_ext_local > 0) { mbx_impl->ptr_mbx_local->SetExternalChargesAndPositions(chg_ext, xyz_ext); } + + mbxt_stop(MBXT_LABELS::UPDATE_XYZ_LOCAL); +} + + +/* ---------------------------------------------------------------------- + Initialize dipole history for local molecules + plus halo +------------------------------------------------------------------------- */ + +void FixMBX::mbx_init_dipole_history_local() +{ + + if (aspc_num_hist == 0) return; + + // sync dipole histories of ghost particles + + comm->forward_comm(this); + + // update coordinates + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + tagint *tag = atom->tag; + double **x = atom->x; + + if (mbx_num_atoms_local == 0) { + return; + } + + const double xlo = domain->boxlo[0]; + const double ylo = domain->boxlo[1]; + const double zlo = domain->boxlo[2]; + + double ximage[3]; + + mbx_impl->ptr_mbx_local->SetNumDipoleHistory(aspc_num_hist); + + std::vector mbx_dip_history = std::vector(mbx_num_atoms_local * 3); + + // following debug only works if all ranks contribute + + for (int h = 0; h < aspc_num_hist; ++h) { + + int indx = 0; + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i] && mol_local[i]) { + const int mtype = mol_type[i]; + + bool is_ext = false; + int na = get_num_atoms_per_monomer(mol_names[mtype], is_ext); + + // ids of particles in molecule on proc + + tagint anchor = tag[i]; + + int amap[_MAX_ATOMS_PER_MONOMER]; + bool add_monomer = true; + for (int j = 1; j < na; ++j) { + amap[j] = atom->map(anchor + j); + if (amap[j] == -1) add_monomer = false; + } + + // add info + + if (add_monomer) { + // add coordinates + + for (int j = 0; j < na; ++j) { + const int ii = atom->map(anchor + j); + mbx_dip_history[indx++] = aspc_dip_hist[ii][h * 3]; + mbx_dip_history[indx++] = aspc_dip_hist[ii][h * 3 + 1]; + mbx_dip_history[indx++] = aspc_dip_hist[ii][h * 3 + 2]; + + } // for(na) + + } // if(add_monomer) + + } // if(mol_anchor) + + } // for(ione(FLERR, "Inconsistent # of atoms"); + // printf("calling SetDipoleHistory"); + mbx_impl->ptr_mbx_local->SetDipoleHistory(h, mbx_dip_history); + + } // for(hist) + +} + +/* ---------------------------------------------------------------------- + Helper functions for timing +------------------------------------------------------------------------- */ + +void FixMBX::mbxt_start(int T) +{ + mbxt_time_start[T] = MPI_Wtime(); +} + +void FixMBX::mbxt_stop(int T) +{ + mbxt_time[T] += MPI_Wtime() - mbxt_time_start[T]; + mbxt_count[T]++; +} + +void FixMBX::mbxt_print_time(const char *name, int T, double *d) +{ + double tavg = d[T]; + double tmin = d[MBXT_LABELS::NUM_TIMERS + T]; + double tmax = d[MBXT_LABELS::NUM_TIMERS * 2 + T]; + + double p = tmax / d[MBXT_LABELS::NUM_TIMERS * 3] * 100.0; + + if (screen) + fprintf(screen, "[MBX] %-20s: %12.5g %12.5g %12.5g %8i %8.2f%%\n", name, tmin, tavg, tmax, + mbxt_count[T], p); + + if (logfile) + fprintf(logfile, "[MBX] %-20s: %12.5g %12.5g %12.5g %8i %8.2f%%\n", name, tmin, tavg, tmax, + mbxt_count[T], p); +} + +void FixMBX::mbxt_write_summary() +{ + double t[MBXT_LABELS::NUM_TIMERS * 3 + 1]; + double *tavg = &t[0]; + double *tmin = &t[MBXT_LABELS::NUM_TIMERS]; + double *tmax = &t[MBXT_LABELS::NUM_TIMERS * 2]; + + // total runtime since fix created + + t[MBXT_LABELS::NUM_TIMERS * 3] = MPI_Wtime() - mbxt_initial_time; + + MPI_Reduce(mbxt_time, tavg, MBXT_LABELS::NUM_TIMERS, MPI_DOUBLE, MPI_SUM, 0, world); + MPI_Reduce(mbxt_time, tmin, MBXT_LABELS::NUM_TIMERS, MPI_DOUBLE, MPI_MIN, 0, world); + MPI_Reduce(mbxt_time, tmax, MBXT_LABELS::NUM_TIMERS, MPI_DOUBLE, MPI_MAX, 0, world); + + if (me) return; + + for (int i = 0; i < MBXT_LABELS::NUM_TIMERS; ++i) tavg[i] /= (double) nprocs; + + if (screen) { + fprintf(screen, "\n[MBX] Total MBX fix/pair time= %f seconds\n", t[MBXT_LABELS::NUM_TIMERS * 3]); + fprintf(screen, "[MBX] Timing Summary\n"); + fprintf(screen, + "[MBX] kernel tmin tavg tmax count " + "%%total\n"); + fprintf( + screen, + "[MBX] " + "-----------------------------------------------------------------------------------\n"); + } + if (logfile) { + fprintf(logfile, "\n[MBX] Total MBX fix/pair time= %f seconds\n", t[MBXT_LABELS::NUM_TIMERS * 3]); + fprintf(logfile, "[MBX] Timing Summary\n"); + fprintf(logfile, + "[MBX] kernel tmin tavg tmax count " + "%%total\n"); + fprintf( + logfile, + "[MBX] " + "-----------------------------------------------------------------------------------\n"); + } + + mbxt_print_time("INIT", MBXT_LABELS::INIT, t); + mbxt_print_time("UPDATE_XYZ", MBXT_LABELS::UPDATE_XYZ, t); + mbxt_print_time("ACCUMULATE_F", MBXT_LABELS::ACCUMULATE_F, t); + + mbxt_print_time("E1B", MBXT_LABELS::E1B, t); + mbxt_print_time("E2B", MBXT_LABELS::E2B_GHOST, t); + mbxt_print_time("E3B", MBXT_LABELS::E3B_GHOST, t); + mbxt_print_time("E4B", MBXT_LABELS::E4B_GHOST, t); + mbxt_print_time("DISP", MBXT_LABELS::DISP, t); + mbxt_print_time("DISP_PME", MBXT_LABELS::DISP_PME, t); + mbxt_print_time("BUCK", MBXT_LABELS::BUCK, t); + mbxt_print_time("ELE", MBXT_LABELS::ELE, t); + mbxt_print_time("INIT_LOCAL", MBXT_LABELS::INIT_LOCAL, t); + mbxt_print_time("UPDATE_XYZ_LOCAL", MBXT_LABELS::UPDATE_XYZ_LOCAL, t); + mbxt_print_time("ACCUMULATE_F_LOCAL", MBXT_LABELS::ACCUMULATE_F_LOCAL, t); + + if (screen) { + fprintf(screen, "\n\n[MBX] Electrostatics Summary\n"); + fprintf(screen, + "[MBX] kernel tmin tavg tmax count " + "%%total\n"); + fprintf( + screen, + "[MBX] " + "-----------------------------------------------------------------------------------\n"); + } + if (logfile) { + fprintf(logfile, "\n\n[MBX] Electrostatics Summary\n"); + fprintf(logfile, + "[MBX] kernel tmin tavg tmax count " + "%%total\n"); + fprintf( + logfile, + "[MBX] " + "-----------------------------------------------------------------------------------\n"); + } + + mbxt_print_time("ELE_PERMDIP_REAL", MBXT_LABELS::ELE_PERMDIP_REAL, t); + mbxt_print_time("ELE_PERMDIP_PME", MBXT_LABELS::ELE_PERMDIP_PME, t); + + mbxt_print_time("ELE_DIPFIELD_REAL", MBXT_LABELS::ELE_DIPFIELD_REAL, t); + mbxt_print_time("ELE_DIPFIELD_PME", MBXT_LABELS::ELE_DIPFIELD_PME, t); + + mbxt_print_time("ELE_GRAD_REAL", MBXT_LABELS::ELE_GRAD_REAL, t); + mbxt_print_time("ELE_GRAD_PME", MBXT_LABELS::ELE_GRAD_PME, t); + mbxt_print_time("ELE_GRAD_FIN", MBXT_LABELS::ELE_GRAD_FIN, t); + + mbxt_print_time("ELE_PME_SETUP", MBXT_LABELS::ELE_PME_SETUP, t); + mbxt_print_time("ELE_PME_C", MBXT_LABELS::ELE_PME_C, t); + mbxt_print_time("ELE_PME_D", MBXT_LABELS::ELE_PME_D, t); + mbxt_print_time("ELE_PME_E", MBXT_LABELS::ELE_PME_E, t); + + mbxt_print_time("DISP_PME_SETUP", MBXT_LABELS::DISP_PME_SETUP, t); + mbxt_print_time("DISP_PME_E", MBXT_LABELS::DISP_PME_E, t); + + mbxt_print_time("ELE_COMM_REVFOR", MBXT_LABELS::ELE_COMM_REVFOR, t); + mbxt_print_time("ELE_COMM_REVSET", MBXT_LABELS::ELE_COMM_REVSET, t); + mbxt_print_time("ELE_COMM_REV", MBXT_LABELS::ELE_COMM_REV, t); + mbxt_print_time("ELE_COMM_FORSET", MBXT_LABELS::ELE_COMM_FORSET, t); + mbxt_print_time("ELE_COMM_FOR", MBXT_LABELS::ELE_COMM_FOR, t); +} + +/* ---------------------------------------------------------------------- + Helper functions for monomers +------------------------------------------------------------------------- */ + +int FixMBX::get_num_atoms_per_monomer(char *name, bool &inc_e) +{ + int na; + inc_e = false; + + if (strcmp("h2o", name) == 0) + na = 3; + else if (strcmp("li+", name) == 0) + na = 1; + else if (strcmp("na+", name) == 0) + na = 1; + else if (strcmp("k+", name) == 0) + na = 1; + else if (strcmp("rb+", name) == 0) + na = 1; + else if (strcmp("cs+", name) == 0) + na = 1; + else if (strcmp("dp1", name) == 0) { + na = 1; + inc_e = true; + } else if (strcmp("f-", name) == 0) + na = 1; + else if (strcmp("cl-", name) == 0) + na = 1; + else if (strcmp("br-", name) == 0) + na = 1; + else if (strcmp("i-", name) == 0) + na = 1; + else if (strcmp("co2", name) == 0) + na = 3; + else if (strcmp("ch4", name) == 0) + na = 5; + else if (strcmp("he", name) == 0) + na = 1; + else if (strcmp("ar", name) == 0) + na = 1; + else if (strcmp("h2", name) == 0) + na = 2; + else if (strcmp("n2o5", name) == 0) + na = 7; + else if (strcmp("so4a", name) == 0) + na = 5; + else if (strcmp("co3a", name) == 0) + na = 4; + else if (strcmp("no3a", name) == 0) + na = 4; + else if (strcmp("dp2", name) == 0) + na = 2; + else + error->one(FLERR, "Unsupported molecule type in MBX"); + + return na; +} + +/* ---------------------------------------------------------------------- +------------------------------------------------------------------------- */ + +int FixMBX::get_include_monomer(char *name, int anchor, bool &inc, bool &inc_e) +{ + inc = true; + inc_e = false; + int na = get_num_atoms_per_monomer(name, inc_e); + + for (int ii = 1; ii < na; ii++) { + if (atom->map(anchor + ii) < 0) { + inc = false; + break; + } + } + + if (strcmp("dp1", name) == 0) { + inc = false; + inc_e = true; + } + + return na; +} + +/* ---------------------------------------------------------------------- +------------------------------------------------------------------------- */ + +void FixMBX::add_monomer_atom_types(char *name, std::vector &n) +{ + if (strcmp("h2o", name) == 0) { + n.push_back("O"); + n.push_back("H"); + n.push_back("H"); + } else if (strcmp("li+", name) == 0) { + n.push_back("Li"); + } else if (strcmp("na+", name) == 0) { + n.push_back("Na"); + } else if (strcmp("k+", name) == 0) { + n.push_back("K"); + } else if (strcmp("rb+", name) == 0) { + n.push_back("Rb"); + } else if (strcmp("cs+", name) == 0) { + n.push_back("Cs"); + } else if (strcmp("f-", name) == 0) { + n.push_back("F"); + } else if (strcmp("cl-", name) == 0) { + n.push_back("Cl"); + } else if (strcmp("br-", name) == 0) { + n.push_back("Br"); + } else if (strcmp("i-", name) == 0) { + n.push_back("I"); + } else if (strcmp("he", name) == 0) { + n.push_back("He"); + } else if (strcmp("co2", name) == 0) { + n.push_back("C"); + n.push_back("O"); + n.push_back("O"); + } else if (strcmp("ch4", name) == 0) { + n.push_back("C"); + n.push_back("H"); + n.push_back("H"); + n.push_back("H"); + n.push_back("H"); + } else if (strcmp("ar", name) == 0) { + n.push_back("Ar"); + } else if (strcmp("h2", name) == 0) { + n.push_back("H"); + n.push_back("H"); + } else if (strcmp("n2o5", name) == 0) { + n.push_back("O"); + n.push_back("N"); + n.push_back("N"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + } else if (strcmp("so4a", name) == 0) { + n.push_back("S"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + } else if (strcmp("co3a", name) == 0) { + n.push_back("C"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + } else if (strcmp("no3a", name) == 0) { + n.push_back("N"); + n.push_back("O"); + n.push_back("O"); + n.push_back("O"); + } else if (strcmp("dp2", name) == 0) { + n.push_back("X"); + n.push_back("X"); + } + else + error->one(FLERR, "Unsupported molecule type in MBX"); +} diff --git a/src/MBX/fix_mbx.h b/src/MBX/fix_mbx.h new file mode 100644 index 00000000000..11b3d7e74db --- /dev/null +++ b/src/MBX/fix_mbx.h @@ -0,0 +1,182 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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 FIX_CLASS + +FixStyle(MBX, FixMBX) + +#else + +#ifndef LMP_FIX_MBX_H +#define LMP_FIX_MBX_H + +#include "fix.h" + + + +namespace LAMMPS_NS { + +class FixMBX : public Fix { + friend class PairMBX; + + public: + FixMBX(class LAMMPS *, int, char **); + ~FixMBX(); + int setmask(); + virtual void post_constructor(); + virtual void init(); + virtual void init_storage(); + void setup(int); + void min_setup(int); + virtual void setup_post_neighbor(); + virtual void post_neighbor(); + void min_post_neighbor(); + void setup_pre_force(int); + virtual void pre_force(int); + + void min_setup_pre_force(int); + void min_pre_force(int); + + void setup_pre_exchange(); + void pre_exchange(); + + void post_force(int); + void min_post_force(int); + + protected: + struct MBXImpl *mbx_impl; + class PairMBX *pair_mbx; // pointer to MBX pair_style + + static std::string cite_pair_mbx; + int me, nprocs; + bigint ngroup; + + bool mbx_aspc_enabled; + bool print_dipoles; + + bool first_step; + bool has_gcmc; + + int use_json; + std::string json_settings; + + int print_verbose; + + int num_mol_types; // # of unique molecule types + int num_molecules; // total # of molecules + int *num_atoms_per_mol; // array of # of atoms per molecule for each type + int *lower_atom_type_index_in_mol; // array with the lowest atom type index in the monomer + int *higher_atom_type_index_in_mol; // array with the highest atom type index in the monomer + int **order_in_mol; // array with the atom order for each monomer + char **mol_names; // array of molecule names + + int *mol_type; // per-atom array of molecule type + int *mol_anchor; // per-atom array 1/0 if anchor atom of a molecule + int *mol_local; // per-molecule array 1/0 if molecule has at least one local particle + + int mbx_num_atoms, mbx_num_ext; + int mbx_num_atoms_local, mbx_num_ext_local; + + int *mbxt_count; + double *mbxt_time; + double *mbxt_time_start; + double mbxt_initial_time; + void mbxt_start(int); + void mbxt_stop(int); + void mbxt_write_summary(); + void mbxt_print_time(const char *, int, double *); + enum MBXT_LABELS : int { + INIT = 0, + UPDATE_XYZ, + INIT_LOCAL, + UPDATE_XYZ_LOCAL, + E1B, + E2B_GHOST, + E3B_GHOST, + E4B_GHOST, + DISP, + DISP_PME, + BUCK, + ELE, + ACCUMULATE_F, + ACCUMULATE_F_LOCAL, + + ELE_PERMDIP_REAL, + ELE_PERMDIP_PME, + + ELE_DIPFIELD_REAL, + ELE_DIPFIELD_PME, + + ELE_GRAD_REAL, + ELE_GRAD_PME, + ELE_GRAD_FIN, + + ELE_COMM_REVFOR, + ELE_COMM_REVSET, + ELE_COMM_REV, + ELE_COMM_FORSET, + ELE_COMM_FOR, + + ELE_PME_SETUP, + ELE_PME_C, + ELE_PME_D, + ELE_PME_E, + + DISP_PME_SETUP, + DISP_PME_E, + + NUM_TIMERS + }; + + bool validateMBXFixParameters(int narg, char **arg); + + int aspc_order; + int aspc_num_hist; + int aspc_max_num_hist; + int aspc_per_atom_size; + double **aspc_dip_hist; + + int aspc_step; + int aspc_step_reset; + + double **mbx_dip; + + void mbx_init(); + void mbx_init_local(); + + void mbx_update_xyz(); + void mbx_update_xyz_local(); + + void mbx_fill_system_information_from_atom(); + + void mbx_init_dipole_history_local(); + + void mbx_get_dipoles_local(); + + int get_num_atoms_per_monomer(char *, bool &); + int get_include_monomer(char *, int, bool &, bool &); + void add_monomer_atom_types(char *, std::vector &); + std::pair parse_dp1_range(const std::string &); + + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual void grow_arrays(int); + virtual void copy_arrays(int, int, int); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(int, double *); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/MBX/pair_mbx.cpp b/src/MBX/pair_mbx.cpp new file mode 100644 index 00000000000..6470c42a911 --- /dev/null +++ b/src/MBX/pair_mbx.cpp @@ -0,0 +1,528 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: +------------------------------------------------------------------------- */ + +#include "pair_mbx.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include + +#include "fix_mbx.h" +#include "bblock/system.h" + +#define TTMNRG + +// subject for removal +// Systems::DispersionPME() +// Systems::ElectrostaticsMPI() + +namespace LAMMPS_NS{ +//PImpl idiom to hide MBX implementation details +struct MBXImpl { + MBXImpl() : ptr_mbx(nullptr), ptr_mbx_local(nullptr) {} + ~MBXImpl() + { + delete ptr_mbx; + delete ptr_mbx_local; + } + bblock::System *ptr_mbx; + bblock::System *ptr_mbx_local; +}; +} // namespace LAMMPS_NS + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairMBX::PairMBX(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + no_virial_fdotr_compute = 1; + one_coeff = 1; + + mbx_total_energy = 0; + + me = comm->me; + + // energy terms available to pair compute + + nextra = 10; + pvector = new double[nextra]; +} + +/* ---------------------------------------------------------------------- */ + +PairMBX::~PairMBX() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } + + delete[] pvector; +} + +/* ---------------------------------------------------------------------- */ + +void PairMBX::compute(int eflag, int vflag) +{ + + ev_init(eflag, vflag); + + // compute energy+gradients in parallel + + bblock::System *ptr_mbx = fix_MBX->mbx_impl->ptr_mbx; // compute terms in parallel + bblock::System *ptr_mbx_local = + fix_MBX->mbx_impl->ptr_mbx_local; // compute PME terms in parallel w/ sub-domains + + double mbx_e2b_local, mbx_e2b_ghost; + double mbx_e3b_local, mbx_e3b_ghost; + double mbx_e4b_local, mbx_e4b_ghost; + double mbx_disp_real, mbx_disp_pme; + + // compute energy + + mbx_e1b = 0.0; + mbx_e2b = 0.0; + mbx_e3b = 0.0; + mbx_e4b = 0.0; + + mbx_e2b_local = 0.0; + mbx_e2b_ghost = 0.0; + mbx_e3b_local = 0.0; + mbx_e3b_ghost = 0.0; + mbx_e4b_local = 0.0; + mbx_e4b_ghost = 0.0; + + mbx_disp_real = 0.0; + mbx_disp_pme = 0.0; + + mbx_disp = 0.0; + mbx_buck = 0.0; + mbx_ele = 0.0; + + for (int i = 0; i < 6; ++i) mbx_virial[i] = 0.0; + + if (fix_MBX->mbx_num_atoms > 0) { + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::E1B); + mbx_e1b = ptr_mbx->OneBodyEnergy(true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::E1B); + accumulate_f(false); + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::E2B_GHOST); + mbx_e2b_ghost = ptr_mbx->TwoBodyEnergy(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::E2B_GHOST); + accumulate_f_all(false); + mbx_e2b = mbx_e2b_ghost; + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::E3B_GHOST); + mbx_e3b_ghost = ptr_mbx->ThreeBodyEnergy(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::E3B_GHOST); + accumulate_f_all(false); + mbx_e3b = mbx_e3b_ghost; + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::E4B_GHOST); + mbx_e4b_ghost = ptr_mbx->FourBodyEnergy(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::E4B_GHOST); + accumulate_f_all(false); + + mbx_e4b = mbx_e4b_ghost; + } + + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::ELE); + mbx_ele = ptr_mbx_local->ElectrostaticsMPIlocal(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::ELE); + accumulate_f_local(true); + + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::DISP); + mbx_disp_real = ptr_mbx_local->Dispersion( + true, true); // computes real-space with local-local & local-ghost pairs + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::DISP); + accumulate_f_local(false); + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::DISP_PME); + mbx_disp_pme = ptr_mbx_local->DispersionPMElocal( + true, true); // computes PME-space with local-local & local-ghost pairs + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::DISP_PME); + accumulate_f_local(false); + + + if (fix_MBX->mbx_num_atoms > 0) { + +#ifdef TTMNRG + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::BUCK); + mbx_buck = ptr_mbx->Buckingham(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::BUCK); + accumulate_f(false); + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::BUCK); + mbx_buck += ptr_mbx_local->LennardJones(true, true); + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::BUCK); + accumulate_f_local(false); +#else + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::BUCK); + mbx_buck = 0.0; + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::BUCK); +#endif + } + + mbx_disp = mbx_disp_real + mbx_disp_pme; + + mbx_total_energy = mbx_e1b + mbx_e2b + mbx_disp + mbx_buck + mbx_e3b + mbx_e4b + mbx_ele; + + for (int i = 0; i < 6; ++i) virial[i] += mbx_virial[i]; + + // save total energy from mbx as vdwl + + if (evflag) { + eng_vdwl = mbx_total_energy; + + // generally useful + + pvector[0] = mbx_e1b; + pvector[1] = mbx_e2b; + pvector[2] = mbx_e3b; + pvector[3] = mbx_e4b; + pvector[4] = mbx_disp; + pvector[5] = mbx_buck; + pvector[6] = ptr_mbx_local->GetPermanentElectrostaticEnergy(); + pvector[7] = ptr_mbx_local->GetInducedElectrostaticEnergy(); + pvector[8] = mbx_ele; + pvector[9] = mbx_total_energy; + + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMBX::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMBX::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); + + cut_global = utils::numeric(FLERR, arg[0], false, lmp); + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMBX::coeff(int narg, char **arg) +{ + if (narg < 2) error->all(FLERR, "Incorrect num args for pair coefficients"); + if (!allocated) allocate(); + + int count = 0; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + setflag[i][j] = 1; + count++; + } + } + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + + std::string fix_args = ""; + for (int i = 2; i < narg; ++i) { fix_args += std::string(arg[i]) + " "; } + + fix_args = fmt::format("_FIX_MBX_INTERNAL all MBX {}", fix_args); + + fix_MBX = dynamic_cast(modify->add_fix(fix_args)); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMBX::init_one(int i, int j) +{ + return cut_global; +} + + +/* ---------------------------------------------------------------------- + update forces with MBX contribution +------------------------------------------------------------------------- */ + +void PairMBX::accumulate_f(bool include_ext) +{ + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::ACCUMULATE_F); + + bblock::System *ptr_mbx = fix_MBX->mbx_impl->ptr_mbx; + + const int nlocal = atom->nlocal; + double **f = atom->f; + + const int *const mol_anchor = fix_MBX->mol_anchor; + const int *const mol_type = fix_MBX->mol_type; + char **mol_names = fix_MBX->mol_names; + + std::vector grads = ptr_mbx->GetRealGrads(); + + std::vector grads_ext; + if (include_ext) + grads_ext = ptr_mbx->GetExternalChargesGradients(); + else + grads_ext = std::vector(fix_MBX->mbx_num_ext * 3, 0.0); + + // accumulate forces on local particles + // -- forces on ghost particles ignored/not needed + // -- should use a map created from earlier loop loading particles into mbx + + int indx = 0; + int indx_ext = 0; + + for (int i = 0; i < nlocal; ++i) { + if (mol_anchor[i]) { + const int mtype = mol_type[i]; + + // to be replaced with integer comparison + + bool include_monomer = true; + bool is_ext = false; + tagint anchor = atom->tag[i]; + + int na = fix_MBX->get_include_monomer(mol_names[mtype], anchor, include_monomer, is_ext); + + if (include_monomer) { + for (int j = 0; j < na; ++j) { + const int ii = atom->map(anchor + j); + f[ii][0] -= grads[indx++]; + f[ii][1] -= grads[indx++]; + f[ii][2] -= grads[indx++]; + } + } else if (is_ext) { + f[i][0] -= grads_ext[indx_ext++]; + f[i][1] -= grads_ext[indx_ext++]; + f[i][2] -= grads_ext[indx_ext++]; + } + + } // if(anchor) + } + + // accumulate virial: only global is supported + // MBX: xx, xy, xz, yx, yy, yz, zx, zy, zz + // LAMMPS: xx, yy, zz, xy, xz, yz + + if (vflag_either) { + std::vector mbx_vir = ptr_mbx->GetVirial(); + + mbx_virial[0] += mbx_vir[0]; + mbx_virial[1] += mbx_vir[4]; + mbx_virial[2] += mbx_vir[8]; + mbx_virial[3] += mbx_vir[1]; + mbx_virial[4] += mbx_vir[2]; + mbx_virial[5] += mbx_vir[5]; + } + + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::ACCUMULATE_F); +} + +/* ---------------------------------------------------------------------- + update forces with MBX contribution +------------------------------------------------------------------------- */ + +void PairMBX::accumulate_f_all(bool include_ext) +{ + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::ACCUMULATE_F); + + bblock::System *ptr_mbx = fix_MBX->mbx_impl->ptr_mbx; + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + double **f = atom->f; + + const int *const mol_anchor = fix_MBX->mol_anchor; + const int *const mol_type = fix_MBX->mol_type; + char **mol_names = fix_MBX->mol_names; + + std::vector grads = ptr_mbx->GetRealGrads(); + + std::vector grads_ext; + if (include_ext) + grads_ext = ptr_mbx->GetExternalChargesGradients(); + else + grads_ext = std::vector(fix_MBX->mbx_num_ext * 3, 0.0); + + // accumulate forces on local + ghost particles + // -- should use a map created from earlier loop loading particles into mbx + + int indx = 0; + int indx_ext = 0; + + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i]) { + const int mtype = mol_type[i]; + + // to be replaced with integer comparison + + bool include_monomer = true; + bool is_ext = false; + tagint anchor = atom->tag[i]; + + int na = fix_MBX->get_include_monomer(mol_names[mtype], anchor, include_monomer, is_ext); + + if (include_monomer) { + for (int j = 0; j < na; ++j) { + const int ii = atom->map(anchor + j); + f[ii][0] -= grads[indx++]; + f[ii][1] -= grads[indx++]; + f[ii][2] -= grads[indx++]; + } + } else if (is_ext) { + f[i][0] -= grads_ext[indx_ext++]; + f[i][1] -= grads_ext[indx_ext++]; + f[i][2] -= grads_ext[indx_ext++]; + } + + } // if(anchor) + } + + // accumulate virial: only global is supported + // MBX: xx, xy, xz, yx, yy, yz, zx, zy, zz + // LAMMPS: xx, yy, zz, xy, xz, yz + + if (vflag_either) { + std::vector mbx_vir = ptr_mbx->GetVirial(); + + mbx_virial[0] += mbx_vir[0]; + mbx_virial[1] += mbx_vir[4]; + mbx_virial[2] += mbx_vir[8]; + mbx_virial[3] += mbx_vir[1]; + mbx_virial[4] += mbx_vir[2]; + mbx_virial[5] += mbx_vir[5]; + } + + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::ACCUMULATE_F); +} + +/* ---------------------------------------------------------------------- + update forces with MBX contribution +------------------------------------------------------------------------- */ + +void PairMBX::accumulate_f_local(bool include_ext) +{ + + fix_MBX->mbxt_start(FixMBX::MBXT_LABELS::ACCUMULATE_F_LOCAL); + + bblock::System *ptr_mbx = fix_MBX->mbx_impl->ptr_mbx_local; + + const int nlocal = atom->nlocal; + const int nall = nlocal + atom->nghost; + double **f = atom->f; + + const int *const mol_anchor = fix_MBX->mol_anchor; + const int *const mol_local = fix_MBX->mol_local; + const int *const mol_type = fix_MBX->mol_type; + char **mol_names = fix_MBX->mol_names; + + std::vector grads = ptr_mbx->GetRealGrads(); + + std::vector grads_ext; + if (include_ext) + grads_ext = ptr_mbx->GetExternalChargesGradients(); + else + grads_ext = std::vector(fix_MBX->mbx_num_ext_local * 3, 0.0); + + // accumulate forces on monomers with at least one local particle + // -- forces on ghost particles ignored/not needed ?? + // -- should use a map created from earlier loop loading particles into mbx + + int indx = 0; + int indx_ext = 0; + + for (int i = 0; i < nall; ++i) { + if (mol_anchor[i] && mol_local[i]) { + const int mtype = mol_type[i]; + + // to be replaced with integer comparison + + bool include_monomer = true; + bool is_ext = false; + tagint anchor = atom->tag[i]; + + int na = fix_MBX->get_include_monomer(mol_names[mtype], anchor, include_monomer, is_ext); + + if (include_monomer) { + for (int j = 0; j < na; ++j) { + const int ii = atom->map(anchor + j); + f[ii][0] -= grads[indx++]; + f[ii][1] -= grads[indx++]; + f[ii][2] -= grads[indx++]; + } + } else if (is_ext) { + f[i][0] -= grads_ext[indx_ext++]; + f[i][1] -= grads_ext[indx_ext++]; + f[i][2] -= grads_ext[indx_ext++]; + } + + } // if(anchor) + } + + // accumulate virial: only global is supported + // MBX: xx, xy, xz, yx, yy, yz, zx, zy, zz + // LAMMPS: xx, yy, zz, xy, xz, yz + + if (vflag_either) { + std::vector mbx_vir = ptr_mbx->GetVirial(); + + mbx_virial[0] += mbx_vir[0]; + mbx_virial[1] += mbx_vir[4]; + mbx_virial[2] += mbx_vir[8]; + mbx_virial[3] += mbx_vir[1]; + mbx_virial[4] += mbx_vir[2]; + mbx_virial[5] += mbx_vir[5]; + } + + fix_MBX->mbxt_stop(FixMBX::MBXT_LABELS::ACCUMULATE_F_LOCAL); +} + diff --git a/src/MBX/pair_mbx.h b/src/MBX/pair_mbx.h new file mode 100644 index 00000000000..6fe6065b86b --- /dev/null +++ b/src/MBX/pair_mbx.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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 + +PairStyle(mbx, PairMBX) + +#else + +#ifndef LMP_PAIR_MBX_H +#define LMP_PAIR_MBX_H + +#include "pair.h" + + +namespace LAMMPS_NS { + class FixMBX; + +class PairMBX : public Pair { + friend FixMBX; // accesses cut_global + + public: + PairMBX(class LAMMPS *); + virtual ~PairMBX(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + + protected: + double cut_global; + + int me; + + FixMBX *fix_MBX; // owner of MBX objects + + int nmolecule; // # of molecules in system (would break if number of molecules can change) + + double mbx_e1b; + double mbx_e2b; + double mbx_e3b; + double mbx_e4b; + double mbx_disp; + double mbx_buck; + double mbx_ele; + double mbx_total_energy; + + double mbx_virial[6]; + + virtual void allocate(); + + void accumulate_f(bool); + void accumulate_f_all(bool); // local + ghost + void accumulate_f_local(bool); +}; + +} // namespace LAMMPS_NS + +#endif +#endif