Merge branch 'develop' into remove-message-package

bench/README

@@ -4,10 +4,8 @@ This directory contains 5 benchmark problems which are discussed in
 the Benchmark section of the LAMMPS documentation, and on the
 Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
-This directory also has several sub-directories:
+This directory also has one sub-directories:
 
-FERMI           benchmark scripts for desktop machine with Fermi GPUs (Tesla)
-KEPLER          benchmark scripts for GPU cluster with Kepler GPUs
 POTENTIALS      benchmarks scripts for various potentials in LAMMPS
 
 The results for all of these benchmarks are displayed and discussed on

cmake/Modules/Packages/GPU.cmake

@@ -347,6 +347,10 @@ elseif(GPU_API STREQUAL "HIP")
   target_link_libraries(gpu PRIVATE hip::host)
 
   if(HIP_USE_DEVICE_SORT)
+    if(HIP_PLATFORM STREQUAL "amd")
+      # newer version of ROCm (5.1+) require c++14 for rocprim
+      set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
+    endif()
     # add hipCUB
     target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
     target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.0.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "8a8da217148bd9b700083b67d795af5e" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)

doc/src/Commands_compute.rst

@@ -63,6 +63,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`
    * :doc:`fep <compute_fep>`
+   * :doc:`fep/ta <compute_fep_ta>`
    * :doc:`force/tally <compute_tally>`
    * :doc:`fragment/atom <compute_cluster_atom>`
    * :doc:`global/atom <compute_global_atom>`

doc/src/Commands_fix.rst

@@ -100,7 +100,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`mdi/engine <fix_mdi_engine>`
+   * :doc:`mdi/aimd <fix_mdi_aimd>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`

doc/src/Commands_pair.rst

@@ -88,12 +88,12 @@ OPT.
    * :doc:`coul/tt <pair_coul_tt>`
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
-   * :doc:`dpd (gio) <pair_dpd>`
+   * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
-   * :doc:`dpd/ext <pair_dpd_ext>`
+   * :doc:`dpd/ext (k) <pair_dpd_ext>`
-   * :doc:`dpd/ext/tstat <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
-   * :doc:`dpd/tstat (go) <pair_dpd>`
+   * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
    * :doc:`e3b <pair_e3b>`
    * :doc:`drip <pair_drip>`

doc/src/Developer_plugins.rst

@@ -262,3 +262,24 @@ A plugin may be registered under an existing style name.  In that case
 the plugin will override the existing code.  This can be used to modify
 the behavior of existing styles or to debug new versions of them without
 having to re-compile or re-install all of LAMMPS.
+
+Compiling plugins
+^^^^^^^^^^^^^^^^^
+
+Plugins need to be compiled with the same compilers and libraries
+(e.g. MPI) and compilation settings (MPI on/off, OpenMP, integer sizes)
+as the LAMMPS executable and library.  Otherwise the plugin will likely
+not load due to mismatches in the function signatures (LAMMPS is C++ so
+scope, type, and number of arguments are encoded into the symbol names
+and thus differences in them will lead to failed plugin load commands.
+Compilation of the plugin can be managed via both, CMake or traditional
+GNU makefiles.  Some examples that can be used as a template are in the
+``examples/plugins`` folder.  The CMake script code has some small
+adjustments to allow building the plugins for running unit tests with
+them. Another example that converts the KIM package into a plugin can be
+found in the ``examples/kim/plugin`` folder.  No changes to the sources
+of the KIM package themselves are needed; only the plugin interface and
+loader code needs to be added.  This example only supports building with
+CMake, but is probably a more typical example. To compile you need to
+run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
+configuration setting are identical to those for compiling LAMMPS.

doc/src/Examples.rst

@@ -94,6 +94,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | latte       | examples for using fix latte for DFTB via the LATTE library      |
 +-------------+------------------------------------------------------------------+
+| mdi         | use of the MDI package and MolSSI MDI code coupling library      |
++-------------+------------------------------------------------------------------+
 | meam        | MEAM test for SiC and shear (same as shear examples)             |
 +-------------+------------------------------------------------------------------+
 | melt        | rapid melt of 3d LJ system                                       |

doc/src/Howto_couple.rst

@@ -12,16 +12,16 @@ LAMMPS can be coupled to other codes in at least 4 ways.  Each has
 advantages and disadvantages, which you will have to think about in the
 context of your application.
 
-1. Define a new :doc:`fix <fix>` command that calls the other code.  In
+1. Define a new :doc:`fix <fix>` command that calls the other code.
-   this scenario, LAMMPS is the driver code.  During timestepping,
+   In this scenario, LAMMPS is the driver code.  During timestepping,
    the fix is invoked, and can make library calls to the other code,
-   which has been linked to LAMMPS as a library.  This is the way how the
+   which has been linked to LAMMPS as a library.  This is the way the
    :ref:`LATTE <PKG-LATTE>` package, which performs density-functional
-   tight-binding calculations using the `LATTE software <https://github.com/lanl/LATTE>`_
+   tight-binding calculations using the `LATTE software
-   to compute forces, is hooked to LAMMPS.
+   <https://github.com/lanl/LATTE>`_ to compute forces, is hooked to
-   See the :doc:`fix latte <fix_latte>` command for more details.
+   LAMMPS.  See the :doc:`fix latte <fix_latte>` command for more
-   Also see the :doc:`Modify <Modify>` doc pages for info on how to
+   details.  Also see the :doc:`Modify <Modify>` doc pages for info on
-   add a new fix to LAMMPS.
+   how to add a new fix to LAMMPS.
 
 .. spacer
 
@@ -58,5 +58,12 @@ context of your application.
 
 .. spacer
 
-4. Couple LAMMPS with another code in a client/server mode.  This is
+4. Couple LAMMPS with another code in a client/server fashion, using
-   described on the :doc:`Howto MDI library coupling <Howto_mdi>` page.
+   using the `MDI Library
+   <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
+   developed by the `Molecular Sciences Software Institute (MolSSI)
+   <https://molssi.org>`_ to run LAMMPS as either an MDI driver
+   (client) or an MDI engine (server).  The MDI driver issues commands
+   to the MDI server to exchange data between them.  See the
+   :doc:`Howto mdi <Howto_mdi>` page for more information about how
+   LAMMPS can operate in either of these modes.

doc/src/Howto_mdi.rst

@@ -1,127 +1,144 @@
 Using LAMMPS with the MDI library for code coupling
 ===================================================
 
-Client/server coupling of two codes is where one code is the "client"
+Client/server coupling of two (or more) codes is where one code is the
-and sends request messages (data) to a "server" code.  The server
+"client" and sends request messages (data) to one (or more) "server"
-responds to each request with a reply message.  This enables the two
+code(s).  A server responds to each request with a reply message
-codes to work in tandem to perform a simulation.  LAMMPS can act as
+(data).  This enables two (or more) codes to work in tandem to perform
-either a client or server code; it does this by using the `MolSSI
+a simulation.  LAMMPS can act as either a client or server code; it
-Driver Interface (MDI) library
+does this by using the `MolSSI Driver Interface (MDI) library
 <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
 developed by the `Molecular Sciences Software Institute (MolSSI)
-<https://molssi.org>`_.
+<https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
+package.
 
 Alternate methods for code coupling with LAMMPS are described on the
 :doc:`Howto couple <Howto_couple>` doc page.
 
-Some advantages of client/server coupling are that the two codes can run
+Some advantages of client/server coupling are that the codes can run
 as stand-alone executables; they need not be linked together.  Thus
-neither code needs to have a library interface.  This also makes it easy
+neither code needs to have a library interface.  This also makes it
-to run the two codes on different numbers of processors.  If a message
+easy to run the two codes on different numbers of processors.  If a
-protocol (format and content) is defined for a particular kind of
+message protocol (format and content) is defined for a particular kind
-simulation, then in principle any code which implements the client-side
+of simulation, then in principle any code which implements the
-protocol can be used in tandem with any code which implements the
+client-side protocol can be used in tandem with any code which
-server-side protocol.  Neither code needs to know what specific other
+implements the server-side protocol.  Neither code needs to know what
-code it is working with.
+specific other code it is working with.
 
 In MDI nomenclature, a client code is the "driver", and a server code is
 an "engine".  One driver code can communicate with one or more instances
 of one or more engine codes.  Driver and engine codes can be written in
 any language: C, C++, Fortran, Python, etc.
 
-In addition to allowing driver and engine(s) running to run as
+In addition to allowing driver and engine(s) to run as stand-alone
-stand-alone executables, MDI also enables a server code to be a
+executables, MDI also enables an engine to be a *plugin* to the client
-"plugin" to the client code.  In this scenario, server code(s) are
+code.  In this scenario, server code(s) are compiled as shared
-compiled as shared libraries, and one (or more) instances of the
+libraries, and one (or more) instances of the server are instantiated
-server are instantiated by the driver code.  If the driver code runs
+by the driver code.  If the driver code runs in parallel, it can split
-in parallel, it can split its MPI communicator into multiple
+its MPI communicator into multiple sub-communicators, and launch each
-sub-communicators, and launch each plugin engine instance on a
+plugin engine instance on a sub-communicator.  Driver processors
-sub-communicator.  Driver processors in that sub-communicator exchange
+within that sub-communicator exchange messages with the corresponding
-messages with that engine instance, and can also send MPI messages to
+engine instance, and can also send MPI messages to other processors in
-other processors in the driver.  The driver code can also destroy
+the driver.  The driver code can also destroy engine instances and
-engine instances and re-instantiate them.
+re-instantiate them.  LAMMPS can operate as either a stand-alone or
+plugin MDI engine.  When it operates as a driver, if can use either
+stand-alone or plugin MDI engines.
 
-The way that a driver communicates with an engine is by making
+The way in which an MDI driver communicates with an MDI engine is by
-MDI_Send() and MDI_Recv() calls, which are conceptually similar to
+making MDI_Send() and MDI_Recv() calls, which are conceptually similar
-MPI_Send() and MPI_Recv() calls.  Each send or receive has a string
+to MPI_Send() and MPI_Recv() calls.  Each send or receive operation
-which identifies the command name, and optionally some data, which can
+uses a string to identify the command name, and optionally some data,
-be a single value or vector of values of any data type.  Inside the
+which can be a single value or vector of values of any data type.
-MDI library, data is exchanged between the driver and engine via MPI
+Inside the MDI library, data is exchanged between the driver and
-calls or sockets.  This a run-time choice by the user.
+engine via MPI calls or sockets.  This a run-time choice by the user.
+
+----------
+
+The :ref:`MDI <PKG-MDI>` package provides a :doc:`mdi engine <mdi>`
+command which enables LAMMPS to operate as an MDI engine.  Its doc
+page explains the variety of standard and custom MDI commands which
+the LAMMPS engine recognizes and can respond to.
+
+The package also provides a :doc:`mdi plugin <mdi>` command which
+enables LAMMPS to operate as an MDI driver and load an MDI engine as a
+plugin library.
+
+The package also has a `fix mdi/aimd <fix_mdi_aimd>` command in which
+LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
+in conjunction with a quantum mechanics code.  Its post_force() method
+illustrates how a driver issues MDI commands to another code.  This
+command can be used to couple to an MDI engine which is either a
+stand-alone code or a plugin library.
+
+----------
+
+The examples/mdi directory contains Python scripts and LAMMPS input
+script which use LAMMPS as either an MDI driver or engine or both.
+Three example use cases are provided:
+
+* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
+  and one as an engine.  As an engine, LAMMPS is a surrogate for a
+  quantum code.
+
+* A Python script driver invokes a sequence of unrelated LAMMPS
+  calculations.  Calculations can be single-point energy/force
+  evaluations, MD runs, or energy minimizations.
+
+* Run AIMD with a Python driver code and 2 LAMMPS instances as
+  engines.  The first LAMMPS instance performs MD timestepping.  The
+  second LAMMPS instance acts as a surrogate QM code to compute
+  forces.
+
+Note that in any of these example where LAMMPS is used as an engine,
+an actual QM code (which supports MDI) could be used in its place,
+without modifying other code or scripts, except to specify the name of
+the QM code.
+
+The examples/mdi/README file explains how to launch both driver and
+engine codes so that they communicate using the MDI library via either
+MPI or sockets.
 
 -------------
 
-As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
+Currently there are two quantum DFT codes which have direct MDI
-suite of quantum DFT codes), can work together via the MDI library to
+support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
-perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
+and `INQ <https://qsg.llnl.gov/node/101.html>`_.  There are also
-simulation and sends a message each timestep to ``pw.x`` asking it to
+several QM codes which have indirect support through QCEngine or i-PI.
-compute quantum forces on the current configuration of atoms.  Here is
+The former means they require a wrapper program (QCEngine) with MDI
-how the 2 codes are launched to communicate by MPI:
+support which writes/read files to pass data to the quantum code
+itself.  The list of QCEngine-supported and i-PI-supported quantum
+codes is on the `MDI webpage
+<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
+
+Here is how to build QE as a stand-alone ``pw.x`` file which can be
+used in stand-alone mode:
 
 .. code-block:: bash
 
-   % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
+   % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
-     -in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
+   % build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
 
-In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
+Here is how to build QE as a shared library which can be used in plugin mode,
-processors.
+which results in a libqemdi.so file in <base_path>/q-e/MDI/src:
-
-Here is how the 2 codes are launched to communicate by sockets:
 
 .. code-block:: bash
 
-   % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
+   % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
-   % mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
+   % cd <base_path>/q-e
+   % ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
+   % make -j 4 mdi
 
-These commands could be issued in different windows on a desktop
+INQ cannot be built as a stand-alone code; it is by design a library.
-machine.  Or in the same window, if the first command is ended with
+Here is how to build INQ as a shared library which can be used in
-"&" so as to run in the background.  If "localhost" is replaced by an
+plugin mode, which results in a libinqmdi.so file in
-IP address, ``pw.x`` could be run on another machine on the same network, or
+<base_path>/inq/build/examples:
-even on another machine across the country.
 
-After both codes initialize themselves to model the same system, this is
+.. code-block:: bash
-what occurs each timestep:
 
-* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
+   % git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
-* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
+   % cd <base_path>/inq
-* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
+   % mkdir -p build
-* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
+   % cd build
-* LAMMPS receives the forces and time integrates to complete a single timestep
+   % ../configure --prefix=<install_path>/install
-
+   % make -j 4
--------------
+   % make install
-
-Examples scripts for using LAMMPS as an MDI engine are in the
-examples/mdi directory.  See the README file in that directory for
-instructions on how to run the examples.
-
-.. note::
-
-  Work is underway to add commands that allow LAMMPS to be used as an
-  MDI driver, e.g. for the AIMD example discussed above.  Example
-  scripts for this usage mode will be added the same directory when
-  available.
-
-If LAMMPS is used as a stand-alone engine it should set up the system
-it will be modeling in its input script, then invoke the
-:doc:`mdi/engine <mdi_engine>` command.  This will put LAMMPS into
-"engine mode" where it waits for messages and data from the driver.
-When the driver sends an "EXIT" command, LAMMPS will exit engine mode
-and the input script will continue.
-
-If LAMMPS is used as a plugin engine it operates the same way, except
-that the driver will pass LAMMPS an input script to initialize itself.
-Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
-input script will continue.  After finishing execution of the input
-script, the instance of LAMMPS will be destroyed.
-
-LAMMPS supports the full set of MD-appropriate engine commands defined
-by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` page for
-a list of these.
-
-If those commands are not sufficient for a user-developed driver to use
-LAMMPS as an engine, then new commands can be easily added.  See these
-two files which implement the definition of MDI commands and the logic
-for responding to them:
-
-* src/MDI/mdi_engine.cpp
-* src/MDI/fix_mdi_engine.cpp

doc/src/Howto_structured_data.rst

@@ -79,6 +79,10 @@ This data can be extracted and parsed from a log file using python with:
 .. code-block:: python
 
    import re, yaml
+   try:
+       from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
+   except ImportError:
+       from yaml import SafeLoader as Loader, SafeDumper as Dumper
 
    docs = ""
    with open("log.lammps") as f:
@@ -86,7 +90,7 @@ This data can be extracted and parsed from a log file using python with:
            m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$|  - \[.*\]$)", line)
            if m: docs += m.group(0) + '\n'
 
-   thermo = list(yaml.load_all(docs, Loader=yaml.SafeLoader))
+   thermo = list(yaml.load_all(docs, Loader=Loader))
 
    print("Number of runs: ", len(thermo))
    print(thermo[1]['keywords'][4], ' = ', thermo[1]['data'][2][4])

doc/src/Packages_details.rst

@@ -1395,17 +1395,24 @@ MDI package
 
 **Contents:**
 
-A LAMMPS command and fix to allow client-server coupling of LAMMPS to
+A LAMMPS command and fixes to allow client-server coupling of LAMMPS
-other atomic or molecular simulation codes via the `MolSSI Driver Interface
+to other atomic or molecular simulation codes or materials modeling
+workflows via the `MolSSI Driver Interface
 (MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
 
 **Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
 
+**Install:**
+
+This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` page.
+
 **Supporting info:**
 
 * src/MDI/README
-* :doc:`mdi/engine <mdi_engine>`
+* lib/mdi/README
-* :doc:`fix mdi/engine <fix_mdi_engine>`
+* :doc:`Howto MDI <Howto_mdi>`
+* :doc:`mdi <mdi>`
+* :doc:`fix mdi/aimd <fix_mdi_aimd>`
 * examples/PACKAGES/mdi
 
 ----------

doc/src/Packages_list.rst

@@ -244,7 +244,7 @@ whether an extra library is needed to build and use the package:
      - n/a
      - no
    * - :ref:`MDI <PKG-MDI>`
-     - client-server coupling
+     - client-server code coupling
      - :doc:`MDI Howto <Howto_mdi>`
      - PACKAGES/mdi
      - ext

doc/src/compute.rst

@@ -208,7 +208,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` - rotational energy for each spherical particle
 * :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
 * :doc:`fabric <compute_fabric>` - calculates fabric tensors from pair interactions
-* :doc:`fep <compute_fep>` -
+* :doc:`fep <compute_fep>` - compute free energies for alchemical transformation from perturbation theory
+* :doc:`fep/ta <compute_fep_ta>` - compute free energies for a test area perturbation
 * :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
 * :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
 * :doc:`global/atom <compute_global_atom>` -

doc/src/compute_fep_ta.rst

@@ -0,0 +1,99 @@
+.. index:: compute fep/ta
+
+compute fep/ta command
+======================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID fep/ta temp plane scale_factor keyword value ...
+
+* ID, group-ID are documented in the :doc:`compute <compute>` command
+* fep/ta = name of this compute command
+* temp = external temperature (as specified for constant-temperature run)
+* plane = *xy* or *xz* or *yz*
+* scale_factor = multiplicative factor for change in plane area
+* zero or more keyword/value pairs may be appended
+* keyword = *tail*
+
+  .. parsed-literal::
+
+       *tail* value = *no* or *yes*
+         *no* = ignore tail correction to pair energies (usually small in fep)
+         *yes* = include tail correction to pair energies
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all fep/ta 298 xy 1.0005
+
+Description
+"""""""""""
+
+Define a computation that calculates the change in the free energy due
+to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area
+approach can be used to determine the interfacial tension of the system
+in a single simulation:
+
+.. math::
+
+   \gamma = \lim_{\Delta \mathcal{A} \to 0} \left( \frac{\Delta A_{0 \to 1 }}{\Delta \mathcal{A}}\right)_{N,V,T}
+   = - \frac{kT}{\Delta \mathcal{A}} \ln \left< \exp(-(U_1 - U_0)/kT) \right>_0
+
+During the perturbation, both axes of *plane* are scaled by multiplying
+:math:`\sqrt{scale\_factor}`, while the other axis divided by
+*scale_factor* such that the overall volume of the system is maintained.
+
+The *tail* keyword controls the calculation of the tail correction to
+"van der Waals" pair energies beyond the cutoff, if this has been
+activated via the :doc:`pair_modify <pair_modify>` command. If the
+perturbation is small, the tail contribution to the energy difference
+between the reference and perturbed systems should be negligible.
+
+----------
+
+Output info
+"""""""""""
+
+This compute calculates a global vector of length 3 which contains the
+energy difference ( :math:`U_1-U_0` ) as c_ID[1], the Boltzmann factor
+:math:`\exp(-(U_1-U_0)/kT)`, as c_ID[2] and the change in the *plane*
+area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the potential
+energy of the perturbed state and :math:`U_0` is the potential energy of
+the reference state.  The energies include kspace terms if these are
+used in the simulation.
+
+These output results can be used by any command that uses a global
+scalar or vector from a compute as input.  See the :doc:`Howto output
+<Howto_output>` page for an overview of LAMMPS output options. For
+example, the computed values can be averaged using :doc:`fix ave/time
+<fix_ave_time>`.
+
+Restrictions
+""""""""""""
+
+Constraints, like fix shake, may lead to incorrect values for energy difference.
+
+This compute is distributed as the FEP package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute fep <compute_fep>`
+
+Default
+"""""""
+
+The option defaults are *tail* = *no*\ .
+
+----------
+
+.. _Gloor:
+
+**(Gloor)** Gloor, J Chem Phys, 123, 134703 (2005)

doc/src/dump.rst

@@ -36,7 +36,7 @@ Syntax
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be dumped
-* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio*
+* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
 * N = dump every this many timesteps
 * file = name of file to write dump info to
 * args = list of arguments for a particular style
@@ -68,8 +68,9 @@ Syntax
        *xyz/gz* args = none
        *xyz/zstd* args = none
        *xyz/mpiio* args = none
+       *yaml* args = same as *custom* args, see below
 
-* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* args = list of atom attributes
+* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes
 
   .. parsed-literal::
 
@@ -386,6 +387,70 @@ from using the (numerical) atom type to an element name (or some
 other label). This will help many visualization programs to guess
 bonds and colors.
 
+Dump style *yaml* has the same command syntax as style *custom* and
+writes YAML format files that can be easily parsed by a variety of data
+processing tools and programming languages.  Each timestep will be
+written as a YAML "document" (i.e. starts with "---" and ends with
+"...").  The style supports writing one file per timestep through the
+"\*" wildcard but not multi-processor outputs with the "%" token in the
+filename.  In addition to per-atom data, :doc:`thermo <thermo>` data can
+be included in the *yaml* style dump file using the :doc:`dump_modify
+thermo yes <dump_modify>`. The data included in the dump file uses the
+"thermo" tag and is otherwise identical to data specified by the
+:doc:`thermo_style <thermo_style>` command.
+
+Below is an example for a YAML format dump created by the following commands.
+
+.. code-block:: LAMMPS
+
+   dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
+   dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
+
+The tags "time", "units", and "thermo" are optional and enabled by the
+dump_modify command. The list under the "box" tag has 3 lines for
+orthogonal boxes and 4 lines with triclinic boxes, where the first 3 are
+the box boundaries and the 4th the three tilt factors (xy, xz, yz).  The
+"thermo" data follows the format of the *yaml* thermo style.  The
+"keywords" tag lists the per-atom properties contained in the "data"
+columns, which contain a list with one line per atom.  The keywords may
+be renamed using the dump_modify command same as for the *custom* dump
+style.
+
+.. code-block:: yaml
+
+   ---
+   timestep: 0
+   units: lj
+   time: 0
+   natoms: 4000
+   boundary: [ p, p, p, p, p, p, ]
+   thermo:
+     - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+     - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+   box:
+     - [ 0, 16.795961913825074 ]
+     - [ 0, 16.795961913825074 ]
+     - [ 0, 16.795961913825074 ]
+     - [ 0, 0, 0 ]
+   keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+   data:
+     - [     1 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0 , 0 , 0, ]
+     - [     2 , 1 ,  8.397981e-01 ,  8.397981e-01 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0 , 0 , 0, ]
+     - [     3 , 1 ,  8.397981e-01 ,  0.000000e+00 ,  8.397981e-01 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+
+     [...]
+   ...
+   ---
+   timestep: 100
+   units: lj
+   time: 0.5
+
+     [...]
+
+   ...
+
+----------
+
 Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
 can be read directly by `VMD <http://www.ks.uiuc.edu/Research/vmd>`_, a
 popular molecular viewing program.
@@ -427,9 +492,9 @@ If a "%" character appears in the filename, then each of P processors
 writes a portion of the dump file, and the "%" character is replaced
 with the processor ID from 0 to P-1.  For example, tmp.dump.% becomes
 tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc.  This creates smaller
-files and can be a fast mode of output on parallel machines that
+files and can be a fast mode of output on parallel machines that support
-support parallel I/O for output. This option is not available for the
+parallel I/O for output. This option is **not** available for the *dcd*,
-*dcd*, *xtc*, and *xyz* styles.
+*xtc*, *xyz*, and *yaml* styles.
 
 By default, P = the number of processors meaning one file per
 processor, but P can be set to a smaller value via the *nfile* or
@@ -722,8 +787,8 @@ are part of the MPIIO package.  They are only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
-The *xtc* and *dcd* styles are part of the EXTRA-DUMP package.  They
+The *xtc*, *dcd* and *yaml* styles are part of the EXTRA-DUMP package.
-are only enabled if LAMMPS was built with that package.  See the
+They are only enabled if LAMMPS was built with that package.  See the
 :doc:`Build package <Build_package>` page for more info.
 
 Related commands

doc/src/dump_modify.rst

@@ -26,6 +26,10 @@ Syntax
          N = index of frame written upon first dump
        *balance* arg = *yes* or *no*
        *buffer* arg = *yes* or *no*
+       *colname* values =  ID string, or *default*
+         string = new column header name
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a custom dump keyword or reference to compute, fix, property or variable.
        *delay* arg = Dstep
          Dstep = delay output until this timestep
        *element* args = E1 E2 ... EN, where N = # of atom types
@@ -40,9 +44,10 @@ Syntax
          Np = write one file for every this many processors
        *first* arg = *yes* or *no*
        *flush* arg = *yes* or *no*
-       *format* args = *line* string, *int* string, *float* string, M string, or *none*
+       *format* args = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
-         M = integer from 1 to N, where N = # of per-atom quantities being output
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a custom dump keyword or reference to compute, fix, property or variable.
        *header* arg = *yes* or *no*
          *yes* to write the header
          *no* to not write the header
@@ -375,6 +380,29 @@ performed with dump style *xtc*\ .
 
 ----------
 
+The *colname* keyword can be used to change the default header keyword
+for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
+and MPIIO variants.  The setting for *ID string* replaces the default
+text with the provided string.  *ID* can be a positive integer when it
+represents the column number counting from the left, a negative integer
+when it represents the column number from the right (i.e. -1 is the last
+column/keyword), or a custom dump keyword (or compute, fix, property, or
+variable reference) and then it replaces the string for that specific
+keyword. For *atom* dump styles only the keywords "id", "type", "x",
+"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
+whether scaled or unwrapped coordinates were enabled or disabled, and
+it always assumes 8 columns for indexing regardless of whether image
+flags are enabled or not.  For dump style *cfg* only the "auxiliary"
+keywords (6th or later keyword) may be changed and the column indexing
+considers only them (i.e. the 6th keyword is the the 1st column).
+
+The *colname* keyword can be used multiple times. If multiple *colname*
+settings refer to the same keyword, the last setting has precedence.  A
+setting of *default* clears all previous settings, reverting all values
+to their default names.
+
+----------
+
 The *format* keyword can be used to change the default numeric format output
 by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
 *xyz* styles, and their MPIIO variants. Only the *line* or *none*
@@ -684,8 +712,8 @@ run, this option is ignored since the output is already balanced.
 
 ----------
 
-The *thermo* keyword only applies the dump *netcdf* style.  It
+The *thermo* keyword only applies the dump styles *netcdf* and *yaml*.
-triggers writing of :doc:`thermo <thermo>` information to the dump file
+It triggers writing of :doc:`thermo <thermo>` information to the dump file
 alongside per-atom data.  The values included in the dump file are
 identical to the values specified by :doc:`thermo_style <thermo_style>`.
 

doc/src/fix.rst

@@ -243,7 +243,7 @@ accelerated styles exist.
 * :doc:`lb/viscous <fix_lb_viscous>` -
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
-* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
+* :doc:`mdi/aimd <fix_mdi_aimd>` - LAMMPS operates as driver for ab initio MD (AIMD) via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
 * :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms

doc/src/fix_mdi_aimd.rst

@@ -0,0 +1,103 @@
+.. index:: fix mdi/aimd
+
+fix mdi/aimd command
+======================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID mdi/aimd keyword
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* mdi/aimd = style name of this fix command
+* optional keyword = *plugin*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all mdi/aimd
+   fix 1 all mdi/aimd plugin
+
+Description
+"""""""""""
+
+This command enables LAMMPS to act as a client with another server
+code to couple the two codes together to perform ab initio MD (AIMD)
+simulations.
+
+More specifically, this command causes LAMMPS to begin using the `MDI
+Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
+to run as an MDI driver (client), which sends MDI commands to an
+external MDI engine code (server) which in the case of AIMD is a
+quantum mechanics (QM) code, or could be LAMMPS itself, acting as a
+surrogate for a QM code.  See the :doc:`Howto mdi <Howto_mdi>` page
+for more information about how LAMMPS can operate as either an MDI
+driver or engine.
+
+The examples/mdi directory contains input scripts performing AIMD in
+this manner with LAMMPS acting as both a driver and an engine
+(surrogate for a QM code).  The examples/mdi/README file explains how
+to launch both driver and engine codes so that they communicate using
+the MDI library via either MPI or sockets.  Any QM code that supports
+MDI could be used in place of LAMMPS acting as a QM surrogate.  See
+the :doc:`Howto mdi <Howto_mdi>` page for a current list (March 2022)
+of such QM codes.
+
+The engine code can run either as a stand-alone code, launched at the
+same time as LAMMPS, or as a plugin library.  See the :doc:`mdi plugin
+<mdi>` command for how to trigger LAMMPS to load the plugin library.
+Again, the examples/mdi/README file explains how to launch both driver
+and engine codes so that engine is used in plugin mode.
+
+To use this fix with a plugin engine, you must specify the
+*plugin* keyword as the last argument, as illustrated above.
+
+.. note::
+
+   As of April 2022, the *plugin* keyword is needed.  In a future
+   version of the MDI library it will no longer be necessary.
+
+----------
+
+This fix performs the timestepping portion of an AIMD simulation.
+Both LAMMPS and the engine code (QM or LAMMPS) should define the same
+system (simulation box, atoms and their types) in their respective
+input scripts.  LAMMPS then begins its timestepping.
+
+At the point in each timestep when LAMMPS needs the force on each
+atom, it communicates with the engine code.  It sends the current
+simulation box size and shape (if they change dynamically, e.g. during
+an NPT simulation), and the current atom coordinates.  The engine code
+computes quantum forces on each atom and returns them to LAMMPS.  If
+LAMMPS also needs the system energy and/or virial, it requests those
+values from the engine code as well.
+
+Restrictions
+""""""""""""
+
+This command is part of the MDI package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
+atomistic codes, the :doc:`units <units>` command should be used to
+specify *real* or *metal* units.  This will ensure the correct unit
+conversions between LAMMPS and MDI units, which the other codes will
+also perform in their preferred units.
+
+LAMMPS can also be used as an MDI driver in other unit choices it
+supports, e.g. *lj*, but then no unit conversion is performed.
+
+Related commands
+""""""""""""""""
+
+:doc:`mdi engine <mdi>`
+
+Default
+"""""""
+
+none

doc/src/fix_mdi_engine.rst

@@ -1,59 +0,0 @@
-.. index:: fix mdi/engine
-
-fix mdi/engine command
-======================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID mdi/engine
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* mdi/engine = style name of this fix command
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all mdi/engine
-
-Description
-"""""""""""
-
-This fix is used along with the :doc:`mdi/engine <mdi_engine>` command
-to enable LAMMPS to use the `MDI Library
-<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ to run as
-an MDI engine.  The fix provides hooks that enable MDI driver codes to
-communicate with LAMMPS at various points within a LAMMPS timestep.
-
-It is not generally necessary to add this fix to a LAMMPS input file,
-even when using the :doc:`mdi/engine <mdi_engine>` command.  If the
-:doc:`mdi/engine <mdi_engine>` command is executed and this fix is not
-present, it will automatically be added and applied as a new fix for
-all atoms for the duration of the command.  Thus it is only necessary
-to add this fix to an input file when you want to modify the group-ID
-or the ordering of this fix relative to other fixes in the input script.
-
-For more information about running LAMMPS as an MDI engine, see the
-:doc:`mdi/engine <mdi_engine>` command and the :doc:`Howto mdi
-<Howto_mdi>` doc page.
-
-Restrictions
-""""""""""""
-
-This command is part of the MDI package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package
-<Build_package>` page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`mdi/engine <mdi_engine>`
-
-Default
-"""""""
-
-none

doc/src/fix_tmd.rst

@@ -29,10 +29,10 @@ Description
 """""""""""
 
 Perform targeted molecular dynamics (TMD) on a group of atoms.  A
-holonomic constraint is used to force the atoms to move towards (or
+holonomic constraint is used to force the atoms to move towards (or away
-away from) the target configuration.  The parameter "rho" is
+from) the target configuration.  The parameter "rho" is monotonically
-monotonically decreased (or increased) from its initial value to
+decreased (or increased) from its initial value to rho_final at the end
-rho_final at the end of the run.
+of the run.
 
 Rho has distance units and is a measure of the root-mean-squared
 distance (RMSD) between the current configuration of the atoms in the
@@ -55,22 +55,25 @@ a .gz suffix).  The format of the target file1 is as follows:
 
 The first 3 lines may or may not be needed, depending on the format of
 the atoms to follow.  If image flags are included with the atoms, the
-first 3 lo/hi lines must appear in the file.  If image flags are not
+first 3 lo/hi lines **must** appear in the file.  If image flags are not
-included, the first 3 lines should not appear.  The 3 lines contain the
+included, the first 3 lines **must not** appear.  The 3 lines contain the
 simulation box dimensions for the atom coordinates, in the same format
 as in a LAMMPS data file (see the :doc:`read_data <read_data>` command).
 
 The remaining lines each contain an atom ID and its target x,y,z
 coordinates.  The atom lines (all or none of them) can optionally be
-followed by 3 integer values: nx,ny,nz.  For periodic dimensions, they
+followed by 3 integer values: nx,ny,nz.For periodic dimensions, they
 specify which image of the box the atom is considered to be in, i.e. a
 value of N (positive or negative) means add N times the box length to
-the coordinate to get the true value.
+the coordinate to get the true value.  Those 3 integers either must
+be given for all atoms or none.
 
 The atom lines can be listed in any order, but every atom in the group
 must be listed in the file.  Atoms not in the fix group may also be
 listed; they will be ignored.
 
+Comments starting with '#' and empty lines may be included as well.
+
 TMD statistics are written to file2 every N timesteps, unless N is
 specified as 0, which means no statistics.
 

doc/src/fix_ttm.rst

@@ -154,7 +154,7 @@ of the electronic specific heat, but ignored temperature dependencies
 of any of the other parameters.  See more discussion below for fix
 ttm/mod.
 
-..note::
+.. note::
 
   These fixes do not perform time integration of the atoms in the fix
   group, they only rescale their velocities.  Thus a time integration
@@ -164,7 +164,7 @@ ttm/mod.
   fix, e.g. :doc:`fix nvt <fix_nh>` or :doc:`fix langevin
   <fix_langevin>`.
 
-..note::
+.. note::
 
   These fixes require use of an orthogonal 3d simulation box with
   periodic boundary conditions in all dimensions.  They also require
@@ -305,8 +305,8 @@ is calculated as
 where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
 :ref:`(Pisarev) <Pisarev>`)
 
-The fix ttm/mod parameter file *init_file* has the following syntax/
+The fix ttm/mod parameter file *init_file* has the following syntax.
-Every line with the odd number is considered as a comment and
+Every line with an odd number is considered as a comment and
 ignored. The lines with the even numbers are treated as follows:
 
 .. parsed-literal::

doc/src/mdi.rst

@@ -0,0 +1,312 @@
+.. index:: mdi
+
+mdi command
+==================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   mdi mode args
+
+* mode = *engine* or *plugin*
+
+  .. parsed-literal::
+
+     *engine* args = none
+     *plugin* args = name keyword value keyword value
+       name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
+       keywords = *mdi* or *infile* or *extra* or *command*
+         *mdi* value = args passed to MDI for driver to operate with plugins
+         *infile* value = filename the engine will read at start-up
+         *extra* value = aditional command-line args to pass to engine library when loaded
+         *command* value = a LAMMPS input script command to execute
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   mdi engine
+   mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
+              infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
+              command "run 5"
+
+Description
+"""""""""""
+
+This command implements two high-level operations within LAMMPS to use
+the `MDI Library
+<https://molssi-mdi.github.io/MDI_Library/html/index.html>` for
+coupling to other codes in a client/server protocol.
+
+The *engine* mode enables LAMMPS to act as an MDI engine (server),
+responding to requests from an MDI driver (client) code.
+
+The *plugin* mode enables LAMMPS to act as an MDI driver (client), and
+load the MDI engine (server) code as a library plugin.  In this case
+the MDI engine is a library plugin.  It can also be a stand-alone
+code, launched separately from LAMMPS, in which case the mdi plugin
+command is not used.
+
+See the Howto MDI doc page for a discussion of all the different ways
+2 or more codes can interact via MDI.
+
+The examples/mdi directory has examples which use LAMMPS in 4
+different modes: as a driver using an engine as either a stand-alone
+code or as a plugin, and as an engine operating as either a
+stand-alone code or as a plugin.  The README file in that directory
+shows how to launch and couple codes for all the 4 usage modes, and so
+they communicate via the MDI library using either MPI or sockets.
+
+----------
+
+The *mdi engine* command is used to make LAMMPS operate as an MDI
+engine.  It is typically used in an input script after LAMMPS has
+setup the system it is going to model consistent with what the driver
+code expects.  Depending on when the driver code tells the LAMMPS
+engine to exit, other commands can be executed after this command, but
+typically it is used at the end of a LAMMPS input script.
+
+To act as an MDI engine operating as an MD code (or surrogate QM
+code), this is the list of standard MDI commands issued by a driver
+code which LAMMPS currently recognizes.  Using standard commands
+defined by the MDI library means that a driver code can work
+interchangeably with LAMMPS or other MD codes or with QM codes which
+support the MDI standard.  See more details about these commands in
+the `MDI library documentation
+<https://molssi-mdi.github.io/MDI_Library/html/mdi_standard.html>`_
+
+These commands are valid at the @DEFAULT node defined by MDI.
+Commands that start with ">" mean the driver is sending information to
+LAMMPS.  Commands that start with "<" are requests by the driver for
+LAMMPS to send it information.  Commands that start with an alphabetic
+letter perform actions.  Commands that start with "@" are MDI "node"
+commands, which are described further below.
+
+.. list-table::
+   :widths: 20 80
+   :header-rows: 1
+
+   * - Command name
+     - Action
+   * - >CELL or <CELL
+     - Send/request 3 simulation box edge vectors (9 values)
+   * - >CELL_DISPL or <CELL_DISPL
+     - Send/request displacement of the simulation box from the origin (3 values)
+   * - >CHARGES or <CHARGES
+     - Send/request charge on each atom (N values)
+   * - >COORDS or <COORDS
+     - Send/request coordinates of each atom (3N values)
+   * - <ENERGY
+     - Request total energy (potential + kinetic) of the system (1 value)
+   * - >FORCES or <FORCES
+     - Send/request forces on each atom (3N values)
+   * - >+FORCES
+     - Send forces to add to each atom (3N values)
+   * - <LABELS
+     - Request string label of each atom (N values)
+   * - <MASSES
+     - Request mass of each atom (N values)
+   * - MD
+     - Perform an MD simulation for N timesteps (most recent >NSTEPS value)
+   * - OPTG
+     - Perform an energy minimization to convergence (most recent >TOLERANCE values)
+   * - >NATOMS or <NATOMS
+     - Sends/request number of atoms in the system (1 value)
+   * - >NSTEPS
+     - Send number of timesteps for next MD dynamics run via MD command
+   * - <PE
+     - Request potential energy of the system (1 value)
+   * - <STRESS
+     - Request stress tensor (virial) of the system (6 values)
+   * - >TOLERANCE
+     - Send 4 tolerance parameters for next MD minimization via OPTG command
+   * - >TYPES or <TYPES
+     - Send/request the numeric type of each atom (N values)
+   * - >VELOCITIES or <VELOCITIES
+     - Send/request the velocity of each atom (3N values)
+   * - @INIT_MD or @INIT_OPTG
+     - Driver tells LAMMPS to start single-step dynamics or minimization (see below)
+   * - EXIT
+     - Driver tells LAMMPS to exit engine mode
+
+.. note::
+
+   The <ENERGY, <FORCES, <PE, and <STRESS commands trigger LAMMPS to
+   compute atomic interactions for the current configuration of atoms
+   and size/shape of the simulation box.  I.e. LAMMPS invokes its
+   pair, bond, angle, ..., kspace styles.  If the driver is updating
+   the atom coordinates and/or box incrementally (as in an MD
+   simulation which the driver is managing), then the LAMMPS engine
+   will do the same, and only occasionally trigger neighbor list
+   builds.  If the change in atom positions is large (since the
+   previous >COORDS command), then LAMMPS will do a more expensive
+   operation to migrate atoms to new processors as needed and
+   re-neighbor.  If the >NATOMS or >TYPES commands have been sent
+   (since the previous >COORDS command), then LAMMPS assumes the
+   system is new and re-initializes an entirely new simulation.
+
+The MD and OPTG commands perform an entire MD simulation or energy
+minimization (to convergence) with no communication from the driver
+until the simulation is complete.  By contrast, the @INIT_MD and
+@INIT_OPTG commands allow the driver to communicate with the engine at
+each timestep of a dynamics run or iteration of a minimization; see
+more info below.
+
+The MD command performs a simulation using the most recent >NSTEPS
+value.  The OPTG command performs a minimization using the 4
+convergence parameters from the most recent >TOLERANCE command.  The 4
+parameters sent are those used by the :doc:`minimize <minimize>`
+command in LAMMPS: etol, ftol, maxiter, and maxeval.
+
+The mdi engine command also implements the following custom MDI
+commands which are LAMMPS-specific.  These commands are also valid at
+the @DEFAULT node defined by MDI:
+
+   * - Command name
+     - Action
+   * - >NBYTES
+     - Send # of datums in a subsequent command (1 value)
+   * - >COMMAND
+     - Send a LAMMPS input script command as a string (Nbytes in length)
+   * - >COMMANDS
+     - Send multiple LAMMPS input script commands as a newline-separated string (Nbytes in length)
+   * - >INFILE
+     - Send filename of an input script to execute (filename Nbytes in length)
+   * - <KE
+     - Request kinetic energy of the system (1 value)
+
+Note that other custom commands can easily be added if these are not
+sufficient to support what a user-written driver code needs.  Code to
+support new commands can be added to the MDI package within LAMMPS,
+specifically to the src/MDI/mdi_engine.cpp file.
+
+MDI also defines a standard mechanism for the driver to request that
+an MD engine (LAMMPS) perform a dynamics simulation one step at a time
+or an energy minimization one iteration at a time.  This is so that
+the driver can (optionally) communicate with LAMMPS at intermediate
+points of the timestep or iteration by issuing MDI node commands which
+start with "@".
+
+To tell LAMMPS to run dynamics in single-step mode, the driver sends
+as @INIT_MD command followed by the these commands.  The driver
+can interact with LAMMPS at 3 node locations within each
+timestep: @COORDS, @FORCES, @ENDSTEP:
+
+   * - Command name
+     - Action
+   * - @COORDS
+     - Proceed to next @COORDS node = post-integrate location in LAMMPS timestep
+   * - @FORCES
+     - Proceed to next @FORCES node = post-force location in LAMMPS timestep
+   * - @ENDSTEP
+     - Proceed to next @ENDSTEP node = end-of-step location in LAMMPS timestep
+   * - @DEFAULT
+     - Exit MD simulation, return to @DEFAULT node
+   * - EXIT
+     - Driver tells LAMMPS to exit the MD simulation and engine mode
+
+To tell LAMMPS to run an energy minimization in single-iteration mode.
+The driver can interact with LAMMPS at 2 node locations within each
+iteration of the minimizer: @COORDS, @FORCES:
+
+   * - Command name
+     - Action
+   * - @COORDS
+     - Proceed to next @COORDS node = min-pre-force location in LAMMPS min iteration
+   * - @FORCES
+     - Proceed to next @FORCES node = min-post-force location in LAMMPS min iteration
+   * - @DEFAULT
+     - Exit minimization, return to @DEFAULT node
+   * - EXIT
+     - Driver tells LAMMPS to exit the minimization and engine mode
+
+While LAMMPS is at its @COORDS node, the following standard MDI
+commands are supported, as documented above: >COORDS or <COORDS,
+@COORDS, @FORCES, @ENDSTEP, @DEFAULT, EXIT.
+
+While LAMMPS is at its @FORCES node, the following standard MDI
+commands are supported, as documented above: <COORDS, <ENERGY, >FORCES
+or >+FORCES or <FORCES, <KE, <PE, <STRESS, @COORDS, @FORCES, @ENDSTEP,
+@DEFAULT, EXIT.
+
+While LAMMPS is at its @ENDSTEP node, the following standard MDI
+commands are supported, as documented above: <ENERGY, <FORCES, <KE,
+<PE, <STRESS, @COORDS, @FORCES, @ENDSTEP, @DEFAULT, EXIT.
+
+----------
+
+The *mdi plugin* command is used to make LAMMPS operate as an MDI
+driver which loads an MDI engine as a plugin library.  It is typically
+used in an input script after LAMMPS has setup the system it is going
+to model consistent with the engine code.
+
+The *name* argument specifies which plugin library to load.  A name
+like "lammps" is converted to a filename liblammps.so.  The path for
+where this file is located is specified by the -plugin_path switch
+within the -mdi command-line switch, which is specified when LAMMPS is
+launched.  See the examples/mdi/README files for examples of how this
+is done.
+
+The *mdi* keyword is required and is used as the -mdi argument passed
+to the library when it is launched.  The -role and -method settings
+are required.  The -name setting can be anything you choose.  MDI
+drivers and engines can query their names to verify they are values
+they expect.
+
+The *infile* keyword is also required.  It is the name of an input
+script which the engine will open and process.  MDI will pass it as a
+command-line argument to the library when it is launched.  The file
+typically contains settings that an MD or QM code will use for its
+subsequent calculations.
+
+The *extra* keyword is optional.  It contains additional command-line
+arguments which MDI will pass to the library when it is launched.
+
+The *command* keyword is required.  It specifies a LAMMPS input script
+command (as a single argument in quotes if it is multiple words).
+Once the plugin library is launched, LAMMPS will execute this command.
+Other previously-defined commands in the input script, such as the
+:doc:`fix mdi/aimd <fix_mdi_aimd>` command, should perform MDI
+communication with the engine, while the specified *command* executes.
+Note that if *command* is an :doc:`include <include>` command, then it
+could specify a filename with multiple LAMMPS commands.
+
+.. note::
+
+   When the single *command* is complete, LAMMPS will send an MDI
+   EXIT command to the plugin engine and the plugin will be removed.
+   The "mdi plugin" command will then exit and the next command
+   (if any) in the LAMMPS input script will be processed.  A subsequent
+   "mdi plugin" command could then load the same library plugin or
+   a different one if desired.
+
+
+Restrictions
+""""""""""""
+
+This command is part of the MDI package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+To use LAMMPS in conjunction with other MDI-enabled atomistic codes,
+the :doc:`units <units>` command should be used to specify *real* or
+*metal* units.  This will ensure the correct unit conversions between
+LAMMPS and MDI units, which the other codes will also perform in their
+preferred units.
+
+LAMMPS can also be used as an MDI engine in other unit choices it
+supports, e.g. *lj*, but then no unit conversion is performed.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix mdi/aimd <fix_mdi_aimd>`
+
+Default
+"""""""
+
+None

doc/src/mdi_engine.rst

@@ -1,88 +0,0 @@
-.. index:: mdi/engine
-
-mdi_engine command
-==================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   mdi_engine
-
-Description
-"""""""""""
-
-This command is used to have LAMMPS act as a server with another
-client code to effectively couple the two codes together in
-client/server mode.
-
-More specifically, this command causes LAMMPS to begin using the `MDI
-Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
-to run as an MDI engine (server), responding to commands made by an
-external MDI driver code (client).  See the :doc:`Howto mdi
-<Howto_mdi>` page for more information about how LAMMPS can work
-as both an MDI driver or engine.
-
-General information about launching codes that communicate using the
-MDI Library can be found in the `corresponding page
-<https://molssi-mdi.github.io/MDI_Library/html/library_page.html#library_launching_sec>`_
-of the MDI Library's documentation.
-
-----------
-
-This command should typically be used in an input script after LAMMPS
-has setup the system it is going to model in collaboration with the
-driver code.  Depending on how the driver code tells the LAMMPS engine
-to exit, other commands can be executed after this command, but
-typically it should be used at the end of the LAMMPS input script.
-
-To act as a MD-based MDI engine, this is the list of MDI commands from
-a driver code which LAMMPS currently recognizes.  See more details
-about these commands in the `MDI library documentation
-<https://molssi-mdi.github.io/MDI_Library/html/mdi_standard.html>`_
-.. NOTE: Taylor - is this the best link for this info?  Can we flesh this
-.. out with the full list of supported commands?  Maybe the distinction
-.. of what "node" the commands refer to is not needed in this table?
-
-.. list-table::
-   :widths: 20 80
-   :header-rows: 1
-
-   * - Command name
-     - Action
-   * - >NATOMS
-     - Driver sends the number of atoms in the system
-   * - <NATOMS
-     - Driver requests the number of atoms in the system
-   * - <COORDS
-     - Driver requests 3*N double-precision atom coordinates
-   * - >FORCES
-     - Driver sends 3*N double-precision atom forces
-   * - <COORDS
-     - Driver requests 3*N double-precision atom forces
-   * - EXIT
-     - Driver tells the engine (LAMMPS) to exit engine mode
-
-If these commands are not sufficient to support what a driver which
-you write needs, additional commands can be defined by simply using a
-new command name not in this list.  Code to support the new command
-needs to be added to the MDI package within LAMMPS; see its
-src/MDI/mdi_engine.cpp and fix_mdi_engine.cpp files.
-
-Restrictions
-""""""""""""
-
-This command is part of the MDI package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package
-<Build_package>` page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`fix mdi/engine <fix_mdi_engine>`
-
-Default
-"""""""
-
-None

doc/src/package.rst

@@ -467,14 +467,14 @@ simple pairwise potentials such as Lennard-Jones do support threading
 over both atoms and neighbors.
 
 If the *neigh/transpose* keyword is set to *off*, then the KOKKOS
-package will use the same memory layout for building the neigh list on
+package will use the same memory layout for building the neighbor list on
 GPUs as used for the pair style. When this keyword is set to *on* it
-will use a different (transposed) memory layout to build the neigh
+will use a different (transposed) memory layout to build the neighbor
 list on GPUs. This can be faster in some cases (e.g. ReaxFF HNS
 benchmark) but slower in others (e.g. Lennard Jones benchmark). The
 copy between different memory layouts is done out of place and
-therefore doubles the memory overhead of the neigh list, which can be
+therefore doubles the memory overhead of the neighbor list, which can
-signicant.
+be significant.
 
 The *newton* keyword sets the Newton flags for pairwise and bonded
 interactions to *off* or *on*, the same as the :doc:`newton <newton>`
@@ -484,11 +484,12 @@ computation is done, but less communication. However, when running on
 CPUs a value of *on* is the default since it can often be faster, just
 as it is for non-accelerated pair styles
 
-The *binsize* keyword sets the size of bins used to bin atoms in
+The *binsize* keyword sets the size of bins used to bin atoms during
-neighbor list builds. The same value can be set by the :doc:`neigh_modify binsize <neigh_modify>` command. Making it an option in the package
+ neighbor list builds. The same value can be set by the
-kokkos command allows it to be set from the command line. The default
+:doc:`neigh_modify binsize <neigh_modify>` command. Making it an option
-value for CPUs is 0.0, which means the LAMMPS default will be used,
+in the package kokkos command allows it to be set from the command line.
-which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
+The default value for CPUs is 0.0, which means the LAMMPS default will be
+used, which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
 distance. This is fine when neighbor lists are built on the CPU. For GPU
 builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
 is often faster, which is the default. Note that if you use a

doc/src/pair_dpd.rst

@@ -1,20 +1,22 @@
 .. index:: pair_style dpd
 .. index:: pair_style dpd/gpu
 .. index:: pair_style dpd/intel
+.. index:: pair_style dpd/kk
 .. index:: pair_style dpd/omp
 .. index:: pair_style dpd/tstat
 .. index:: pair_style dpd/tstat/gpu
+.. index:: pair_style dpd/tstat/kk
 .. index:: pair_style dpd/tstat/omp
 
 pair_style dpd command
 ======================
 
-Accelerator Variants: *dpd/gpu*, *dpd/intel*, *dpd/omp*
+Accelerator Variants: *dpd/gpu*, *dpd/intel*, *dpd/kk*, *dpd/omp*
 
 pair_style dpd/tstat command
 ============================
 
-Accelerator Variants: *dpd/tstat/gpu*, *dpd/tstat/omp*
+Accelerator Variants: *dpd/tstat/gpu*, *dpd/tstat/kk*, *dpd/tstat/omp*
 
 Syntax
 """"""

doc/src/pair_dpd_ext.rst

@@ -1,12 +1,18 @@
 .. index:: pair_style dpd/ext
+.. index:: pair_style dpd/ext/kk
 .. index:: pair_style dpd/ext/tstat
+.. index:: pair_style dpd/ext/tstat/kk
 
 pair_style dpd/ext command
 ==========================
 
+Accelerator Variants: dpd/ext/kk
+
 pair_style dpd/ext/tstat command
 ================================
 
+Accelerator Variants: dpd/ext/tstat/kk
+
 Syntax
 """"""
 
@@ -137,6 +143,10 @@ except that A is not included.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 
 **Mixing, shift, table, tail correction, restart, rRESPA info**\ :
 

doc/src/plugin.rst

@@ -70,12 +70,11 @@ Restrictions
 """"""""""""
 
 The *plugin* command is part of the PLUGIN package.  It is
-only enabled if LAMMPS was built with that package.
+only enabled if LAMMPS was built with that package.  See
-See the :doc:`Build package <Build_package>` page for
+the :doc:`Build package <Build_package>` page for more info.
-more info. Plugins are not available on Windows.
 
-If plugins access functions or classes from a package, LAMMPS must
+If plugins access functions or classes from a package,
-have been compiled with that package included.
+LAMMPS must have been compiled with that package included.
 
 Plugins are dependent on the LAMMPS binary interface (ABI)
 and particularly the MPI library used. So they are not guaranteed

doc/src/thermo_modify.rst

@@ -21,9 +21,14 @@ Syntax
        *norm* value = *yes* or *no*
        *flush* value = *yes* or *no*
        *line* value = *one* or *multi* or *yaml*
-       *format* values = *line* string, *int* string, *float* string, M string, or *none*
+       *colname* values =  ID string, or *default*
+         string = new column header name
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a thermo keyword or reference to compute, fix, property or variable.
+       *format* values = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
-         M = integer from 1 to N, where N = # of quantities being output
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a thermo keyword or reference to compute, fix, property or variable.
        *temp* value = compute ID that calculates a temperature
        *press* value = compute ID that calculates a pressure
 
@@ -36,7 +41,8 @@ Examples
    thermo_modify temp myTemp format 3 %15.8g
    thermo_modify temp myTemp format line "%ld %g %g %15.8g"
    thermo_modify line multi format float %g
-   themos_modify line yaml format none
+   thermo_modify line yaml format none
+   thermo_modify colname 1 Timestep colname -2 Pressure colname f_1[1] AvgDensity
 
 Description
 """""""""""
@@ -147,6 +153,20 @@ containing the timestep and CPU time ("multi"), or in a YAML format
 block ("yaml").  This modify option overrides the *one*, *multi*, or
 *yaml* thermo_style settings.
 
+The *colname* keyword can be used to change the default header keyword
+for a column or field of thermodynamic output.  The setting for *ID
+string* replaces the default text with the provided string.  *ID* can be
+a positive integer when it represents the column number counting from
+the left, a negative integer when it represents the column number from
+the right (i.e. -1 is the last column/keyword), or a thermo keyword (or
+compute, fix, property, or variable reference) and then it replaces the
+string for that specific thermo keyword.
+
+The *colname* keyword can be used multiple times. If multiple *colname*
+settings refer to the same keyword, the last setting has precedence.  A
+setting of *default* clears all previous settings, reverting all values
+to their default values.
+
 The *format* keyword can be used to change the default numeric format of
 any of quantities the :doc:`thermo_style <thermo_style>` command
 outputs.  All the specified format strings are C-style formats, e.g. as
@@ -155,12 +175,16 @@ argument which is the format string for the entire line of thermo
 output, with N fields, which you must enclose in quotes if it is more
 than one field.  The *int* and *float* keywords take a single format
 argument and are applied to all integer or floating-point quantities
-output.  The setting for *M string* also takes a single format argument
+output.  The setting for *ID string* also takes a single format argument
-which is used for the Mth value output in each line, e.g. the fifth
+which is used for the indexed value in each line.  The interpretation is
-column is output in high precision for "format 5 %20.15g".
+the same as for *colname*, i.e. a positive integer is the n-th value
+corresponding to the n-th thermo keyword, a negative integer is counting
+backwards, and a string matches the entry with the thermo keyword.,
+e.g. the fifth column is output in high precision for "format 5 %20.15g"
+and the pair energy for "format epair %20.15g".
 
 The *format* keyword can be used multiple times.  The precedence is
-that for each value in a line of output, the *M* format (if specified)
+that for each value in a line of output, the *ID* format (if specified)
 is used, else the *int* or *float* setting (if specified) is used,
 else the *line* setting (if specified) for that value is used, else
 the default setting is used.  A setting of *none* clears all previous
@@ -173,9 +197,10 @@ settings, reverting all values to their default format.
    When specifying the *format int* option you can use a "%d"-style
    format identifier in the format string and LAMMPS will convert this
    to the corresponding 8-byte form when it is applied to those
-   keywords.  However, when specifying the *line* option or *format M
+   keywords.  However, when specifying the *line* option or *format ID
    string* option for *step* and *natoms*, you should specify a format
-   string appropriate for an 8-byte signed integer, e.g. one with "%ld".
+   string appropriate for an 8-byte signed integer, e.g. one with "%ld"
+   or "%lld" depending on the platform.
 
 The *temp* keyword is used to determine how thermodynamic temperature is
 calculated, which is used by all thermo quantities that require a

doc/utils/sphinx-config/false_positives.txt

@@ -1180,6 +1180,7 @@ Gladky
 gld
 gle
 globbing
+Gloor
 Glosli
 Glotzer
 gmail
@@ -1417,6 +1418,7 @@ initializations
 InitiatorIDs
 initio
 InP
+inq
 inregion
 instantiation
 Institut
@@ -1428,6 +1430,7 @@ interal
 interatomic
 Interatomic
 interconvert
+interfacial
 interial
 interlayer
 intermolecular
@@ -1738,6 +1741,7 @@ libdl
 libfftw
 libgcc
 libgpu
+libinqmdi
 libjpeg
 libkim
 liblammps
@@ -1752,6 +1756,7 @@ libplumed
 libplumedKernel
 libpng
 libpoems
+libqemdi
 libqmmm
 librar
 libreax
@@ -1787,6 +1792,7 @@ Liu
 Livermore
 lj
 llammps
+lld
 LLVM
 lm
 lmp
@@ -2205,6 +2211,7 @@ Nbondtypes
 nBOt
 nbrhood
 Nbtypes
+Nbytes
 nc
 Nc
 nchunk
@@ -3649,6 +3656,7 @@ Wittmaack
 wn
 Wolde
 workflow
+workflows
 Worley
 Wriggers
 Wuppertal

examples/PACKAGES/dpd-basic/README

@@ -1,10 +1,16 @@
-Examples for Extended Dissipative Particle Dynamics (DPD)
+Examples for Basic Dissipative Particle Dynamics (DPD)
----------------------------------------------------------
+------------------------------------------------------
-This directory contains examples for extended DPD simulations
+This directory contains examples for DPD simulations using
+pair styles from the DPD-BASIC package.
 
-1)  'dpdext' - test case (DPD fluid) for 'dpdext' pair style (in.dpdext) and an initial 
+1)  'dpd' - simple example (DPD fluid) for 'dpd' pair style (in.dpd)
-    configuration (dpdext.data)
 
-2)  'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style 
+2)  'dpd_tstat' - coarse-grained SPC/E water example for 'dpd/tstat' pair style
-    (in.cg_spce), an initial configuration (dpdext.data) and tabulated potential 
+    (in.dpd_tstat), an initial configuration (dpdext.data) and tabulated potential
+    (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
+
+3)  'dpdext' - simple example (DPD fluid) for 'dpd/ext' pair style (in.dpdext)
+
+4)  'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
+    (in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
     (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.

examples/PACKAGES/dpd-basic/dpd/in.dpd

@@ -0,0 +1,43 @@
+# DPD Fluid
+
+variable T    equal 1.0
+variable rc   equal 1.0
+variable rcD  equal 1.2
+
+units        lj
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+### create box and configuration
+variable     L equal 5.0
+lattice      fcc 3.0
+region       simBox block 0 ${L} 0 ${L} 0 ${L}
+create_box   2 simBox
+#create_atoms 1 region simBox
+create_atoms 1 random 100 12456 simBox
+create_atoms 2 random 100 13245 simBox
+mass         1 1.0
+mass         2 2.0
+###
+
+pair_style       dpd ${T} ${rc} 3854262
+
+pair_coeff   1 1 25.0 4.5  1.2
+pair_coeff   1 2 25.1 4.51 1.21
+pair_coeff   2 2 25.2 4.52 1.22
+
+timestep     0.01
+run_style    verlet
+
+velocity all create ${T} 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          5000
+

examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1

@@ -0,0 +1,154 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Fluid
+
+variable T    equal 1.0
+variable rc   equal 1.0
+variable rcD  equal 1.2
+
+units        lj
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+### create box and configuration
+variable     L equal 5.0
+lattice      fcc 3.0
+Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
+region       simBox block 0 ${L} 0 ${L} 0 ${L}
+region       simBox block 0 5 0 ${L} 0 ${L}
+region       simBox block 0 5 0 5 0 ${L}
+region       simBox block 0 5 0 5 0 5
+create_box   2 simBox
+Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  1 by 1 by 1 MPI processor grid
+#create_atoms 1 region simBox
+create_atoms 1 random 100 12456 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+create_atoms 2 random 100 13245 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+mass         1 1.0
+mass         2 2.0
+###
+
+pair_style       dpd ${T} ${rc} 3854262
+pair_style       dpd 1 ${rc} 3854262
+pair_style       dpd 1 1 3854262
+
+pair_coeff   1 1 25.0 4.5  1.2
+pair_coeff   1 2 25.1 4.51 1.21
+pair_coeff   2 2 25.2 4.52 1.22
+
+timestep     0.01
+run_style    verlet
+
+velocity all create ${T} 68768932
+velocity all create 1 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          5000
+  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 = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes
+   Step          Time           Temp          Press     
+         0   0              1              9.5226009    
+       100   1              1.9913643      9.2036029    
+       200   2              1.6321732      9.2787957    
+       300   3              1.3533438      8.3081433    
+       400   4              1.2125884      8.0809065    
+       500   5              1.0682216      8.0877925    
+       600   6              0.99100473     8.1100319    
+       700   7              0.99731243     7.8225195    
+       800   8              1.0597693      7.8368218    
+       900   9              0.99038588     7.9450569    
+      1000   10             1.077129       7.5857015    
+      1100   11             0.99070336     7.5138128    
+      1200   12             1.013894       7.2794857    
+      1300   13             1.0433203      7.7439871    
+      1400   14             1.0285528      7.5662235    
+      1500   15             0.99180601     7.8376313    
+      1600   16             0.98059071     8.0243735    
+      1700   17             1.0070947      8.3186893    
+      1800   18             0.99507569     7.0786393    
+      1900   19             1.0040168      7.8120389    
+      2000   20             0.98636164     7.472185     
+      2100   21             0.95811165     7.7085985    
+      2200   22             0.93568327     6.9424246    
+      2300   23             0.92804144     8.1239435    
+      2400   24             0.94940276     7.6108611    
+      2500   25             1.0535153      8.0772721    
+      2600   26             1.0902144      7.5609768    
+      2700   27             1.0737336      7.8706755    
+      2800   28             0.93074581     7.3699993    
+      2900   29             1.0440705      7.6454988    
+      3000   30             0.93868164     7.841168     
+      3100   31             1.0172025      7.6856163    
+      3200   32             1.0405368      7.5325735    
+      3300   33             0.96721201     7.8262809    
+      3400   34             0.90430758     7.1693921    
+      3500   35             0.89938433     7.865845     
+      3600   36             0.9907178      7.3462971    
+      3700   37             1.0311879      7.8876401    
+      3800   38             0.98339132     7.3413929    
+      3900   39             1.2111264      8.0968408    
+      4000   40             1.062489       7.7315959    
+      4100   41             0.94737492     7.3386028    
+      4200   42             1.0453816      8.2017304    
+      4300   43             0.97024897     7.7379624    
+      4400   44             0.9553861      7.8047635    
+      4500   45             1.043252       7.7486215    
+      4600   46             0.98611474     8.1237053    
+      4700   47             0.98624285     8.5801642    
+      4800   48             0.97176754     7.1540299    
+      4900   49             1.0165401      7.3853841    
+      5000   50             0.88359115     7.5541592    
+Loop time of 0.359916 on 1 procs for 5000 steps with 200 atoms
+
+Performance: 12002788.048 tau/day, 13892.116 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24932    | 0.24932    | 0.24932    |   0.0 | 69.27
+Neigh   | 0.068726   | 0.068726   | 0.068726   |   0.0 | 19.10
+Comm    | 0.028691   | 0.028691   | 0.028691   |   0.0 |  7.97
+Output  | 0.00066318 | 0.00066318 | 0.00066318 |   0.0 |  0.18
+Modify  | 0.0078062  | 0.0078062  | 0.0078062  |   0.0 |  2.17
+Other   |            | 0.004713   |            |       |  1.31
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            546 ave         546 max         546 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1649 ave        1649 max        1649 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1649
+Ave neighs/atom = 8.245
+Neighbor list builds = 500
+Dangerous builds = 500
+
+Total wall time: 0:00:00

examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4

@@ -0,0 +1,154 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Fluid
+
+variable T    equal 1.0
+variable rc   equal 1.0
+variable rcD  equal 1.2
+
+units        lj
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+### create box and configuration
+variable     L equal 5.0
+lattice      fcc 3.0
+Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
+region       simBox block 0 ${L} 0 ${L} 0 ${L}
+region       simBox block 0 5 0 ${L} 0 ${L}
+region       simBox block 0 5 0 5 0 ${L}
+region       simBox block 0 5 0 5 0 5
+create_box   2 simBox
+Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  1 by 2 by 2 MPI processor grid
+#create_atoms 1 region simBox
+create_atoms 1 random 100 12456 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+create_atoms 2 random 100 13245 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+mass         1 1.0
+mass         2 2.0
+###
+
+pair_style       dpd ${T} ${rc} 3854262
+pair_style       dpd 1 ${rc} 3854262
+pair_style       dpd 1 1 3854262
+
+pair_coeff   1 1 25.0 4.5  1.2
+pair_coeff   1 2 25.1 4.51 1.21
+pair_coeff   2 2 25.2 4.52 1.22
+
+timestep     0.01
+run_style    verlet
+
+velocity all create ${T} 68768932
+velocity all create 1 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          5000
+  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 = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes
+   Step          Time           Temp          Press     
+         0   0              1              8.603339     
+       100   1              1.8691059      8.9058297    
+       200   2              1.4500635      8.7420141    
+       300   3              1.3089453      8.3985981    
+       400   4              1.1647803      8.2948808    
+       500   5              1.1399445      7.7421817    
+       600   6              1.0297918      7.2040397    
+       700   7              1.046713       7.6115758    
+       800   8              0.93523712     7.6885563    
+       900   9              0.94701493     7.9662712    
+      1000   10             0.99302416     7.7606189    
+      1100   11             0.98975674     7.5207427    
+      1200   12             0.98661662     7.3565222    
+      1300   13             1.0289377      7.6110453    
+      1400   14             0.9982501      7.8065701    
+      1500   15             1.0043888      7.3957185    
+      1600   16             1.0175816      7.7885955    
+      1700   17             1.0252117      7.5076258    
+      1800   18             1.0275139      8.1052823    
+      1900   19             1.0021054      7.0385989    
+      2000   20             1.0489009      7.7138149    
+      2100   21             0.91250488     7.3540839    
+      2200   22             0.92470996     7.9600233    
+      2300   23             0.96932725     7.3106045    
+      2400   24             0.93443088     7.4594635    
+      2500   25             0.95596038     7.2544715    
+      2600   26             1.0368594      7.6229263    
+      2700   27             0.94639332     7.4869636    
+      2800   28             0.99917354     7.9806636    
+      2900   29             0.95048071     7.0086404    
+      3000   30             0.95226181     7.7807205    
+      3100   31             0.95864429     7.8059442    
+      3200   32             0.85678761     7.3416027    
+      3300   33             0.95951096     7.3467158    
+      3400   34             0.97665772     8.2900991    
+      3500   35             0.92885927     7.5385993    
+      3600   36             1.0455015      8.0627999    
+      3700   37             0.91911809     8.0371736    
+      3800   38             0.92022241     7.5803999    
+      3900   39             1.0465522      7.6920189    
+      4000   40             0.98568475     7.4529825    
+      4100   41             1.0389372      7.2273346    
+      4200   42             1.0257545      7.6081878    
+      4300   43             1.0937573      8.2158237    
+      4400   44             1.0908817      7.5021567    
+      4500   45             1.0482874      7.5924368    
+      4600   46             1.1468439      8.0285157    
+      4700   47             1.119683       8.3365123    
+      4800   48             1.0963877      7.51772      
+      4900   49             1.0766762      7.3137035    
+      5000   50             1.0359203      7.7354572    
+Loop time of 0.148597 on 4 procs for 5000 steps with 200 atoms
+
+Performance: 29071936.422 tau/day, 33648.075 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.059602   | 0.063397   | 0.068622   |   1.3 | 42.66
+Neigh   | 0.017747   | 0.018193   | 0.018698   |   0.3 | 12.24
+Comm    | 0.055145   | 0.061014   | 0.065369   |   1.5 | 41.06
+Output  | 0.00042708 | 0.00050725 | 0.00071024 |   0.0 |  0.34
+Modify  | 0.0023494  | 0.002532   | 0.0026434  |   0.2 |  1.70
+Other   |            | 0.002953   |            |       |  1.99
+
+Nlocal:             50 ave          52 max          48 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:         292.75 ave         299 max         287 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:          413.5 ave         441 max         399 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 1654
+Ave neighs/atom = 8.27
+Neighbor list builds = 500
+Dangerous builds = 500
+
+Total wall time: 0:00:00

examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce.data

@@ -1,4 +1,4 @@
- DPD Fluid
+ Coarse-Grained SPC/E Water
  
         2180 atoms
  

examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot

@@ -0,0 +1,354 @@
+VOTCA				
+N	351	R	2.0	9.0
+				
+1	2.000000E+00	2.190202E+01	7.229762E+01	
+2	2.020000E+00	2.048957E+01	6.887333E+01	
+3	2.040000E+00	1.915004E+01	6.500604E+01	
+4	2.060000E+00	1.789228E+01	6.069573E+01	
+5	2.080000E+00	1.672516E+01	5.594242E+01	
+6	2.100000E+00	1.565754E+01	5.074609E+01	
+7	2.120000E+00	1.467088E+01	4.787307E+01	
+8	2.140000E+00	1.374450E+01	4.471740E+01	
+9	2.160000E+00	1.288407E+01	4.127908E+01	
+10	2.180000E+00	1.209522E+01	3.755811E+01	
+11	2.200000E+00	1.138363E+01	3.355449E+01	
+12	2.220000E+00	1.072913E+01	3.188695E+01	
+13	2.240000E+00	1.010845E+01	3.017359E+01	
+14	2.260000E+00	9.522496E+00	2.841440E+01	
+15	2.280000E+00	8.972182E+00	2.660938E+01	
+16	2.300000E+00	8.458426E+00	2.475854E+01	
+17	2.320000E+00	8.014166E+00	2.006698E+01	
+18	2.340000E+00	7.639767E+00	1.777244E+01	
+19	2.360000E+00	7.287288E+00	1.787493E+01	
+20	2.380000E+00	6.908790E+00	2.037445E+01	
+21	2.400000E+00	6.456330E+00	2.527099E+01	
+22	2.420000E+00	5.858025E+00	3.384695E+01	
+23	2.440000E+00	5.130955E+00	3.814748E+01	
+24	2.460000E+00	4.360629E+00	3.817257E+01	
+25	2.480000E+00	3.632555E+00	3.392224E+01	
+26	2.500000E+00	3.032242E+00	2.539647E+01	
+27	2.520000E+00	2.547993E+00	2.297813E+01	
+28	2.540000E+00	2.115131E+00	2.025763E+01	
+29	2.560000E+00	1.739702E+00	1.723497E+01	
+30	2.580000E+00	1.427747E+00	1.391013E+01	
+31	2.600000E+00	1.185311E+00	1.028314E+01	
+32	2.620000E+00	9.860176E-01	9.578245E+00	
+33	2.640000E+00	8.048986E-01	8.465708E+00	
+34	2.660000E+00	6.501069E-01	6.945526E+00	
+35	2.680000E+00	5.297952E-01	5.017699E+00	
+36	2.700000E+00	4.521166E-01	2.682227E+00	
+37	2.720000E+00	3.986447E-01	2.615311E+00	
+38	2.740000E+00	3.494900E-01	2.250522E+00	
+39	2.760000E+00	3.106097E-01	1.587859E+00	
+40	2.780000E+00	2.879614E-01	6.273237E-01	
+41	2.800000E+00	2.875026E-01	-6.310851E-01	
+42	2.820000E+00	3.002733E-01	-6.543549E-01	
+43	2.840000E+00	3.140112E-01	-7.277911E-01	
+44	2.860000E+00	3.297194E-01	-8.513935E-01	
+45	2.880000E+00	3.484014E-01	-1.025162E+00	
+46	2.900000E+00	3.710604E-01	-1.249097E+00	
+47	2.920000E+00	3.974884E-01	-1.380483E+00	
+48	2.940000E+00	4.257507E-01	-1.432530E+00	
+49	2.960000E+00	4.542607E-01	-1.405240E+00	
+50	2.980000E+00	4.814314E-01	-1.298611E+00	
+51	3.000000E+00	5.056762E-01	-1.112645E+00	
+52	3.020000E+00	5.266502E-01	-9.832894E-01	
+53	3.040000E+00	5.449492E-01	-8.451544E-01	
+54	3.060000E+00	5.603978E-01	-6.982396E-01	
+55	3.080000E+00	5.728203E-01	-5.425450E-01	
+56	3.100000E+00	5.820411E-01	-3.780706E-01	
+57	3.120000E+00	5.882509E-01	-2.409307E-01	
+58	3.140000E+00	5.915991E-01	-9.190908E-02	
+59	3.160000E+00	5.918481E-01	6.899430E-02	
+60	3.180000E+00	5.887601E-01	2.417794E-01	
+61	3.200000E+00	5.820977E-01	4.264463E-01	
+62	3.220000E+00	5.733491E-01	4.528343E-01	
+63	3.240000E+00	5.638075E-01	5.057356E-01	
+64	3.260000E+00	5.529429E-01	5.851503E-01	
+65	3.280000E+00	5.402248E-01	6.910784E-01	
+66	3.300000E+00	5.251230E-01	8.235199E-01	
+67	3.320000E+00	5.086524E-01	8.236482E-01	
+68	3.340000E+00	4.921725E-01	8.244583E-01	
+69	3.360000E+00	4.756696E-01	8.259503E-01	
+70	3.380000E+00	4.591299E-01	8.281240E-01	
+71	3.400000E+00	4.425400E-01	8.309796E-01	
+72	3.420000E+00	4.259181E-01	8.311861E-01	
+73	3.440000E+00	4.092937E-01	8.312292E-01	
+74	3.460000E+00	3.926700E-01	8.311089E-01	
+75	3.480000E+00	3.760504E-01	8.308252E-01	
+76	3.500000E+00	3.594381E-01	8.303781E-01	
+77	3.520000E+00	3.428394E-01	8.295412E-01	
+78	3.540000E+00	3.262547E-01	8.289646E-01	
+79	3.560000E+00	3.096790E-01	8.286483E-01	
+80	3.580000E+00	2.931071E-01	8.285923E-01	
+81	3.600000E+00	2.765336E-01	8.287966E-01	
+82	3.620000E+00	2.599901E-01	8.254306E-01	
+83	3.640000E+00	2.435212E-01	8.213359E-01	
+84	3.660000E+00	2.271415E-01	8.165124E-01	
+85	3.680000E+00	2.108656E-01	8.109603E-01	
+86	3.700000E+00	1.947080E-01	8.046794E-01	
+87	3.720000E+00	1.790243E-01	7.653050E-01	
+88	3.740000E+00	1.640312E-01	7.356166E-01	
+89	3.760000E+00	1.495351E-01	7.156143E-01	
+90	3.780000E+00	1.353421E-01	7.052980E-01	
+91	3.800000E+00	1.212586E-01	7.046676E-01	
+92	3.820000E+00	1.072429E-01	6.965706E-01	
+93	3.840000E+00	9.340878E-02	6.865180E-01	
+94	3.860000E+00	7.979524E-02	6.745098E-01	
+95	3.880000E+00	6.644142E-02	6.605462E-01	
+96	3.900000E+00	5.338643E-02	6.446270E-01	
+97	3.920000E+00	4.067486E-02	6.268536E-01	
+98	3.940000E+00	2.829935E-02	6.110218E-01	
+99	3.960000E+00	1.622105E-02	5.971317E-01	
+100	3.980000E+00	4.401131E-03	5.851833E-01	
+101	4.000000E+00	-7.199230E-03	5.751764E-01	
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examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat

@@ -0,0 +1,31 @@
+# Coarse-Grained SPC/E Water
+
+variable T   equal 300.0
+variable rc  equal   9.0
+variable rcD equal  10.0
+
+units            real
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+read_data    cg_spce.data
+
+pair_style       hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
+
+pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
+pair_coeff   1 1 dpd/tstat 10.0 ${rcD}
+
+timestep    1.0
+run_style   verlet
+
+velocity all create ${T} 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          1000

examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.1

@@ -0,0 +1,106 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Coarse-Grained SPC/E Water
+
+variable T   equal 300.0
+variable rc  equal   9.0
+variable rcD equal  10.0
+
+units            real
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+read_data    cg_spce.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (40.31 40.31 40.31)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2180 atoms
+  read_data CPU = 0.003 seconds
+
+pair_style       hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
+
+pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
+pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
+WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+pair_coeff   1 1 dpd/tstat 10.0 ${rcD}
+pair_coeff   1 1 dpd/tstat 10.0 10
+
+timestep    1.0
+run_style   verlet
+
+velocity all create ${T} 68768932
+velocity all create 300 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          1000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair dpd/tstat, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
+   Step          Time           Temp          Press     
+         0   0              300            7459.7935    
+       100   100            309.27219      6997.2438    
+       200   200            311.23318      9940.3922    
+       300   300            300.14145      7970.3486    
+       400   400            293.17924      8390.7272    
+       500   500            285.9647       7304.1147    
+       600   600            291.15512      6605.1675    
+       700   700            294.54557      7708.3815    
+       800   800            288.72442      8641.2675    
+       900   900            294.83288      7145.1684    
+      1000   1000           291.12446      8525.4556    
+Loop time of 10.1894 on 1 procs for 1000 steps with 2180 atoms
+
+Performance: 8.479 ns/day, 2.830 hours/ns, 98.141 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 10.02      | 10.02      | 10.02      |   0.0 | 98.34
+Neigh   | 0.087623   | 0.087623   | 0.087623   |   0.0 |  0.86
+Comm    | 0.055526   | 0.055526   | 0.055526   |   0.0 |  0.54
+Output  | 0.00026505 | 0.00026505 | 0.00026505 |   0.0 |  0.00
+Modify  | 0.013958   | 0.013958   | 0.013958   |   0.0 |  0.14
+Other   |            | 0.01163    |            |       |  0.11
+
+Nlocal:           2180 ave        2180 max        2180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           6741 ave        6741 max        6741 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         261567 ave      261567 max      261567 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 261567
+Ave neighs/atom = 119.98486
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.4

@@ -0,0 +1,106 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Coarse-Grained SPC/E Water
+
+variable T   equal 300.0
+variable rc  equal   9.0
+variable rcD equal  10.0
+
+units            real
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+read_data    cg_spce.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (40.31 40.31 40.31)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2180 atoms
+  read_data CPU = 0.003 seconds
+
+pair_style       hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
+
+pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
+pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
+WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+pair_coeff   1 1 dpd/tstat 10.0 ${rcD}
+pair_coeff   1 1 dpd/tstat 10.0 10
+
+timestep    1.0
+run_style   verlet
+
+velocity all create ${T} 68768932
+velocity all create 300 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          1000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair dpd/tstat, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
+   Step          Time           Temp          Press     
+         0   0              300            7929.9249    
+       100   100            305.51763      8531.8105    
+       200   200            304.43334      8697.989     
+       300   300            292.42805      6865.4712    
+       400   400            300.66447      7606.6995    
+       500   500            298.43456      8713.2403    
+       600   600            298.10981      6913.5475    
+       700   700            297.39737      9121.8642    
+       800   800            298.23888      7833.1307    
+       900   900            293.91793      8423.8417    
+      1000   1000           299.65933      7974.9976    
+Loop time of 2.82436 on 4 procs for 1000 steps with 2180 atoms
+
+Performance: 30.591 ns/day, 0.785 hours/ns, 354.062 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.6238     | 2.644      | 2.6909     |   1.7 | 93.61
+Neigh   | 0.021524   | 0.021958   | 0.022778   |   0.3 |  0.78
+Comm    | 0.10035    | 0.1479     | 0.16842    |   7.2 |  5.24
+Output  | 0.00019058 | 0.00021173 | 0.00026852 |   0.0 |  0.01
+Modify  | 0.0041395  | 0.0041846  | 0.0042798  |   0.1 |  0.15
+Other   |            | 0.006091   |            |       |  0.22
+
+Nlocal:            545 ave         559 max         536 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:         3613.5 ave        3634 max        3604 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Neighs:          65402 ave       68101 max       63621 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 261608
+Ave neighs/atom = 120.00367
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/PACKAGES/dpd-basic/dpdext/in.dpdext

@@ -4,9 +4,9 @@ variable T    equal 1.0
 variable rc   equal 1.0
 variable rcD  equal 1.2
 
-units		 lj
+units            lj
 boundary     p p p
-atom_style	 atomic
+atom_style       atomic
 dimension    3
 newton       on
 comm_modify  vel yes
@@ -16,29 +16,27 @@ variable     L equal 5.0
 lattice      fcc 3.0
 region       simBox block 0 ${L} 0 ${L} 0 ${L}
 create_box   2 simBox
-#create_atoms 1 region simBox
+create_atoms 1 random 100 12456 simBox
-create_atoms 1 random 100 132456 simBox
+create_atoms 2 random 100 13245 simBox
-create_atoms 2 random 100 132456 simBox
 mass         1 1.0
 mass         2 2.0
 ###
 
-pair_style	 dpd/ext ${T} ${rc} 3854262
+pair_style       dpd/ext ${T} ${rc} 3854262
 
 pair_coeff   1 1 25.0 4.5 4.53 0.5 0.53   1.2 #${rcD}
 pair_coeff   1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
 pair_coeff   2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
 
-timestep     0.01 
+timestep     0.01
 run_style    verlet
 
 velocity all create ${T} 68768932
 
 thermo_style custom step time temp press
-thermo       500
+thermo       100
 
 fix 1 all    nve
 
-run	     50000
+run          5000
 
-write_data final.data pair ij

examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.1

@@ -0,0 +1,153 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Fluid
+
+variable T    equal 1.0
+variable rc   equal 1.0
+variable rcD  equal 1.2
+
+units            lj
+boundary     p p p
+atom_style       atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+### create box and configuration
+variable     L equal 5.0
+lattice      fcc 3.0
+Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
+region       simBox block 0 ${L} 0 ${L} 0 ${L}
+region       simBox block 0 5 0 ${L} 0 ${L}
+region       simBox block 0 5 0 5 0 ${L}
+region       simBox block 0 5 0 5 0 5
+create_box   2 simBox
+Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  1 by 1 by 1 MPI processor grid
+create_atoms 1 random 100 12456 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+create_atoms 2 random 100 13245 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+mass         1 1.0
+mass         2 2.0
+###
+
+pair_style       dpd/ext ${T} ${rc} 3854262
+pair_style       dpd/ext 1 ${rc} 3854262
+pair_style       dpd/ext 1 1 3854262
+
+pair_coeff   1 1 25.0 4.5 4.53 0.5 0.53   1.2 #${rcD}
+pair_coeff   1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
+pair_coeff   2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
+
+timestep     0.01
+run_style    verlet
+
+velocity all create ${T} 68768932
+velocity all create 1 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          5000
+  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 = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/ext, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes
+   Step          Time           Temp          Press     
+         0   0              1              10.864186    
+       100   1              1.1314376      7.1955963    
+       200   2              1.0058948      8.4574538    
+       300   3              0.93292241     7.7033353    
+       400   4              0.93599378     7.9649888    
+       500   5              1.0390423      7.9498546    
+       600   6              1.0750333      7.3594973    
+       700   7              1.119325       7.1843859    
+       800   8              0.96727219     6.8327896    
+       900   9              0.98826001     8.1974994    
+      1000   10             1.105819       7.8830702    
+      1100   11             0.99559202     7.8295372    
+      1200   12             0.9210428      8.2045593    
+      1300   13             0.96628584     8.6531905    
+      1400   14             1.1808689      7.7659964    
+      1500   15             0.96208743     7.9977415    
+      1600   16             1.0080123      7.6254557    
+      1700   17             0.96910957     8.3643075    
+      1800   18             1.0562621      7.5966268    
+      1900   19             0.93109173     7.7944606    
+      2000   20             1.1126085      9.3753501    
+      2100   21             1.1328553      7.6293793    
+      2200   22             0.8964042      7.5985061    
+      2300   23             1.0043044      8.0016943    
+      2400   24             1.0319521      8.1249684    
+      2500   25             0.95913468     7.2383318    
+      2600   26             0.99480311     7.6491295    
+      2700   27             0.9735191      7.5004628    
+      2800   28             0.96145308     8.222045     
+      2900   29             1.0131071      6.6390842    
+      3000   30             0.99463836     7.0147693    
+      3100   31             0.96803993     8.2738796    
+      3200   32             0.94066026     9.476403     
+      3300   33             0.97401823     6.409563     
+      3400   34             1.0548493      7.7301555    
+      3500   35             0.98567796     8.2949868    
+      3600   36             0.86621746     7.4759028    
+      3700   37             0.94934175     8.1189998    
+      3800   38             0.9626774      7.7986715    
+      3900   39             0.95728518     6.8669836    
+      4000   40             1.0866412      7.41281      
+      4100   41             0.98873564     6.4612262    
+      4200   42             0.9109925      7.1806331    
+      4300   43             1.0344723      8.4617679    
+      4400   44             0.98920584     7.3622901    
+      4500   45             0.99386139     6.8002442    
+      4600   46             1.0947487      6.8868352    
+      4700   47             0.98789482     7.8428621    
+      4800   48             1.0035907      8.3878628    
+      4900   49             1.0336467      8.1592349    
+      5000   50             1.0870964      8.217988     
+Loop time of 0.907286 on 1 procs for 5000 steps with 200 atoms
+
+Performance: 4761453.941 tau/day, 5510.942 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.79672    | 0.79672    | 0.79672    |   0.0 | 87.81
+Neigh   | 0.066416   | 0.066416   | 0.066416   |   0.0 |  7.32
+Comm    | 0.029801   | 0.029801   | 0.029801   |   0.0 |  3.28
+Output  | 0.0010415  | 0.0010415  | 0.0010415  |   0.0 |  0.11
+Modify  | 0.0078915  | 0.0078915  | 0.0078915  |   0.0 |  0.87
+Other   |            | 0.005414   |            |       |  0.60
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            563 ave         563 max         563 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1624 ave        1624 max        1624 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1624
+Ave neighs/atom = 8.12
+Neighbor list builds = 500
+Dangerous builds = 500
+
+Total wall time: 0:00:00

examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.4

@@ -0,0 +1,153 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Fluid
+
+variable T    equal 1.0
+variable rc   equal 1.0
+variable rcD  equal 1.2
+
+units            lj
+boundary     p p p
+atom_style       atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+### create box and configuration
+variable     L equal 5.0
+lattice      fcc 3.0
+Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
+region       simBox block 0 ${L} 0 ${L} 0 ${L}
+region       simBox block 0 5 0 ${L} 0 ${L}
+region       simBox block 0 5 0 5 0 ${L}
+region       simBox block 0 5 0 5 0 5
+create_box   2 simBox
+Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  1 by 2 by 2 MPI processor grid
+create_atoms 1 random 100 12456 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+create_atoms 2 random 100 13245 simBox
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
+  create_atoms CPU = 0.000 seconds
+mass         1 1.0
+mass         2 2.0
+###
+
+pair_style       dpd/ext ${T} ${rc} 3854262
+pair_style       dpd/ext 1 ${rc} 3854262
+pair_style       dpd/ext 1 1 3854262
+
+pair_coeff   1 1 25.0 4.5 4.53 0.5 0.53   1.2 #${rcD}
+pair_coeff   1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
+pair_coeff   2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
+
+timestep     0.01
+run_style    verlet
+
+velocity all create ${T} 68768932
+velocity all create 1 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          5000
+  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 = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/ext, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes
+   Step          Time           Temp          Press     
+         0   0              1              9.2729849    
+       100   1              1.1416138      7.7058466    
+       200   2              0.91696292     8.1601454    
+       300   3              0.96358166     6.7987934    
+       400   4              0.94726377     7.6196059    
+       500   5              1.0941462      7.5974711    
+       600   6              0.91469027     8.3921536    
+       700   7              1.0912559      7.362721     
+       800   8              0.96537861     9.2089379    
+       900   9              0.9986577      8.0072887    
+      1000   10             0.9580071      7.2399027    
+      1100   11             0.94763774     7.8075521    
+      1200   12             0.9942368      7.5215461    
+      1300   13             1.0312465      8.2684258    
+      1400   14             0.95133276     7.2734722    
+      1500   15             0.97273431     7.1831939    
+      1600   16             1.0052028      7.929104     
+      1700   17             0.93909435     8.2831308    
+      1800   18             1.0647294      8.850861     
+      1900   19             1.0268112      7.2828461    
+      2000   20             0.91293528     8.208191     
+      2100   21             0.94719411     8.3353929    
+      2200   22             0.90507637     9.1708397    
+      2300   23             1.0663386      7.1415871    
+      2400   24             1.0132089      9.2210634    
+      2500   25             1.0633849      8.3368039    
+      2600   26             0.95803955     8.8247976    
+      2700   27             0.95264552     7.3204561    
+      2800   28             0.93548595     7.290555     
+      2900   29             0.96876322     7.4969147    
+      3000   30             0.99554648     8.2055023    
+      3100   31             1.0190751      7.907751     
+      3200   32             1.0887502      7.7247246    
+      3300   33             1.0059692      7.4039814    
+      3400   34             1.0055991      7.3469353    
+      3500   35             1.0067689      7.2161248    
+      3600   36             1.1103667      8.4373236    
+      3700   37             1.0668979      7.1922528    
+      3800   38             0.97902043     5.5426601    
+      3900   39             1.0268733      6.7786635    
+      4000   40             1.0036613      7.8078466    
+      4100   41             1.0714377      7.4129166    
+      4200   42             0.99168608     6.0096099    
+      4300   43             1.084818       7.4932992    
+      4400   44             0.98348896     8.9950057    
+      4500   45             1.045253       6.1309568    
+      4600   46             1.0266723      6.3227645    
+      4700   47             1.0183525      8.1505786    
+      4800   48             1.0527309      8.2824928    
+      4900   49             0.96877903     7.6341751    
+      5000   50             1.0178917      7.5037327    
+Loop time of 0.320182 on 4 procs for 5000 steps with 200 atoms
+
+Performance: 13492326.176 tau/day, 15616.118 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.20185    | 0.21019    | 0.2166     |   1.4 | 65.65
+Neigh   | 0.017652   | 0.018339   | 0.019085   |   0.5 |  5.73
+Comm    | 0.076802   | 0.084707   | 0.094197   |   2.6 | 26.46
+Output  | 0.00057039 | 0.00066408 | 0.00093301 |   0.0 |  0.21
+Modify  | 0.0025036  | 0.0027709  | 0.0030403  |   0.5 |  0.87
+Other   |            | 0.003508   |            |       |  1.10
+
+Nlocal:             50 ave          53 max          45 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:          288.5 ave         300 max         279 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs:         418.25 ave         438 max         384 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+
+Total # of neighbors = 1673
+Ave neighs/atom = 8.365
+Neighbor list builds = 500
+Dangerous builds = 500
+
+Total wall time: 0:00:00

examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data

@@ -0,0 +1 @@
+../dpd_tstat/cg_spce.data

examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot

@@ -1,354 +0,0 @@
-VOTCA				
-N	351	R	2.0	9.0
-				
-1	2.000000E+00	2.190202E+01	7.229762E+01	
-2	2.020000E+00	2.048957E+01	6.887333E+01	
-3	2.040000E+00	1.915004E+01	6.500604E+01	
-4	2.060000E+00	1.789228E+01	6.069573E+01	
-5	2.080000E+00	1.672516E+01	5.594242E+01	
-6	2.100000E+00	1.565754E+01	5.074609E+01	
-7	2.120000E+00	1.467088E+01	4.787307E+01	
-8	2.140000E+00	1.374450E+01	4.471740E+01	
-9	2.160000E+00	1.288407E+01	4.127908E+01	
-10	2.180000E+00	1.209522E+01	3.755811E+01	
-11	2.200000E+00	1.138363E+01	3.355449E+01	
-12	2.220000E+00	1.072913E+01	3.188695E+01	
-13	2.240000E+00	1.010845E+01	3.017359E+01	
-14	2.260000E+00	9.522496E+00	2.841440E+01	
-15	2.280000E+00	8.972182E+00	2.660938E+01	
-16	2.300000E+00	8.458426E+00	2.475854E+01	
-17	2.320000E+00	8.014166E+00	2.006698E+01	
-18	2.340000E+00	7.639767E+00	1.777244E+01	
-19	2.360000E+00	7.287288E+00	1.787493E+01	
-20	2.380000E+00	6.908790E+00	2.037445E+01	
-21	2.400000E+00	6.456330E+00	2.527099E+01	
-22	2.420000E+00	5.858025E+00	3.384695E+01	
-23	2.440000E+00	5.130955E+00	3.814748E+01	
-24	2.460000E+00	4.360629E+00	3.817257E+01	
-25	2.480000E+00	3.632555E+00	3.392224E+01	
-26	2.500000E+00	3.032242E+00	2.539647E+01	
-27	2.520000E+00	2.547993E+00	2.297813E+01	
-28	2.540000E+00	2.115131E+00	2.025763E+01	
-29	2.560000E+00	1.739702E+00	1.723497E+01	
-30	2.580000E+00	1.427747E+00	1.391013E+01	
-31	2.600000E+00	1.185311E+00	1.028314E+01	
-32	2.620000E+00	9.860176E-01	9.578245E+00	
-33	2.640000E+00	8.048986E-01	8.465708E+00	
-34	2.660000E+00	6.501069E-01	6.945526E+00	
-35	2.680000E+00	5.297952E-01	5.017699E+00	
-36	2.700000E+00	4.521166E-01	2.682227E+00	
-37	2.720000E+00	3.986447E-01	2.615311E+00	
-38	2.740000E+00	3.494900E-01	2.250522E+00	
-39	2.760000E+00	3.106097E-01	1.587859E+00	
-40	2.780000E+00	2.879614E-01	6.273237E-01	
-41	2.800000E+00	2.875026E-01	-6.310851E-01	
-42	2.820000E+00	3.002733E-01	-6.543549E-01	
-43	2.840000E+00	3.140112E-01	-7.277911E-01	
-44	2.860000E+00	3.297194E-01	-8.513935E-01	
-45	2.880000E+00	3.484014E-01	-1.025162E+00	
-46	2.900000E+00	3.710604E-01	-1.249097E+00	
-47	2.920000E+00	3.974884E-01	-1.380483E+00	
-48	2.940000E+00	4.257507E-01	-1.432530E+00	
-49	2.960000E+00	4.542607E-01	-1.405240E+00	
-50	2.980000E+00	4.814314E-01	-1.298611E+00	
-51	3.000000E+00	5.056762E-01	-1.112645E+00	
-52	3.020000E+00	5.266502E-01	-9.832894E-01	
-53	3.040000E+00	5.449492E-01	-8.451544E-01	
-54	3.060000E+00	5.603978E-01	-6.982396E-01	
-55	3.080000E+00	5.728203E-01	-5.425450E-01	
-56	3.100000E+00	5.820411E-01	-3.780706E-01	
-57	3.120000E+00	5.882509E-01	-2.409307E-01	
-58	3.140000E+00	5.915991E-01	-9.190908E-02	
-59	3.160000E+00	5.918481E-01	6.899430E-02	
-60	3.180000E+00	5.887601E-01	2.417794E-01	
-61	3.200000E+00	5.820977E-01	4.264463E-01	
-62	3.220000E+00	5.733491E-01	4.528343E-01	
-63	3.240000E+00	5.638075E-01	5.057356E-01	
-64	3.260000E+00	5.529429E-01	5.851503E-01	
-65	3.280000E+00	5.402248E-01	6.910784E-01	
-66	3.300000E+00	5.251230E-01	8.235199E-01	
-67	3.320000E+00	5.086524E-01	8.236482E-01	
-68	3.340000E+00	4.921725E-01	8.244583E-01	
-69	3.360000E+00	4.756696E-01	8.259503E-01	
-70	3.380000E+00	4.591299E-01	8.281240E-01	
-71	3.400000E+00	4.425400E-01	8.309796E-01	
-72	3.420000E+00	4.259181E-01	8.311861E-01	
-73	3.440000E+00	4.092937E-01	8.312292E-01	
-74	3.460000E+00	3.926700E-01	8.311089E-01	
-75	3.480000E+00	3.760504E-01	8.308252E-01	
-76	3.500000E+00	3.594381E-01	8.303781E-01	
-77	3.520000E+00	3.428394E-01	8.295412E-01	
-78	3.540000E+00	3.262547E-01	8.289646E-01	
-79	3.560000E+00	3.096790E-01	8.286483E-01	
-80	3.580000E+00	2.931071E-01	8.285923E-01	
-81	3.600000E+00	2.765336E-01	8.287966E-01	
-82	3.620000E+00	2.599901E-01	8.254306E-01	
-83	3.640000E+00	2.435212E-01	8.213359E-01	
-84	3.660000E+00	2.271415E-01	8.165124E-01	
-85	3.680000E+00	2.108656E-01	8.109603E-01	
-86	3.700000E+00	1.947080E-01	8.046794E-01	
-87	3.720000E+00	1.790243E-01	7.653050E-01	
-88	3.740000E+00	1.640312E-01	7.356166E-01	
-89	3.760000E+00	1.495351E-01	7.156143E-01	
-90	3.780000E+00	1.353421E-01	7.052980E-01	
-91	3.800000E+00	1.212586E-01	7.046676E-01	
-92	3.820000E+00	1.072429E-01	6.965706E-01	
-93	3.840000E+00	9.340878E-02	6.865180E-01	
-94	3.860000E+00	7.979524E-02	6.745098E-01	
-95	3.880000E+00	6.644142E-02	6.605462E-01	
-96	3.900000E+00	5.338643E-02	6.446270E-01	
-97	3.920000E+00	4.067486E-02	6.268536E-01	
-98	3.940000E+00	2.829935E-02	6.110218E-01	
-99	3.960000E+00	1.622105E-02	5.971317E-01	
-100	3.980000E+00	4.401131E-03	5.851833E-01	
-101	4.000000E+00	-7.199230E-03	5.751764E-01	
-102	4.020000E+00	-1.856170E-02	5.611971E-01	
-103	4.040000E+00	-2.965216E-02	5.479743E-01	
-104	4.060000E+00	-4.048572E-02	5.355079E-01	
-105	4.080000E+00	-5.107752E-02	5.237981E-01	
-106	4.100000E+00	-6.144268E-02	5.128447E-01	
-107	4.120000E+00	-7.151117E-02	4.939504E-01	
-108	4.140000E+00	-8.119856E-02	4.747353E-01	
-109	4.160000E+00	-9.049845E-02	4.551994E-01	
-110	4.180000E+00	-9.940440E-02	4.353427E-01	
-111	4.200000E+00	-1.079100E-01	4.151651E-01	
-112	4.220000E+00	-1.159565E-01	3.900062E-01	
-113	4.240000E+00	-1.235312E-01	3.679865E-01	
-114	4.260000E+00	-1.306969E-01	3.491061E-01	
-115	4.280000E+00	-1.375164E-01	3.333651E-01	
-116	4.300000E+00	-1.440524E-01	3.207633E-01	
-117	4.320000E+00	-1.503014E-01	3.040292E-01	
-118	4.340000E+00	-1.562092E-01	2.866389E-01	
-119	4.360000E+00	-1.617626E-01	2.685925E-01	
-120	4.380000E+00	-1.669485E-01	2.498899E-01	
-121	4.400000E+00	-1.717538E-01	2.305311E-01	
-122	4.420000E+00	-1.760941E-01	2.036400E-01	
-123	4.440000E+00	-1.799054E-01	1.776469E-01	
-124	4.460000E+00	-1.832059E-01	1.525518E-01	
-125	4.480000E+00	-1.860135E-01	1.283546E-01	
-126	4.500000E+00	-1.883461E-01	1.050554E-01	
-127	4.520000E+00	-1.902569E-01	8.558005E-02	
-128	4.540000E+00	-1.917515E-01	6.344105E-02	
-129	4.560000E+00	-1.927768E-01	3.863842E-02	
-130	4.580000E+00	-1.932793E-01	1.117216E-02	
-131	4.600000E+00	-1.932059E-01	-1.895774E-02	
-132	4.620000E+00	-1.926829E-01	-3.331832E-02	
-133	4.640000E+00	-1.918741E-01	-4.753697E-02	
-134	4.660000E+00	-1.907824E-01	-6.161370E-02	
-135	4.680000E+00	-1.894105E-01	-7.554851E-02	
-136	4.700000E+00	-1.877614E-01	-8.934140E-02	
-137	4.720000E+00	-1.859159E-01	-9.580751E-02	
-138	4.740000E+00	-1.839049E-01	-1.058976E-01	
-139	4.760000E+00	-1.816559E-01	-1.196116E-01	
-140	4.780000E+00	-1.790963E-01	-1.369495E-01	
-141	4.800000E+00	-1.761537E-01	-1.579114E-01	
-142	4.820000E+00	-1.728280E-01	-1.744216E-01	
-143	4.840000E+00	-1.691864E-01	-1.895036E-01	
-144	4.860000E+00	-1.652574E-01	-2.031575E-01	
-145	4.880000E+00	-1.610696E-01	-2.153832E-01	
-146	4.900000E+00	-1.566516E-01	-2.261808E-01	
-147	4.920000E+00	-1.521084E-01	-2.290714E-01	
-148	4.940000E+00	-1.474515E-01	-2.375453E-01	
-149	4.960000E+00	-1.425693E-01	-2.516026E-01	
-150	4.980000E+00	-1.373502E-01	-2.712432E-01	
-151	5.000000E+00	-1.316824E-01	-2.964672E-01	
-152	5.020000E+00	-1.257009E-01	-3.016666E-01	
-153	5.040000E+00	-1.196162E-01	-3.067953E-01	
-154	5.060000E+00	-1.134296E-01	-3.118535E-01	
-155	5.080000E+00	-1.071425E-01	-3.168409E-01	
-156	5.100000E+00	-1.007564E-01	-3.217577E-01	
-157	5.120000E+00	-9.430843E-02	-3.230025E-01	
-158	5.140000E+00	-8.783782E-02	-3.240216E-01	
-159	5.160000E+00	-8.134907E-02	-3.248150E-01	
-160	5.180000E+00	-7.484672E-02	-3.253827E-01	
-161	5.200000E+00	-6.833527E-02	-3.257248E-01	
-162	5.220000E+00	-6.171989E-02	-3.350608E-01	
-163	5.240000E+00	-5.496291E-02	-3.398853E-01	
-164	5.260000E+00	-4.815456E-02	-3.401983E-01	
-165	5.280000E+00	-4.138506E-02	-3.359997E-01	
-166	5.300000E+00	-3.474465E-02	-3.272895E-01	
-167	5.320000E+00	-2.866480E-02	-2.819209E-01	
-168	5.340000E+00	-2.341879E-02	-2.439062E-01	
-169	5.360000E+00	-1.885953E-02	-2.132454E-01	
-170	5.380000E+00	-1.483994E-02	-1.899386E-01	
-171	5.400000E+00	-1.121296E-02	-1.739857E-01	
-172	5.420000E+00	-7.974056E-03	-1.497398E-01	
-173	5.440000E+00	-5.229953E-03	-1.245058E-01	
-174	5.460000E+00	-3.000413E-03	-9.828350E-02	
-175	5.480000E+00	-1.305201E-03	-7.107305E-02	
-176	5.500000E+00	-1.640790E-04	-4.287441E-02	
-177	5.520000E+00	6.371635E-04	-3.612657E-02	
-178	5.540000E+00	1.236053E-03	-2.263906E-02	
-179	5.560000E+00	1.497795E-03	-2.411882E-03	
-180	5.580000E+00	1.287597E-03	2.455496E-02	
-181	5.600000E+00	4.706651E-04	5.826147E-02	
-182	5.620000E+00	-7.026386E-04	5.910929E-02	
-183	5.640000E+00	-1.895322E-03	6.019943E-02	
-184	5.660000E+00	-3.112231E-03	6.153190E-02	
-185	5.680000E+00	-4.358213E-03	6.310668E-02	
-186	5.700000E+00	-5.638114E-03	6.492378E-02	
-187	5.720000E+00	-6.949688E-03	6.610584E-02	
-188	5.740000E+00	-8.277238E-03	6.652145E-02	
-189	5.760000E+00	-9.605436E-03	6.617062E-02	
-190	5.780000E+00	-1.091895E-02	6.505335E-02	
-191	5.800000E+00	-1.220246E-02	6.316963E-02	
-192	5.820000E+00	-1.341489E-02	5.820182E-02	
-193	5.840000E+00	-1.453566E-02	5.400257E-02	
-194	5.860000E+00	-1.558012E-02	5.057189E-02	
-195	5.880000E+00	-1.656366E-02	4.790978E-02	
-196	5.900000E+00	-1.750164E-02	4.601622E-02	
-197	5.920000E+00	-1.840088E-02	4.358369E-02	
-198	5.940000E+00	-1.923199E-02	3.920163E-02	
-199	5.960000E+00	-1.995595E-02	3.287003E-02	
-200	5.980000E+00	-2.053379E-02	2.458889E-02	
-201	6.000000E+00	-2.092651E-02	1.435822E-02	
-202	6.020000E+00	-2.120502E-02	1.352840E-02	
-203	6.040000E+00	-2.146907E-02	1.291186E-02	
-204	6.060000E+00	-2.172292E-02	1.250861E-02	
-205	6.080000E+00	-2.197084E-02	1.231865E-02	
-206	6.100000E+00	-2.221709E-02	1.234198E-02	
-207	6.120000E+00	-2.246474E-02	1.237271E-02	
-208	6.140000E+00	-2.270998E-02	1.210114E-02	
-209	6.160000E+00	-2.294677E-02	1.152726E-02	
-210	6.180000E+00	-2.316905E-02	1.065107E-02	
-211	6.200000E+00	-2.337079E-02	9.472569E-03	
-212	6.220000E+00	-2.332237E-02	-1.276224E-02	
-213	6.240000E+00	-2.292243E-02	-2.567822E-02	
-214	6.260000E+00	-2.235736E-02	-2.927535E-02	
-215	6.280000E+00	-2.181354E-02	-2.355364E-02	
-216	6.300000E+00	-2.147734E-02	-8.513096E-03	
-217	6.320000E+00	-2.141633E-02	1.466366E-03	
-218	6.340000E+00	-2.149820E-02	5.775798E-03	
-219	6.360000E+00	-2.160956E-02	4.415202E-03	
-220	6.380000E+00	-2.163701E-02	-2.615423E-03	
-221	6.400000E+00	-2.146714E-02	-1.531608E-02	
-222	6.420000E+00	-2.107402E-02	-2.337955E-02	
-223	6.440000E+00	-2.055660E-02	-2.774728E-02	
-224	6.460000E+00	-1.998877E-02	-2.841924E-02	
-225	6.480000E+00	-1.944446E-02	-2.539546E-02	
-226	6.500000E+00	-1.899759E-02	-1.867591E-02	
-227	6.520000E+00	-1.869042E-02	-1.259095E-02	
-228	6.540000E+00	-1.847196E-02	-9.804901E-03	
-229	6.560000E+00	-1.827623E-02	-1.031775E-02	
-230	6.580000E+00	-1.803726E-02	-1.412951E-02	
-231	6.600000E+00	-1.768906E-02	-2.124018E-02	
-232	6.620000E+00	-1.710949E-02	-3.551655E-02	
-233	6.640000E+00	-1.631641E-02	-4.259122E-02	
-234	6.660000E+00	-1.545385E-02	-4.246419E-02	
-235	6.680000E+00	-1.466585E-02	-3.513545E-02	
-236	6.700000E+00	-1.409644E-02	-2.060502E-02	
-237	6.720000E+00	-1.374966E-02	-1.461056E-02	
-238	6.740000E+00	-1.349054E-02	-1.183851E-02	
-239	6.760000E+00	-1.325464E-02	-1.228886E-02	
-240	6.780000E+00	-1.297750E-02	-1.596163E-02	
-241	6.800000E+00	-1.259469E-02	-2.285680E-02	
-242	6.820000E+00	-1.213049E-02	-2.349903E-02	
-243	6.840000E+00	-1.165728E-02	-2.375897E-02	
-244	6.860000E+00	-1.118268E-02	-2.363664E-02	
-245	6.880000E+00	-1.071436E-02	-2.313203E-02	
-246	6.900000E+00	-1.025995E-02	-2.224514E-02	
-247	6.920000E+00	-9.817276E-03	-2.203990E-02	
-248	6.940000E+00	-9.377653E-03	-2.193988E-02	
-249	6.960000E+00	-8.938979E-03	-2.194508E-02	
-250	6.980000E+00	-8.499148E-03	-2.205550E-02	
-251	7.000000E+00	-8.056057E-03	-2.227113E-02	
-252	7.020000E+00	-7.597830E-03	-2.345789E-02	
-253	7.040000E+00	-7.121492E-03	-2.408210E-02	
-254	7.060000E+00	-6.638296E-03	-2.414376E-02	
-255	7.080000E+00	-6.159492E-03	-2.364288E-02	
-256	7.100000E+00	-5.696331E-03	-2.257946E-02	
-257	7.120000E+00	-5.301441E-03	-1.729553E-02	
-258	7.140000E+00	-4.989070E-03	-1.432759E-02	
-259	7.160000E+00	-4.712898E-03	-1.367562E-02	
-260	7.180000E+00	-4.426605E-03	-1.533964E-02	
-261	7.200000E+00	-4.083872E-03	-1.931964E-02	
-262	7.220000E+00	-3.631995E-03	-2.538390E-02	
-263	7.240000E+00	-3.087883E-03	-2.854317E-02	
-264	7.260000E+00	-2.509635E-03	-2.879748E-02	
-265	7.280000E+00	-1.955351E-03	-2.614680E-02	
-266	7.300000E+00	-1.483130E-03	-2.059115E-02	
-267	7.320000E+00	-1.113389E-03	-1.639767E-02	
-268	7.340000E+00	-8.266321E-04	-1.229279E-02	
-269	7.360000E+00	-6.210869E-04	-8.276492E-03	
-270	7.380000E+00	-4.949818E-04	-4.348786E-03	
-271	7.400000E+00	-4.465449E-04	-5.096684E-04	
-272	7.420000E+00	-5.304321E-04	8.162452E-03	
-273	7.440000E+00	-7.436056E-04	1.241897E-02	
-274	7.460000E+00	-9.977534E-04	1.225988E-02	
-275	7.480000E+00	-1.204563E-03	7.685191E-03	
-276	7.500000E+00	-1.275724E-03	-1.305104E-03	
-277	7.520000E+00	-1.199415E-03	-5.916706E-03	
-278	7.540000E+00	-1.055417E-03	-8.074089E-03	
-279	7.560000E+00	-8.928131E-04	-7.777253E-03	
-280	7.580000E+00	-7.606883E-04	-5.026198E-03	
-281	7.600000E+00	-7.081267E-04	1.790768E-04	
-282	7.620000E+00	-7.213835E-04	1.157786E-03	
-283	7.640000E+00	-7.548855E-04	2.203601E-03	
-284	7.660000E+00	-8.099749E-04	3.316523E-03	
-285	7.680000E+00	-8.879938E-04	4.496550E-03	
-286	7.700000E+00	-9.902843E-04	5.743685E-03	
-287	7.720000E+00	-1.122403E-03	7.421734E-03	
-288	7.740000E+00	-1.285295E-03	8.820936E-03	
-289	7.760000E+00	-1.473382E-03	9.941291E-03	
-290	7.780000E+00	-1.681087E-03	1.078280E-02	
-291	7.800000E+00	-1.902835E-03	1.134546E-02	
-292	7.820000E+00	-2.225281E-03	2.008573E-02	
-293	7.840000E+00	-2.673724E-03	2.394500E-02	
-294	7.860000E+00	-3.150542E-03	2.292328E-02	
-295	7.880000E+00	-3.558115E-03	1.702056E-02	
-296	7.900000E+00	-3.798824E-03	6.236836E-03	
-297	7.920000E+00	-3.844315E-03	-1.142168E-03	
-298	7.940000E+00	-3.774961E-03	-5.247538E-03	
-299	7.960000E+00	-3.656237E-03	-6.079274E-03	
-300	7.980000E+00	-3.553615E-03	-3.637376E-03	
-301	8.000000E+00	-3.532566E-03	2.078155E-03	
-302	8.020000E+00	-3.611956E-03	5.494873E-03	
-303	8.040000E+00	-3.737724E-03	6.716053E-03	
-304	8.060000E+00	-3.865961E-03	5.741694E-03	
-305	8.080000E+00	-3.952755E-03	2.571796E-03	
-306	8.100000E+00	-3.954196E-03	-2.793640E-03	
-307	8.120000E+00	-3.873685E-03	-5.086591E-03	
-308	8.140000E+00	-3.757567E-03	-6.354313E-03	
-309	8.160000E+00	-3.626347E-03	-6.596805E-03	
-310	8.180000E+00	-3.500530E-03	-5.814068E-03	
-311	8.200000E+00	-3.400620E-03	-4.006101E-03	
-312	8.220000E+00	-3.334411E-03	-2.730570E-03	
-313	8.240000E+00	-3.286762E-03	-2.150229E-03	
-314	8.260000E+00	-3.243768E-03	-2.265076E-03	
-315	8.280000E+00	-3.191524E-03	-3.075114E-03	
-316	8.300000E+00	-3.116129E-03	-4.580340E-03	
-317	8.320000E+00	-2.964210E-03	-1.014102E-02	
-318	8.340000E+00	-2.729309E-03	-1.287854E-02	
-319	8.360000E+00	-2.467889E-03	-1.279292E-02	
-320	8.380000E+00	-2.236413E-03	-9.884157E-03	
-321	8.400000E+00	-2.091344E-03	-4.152240E-03	
-322	8.420000E+00	-2.034875E-03	-1.692189E-03	
-323	8.440000E+00	-2.015752E-03	-4.177491E-04	
-324	8.460000E+00	-2.010261E-03	-3.289192E-04	
-325	8.480000E+00	-1.994691E-03	-1.425700E-03	
-326	8.500000E+00	-1.945329E-03	-3.708091E-03	
-327	8.520000E+00	-1.867098E-03	-4.115259E-03	
-328	8.540000E+00	-1.780711E-03	-4.523663E-03	
-329	8.560000E+00	-1.686143E-03	-4.933304E-03	
-330	8.580000E+00	-1.583370E-03	-5.344181E-03	
-331	8.600000E+00	-1.472368E-03	-5.756296E-03	
-332	8.620000E+00	-1.328792E-03	-8.394009E-03	
-333	8.640000E+00	-1.144899E-03	-9.787974E-03	
-334	8.660000E+00	-9.455644E-04	-9.938189E-03	
-335	8.680000E+00	-7.556630E-04	-8.844656E-03	
-336	8.700000E+00	-6.000698E-04	-6.507373E-03	
-337	8.720000E+00	-5.364035E-04	-3.286769E-04	
-338	8.740000E+00	-5.681458E-04	3.033482E-03	
-339	8.760000E+00	-6.389659E-04	3.579102E-03	
-340	8.780000E+00	-6.925330E-04	1.308185E-03	
-341	8.800000E+00	-6.725164E-04	-3.779270E-03	
-342	8.820000E+00	-5.113768E-04	-1.169180E-02	
-343	8.840000E+00	-2.305599E-04	-1.574700E-02	
-344	8.860000E+00	9.278768E-05	-1.594487E-02	
-345	8.880000E+00	3.815195E-04	-1.228542E-02	
-346	8.900000E+00	5.584889E-04	-4.768636E-03	
-347	8.920000E+00	6.079481E-04	-2.335309E-04	
-348	8.940000E+00	5.700798E-04	3.964121E-03	
-349	8.960000E+00	4.516330E-04	7.824320E-03	
-350	8.980000E+00	2.593567E-04	1.134707E-02	
-351	9.000000E+00	0.000000E+00	1.453236E-02	

examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot

@@ -0,0 +1 @@
+../dpd_tstat/cg_spce_table.pot

examples/PACKAGES/dpd-basic/dpdext_tstat/in.dpdext_tstat

@@ -4,7 +4,7 @@ variable T   equal 300.0
 variable rc  equal   9.0
 variable rcD equal  10.0
 
-units		 real
+units            real
 boundary     p p p
 atom_style   atomic
 dimension    3
@@ -13,7 +13,7 @@ comm_modify  vel yes
 
 read_data    cg_spce.data
 
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
 
 pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
 pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
@@ -24,8 +24,8 @@ run_style   verlet
 velocity all create ${T} 68768932
 
 thermo_style custom step time temp press
-thermo       10
+thermo       100
 
 fix 1 all    nve
 
-run	     2000
+run          1000

examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1

@@ -1,293 +0,0 @@
-LAMMPS (8 Apr 2021)
-# Coarse-Grained SPC/E Water
-
-variable T   equal 300.0
-variable rc  equal   9.0
-variable rcD equal  10.0
-
-units		 real
-boundary     p p p
-atom_style   atomic
-dimension    3
-newton       on
-comm_modify  vel yes
-
-read_data    cg_spce.data
-Reading data file ...
-  orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  2180 atoms
-  read_data CPU = 0.020 seconds
-
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
-
-pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
-pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
-WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:461)
-pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
-pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
-
-timestep    1.0
-run_style   verlet
-
-velocity all create ${T} 68768932
-velocity all create 300 68768932
-
-thermo_style custom step time temp press
-thermo       10
-
-fix 1 all    nve
-
-run	     2000
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 7 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair dpd/ext/tstat, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes
-Step Time Temp Press 
-       0            0          300    7368.7186 
-      10           10    298.34842    6443.6033 
-      20           20    303.36187    9303.0158 
-      30           30    301.59356    7533.7912 
-      40           40    300.97217    5623.9089 
-      50           50    300.31652    9105.8093 
-      60           60    296.92173     9213.304 
-      70           70    294.36593    12701.327 
-      80           80    295.30077    6098.4732 
-      90           90    296.35396     8051.719 
-     100          100    293.72532     5555.983 
-     110          110    290.95711    9001.8346 
-     120          120    290.91972    10264.241 
-     130          130    294.14911    11450.959 
-     140          140    299.11994    7244.1639 
-     150          150    301.20082    7675.7516 
-     160          160    300.71883    9718.1901 
-     170          170    295.47176    8931.1414 
-     180          180    290.45284    7381.7674 
-     190          190    291.66922    11028.436 
-     200          200     294.0543    11897.269 
-     210          210    299.17955    8939.2171 
-     220          220    298.45193     8047.038 
-     230          230    300.48548     10033.64 
-     240          240    299.24752    6310.7247 
-     250          250    304.51487    8710.5626 
-     260          260     303.6513    5230.8162 
-     270          270    300.76074    12164.773 
-     280          280    302.60275     11145.98 
-     290          290    297.22957    9521.4384 
-     300          300     297.1365    7446.9006 
-     310          310    292.18323    8021.8344 
-     320          320    295.03958    9130.8594 
-     330          330     293.9622     4647.512 
-     340          340    290.77751     8001.486 
-     350          350    292.34687    11887.668 
-     360          360    295.95968     9262.148 
-     370          370    293.50476     4181.549 
-     380          380    288.69498     7632.071 
-     390          390    289.63957    5130.0205 
-     400          400    295.02212    5643.5024 
-     410          410     296.3944     7267.235 
-     420          420    299.22019    7149.9305 
-     430          430    298.36689     8384.595 
-     440          440    295.33149     10515.75 
-     450          450    294.76959    11569.389 
-     460          460      300.141    7272.4453 
-     470          470    299.14431    7792.5419 
-     480          480     302.3697    5837.8675 
-     490          490    301.94692    6999.1059 
-     500          500    300.25929    4885.3948 
-     510          510    302.50013    8231.0438 
-     520          520    300.76412    8445.0349 
-     530          530     298.5016     9110.432 
-     540          540    301.14513    9348.6421 
-     550          550    297.36425    10753.314 
-     560          560    296.50046    10476.823 
-     570          570    300.57267    9889.7968 
-     580          580     300.4868     8377.423 
-     590          590    296.65103      6859.32 
-     600          600    298.50013    7080.5995 
-     610          610    300.28274    9502.5438 
-     620          620    298.45508    8819.7846 
-     630          630    300.24859    6291.4944 
-     640          640    299.38719    7430.2366 
-     650          650    297.91915    9435.3218 
-     660          660    300.61208    6287.9931 
-     670          670    303.59291    8357.7639 
-     680          680    301.85511    1697.3038 
-     690          690    298.96873    5210.2286 
-     700          700    298.09035    7510.4359 
-     710          710    303.11692    10129.526 
-     720          720    302.65473    10488.388 
-     730          730    300.15444    7118.5953 
-     740          740    300.19245    10582.032 
-     750          750    296.73618    6538.0363 
-     760          760    299.72857    7588.9487 
-     770          770    299.00347    6633.9983 
-     780          780    301.38129    8053.5347 
-     790          790    298.54819    8711.4965 
-     800          800    305.54197    9717.9727 
-     810          810    302.96497    7582.0444 
-     820          820    306.81537    9433.6446 
-     830          830    309.16373    10088.582 
-     840          840    313.53881    9509.8624 
-     850          850    310.82992     5366.015 
-     860          860    306.49798    8499.9157 
-     870          870    308.93421    5690.3242 
-     880          880    302.56668    5526.3636 
-     890          890    306.72501    7380.8469 
-     900          900    308.87199     10388.13 
-     910          910     312.7367    6613.0734 
-     920          920    308.34508    5903.4291 
-     930          930    306.39924    8615.6622 
-     940          940    310.37544    6849.4694 
-     950          950    310.13051    6188.7605 
-     960          960    308.68049     7637.532 
-     970          970    302.85465    6448.7926 
-     980          980    307.40719    8763.0959 
-     990          990    304.02815    8373.6518 
-    1000         1000    300.69539    5682.6678 
-    1010         1010    299.16385     6012.246 
-    1020         1020      305.118    7913.4144 
-    1030         1030    304.20382    10580.788 
-    1040         1040    302.91134    7698.4548 
-    1050         1050    298.08593    8952.6724 
-    1060         1060    302.56196    10602.997 
-    1070         1070    305.98211    12174.358 
-    1080         1080    305.70253    12288.219 
-    1090         1090    303.22805    7922.7166 
-    1100         1100    301.54879    5031.3836 
-    1110         1110    302.57611    8547.4189 
-    1120         1120    302.00845    12966.595 
-    1130         1130    296.10912    4514.1707 
-    1140         1140    295.11601    6543.7239 
-    1150         1150    287.29188    6453.3386 
-    1160         1160    284.83881    7168.9427 
-    1170         1170    289.77871    7895.7434 
-    1180         1180    293.48011    7680.6885 
-    1190         1190    295.69035    8609.6593 
-    1200         1200     296.0653      7343.68 
-    1210         1210    302.72922    6973.6048 
-    1220         1220    304.11805    7322.7664 
-    1230         1230    300.24647    6418.2612 
-    1240         1240    293.24074    9039.1214 
-    1250         1250    300.56214    7877.4055 
-    1260         1260    308.03086    5644.2135 
-    1270         1270    311.12289    6875.5126 
-    1280         1280    307.83182    7204.9894 
-    1290         1290    309.58491    9993.2255 
-    1300         1300    305.36536     8626.859 
-    1310         1310    304.35084    3471.1205 
-    1320         1320    304.40125    2149.2701 
-    1330         1330    295.74547    6252.9592 
-    1340         1340    293.16034    3407.4408 
-    1350         1350     298.6302    10139.977 
-    1360         1360    300.46627    7312.9011 
-    1370         1370    298.00367    2780.8886 
-    1380         1380    300.97807    9403.3451 
-    1390         1390    294.32612    12005.453 
-    1400         1400    296.13403    5569.4907 
-    1410         1410    297.86152    9558.6064 
-    1420         1420    303.01992     8678.345 
-    1430         1430    298.53849    5544.6316 
-    1440         1440    293.60633    12879.765 
-    1450         1450    296.28813    9312.4229 
-    1460         1460    292.64466    8344.5877 
-    1470         1470    295.28975    7689.9396 
-    1480         1480    300.10761    7436.7346 
-    1490         1490     291.6152    8909.6757 
-    1500         1500      286.644    9756.5014 
-    1510         1510    294.52064    10383.164 
-    1520         1520    297.49618      4972.89 
-    1530         1530    295.63379    6192.5729 
-    1540         1540    295.04528    4987.7191 
-    1550         1550    290.41403    7013.6076 
-    1560         1560    295.62326    7222.5009 
-    1570         1570    299.90584    4282.5688 
-    1580         1580    299.04532     7885.433 
-    1590         1590    300.03907    5508.0652 
-    1600         1600    298.05683    9262.3744 
-    1610         1610    297.50015    9544.6913 
-    1620         1620    303.21217    6393.6756 
-    1630         1630    304.44383    9674.6583 
-    1640         1640    302.68977    9065.4408 
-    1650         1650    303.62415    6851.1575 
-    1660         1660    306.11103    8592.0481 
-    1670         1670    300.84566     8483.551 
-    1680         1680    303.92882    10113.096 
-    1690         1690    305.02534    7389.9402 
-    1700         1700    303.52902    5541.9256 
-    1710         1710    299.27905    9547.7344 
-    1720         1720    294.14366    7269.2402 
-    1730         1730    299.49977    8086.0601 
-    1740         1740    298.66942    7026.6067 
-    1750         1750    296.94428    9595.2435 
-    1760         1760    297.36921    6268.7436 
-    1770         1770    299.88423    10598.189 
-    1780         1780    293.76868    7405.7641 
-    1790         1790    297.19444    10837.102 
-    1800         1800    296.46054     8345.699 
-    1810         1810    299.06801    5256.5992 
-    1820         1820    294.17725    5510.7529 
-    1830         1830    286.78527    6310.8881 
-    1840         1840    284.89686    8249.1144 
-    1850         1850    293.79389    4578.9263 
-    1860         1860    298.31279     8752.305 
-    1870         1870    295.31087    8401.2736 
-    1880         1880    298.13297    4354.8694 
-    1890         1890    298.90786    11454.088 
-    1900         1900     299.1416    9121.4138 
-    1910         1910    296.43134    12157.884 
-    1920         1920    292.05445    8613.1522 
-    1930         1930     300.3421    7898.3626 
-    1940         1940    304.55746     6311.259 
-    1950         1950    304.03899    8789.3537 
-    1960         1960    305.08259    7243.5622 
-    1970         1970     304.0858    8712.4796 
-    1980         1980    299.14574    5166.3501 
-    1990         1990    300.07254    10019.769 
-    2000         2000    301.78176    8789.7968 
-Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms
-
-Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 90.668     | 90.668     | 90.668     |   0.0 | 99.41
-Neigh   | 0.23231    | 0.23231    | 0.23231    |   0.0 |  0.25
-Comm    | 0.20819    | 0.20819    | 0.20819    |   0.0 |  0.23
-Output  | 0.0049558  | 0.0049558  | 0.0049558  |   0.0 |  0.01
-Modify  | 0.052906   | 0.052906   | 0.052906   |   0.0 |  0.06
-Other   |            | 0.03904    |            |       |  0.04
-
-Nlocal:        2180.00 ave        2180 max        2180 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        6693.00 ave        6693 max        6693 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        261496.0 ave      261496 max      261496 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 261496
-Ave neighs/atom = 119.95229
-Neighbor list builds = 25
-Dangerous builds = 0
-Total wall time: 0:01:31

examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4

@@ -1,293 +0,0 @@
-LAMMPS (8 Apr 2021)
-# Coarse-Grained SPC/E Water
-
-variable T   equal 300.0
-variable rc  equal   9.0
-variable rcD equal  10.0
-
-units		 real
-boundary     p p p
-atom_style   atomic
-dimension    3
-newton       on
-comm_modify  vel yes
-
-read_data    cg_spce.data
-Reading data file ...
-  orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  2180 atoms
-  read_data CPU = 0.005 seconds
-
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
-pair_style	 hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
-
-pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
-pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
-WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:461)
-pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
-pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
-
-timestep    1.0
-run_style   verlet
-
-velocity all create ${T} 68768932
-velocity all create 300 68768932
-
-thermo_style custom step time temp press
-thermo       10
-
-fix 1 all    nve
-
-run	     2000
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 7 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair dpd/ext/tstat, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
-Step Time Temp Press 
-       0            0          300    5965.5396 
-      10           10    303.16391    8779.1574 
-      20           20     306.9014     8268.573 
-      30           30    305.84291    9976.0547 
-      40           40    301.20527    8832.3902 
-      50           50    305.72012    8041.0146 
-      60           60     305.1676    7118.8042 
-      70           70    305.01132    9423.9307 
-      80           80    308.10236    10781.423 
-      90           90    309.18703    3637.9961 
-     100          100    305.11814    7726.7672 
-     110          110    298.37346    8575.1602 
-     120          120    304.79786    8910.8048 
-     130          130    309.05401    6351.4839 
-     140          140    304.28367     4805.137 
-     150          150    300.28903    7412.6411 
-     160          160    299.39358    10183.593 
-     170          170    296.80729    5437.1054 
-     180          180     295.2755    8317.0414 
-     190          190    303.25949    8338.3453 
-     200          200    303.24607    9636.5224 
-     210          210    298.56684    10288.264 
-     220          220    293.42999    9001.0482 
-     230          230    293.12497    9083.5194 
-     240          240    291.92847    9659.3388 
-     250          250     299.2202     6328.759 
-     260          260    297.45209    10405.677 
-     270          270    292.12257    7273.9369 
-     280          280    289.81113    8957.8747 
-     290          290    299.06683    6695.3776 
-     300          300    300.75468    6298.5705 
-     310          310    296.26524    7432.4815 
-     320          320    294.21403    9941.7038 
-     330          330    293.01776    4750.2993 
-     340          340    295.22553    4968.3595 
-     350          350    293.95589    9224.5496 
-     360          360    297.94278    8792.0395 
-     370          370    298.99075    5453.7814 
-     380          380     302.1188    6229.2283 
-     390          390    298.48943    8517.5273 
-     400          400     295.3701    11328.394 
-     410          410    287.74238    4058.0382 
-     420          420    288.83732    5706.6773 
-     430          430     298.8242    6178.7142 
-     440          440    304.42682    10138.321 
-     450          450    300.28695    9731.3417 
-     460          460    300.34539    9249.4691 
-     470          470    303.32231    11638.718 
-     480          480    301.46777     4186.402 
-     490          490    292.56069    9184.8386 
-     500          500    297.26162    11766.733 
-     510          510    295.34018      6436.33 
-     520          520    300.16314    9325.3669 
-     530          530    305.00513    5947.6408 
-     540          540    300.88805    5222.7384 
-     550          550    301.56707    6669.1808 
-     560          560    304.89854    10730.053 
-     570          570    299.50424    7956.1042 
-     580          580    301.23382    10192.246 
-     590          590    298.81222    6017.2125 
-     600          600    300.57891     4575.433 
-     610          610    301.95936    6309.7515 
-     620          620    301.09393    5993.6489 
-     630          630    300.47565    4388.7137 
-     640          640    299.31886    9535.6093 
-     650          650    295.06025    7954.5811 
-     660          660    298.72666    8630.7466 
-     670          670    302.53833    5636.1305 
-     680          680    306.32833    12539.149 
-     690          690     296.1951    11345.293 
-     700          700    297.00325    6352.1448 
-     710          710    298.51181    6922.4379 
-     720          720    293.80125    4849.4922 
-     730          730    296.52677    11141.583 
-     740          740    294.15306    3527.8677 
-     750          750    294.74737    8454.0815 
-     760          760    292.53913    8187.9032 
-     770          770    294.37078    7487.5703 
-     780          780    297.50085    9198.7697 
-     790          790    298.37773    8969.0024 
-     800          800    293.29879    6506.6479 
-     810          810    296.58266    8805.7872 
-     820          820    290.85616    5248.8123 
-     830          830    292.29488    5123.8203 
-     840          840    292.77623    8263.5675 
-     850          850    297.88225    6777.7444 
-     860          860    300.01913    10439.087 
-     870          870    295.79578    7318.1322 
-     880          880     301.5994    8242.4774 
-     890          890    306.63208    8090.6106 
-     900          900    303.53759    6831.2666 
-     910          910    300.70481    3811.0498 
-     920          920    299.96274    8351.1573 
-     930          930    299.67435    7046.0534 
-     940          940    310.81742    6887.6925 
-     950          950    305.09984     4811.088 
-     960          960    301.33039     4184.851 
-     970          970    301.19205    6417.6542 
-     980          980     299.6491    7738.2233 
-     990          990    297.33655    9264.0874 
-    1000         1000    302.33418    7166.2751 
-    1010         1010    300.08402    9121.0882 
-    1020         1020    302.82225    6405.7109 
-    1030         1030    304.01683    6944.0839 
-    1040         1040    305.82618    6160.3838 
-    1050         1050    308.12518    4356.0931 
-    1060         1060    307.64811    6954.7245 
-    1070         1070    313.70509    5558.9804 
-    1080         1080    316.09239    7250.6147 
-    1090         1090     310.2845    5441.3722 
-    1100         1100    300.18899    4417.8774 
-    1110         1110    304.02471    5609.1668 
-    1120         1120    303.46016    10355.031 
-    1130         1130    305.68165     6400.913 
-    1140         1140    308.78348    7235.1894 
-    1150         1150    299.30025    9246.4856 
-    1160         1160    302.70799    9866.9536 
-    1170         1170     302.0977    8643.5532 
-    1180         1180    307.15407    8866.4664 
-    1190         1190    305.78146    7562.4911 
-    1200         1200    302.54605    7974.9973 
-    1210         1210    306.14264    9554.2381 
-    1220         1220    308.89843    6219.5361 
-    1230         1230    305.71844    7633.9105 
-    1240         1240    306.51911    7705.4795 
-    1250         1250    304.78473    8590.5595 
-    1260         1260    300.82969    9281.5964 
-    1270         1270     305.9271    4951.1323 
-    1280         1280    310.32728    9446.3989 
-    1290         1290    318.27879    9102.5544 
-    1300         1300    310.45777    5931.5457 
-    1310         1310    304.81268    1214.4291 
-    1320         1320    307.08811    10315.961 
-    1330         1330    306.86917    8584.9658 
-    1340         1340    307.26912     7254.864 
-    1350         1350    310.02754    8508.6256 
-    1360         1360    306.12763    4912.6641 
-    1370         1370    301.67924    6715.8196 
-    1380         1380    298.37239    6149.8821 
-    1390         1390    299.62894    8181.4761 
-    1400         1400    301.60395    6714.4244 
-    1410         1410    297.65752    7035.6575 
-    1420         1420    297.02817    7510.2637 
-    1430         1430    303.59177    10361.937 
-    1440         1440    300.10771    8473.2311 
-    1450         1450    291.21837    6097.9954 
-    1460         1460    291.58663    7729.0841 
-    1470         1470    292.52447    6555.8661 
-    1480         1480    294.48264    6960.0201 
-    1490         1490    298.34869    8044.2321 
-    1500         1500     296.8193    11731.289 
-    1510         1510    296.52073    5452.8935 
-    1520         1520    294.54819    9591.7969 
-    1530         1530    297.36394    5148.5383 
-    1540         1540    289.08137    6057.0981 
-    1550         1550    288.27007    8965.1965 
-    1560         1560    294.84398    8316.9487 
-    1570         1570    299.79573    8760.7322 
-    1580         1580    295.66745    5045.5322 
-    1590         1590    298.14356    7161.1834 
-    1600         1600    297.10402    6529.9938 
-    1610         1610    299.69137    7741.6027 
-    1620         1620    304.93043    11222.109 
-    1630         1630    302.01322    10893.107 
-    1640         1640    295.47422    8400.3124 
-    1650         1650    301.93122    7190.2609 
-    1660         1660    305.02639    6140.5552 
-    1670         1670    302.86047    8651.5366 
-    1680         1680    304.82151     9909.407 
-    1690         1690    300.48426    8428.8845 
-    1700         1700    293.06643    5333.8144 
-    1710         1710    295.43687    9103.4353 
-    1720         1720    298.77208    8162.1053 
-    1730         1730    300.08189    9603.4371 
-    1740         1740    303.16004    10693.291 
-    1750         1750    303.54199     9151.023 
-    1760         1760    300.99281    4641.2985 
-    1770         1770    297.36657    3888.5753 
-    1780         1780    298.32969    7286.2299 
-    1790         1790    297.34183    8975.8956 
-    1800         1800    295.83042    6366.7607 
-    1810         1810    295.92044    9308.4953 
-    1820         1820    298.10087    7117.2369 
-    1830         1830    296.13936    4849.3739 
-    1840         1840     296.5869    8321.4011 
-    1850         1850    296.74513    9530.6806 
-    1860         1860    298.57398    8788.0603 
-    1870         1870    299.12825    6015.4777 
-    1880         1880    301.91639    11706.441 
-    1890         1890    309.85968    10909.493 
-    1900         1900    302.64998    8779.8967 
-    1910         1910    301.62919    9176.3902 
-    1920         1920    300.66238    5369.8681 
-    1930         1930    297.64499      8185.09 
-    1940         1940    296.47852    10188.803 
-    1950         1950      297.802    6679.4466 
-    1960         1960    299.78754    7316.8198 
-    1970         1970    300.09083    6008.9414 
-    1980         1980    297.94119    5615.6403 
-    1990         1990    298.37687     9727.308 
-    2000         2000    296.08394    6400.2746 
-Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms
-
-Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 38.667     | 38.954     | 39.453     |   4.8 | 93.83
-Neigh   | 0.10947    | 0.11039    | 0.11153    |   0.3 |  0.27
-Comm    | 1.8661     | 2.3644     | 2.652      |  19.6 |  5.70
-Output  | 0.0082644  | 0.0094232  | 0.01281    |   2.0 |  0.02
-Modify  | 0.024678   | 0.025206   | 0.025888   |   0.3 |  0.06
-Other   |            | 0.05335    |            |       |  0.13
-
-Nlocal:        545.000 ave         559 max         531 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Nghost:        3619.00 ave        3655 max        3594 min
-Histogram: 1 1 0 0 1 0 0 0 0 1
-Neighs:        65415.5 ave       66835 max       64310 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-
-Total # of neighbors = 261662
-Ave neighs/atom = 120.02844
-Neighbor list builds = 26
-Dangerous builds = 0
-Total wall time: 0:00:41

examples/PACKAGES/dpd-basic/dpdext_tstat/log.5Apr22.dpdext_tstat.g++.1

@@ -0,0 +1,106 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Coarse-Grained SPC/E Water
+
+variable T   equal 300.0
+variable rc  equal   9.0
+variable rcD equal  10.0
+
+units            real
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+read_data    cg_spce.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (40.31 40.31 40.31)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2180 atoms
+  read_data CPU = 0.003 seconds
+
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
+
+pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
+pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
+WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
+pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
+
+timestep    1.0
+run_style   verlet
+
+velocity all create ${T} 68768932
+velocity all create 300 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          1000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair dpd/ext/tstat, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
+   Step          Time           Temp          Press     
+         0   0              300            7353.4129    
+       100   100            303.74025      4964.013     
+       200   200            298.35396      8007.7802    
+       300   300            298.28547      6291.5807    
+       400   400            298.01797      6252.1041    
+       500   500            299.88984      3489.931     
+       600   600            302.5718       9092.203     
+       700   700            305.38722      5909.02      
+       800   800            294.81401      10282.286    
+       900   900            292.40724      8338.6878    
+      1000   1000           293.64788      6951.569     
+Loop time of 28.1058 on 1 procs for 1000 steps with 2180 atoms
+
+Performance: 3.074 ns/day, 7.807 hours/ns, 35.580 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.948     | 27.948     | 27.948     |   0.0 | 99.44
+Neigh   | 0.071647   | 0.071647   | 0.071647   |   0.0 |  0.25
+Comm    | 0.058215   | 0.058215   | 0.058215   |   0.0 |  0.21
+Output  | 0.00026724 | 0.00026724 | 0.00026724 |   0.0 |  0.00
+Modify  | 0.014429   | 0.014429   | 0.014429   |   0.0 |  0.05
+Other   |            | 0.01283    |            |       |  0.05
+
+Nlocal:           2180 ave        2180 max        2180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           6643 ave        6643 max        6643 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         261826 ave      261826 max      261826 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 261826
+Ave neighs/atom = 120.10367
+Neighbor list builds = 12
+Dangerous builds = 0
+Total wall time: 0:00:28

examples/PACKAGES/dpd-basic/dpdext_tstat/log.5Apr22.dpdext_tstat.g++.4

@@ -0,0 +1,106 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Coarse-Grained SPC/E Water
+
+variable T   equal 300.0
+variable rc  equal   9.0
+variable rcD equal  10.0
+
+units            real
+boundary     p p p
+atom_style   atomic
+dimension    3
+newton       on
+comm_modify  vel yes
+
+read_data    cg_spce.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (40.31 40.31 40.31)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2180 atoms
+  read_data CPU = 0.003 seconds
+
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
+pair_style       hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
+
+pair_coeff   1 1 table cg_spce_table.pot VOTCA ${rc}
+pair_coeff   1 1 table cg_spce_table.pot VOTCA 9
+WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
+pair_coeff   1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
+
+timestep    1.0
+run_style   verlet
+
+velocity all create ${T} 68768932
+velocity all create 300 68768932
+
+thermo_style custom step time temp press
+thermo       100
+
+fix 1 all    nve
+
+run          1000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair dpd/ext/tstat, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
+   Step          Time           Temp          Press     
+         0   0              300            5950.2338    
+       100   100            301.15012      9090.2244    
+       200   200            301.28795      10589.557    
+       300   300            293.61974      5971.7781    
+       400   400            310.4217       8198.7972    
+       500   500            299.89888      9140.3132    
+       600   600            305.56607      7783.4481    
+       700   700            295.99415      6276.9444    
+       800   800            296.50051      5058.1115    
+       900   900            288.68499      8637.0269    
+      1000   1000           291.17292      6516.4192    
+Loop time of 7.57429 on 4 procs for 1000 steps with 2180 atoms
+
+Performance: 11.407 ns/day, 2.104 hours/ns, 132.026 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.2745     | 7.3674     | 7.4316     |   2.1 | 97.27
+Neigh   | 0.01863    | 0.018866   | 0.019429   |   0.2 |  0.25
+Comm    | 0.1123     | 0.17708    | 0.27025    |  13.8 |  2.34
+Output  | 0.00019274 | 0.00021224 | 0.00026504 |   0.0 |  0.00
+Modify  | 0.0041691  | 0.0042729  | 0.0043136  |   0.1 |  0.06
+Other   |            | 0.006464   |            |       |  0.09
+
+Nlocal:            545 ave         552 max         531 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost:         3620.5 ave        3656 max        3584 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:          65419 ave       66338 max       64104 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 261676
+Ave neighs/atom = 120.03486
+Neighbor list builds = 12
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/PACKAGES/fep/README.md

@@ -23,3 +23,5 @@ to the final states.
 
 * `quicktests` -- very short runs with charged Lennard-Jones atoms to test
   *compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
+
+* `ta` -- surface tension of SPCE water without constraints. Test-area method.

examples/PACKAGES/fep/ta/in.spce.lmp

@@ -0,0 +1,49 @@
+
+units        real
+boundary p p p
+
+atom_style   full
+bond_style   harmonic
+angle_style  harmonic
+
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style   lj/cut/coul/long 12.0 12.0
+pair_modify tail no
+kspace_style pppm 1.0e-5
+
+read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
+
+bond_coeff   1    517.630258   1.0
+angle_coeff  1    37.950526    109.47
+pair_coeff   1 1  0.1553  3.166 # O O
+pair_coeff   1 2  0.0     1.0   # O H
+pair_coeff   2 2  0.0     1.0   # H H
+
+# don't use fix shake with compute fep/ta
+# fix SHAKE all shake 0.0001 20 0 b 1
+
+neighbor 2.0 bin
+# neigh_modify delay 0 every 1 check yes
+
+timestep 1.0
+
+variable TK equal 300.0
+compute TA all fep/ta ${TK} xy 1.0005
+
+velocity all create ${TK} 12345
+
+thermo_style custom step temp press etotal pe c_TA[*]
+thermo 5000
+
+fix NVT all nvt temp ${TK} ${TK} 100
+run 300000
+
+reset_timestep 0
+
+variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
+
+fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
+
+run 2000000
+

examples/PACKAGES/fep/ta/log.spce

@@ -0,0 +1,689 @@
+LAMMPS (17 Feb 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+package gpu 0
+
+units        real
+boundary p p p
+
+atom_style   full
+bond_style   harmonic
+angle_style  harmonic
+
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style   lj/cut/coul/long 12.0 12.0
+pair_modify tail no
+kspace_style pppm 1.0e-5
+
+read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
+Reading data file ...
+  orthogonal box = (0 0 0) to (30 30 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  3072 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  2048 bonds
+  reading angles ...
+  1024 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0.5     
+  special bond factors coul:  0        0        0.5     
+     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 = 0.001 seconds
+  read_data CPU = 0.006 seconds
+
+bond_coeff   1    517.630258   1.0
+angle_coeff  1    37.950526    109.47
+pair_coeff   1 1  0.1553  3.166 # O O
+pair_coeff   1 2  0.0     1.0   # O H
+pair_coeff   2 2  0.0     1.0   # H H
+
+# don't use fix shake with compute fep/ta
+# fix SHAKE all shake 0.0001 20 0 b 1
+
+neighbor 2.0 bin
+# neigh_modify delay 0 every 1 check yes
+
+timestep 1.0
+
+variable TK equal 300.0
+compute TA all fep/ta ${TK} xy 1.0005
+compute TA all fep/ta 300 xy 1.0005
+
+velocity all create ${TK} 12345
+velocity all create 300 12345
+
+thermo_style custom step temp press etotal pe c_TA[*]
+thermo 5000
+
+fix NVT all nvt temp ${TK} ${TK} 100
+fix NVT all nvt temp 300 ${TK} 100
+fix NVT all nvt temp 300 300 100
+run 300000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- GPU package (short-range, long-range and three-body potentials):
+
+@Article{Brown11,
+ author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2011,
+ volume =  182,
+ pages =   {898--911}
+}
+
+@Article{Brown12,
+ author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2012,
+ volume =  183,
+ pages =   {449--459}
+}
+
+@Article{Brown13,
+ author = {W. M. Brown, Y. Masako},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2013,
+ volume =  184,
+ pages =   {2785--2793}
+}
+
+@Article{Trung15,
+ author = {T. D. Nguyen, S. J. Plimpton},
+ title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
+ journal = {Comput.~Mater.~Sci.},
+ year =    2015,
+ volume =  100,
+ pages =   {173--180}
+}
+
+@Article{Trung17,
+ author = {T. D. Nguyen},
+ title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2017,
+ volume =  212,
+ pages =   {113--122}
+}
+
+@Article{Nikolskiy19,
+ author = {V. Nikolskiy, V. Stegailov},
+ title = {GPU acceleration of four-site water models in LAMMPS},
+ journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
+ year =    2019
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
+  G vector (1/distance) = 0.24270009
+  grid = 20 20 50
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0037271514
+  estimated relative force accuracy = 1.1224206e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 40824 20000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+FEP/TA settings ...
+  temperature = 300.000000
+  scale factor = 1.000500
+  tail no
+Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.59 Mbytes
+   Step         Temp        Press        TotEng       PotEng      c_TA[1]      c_TA[2]      c_TA[3]   
+         0   300          5742.8831    8061.6965    5315.4762   -10.940045    93249708     0.45       
+      5000   301.43029   -118.64017   -7888.4723   -10647.786   -0.13617205   1.2566061    0.45       
+     10000   294.49018   -301.44062   -8063.3808   -10759.164   -0.14897537   1.2838851    0.45       
+     15000   294.36123   -407.07728   -8189.2912   -10883.894    0.34568257   0.55998421   0.45       
+     20000   300.95171    111.50248   -8104.1193   -10859.052    0.11293291   0.82742794   0.45       
+     25000   300.28473    388.00598   -8147.8655   -10896.692    0.11270184   0.82774872   0.45       
+     30000   306.62229   -113.93849   -8191.7529   -10998.594    0.26068823   0.6457922    0.45       
+     35000   303.66349   -426.81556   -8269.8364   -11049.593    0.78191631   0.26939311   0.45       
+     40000   291.70214   -50.50854    -8368.0775   -11038.339    0.20120788   0.71354814   0.45       
+     45000   299.74326   -289.18081   -8346.2716   -11090.142    0.4163404    0.49739645   0.45       
+     50000   300.53193    36.834691   -8367.5726   -11118.662    0.20517137   0.70881996   0.45       
+     55000   298.20207   -107.76906   -8274.386    -11004.148    0.7409946    0.2885342    0.45       
+     60000   298.32558   -65.20542    -8433.4884   -11164.381    0.16210976   0.76191344   0.45       
+     65000   297.3149    -102.87381   -8379.2515   -11100.892    0.21193701   0.70082127   0.45       
+     70000   300.78423   -463.75811   -8381.3317   -11134.731    0.32109349   0.58356406   0.45       
+     75000   299.53099   -53.264996   -8495.159    -11237.086    0.44828935   0.47144212   0.45       
+     80000   295.55879   -590.1244    -8432.3435   -11137.909    0.28788374   0.61699451   0.45       
+     85000   298.73289   -234.73297   -8473.8721   -11208.493   -0.11723275   1.2173128    0.45       
+     90000   307.02709   -264.9035    -8303.7625   -11114.309   -0.098959935  1.1805672    0.45       
+     95000   304.79112    199.8891    -8364.2553   -11154.334    0.036986735  0.93984396   0.45       
+    100000   295.49748   -743.18974   -8453.8066   -11158.811    0.249981     0.65749559   0.45       
+    105000   303.11352   -163.70166   -8324.4846   -11099.206   -0.012286442  1.0208231    0.45       
+    110000   294.30278   -33.731015   -8512.8168   -11206.884   -0.0129379    1.0219392    0.45       
+    115000   293.65421    393.24871   -8481.1933   -11169.324    0.75255277   0.28299408   0.45       
+    120000   300.56448    16.832298   -8507.3819   -11258.769    0.13389897   0.79883437   0.45       
+    125000   297.92506   -398.77893   -8576.4403   -11303.666    0.07292658   0.88485917   0.45       
+    130000   303.007     -589.11865   -8560.7259   -11334.472    0.42876446   0.48713794   0.45       
+    135000   310.82674   -203.4991    -8565.3181   -11410.647    0.075268046  0.88139064   0.45       
+    140000   303.68345   -710.20709   -8570.895    -11350.834   -0.1023741    1.1873476    0.45       
+    145000   293.86825    129.05781   -8457.0747   -11147.165    0.39475138   0.51573896   0.45       
+    150000   296.93136   -734.03863   -8577.2763   -11295.406    0.73600373   0.29095985   0.45       
+    155000   296.67522   -290.20206   -8631.0579   -11346.843   -0.30049664   1.6554154    0.45       
+    160000   301.5685    -656.03394   -8646.3196   -11406.898    0.08494101   0.86720512   0.45       
+    165000   295.8808     342.45206   -8602.0309   -11310.544   -0.30873864   1.6784606    0.45       
+    170000   303.33048   -64.144957   -8580.8446   -11357.552    0.13622456   0.79572423   0.45       
+    175000   300.75245   -908.44969   -8566.8005   -11319.909    0.15795135   0.76724659   0.45       
+    180000   301.34603   -350.00512   -8489.0111   -11247.553    0.21089487   0.70204744   0.45       
+    185000   305.96254    62.840515   -8458.0542   -11258.856   -0.050029338  1.0875408    0.45       
+    190000   300.14392    256.935     -8684.6591   -11432.197    0.40144188   0.50998337   0.45       
+    195000   299.32366   -218.70113   -8505.3328   -11245.362   -0.19428451   1.3852659    0.45       
+    200000   307.89424   -569.89954   -8615.1541   -11433.639    0.55121888   0.39668508   0.45       
+    205000   299.34873    334.69765   -8657.6353   -11397.894    0.17751997   0.74247109   0.45       
+    210000   298.54619   -261.12193   -8601.2439   -11334.156    0.74219016   0.28795615   0.45       
+    215000   304.02395   -306.81112   -8531.9913   -11315.047    0.86987192   0.23244073   0.45       
+    220000   299.95916    278.60921   -8682.394    -11428.24    -0.26474202   1.559051     0.45       
+    225000   302.839     -226.36906   -8515.0815   -11287.29     0.060381353  0.90367684   0.45       
+    230000   299.54085    240.08589   -8636.8991   -11378.916   -0.46699438   2.1887589    0.45       
+    235000   297.62792   -138.20813   -8627.0888   -11351.595   -0.035013312  1.0604901    0.45       
+    240000   299.15558    442.88999   -8749.2731   -11487.763    0.14696819   0.78151268   0.45       
+    245000   291.76323    174.70322   -8597.8808   -11268.701   -0.3979188    1.9492946    0.45       
+    250000   308.21961    37.282506   -8603.7127   -11425.176    0.021882894  0.96395922   0.45       
+    255000   307.18484   -493.77408   -8459.5942   -11271.585    0.16914044   0.75298079   0.45       
+    260000   294.17364   -238.05366   -8677.8379   -11370.723   -0.35710078   1.8202968    0.45       
+    265000   289.14461   -304.12454   -8727.2613   -11374.111    0.18045129   0.73882932   0.45       
+    270000   301.51228   -255.75558   -8640.9577   -11401.022    0.49252861   0.43772444   0.45       
+    275000   294.98349   -351.00974   -8678.3965   -11378.695   -0.31576914   1.6983718    0.45       
+    280000   294.37376    279.87325   -8668.9575   -11363.675    0.26328091   0.64298978   0.45       
+    285000   295.68351    249.3086    -8748.533    -11455.24     0.6820904    0.31849899   0.45       
+    290000   298.74266   -749.43024   -8583.8679   -11318.578    0.030414997  0.95026156   0.45       
+    295000   292.67215   -573.39647   -8713.3223   -11392.463    0.25656615   0.65027291   0.45       
+    300000   302.48853    186.71329   -8655.8918   -11424.892    0.20319721   0.71117107   0.45       
+Loop time of 706.805 on 1 procs for 300000 steps with 3072 atoms
+
+Performance: 36.672 ns/day, 0.654 hours/ns, 424.445 timesteps/s
+95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 149.88     | 149.88     | 149.88     |   0.0 | 21.21
+Bond    | 17.824     | 17.824     | 17.824     |   0.0 |  2.52
+Kspace  | 517.46     | 517.46     | 517.46     |   0.0 | 73.21
+Neigh   | 1.3789     | 1.3789     | 1.3789     |   0.0 |  0.20
+Comm    | 9.412      | 9.412      | 9.412      |   0.0 |  1.33
+Output  | 0.092      | 0.092      | 0.092      |   0.0 |  0.01
+Modify  | 8.3026     | 8.3026     | 8.3026     |   0.0 |  1.17
+Other   |            | 2.458      |            |       |  0.35
+
+Nlocal:           3072 ave        3072 max        3072 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           8370 ave        8370 max        8370 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -1
+Ave neighs/atom = -0.00032552083
+Ave special neighs/atom = 2
+Neighbor list builds = 14698
+Dangerous builds = 21
+
+reset_timestep 0
+
+variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
+
+fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
+
+run 2000000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
+  G vector (1/distance) = 0.24270009
+  grid = 20 20 50
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0037271514
+  estimated relative force accuracy = 1.1224206e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 40824 20000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.61 | 10.61 | 10.61 Mbytes
+   Step         Temp        Press        TotEng       PotEng      c_TA[1]      c_TA[2]      c_TA[3]   
+         0   302.48853    186.71327   -8655.8918   -11424.892    0.20325452   0.71110271   0.45       
+      5000   296.71986   -573.544     -8510.0832   -11226.277    0.43636365   0.48096787   0.45       
+     10000   302.58189    314.36295   -8636.8139   -11406.669    0.005932853  0.99009761   0.45       
+     15000   296.98096   -950.66627   -8635.9066   -11354.49     0.48058674   0.44658101   0.45       
+     20000   297.11923   -474.65836   -8666.9864   -11386.836    0.27933535   0.62590536   0.45       
+     25000   302.26474   -621.83271   -8655.4227   -11422.375    0.01931686   0.96811729   0.45       
+     30000   300.37645   -358.95128   -8568.7732   -11318.44     0.25415456   0.65290873   0.45       
+     35000   296.5436     179.71411   -8665.0335   -11379.614    0.1911473    0.72569185   0.45       
+     40000   300.79459    92.193193   -8617.7807   -11371.275    0.27587113   0.629553     0.45       
+     45000   298.87827    220.06674   -8695.83     -11431.782    0.28715816   0.61774591   0.45       
+     50000   304.4095    -375.31266   -8614.4396   -11401.025   -0.18683272   1.3680584    0.45       
+     55000   305.11287    128.51602   -8559.8245   -11352.848    0.24122754   0.66722084   0.45       
+     60000   296.56241    302.30371   -8725.6357   -11440.388   -0.27104279   1.5756158    0.45       
+     65000   295.78468   -393.18931   -8716.4616   -11424.095    0.39132466   0.51871194   0.45       
+     70000   297.67504    155.75977   -8641.2451   -11366.182    0.031194864  0.94901929   0.45       
+     75000   298.81381   -207.51201   -8622.9859   -11358.348   -0.11330086   1.2093106    0.45       
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+   1745000   306.47487    418.58552   -8590.4226   -11395.914   -0.04975774   1.0870455    0.45       
+   1750000   296.74674   -73.367187   -8727.0183   -11443.458   -0.27066543   1.5746188    0.45       
+   1755000   299.03541    551.77198   -8712.6905   -11450.081   -0.35865936   1.8250619    0.45       
+   1760000   288.98684   -380.17132   -8775.8546   -11421.26    -0.17754854   1.3469184    0.45       
+   1765000   300.76459   -662.80282   -8671.5414   -11424.761    0.078118597  0.87718632   0.45       
+   1770000   301.47287   -498.34628   -8675.582    -11435.285    0.57886218   0.37871122   0.45       
+   1775000   307.18565   -70.676548   -8554.9531   -11366.951    0.38766498   0.52190597   0.45       
+   1780000   302.58164   -329.49774   -8638.9781   -11408.831    0.53149245   0.41003059   0.45       
+   1785000   307.4086     294.59322   -8586.4793   -11400.518    0.34963097   0.55628768   0.45       
+   1790000   295.81491   -366.57154   -8756.8143   -11464.724    0.61653346   0.35552098   0.45       
+   1795000   296.46712    18.92361    -8640.9928   -11354.873    0.21158778   0.70123194   0.45       
+   1800000   290.9851    -805.74081   -8636.1049   -11299.802    0.36361854   0.54338759   0.45       
+   1805000   291.6313    -58.207903   -8707.0768   -11376.689    0.2659117    0.6401586    0.45       
+   1810000   299.14324    327.45026   -8613.3385   -11351.716    0.58264334   0.37631684   0.45       
+   1815000   295.3441     37.594139   -8747.5577   -11451.158    0.10312363   0.84115511   0.45       
+   1820000   297.19616    596.87014   -8601.4315   -11321.985    0.11690702   0.82193051   0.45       
+   1825000   305.23709   -229.45704   -8586.9328   -11381.094   -0.070794327  1.1260885    0.45       
+   1830000   308.48265   -50.225625   -8595.8609   -11419.732    0.28577292   0.61918297   0.45       
+   1835000   301.67215    30.600339   -8561.9509   -11323.478    0.67464985   0.32249901   0.45       
+   1840000   297.44022   -46.915689   -8760.5329   -11483.321    0.20308399   0.71130615   0.45       
+   1845000   294.56439    121.7989    -8819.2766   -11515.739   -0.13859762   1.2617292    0.45       
+   1850000   303.92475    63.511256   -8655.7131   -11437.861   -0.064617898  1.1144821    0.45       
+   1855000   302.36347   -403.0262    -8663.1963   -11431.052    0.63223295   0.34628081   0.45       
+   1860000   292.88227    124.53259   -8622.4528   -11303.517    0.21782313   0.69393587   0.45       
+   1865000   299.49141    1.3922328   -8592.8243   -11334.389    0.024359522  0.95996296   0.45       
+   1870000   295.36403   -1.848842    -8534.7607   -11238.543    0.53331666   0.40877784   0.45       
+   1875000   299.5254    -303.35635   -8642.4199   -11384.296    0.12049946   0.8169925    0.45       
+   1880000   302.15027   -233.4192    -8607.1984   -11373.102    0.42967343   0.48639576   0.45       
+   1885000   293.78387   -312.31798   -8576.6303   -11265.948    0.62050206   0.35316217   0.45       
+   1890000   296.33987    227.42925   -8675.0988   -11387.814   -0.2387251    1.4924762    0.45       
+   1895000   296.4116    -297.41585   -8695.6693   -11409.041    0.1899345    0.72716967   0.45       
+   1900000   305.04631   -744.8928    -8495.6073   -11288.022   -0.092917858  1.1686627    0.45       
+   1905000   299.13767   -233.05542   -8771.8955   -11510.222   -0.053515786  1.0939196    0.45       
+   1910000   301.18529    391.32364   -8594.238    -11351.309    0.17761387   0.74235415   0.45       
+   1915000   304.53139   -205.26743   -8615.1863   -11402.887   -0.65441918   2.9973254    0.45       
+   1920000   304.46794    75.506851   -8696.0461   -11483.166    0.28757039   0.6173189    0.45       
+   1925000   295.83229   -40.226799   -8677.0683   -11385.137    0.34338584   0.56214572   0.45       
+   1930000   298.91694    72.305481   -8662.7622   -11399.068   -0.45255095   2.1363683    0.45       
+   1935000   297.28693   -277.78411   -8678.223    -11399.608    0.32165864   0.58301111   0.45       
+   1940000   295.22194   -153.48885   -8737.0529   -11439.534    0.47753767   0.4488709    0.45       
+   1945000   298.41366    0.98105216  -8615.733    -11347.432    0.061208942  0.90242323   0.45       
+   1950000   298.47932   -461.39566   -8587.8993   -11320.199    0.41883297   0.49532116   0.45       
+   1955000   293.30456   -530.72887   -8712.242    -11397.172   -0.052983042  1.0929425    0.45       
+   1960000   307.27812   -609.68084   -8563.1295   -11375.974    0.10863685   0.83341209   0.45       
+   1965000   309.21876   -661.65884   -8619.5376   -11450.147   -0.00074060514  1.0012431    0.45       
+   1970000   294.16474    130.9219    -8662.5966   -11355.4     -0.048761848  1.0852311    0.45       
+   1975000   293.87023   -652.42226   -8587.2681   -11277.376   -0.42701916   2.0468057    0.45       
+   1980000   302.66906   -396.94893   -8576.3291   -11346.982    0.55938449   0.39128874   0.45       
+   1985000   304.00863    167.22102   -8525.9503   -11308.866   -0.12417188   1.2315647    0.45       
+   1990000   299.53376   -234.11494   -8528.8821   -11270.834    0.58392743   0.37550715   0.45       
+   1995000   296.20959   -99.022727   -8599.3854   -11310.908    0.10920765   0.83261451   0.45       
+   2000000   307.40367   -179.44965   -8545.6064   -11359.6      0.485016     0.44327537   0.45       
+Loop time of 4787.7 on 1 procs for 2000000 steps with 3072 atoms
+
+Performance: 36.092 ns/day, 0.665 hours/ns, 417.737 timesteps/s
+95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1015.1     | 1015.1     | 1015.1     |   0.0 | 21.20
+Bond    | 121.19     | 121.19     | 121.19     |   0.0 |  2.53
+Kspace  | 3455.1     | 3455.1     | 3455.1     |   0.0 | 72.17
+Neigh   | 8.7475     | 8.7475     | 8.7475     |   0.0 |  0.18
+Comm    | 58.679     | 58.679     | 58.679     |   0.0 |  1.23
+Output  | 0.60209    | 0.60209    | 0.60209    |   0.0 |  0.01
+Modify  | 81.328     | 81.328     | 81.328     |   0.0 |  1.70
+Other   |            | 46.88      |            |       |  0.98
+
+Nlocal:           3072 ave        3072 max        3072 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           8395 ave        8395 max        8395 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -1
+Ave neighs/atom = -0.00032552083
+Ave special neighs/atom = 2
+Neighbor list builds = 93794
+Dangerous builds = 0
+
+Total wall time: 1:31:34

examples/PACKAGES/fep/ta/spce.fep.ta

@@ -0,0 +1,22 @@
+# Time-averaged data for fix FEP
+# TimeStep c_TA[1] c_TA[2] c_TA[3] v_gamma_v
+100000 0.168677 0.863546 0.45 65.7437
+200000 0.169722 0.861354 0.45 66.6859
+300000 0.165507 0.868407 0.45 63.1899
+400000 0.162311 0.875704 0.45 60.7859
+500000 0.165468 0.872729 0.45 63.2053
+600000 0.165267 0.873825 0.45 63.1828
+700000 0.167824 0.869356 0.45 65.1722
+800000 0.170332 0.866538 0.45 67.0749
+900000 0.164396 0.875043 0.45 62.4639
+1000000 0.164738 0.87663 0.45 62.5659
+1100000 0.168395 0.870496 0.45 65.415
+1200000 0.170147 0.867104 0.45 66.7132
+1300000 0.170509 0.866709 0.45 66.9833
+1400000 0.171152 0.865294 0.45 67.5598
+1500000 0.172363 0.863433 0.45 68.547
+1600000 0.171538 0.864062 0.45 67.8359
+1700000 0.171662 0.864029 0.45 67.9145
+1800000 0.170202 0.866069 0.45 66.7697
+1900000 0.171403 0.864162 0.45 67.6313
+2000000 0.170962 0.864753 0.45 67.2314

examples/PACKAGES/tmd/data.peptide

@@ -0,0 +1 @@
+../../peptide/data.peptide

examples/PACKAGES/tmd/in.tmd

@@ -0,0 +1,45 @@
+# Solvated 5-mer peptide
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    multi
+thermo          50
+
+group tmd id 1:6
+
+fix             1 all nvt temp 275.0 275.0 100.0 tchain 1
+fix             0 tmd tmd 0.1 tmd.target  100 tmd.log
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+
+group           peptide type <= 12
+
+#dump           1 peptide atom 10 dump.peptide
+
+#dump           2 peptide image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    2 pad 3
+
+#dump           3 peptide movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    3 pad 3
+
+#compute                bnd all property/local btype batom1 batom2
+#dump           2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
+
+run             300
+

examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1

@@ -0,0 +1,210 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+Reading data file ...
+  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     7 = max # of 1-3 neighbors
+    14 = max # of 1-4 neighbors
+    18 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.011 seconds
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    multi
+thermo          50
+
+group tmd id 1:6
+6 atoms in group tmd
+
+fix             1 all nvt temp 275.0 275.0 100.0 tchain 1
+fix             0 tmd tmd 0.1 tmd.target  100 tmd.log
+Reading TMD target file tmd.target ...
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+      19 = # of size 2 clusters
+       6 = # of size 3 clusters
+       3 = # of size 4 clusters
+     640 = # of frozen angles
+  find clusters CPU = 0.000 seconds
+
+group           peptide type <= 12
+84 atoms in group peptide
+
+#dump           1 peptide atom 10 dump.peptide
+
+#dump           2 peptide image 25 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    2 pad 3
+
+#dump           3 peptide movie 25 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    3 pad 3
+
+#compute                bnd all property/local btype batom1 batom2
+#dump           2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
+
+run             300
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
+  G vector (1/distance) = 0.26872465
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.022820853
+  estimated relative force accuracy = 6.872432e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 10648 3375
+  generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:    4   1.111     1.44264e-05        9
+Bond:    6   0.996998  7.26967e-06        6
+Bond:    8   1.08      1.32536e-05        9
+Bond:   10   1.111     1.22749e-05        8
+Bond:   12   1.08      1.11767e-05        9
+Bond:   14   0.96      0                  1
+Bond:   18   0.957206  4.37979e-05     1280
+Angle:  31   104.519   0.00396029       640
+Per MPI rank memory allocation (min/avg/max) = 19.78 | 19.78 | 19.78 Mbytes
+------------ Step              0 ----- CPU =            0 (sec) -------------
+TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005 
+PotEng   =     -6372.3766 E_bond   =        16.5572 E_angle  =        36.3726 
+E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945 
+E_coul   =     26772.2646 E_long   =    -33907.9271 Press    =      -837.0112
+------------ Step             50 ----- CPU =    0.6301453 (sec) -------------
+TotEng   =     -5001.6799 KinEng   =      1319.3760 Temp     =       327.9501 
+PotEng   =     -6321.0559 E_bond   =        17.4415 E_angle  =        42.4509 
+E_dihed  =        25.0839 E_impro  =         4.4025 E_vdwl   =       725.7619 
+E_coul   =     26771.0015 E_long   =    -33907.1980 Press    =        -1.1409
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:    4   1.11096   0.000146572        9
+Bond:    6   0.996997  7.55911e-06        6
+Bond:    8   1.08      8.22449e-06        9
+Bond:   10   1.11099   3.00424e-05        8
+Bond:   12   1.08      6.53505e-06        9
+Bond:   14   0.95999   0                  1
+Bond:   18   0.957195  4.74892e-05     1280
+Angle:  31   104.52    0.00446577       640
+------------ Step            100 ----- CPU =     1.251267 (sec) -------------
+TotEng   =     -5114.3221 KinEng   =      1168.2996 Temp     =       290.3979 
+PotEng   =     -6282.6217 E_bond   =        45.5470 E_angle  =        87.5725 
+E_dihed  =        26.1332 E_impro  =         1.8662 E_vdwl   =       791.5291 
+E_coul   =     26670.6791 E_long   =    -33905.9488 Press    =       -29.3446
+------------ Step            150 ----- CPU =     1.869158 (sec) -------------
+TotEng   =     -5302.3058 KinEng   =      1211.4300 Temp     =       301.1186 
+PotEng   =     -6513.7358 E_bond   =        51.4069 E_angle  =        82.5752 
+E_dihed  =        31.1298 E_impro  =         4.3390 E_vdwl   =       764.0550 
+E_coul   =     26461.8974 E_long   =    -33909.1392 Press    =     -1204.2714
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:    4   1.11094   0.000292869        9
+Bond:    6   0.996989  3.13206e-05        6
+Bond:    8   1.07999   4.4723e-05         9
+Bond:   10   1.111     1.08895e-05        8
+Bond:   12   1.07999   1.42694e-05        9
+Bond:   14   0.959976  0                  1
+Bond:   18   0.957195  8.58256e-05     1280
+Angle:  31   104.52    0.00597861       640
+------------ Step            200 ----- CPU =      2.48933 (sec) -------------
+TotEng   =     -5785.4658 KinEng   =      1048.7220 Temp     =       260.6751 
+PotEng   =     -6834.1879 E_bond   =        21.7304 E_angle  =        48.3249 
+E_dihed  =        20.5973 E_impro  =         2.0603 E_vdwl   =       818.9175 
+E_coul   =     26165.9672 E_long   =    -33911.7854 Press    =     -1228.5741
+------------ Step            250 ----- CPU =     3.119859 (sec) -------------
+TotEng   =     -6108.4578 KinEng   =       828.5247 Temp     =       205.9419 
+PotEng   =     -6936.9825 E_bond   =        26.5971 E_angle  =        68.2771 
+E_dihed  =        36.1232 E_impro  =         5.2092 E_vdwl   =       884.1147 
+E_coul   =     25955.7300 E_long   =    -33913.0338 Press    =     -1365.4744
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:    4   1.11174   0.0109853          9
+Bond:    6   0.996999  1.94772e-06        6
+Bond:    8   1.08      3.97091e-06        9
+Bond:   10   1.111     2.52635e-06        8
+Bond:   12   1.08      1.24444e-06        9
+Bond:   14   0.96      0                  1
+Bond:   18   0.9572    1.22873e-05     1280
+Angle:  31   104.52    0.00134864       640
+------------ Step            300 ----- CPU =      3.74524 (sec) -------------
+TotEng   =     -5492.5012 KinEng   =      1315.6902 Temp     =       327.0339 
+PotEng   =     -6808.1914 E_bond   =        88.7967 E_angle  =       104.4231 
+E_dihed  =        28.2383 E_impro  =        43.5062 E_vdwl   =       992.5311 
+E_coul   =     25849.1502 E_long   =    -33914.8370 Press    =       268.8004
+Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms
+
+Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9399     | 2.9399     | 2.9399     |   0.0 | 78.50
+Bond    | 0.0069522  | 0.0069522  | 0.0069522  |   0.0 |  0.19
+Kspace  | 0.25203    | 0.25203    | 0.25203    |   0.0 |  6.73
+Neigh   | 0.48624    | 0.48624    | 0.48624    |   0.0 | 12.98
+Comm    | 0.016948   | 0.016948   | 0.016948   |   0.0 |  0.45
+Output  | 0.00023689 | 0.00023689 | 0.00023689 |   0.0 |  0.01
+Modify  | 0.039476   | 0.039476   | 0.039476   |   0.0 |  1.05
+Other   |            | 0.003502   |            |       |  0.09
+
+Nlocal:           2004 ave        2004 max        2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          11242 ave       11242 max       11242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         710782 ave      710782 max      710782 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 710782
+Ave neighs/atom = 354.68164
+Ave special neighs/atom = 2.3403194
+Neighbor list builds = 32
+Dangerous builds = 1
+
+Total wall time: 0:00:03

examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4

@@ -0,0 +1,210 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+Reading data file ...
+  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     7 = max # of 1-3 neighbors
+    14 = max # of 1-4 neighbors
+    18 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.017 seconds
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    multi
+thermo          50
+
+group tmd id 1:6
+6 atoms in group tmd
+
+fix             1 all nvt temp 275.0 275.0 100.0 tchain 1
+fix             0 tmd tmd 0.1 tmd.target  100 tmd.log
+Reading TMD target file tmd.target ...
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+      19 = # of size 2 clusters
+       6 = # of size 3 clusters
+       3 = # of size 4 clusters
+     640 = # of frozen angles
+  find clusters CPU = 0.000 seconds
+
+group           peptide type <= 12
+84 atoms in group peptide
+
+#dump           1 peptide atom 10 dump.peptide
+
+#dump           2 peptide image 25 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    2 pad 3
+
+#dump           3 peptide movie 25 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify    3 pad 3
+
+#compute                bnd all property/local btype batom1 batom2
+#dump           2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
+
+run             300
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
+  G vector (1/distance) = 0.26872465
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.022820853
+  estimated relative force accuracy = 6.872432e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 4312 960
+  generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:    4   1.111     1.44264e-05        9
+Bond:    6   0.996998  7.26967e-06        6
+Bond:    8   1.08      1.32536e-05        6
+Bond:   10   1.111     1.22749e-05        8
+Bond:   12   1.08      1.11767e-05        9
+Bond:   14   0.96      0                  1
+Bond:   18   0.957206  4.37979e-05     1280
+Angle:  31   104.519   0.00396029       640
+Per MPI rank memory allocation (min/avg/max) = 16.78 | 16.97 | 17.16 Mbytes
+------------ Step              0 ----- CPU =            0 (sec) -------------
+TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005 
+PotEng   =     -6372.3766 E_bond   =        16.5572 E_angle  =        36.3726 
+E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945 
+E_coul   =     26772.2646 E_long   =    -33907.9271 Press    =      -837.0112
+------------ Step             50 ----- CPU =    0.1916178 (sec) -------------
+TotEng   =     -5001.6799 KinEng   =      1319.3760 Temp     =       327.9501 
+PotEng   =     -6321.0559 E_bond   =        17.4415 E_angle  =        42.4509 
+E_dihed  =        25.0839 E_impro  =         4.4025 E_vdwl   =       725.7619 
+E_coul   =     26771.0015 E_long   =    -33907.1980 Press    =        -1.1409
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:    4   1.11096   0.000146572        9
+Bond:    6   0.996997  7.55911e-06        6
+Bond:    8   1.08      8.22449e-06        6
+Bond:   10   1.11099   3.00424e-05        8
+Bond:   12   1.08      6.53505e-06        9
+Bond:   14   0.95999   0                  1
+Bond:   18   0.957195  4.74892e-05     1280
+Angle:  31   104.52    0.00446577       640
+------------ Step            100 ----- CPU =    0.3672111 (sec) -------------
+TotEng   =     -5114.3221 KinEng   =      1168.2996 Temp     =       290.3979 
+PotEng   =     -6282.6217 E_bond   =        45.5470 E_angle  =        87.5725 
+E_dihed  =        26.1332 E_impro  =         1.8662 E_vdwl   =       791.5291 
+E_coul   =     26670.6792 E_long   =    -33905.9488 Press    =       -29.3446
+------------ Step            150 ----- CPU =    0.5543252 (sec) -------------
+TotEng   =     -5302.3058 KinEng   =      1211.4300 Temp     =       301.1186 
+PotEng   =     -6513.7358 E_bond   =        51.4069 E_angle  =        82.5752 
+E_dihed  =        31.1298 E_impro  =         4.3390 E_vdwl   =       764.0550 
+E_coul   =     26461.8975 E_long   =    -33909.1392 Press    =     -1204.2714
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:    4   1.11094   0.000292869        9
+Bond:    6   0.996989  3.13206e-05        6
+Bond:    8   1.07999   4.4723e-05         6
+Bond:   10   1.111     1.08895e-05        8
+Bond:   12   1.07999   1.42694e-05        9
+Bond:   14   0.959976  0                  1
+Bond:   18   0.957195  8.58257e-05     1280
+Angle:  31   104.52    0.00597861       640
+------------ Step            200 ----- CPU =    0.7449468 (sec) -------------
+TotEng   =     -5785.4658 KinEng   =      1048.7220 Temp     =       260.6751 
+PotEng   =     -6834.1878 E_bond   =        21.7304 E_angle  =        48.3249 
+E_dihed  =        20.5973 E_impro  =         2.0603 E_vdwl   =       818.9173 
+E_coul   =     26165.9673 E_long   =    -33911.7854 Press    =     -1228.5754
+------------ Step            250 ----- CPU =    0.9417257 (sec) -------------
+TotEng   =     -6108.4577 KinEng   =       828.5246 Temp     =       205.9418 
+PotEng   =     -6936.9823 E_bond   =        26.5971 E_angle  =        68.2771 
+E_dihed  =        36.1232 E_impro  =         5.2092 E_vdwl   =       884.1146 
+E_coul   =     25955.7302 E_long   =    -33913.0338 Press    =     -1365.4736
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:    4   1.11174   0.0109854          9
+Bond:    6   0.996999  1.94775e-06        6
+Bond:    8   1.08      3.97089e-06        6
+Bond:   10   1.111     2.52634e-06        8
+Bond:   12   1.08      1.24445e-06        9
+Bond:   14   0.96      0                  1
+Bond:   18   0.9572    1.22873e-05     1280
+Angle:  31   104.52    0.0013486        640
+------------ Step            300 ----- CPU =     1.137003 (sec) -------------
+TotEng   =     -5492.5016 KinEng   =      1315.6899 Temp     =       327.0339 
+PotEng   =     -6808.1915 E_bond   =        88.7968 E_angle  =       104.4228 
+E_dihed  =        28.2384 E_impro  =        43.5061 E_vdwl   =       992.5315 
+E_coul   =     25849.1499 E_long   =    -33914.8370 Press    =       268.8010
+Loop time of 1.13706 on 4 procs for 300 steps with 2004 atoms
+
+Performance: 45.591 ns/day, 0.526 hours/ns, 263.838 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.75407    | 0.80373    | 0.84144    |   3.6 | 70.68
+Bond    | 0.0010088  | 0.0024668  | 0.0045274  |   2.6 |  0.22
+Kspace  | 0.095468   | 0.13434    | 0.18276    |   8.9 | 11.81
+Neigh   | 0.13509    | 0.13515    | 0.13522    |   0.0 | 11.89
+Comm    | 0.024217   | 0.025086   | 0.026404   |   0.5 |  2.21
+Output  | 0.00020952 | 0.00023591 | 0.00031389 |   0.0 |  0.02
+Modify  | 0.033319   | 0.033374   | 0.033436   |   0.0 |  2.94
+Other   |            | 0.00268    |            |       |  0.24
+
+Nlocal:            501 ave         530 max         459 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost:        6562.75 ave        6755 max        6370 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         177696 ave      195050 max      158403 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 710782
+Ave neighs/atom = 354.68164
+Ave special neighs/atom = 2.3403194
+Neighbor list builds = 32
+Dangerous builds = 1
+
+Total wall time: 0:00:01

examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1

@@ -0,0 +1,4 @@
+# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
+100 11.580338717125848 11.637740410711476 0.00432656530431019 -0.0006058453921097923 1295.0393774041895 -7808.460018545273 562.4687334224966
+200 5.840169358562925 5.897571052148553 0.009256742629063092 -0.0004765379201060169 1404.114149312145 -15441.509720360129 1352.9255849946983
+300 0.10000000000000142 0.15740169358562994 -0.030035833473071705 -0.5643261296323345 -121.59623659080042 -22929.738462520727 2299.6676396746325

examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4

@@ -0,0 +1,4 @@
+# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
+100 11.580338717125848 11.637740410711476 0.004326565303381905 -0.0006058453930379918 1295.0393771263327 -7808.46001855425 562.4687334073235
+200 5.840169358562925 5.897571052148553 0.009256742652188668 -0.0004765378969710561 1404.114152819961 -15441.50972264099 1352.9255825827688
+300 0.10000000000000142 0.15740169358562994 -0.03003651537895091 -0.5643268572640833 -121.59899719968097 -22929.73877163682 2299.6674130478946

examples/PACKAGES/tmd/tmd.target

@@ -0,0 +1,13 @@
+# pull a few peptide atoms across the box
+ 36.840194 64.211560 xlo xhi
+ 41.013691 68.385058 ylo yhi
+ 29.768095 57.139462 zlo zhi # comment
+# comment
+      1    53.99993  48.52678  46.78550   0   0   0
+      2    55.10395  48.23499  45.86693   0   0   0
+      3    53.81519  49.54928  47.43995   0   0   0
+      4    55.71714  47.34797  46.13434   0   0   0
+      5    55.72261  49.13657  45.67007   0   0   0
+      6    54.66624  48.09539  44.85538   0   0   0
+      7    53.28193  47.47427  46.91953   0   0   0
+      8    52.07157  47.45486  47.62418   0   0   0

examples/README

@@ -83,6 +83,7 @@ indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
 latte:    use of LATTE density-functional tight-binding quantum code
 mc:       MC package models: GCMC, Widom, fix mol/swap
+mdi:      use of the MDI package and MolSSI MDI code coupling library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
@@ -117,6 +118,7 @@ ttm:      two-temeperature model examples
 vashishta: models using the Vashishta potential
 voronoi:  Voronoi tesselation via compute voronoi/atom command
 wall:     use of reflective walls with different stochastic models
+yaml:     demonstrates use of yaml thermo and dump styles
 
 Here is how you might run and visualize one of the sample problems:
 

examples/kim/plugin/CMakeLists.txt

@@ -0,0 +1,99 @@
+##########################################
+# 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 3.10)
+
+# enforce out-of-source build
+if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+  message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
+    "Please remove CMakeCache.txt and CMakeFiles first.")
+endif()
+
+project(kimplugin VERSION 1.0 LANGUAGES CXX)
+
+set(LAMMPS_SOURCE_DIR ""  CACHE PATH "Location of LAMMPS sources folder")
+if(NOT LAMMPS_SOURCE_DIR)
+  message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
+endif()
+
+# by default, install into $HOME/.local (not /usr/local),
+# so that no root access (and sudo) is needed
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
+# and prints lots of pointless warnings about "unsafe" functions
+if(MSVC)
+  add_compile_options(/Zc:__cplusplus)
+  add_compile_options(/wd4244)
+  add_compile_options(/wd4267)
+  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
+endif()
+
+# C++11 is required
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Need -restrict with Intel compilers
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+include(CheckIncludeFileCXX)
+include(LAMMPSInterfaceCXX)
+
+##########################
+# building the plugins
+
+add_library(kimplugin MODULE kimplugin.cpp ${LAMMPS_SOURCE_DIR}/KIM/pair_kim.cpp
+  ${LAMMPS_SOURCE_DIR}/KIM/fix_store_kim.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_command.cpp
+  ${LAMMPS_SOURCE_DIR}/KIM/kim_init.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_interactions.cpp
+  ${LAMMPS_SOURCE_DIR}/KIM/kim_param.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_property.cpp
+  ${LAMMPS_SOURCE_DIR}/KIM/kim_query.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_units.cpp)
+target_link_libraries(kimplugin PRIVATE lammps)
+target_include_directories(kimplugin PRIVATE ${LAMMPS_SOURCE_DIR}/KIM)
+set_target_properties(kimplugin PROPERTIES PREFIX "" SUFFIX ".so")
+
+find_package(KIM-API 2.2.0 CONFIG REQUIRED)
+target_link_libraries(kimplugin PRIVATE KIM-API::kim-api)
+
+##########################
+# need libcurl
+find_package(CURL)
+if(CURL_FOUND)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(kimplugin PRIVATE ${CURL_INCLUDE_DIRS})
+    target_link_libraries(kimplugin PRIVATE ${CURL_LIBRARIES})
+  else()
+    target_link_libraries(kimplugin PRIVATE CURL::libcurl)
+  endif()
+  target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL)
+  set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+  mark_as_advanced(LMP_DEBUG_CURL)
+  if(LMP_DEBUG_CURL)
+    target_compile_definitions(kimplugin PRIVATE -DLMP_DEBUG_CURL)
+  endif()
+  set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+  mark_as_advanced(LMP_NO_SSL_CHECK)
+  if(LMP_NO_SSL_CHECK)
+    target_compile_definitions(kimplugin PRIVATE -DLMP_NO_SSL_CHECK)
+  endif()
+endif()
+
+# MacOS seems to need this
+if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
+  set_target_properties(kimplugin 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(kimplugin.so PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+  if(CMAKE_CROSSCOMPILING)
+    set_target_properties(kimplugin  PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
+  endif()
+else()
+  set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-rdynamic")
+endif()

examples/kim/plugin/LAMMPSInterfaceCXX.cmake

@@ -0,0 +1,88 @@
+# Cmake script code to define the LAMMPS C++ interface
+# settings required for building LAMMPS plugins
+
+################################################################################
+# helper function
+function(validate_option name values)
+  string(TOLOWER ${${name}} needle_lower)
+  string(TOUPPER ${${name}} needle_upper)
+  list(FIND ${values} ${needle_lower} IDX_LOWER)
+  list(FIND ${values} ${needle_upper} IDX_UPPER)
+  if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+    list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+    message(FATAL_ERROR "\n########################################################################\n"
+      "Invalid value '${${name}}' for option ${name}\n"
+      "\n"
+      "Possible values are:\n"
+      "${POSSIBLE_VALUE_LIST}"
+      "########################################################################")
+  endif()
+endfunction(validate_option)
+
+#################################################################################
+# LAMMPS C++ interface. We only need the header related parts.
+add_library(lammps INTERFACE)
+target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
+endif()
+################################################################################
+# MPI configuration
+if(NOT CMAKE_CROSSCOMPILING)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET)
+  option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
+endif()
+
+if(BUILD_MPI)
+  find_package(MPI REQUIRED)
+  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+  if(LAMMPS_LONGLONG_TO_LONG)
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
+  endif()
+  target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
+else()
+  target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
+endif()
+
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
+validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
+string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
+target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
+
+################################################################################
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
+find_package(OpenMP QUIET)
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
+endif()
+
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+
+if(BUILD_OMP)
+  find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
+  endif()
+
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
+    # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
+    # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
+  else()
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
+  endif()
+  target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
+endif()

examples/kim/plugin/kimplugin.cpp

@@ -0,0 +1,54 @@
+
+#include "lammpsplugin.h"
+#include "version.h"
+
+#include "pair_kim.h"
+#include "fix_store_kim.h"
+#include "kim_command.h"
+
+using namespace LAMMPS_NS;
+
+static Pair *pair_kim_creator(LAMMPS *lmp)
+{
+  return new PairKIM(lmp);
+}
+
+static Fix *fix_store_kim_creator(LAMMPS *lmp, int argc, char **argv)
+{
+  return new FixStoreKIM(lmp, argc, argv);
+}
+
+static Command *kim_command_creator(LAMMPS *lmp)
+{
+  return new KimCommand(lmp);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  // register kim pair style
+  plugin.version = LAMMPS_VERSION;
+  plugin.style = "pair";
+  plugin.name = "kim";
+  plugin.info = "KIM plugin pair style v1.0";
+  plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_kim_creator;
+  plugin.handle = handle;
+  (*register_plugin)(&plugin, lmp);
+
+  // register fix STORE/KIM only need to update changed fields
+  plugin.style = "fix";
+  plugin.name = "STORE/KIM";
+  plugin.info = "Internal settings storage for KIM fix style v1.0";
+  plugin.creator.v2 = (lammpsplugin_factory2 *) &fix_store_kim_creator;
+  (*register_plugin)(&plugin, lmp);
+
+  // register KIM command
+  plugin.style = "command";
+  plugin.name = "kim";
+  plugin.info = "kim command style v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &kim_command_creator;
+  (*register_plugin)(&plugin, lmp);
+}

examples/mdi/README

@@ -0,0 +1,228 @@
+These are examples that work the MDI package in LAMMPS which uses the
+MolSSI MDI library for coupling codes together and communicating
+between them with MDI messages.
+
+In MDI lingo, one code is the driver and another code is the engine.
+The 2 codes can be written in any language; C++ (LAMMPS) and Python
+are illustrated here.  The 2 codes can each be stand-alone codes, in
+which case they can be run on different numbers of processors.  The 2
+codes can communicate either via TCP (sockets) or via MPI.  For the
+TCP case, the driver and engine need to be launched separately,
+e.g. in 2 windows on your desktop machine.  For the MPI case, a single
+mpirun command launches both codes.
+
+Alternatively the engine code can be a plugin library which the driver
+code loads, in which case the driver and engine run on the same
+processors.
+
+LAMMPS supports operating in all these MDI modes.  It can be an engine
+operating either as a stand-alone code or as a plugin.  It can also be
+a driver and couple to an engine that is either a stand-alone code or
+a plugin.  Examples for all these use cases are in this directory.
+The example commands below illustrate how to run all the variants.
+
+To use LAMMPS as a plugin engine, you must build it as a shared library.
+Something like this, which also builds the normal LAMMPS executable
+lmp_mpi:
+
+cd src
+make yes-mdi
+make mode=shlib mpi
+
+To use the serial_driver.py example you will need Python 3 with Numpy
+and mpi4py available in your Python.  Make sure LAMMPS and Python are
+using same the same version of MPI.
+
+-------------------------------------------------
+-------------------------------------------------
+
+* Example #1 = run ab inito MD (AIMD)
+  Two instances of LAMMPS operate as a driver and engine
+  As an engine, LAMMPS is a surrogate for a quantum code
+
+Note that the 2 input scripts in.aimd.alone and in.aimd.driver
+have an option for running in NVE vs NPT mode.  Comment in/out
+the appropriate line to change modes.  Nothing needs to be
+changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
+
+---
+
+Run the entire calculation with a single instance of LAMMPS by itself
+  results should be identical to running this example with MDI
+
+% lmp_mpi < in.aimd.alone
+
+With MDI, the thermo output of the driver should match the thermo
+output of the in.aimd.alone script.
+
+---
+
+Run with TCP: 1 proc each
+
+% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
+
+% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
+
+---
+
+Run with TCP: 3 procs + 4 procs
+
+% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
+
+% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
+
+---
+
+Run with MPI: 1 proc each
+
+% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
+
+---
+
+Run with MPI: 3 procs + 4 procs
+
+% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
+
+---
+
+Run in plugin mode: 1 proc
+
+% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
+
+---
+
+Run in plugin mode: 3 procs
+
+% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
+
+-------------------------------------------------
+-------------------------------------------------
+
+* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
+  Each calculation can be a single-point evaluation, MD run, or minimization
+
+The sequence_driver.py code allows for optional switches in addition
+to -mdi (required) and the -plugin and -plugin_args switches which are
+used to link to an engine as a plugin library.  The example run
+commands below just use the default values of the optional switches.
+The switches are also explained at the top of the file; the info is
+copied here:
+
+#   -n 3
+#     number of calculations to perform, default = 3
+#   -mode eval/run/min
+#     style of calculations: single snapshot evals, dynamics, minimization
+#     default = run
+#   -size Nx Ny Nz
+#     cubic lattice, default = 2 2 2
+#   -rho 0.75 0.1
+#     reduced density and random variation thereof, default = 0.75 0.1
+#   -delta 0.1
+#     randomly perturb atoms initially by this distance, default 0.1
+#   -nsteps 100
+#     number of timesteps in dynamics runs, default = 100
+#   -temp 1.0
+#     initial temperature in dynamics runs, default = 1.0
+#   -tol 0.001
+#     tolerance for minimizations, default = 0.001
+#   -seed 12345
+#     random number seed > 0, default = 12345
+
+---
+
+Run with TCP: 1 proc each
+
+% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
+
+% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
+
+---
+
+Run with TCP: 2 proc + 4 procs
+
+% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
+
+% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
+
+---
+
+Run with MPI: 1 proc each
+
+% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
+
+---
+
+Run with MPI: 2 procs + 4 procs
+
+% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
+
+---
+
+Run in plugin mode: 1 proc
+
+% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
+
+---
+
+Run in plugin mode: 3 procs
+
+% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
+
+-------------------------------------------------
+-------------------------------------------------
+
+* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
+  First LAMMPS instance performs the MD timestepping
+  Second LAMMPS instance is surrogate QM = computes forces
+
+The aimd_driver.py code allows for an optional switch in addition to
+-mdi (required) and the -plugin and -plugin_args swiches which are
+used to link to the 2 engines as a plugin libraries.  The example run
+commands below use the default values of the optional switch.  The
+switch is also explained the top of the file; the info is copied
+here:
+
+#   -nsteps 5
+#     number of timesteps in dynamics runs, default = 5
+
+---
+
+Run the entire calculation with a single instance of LAMMPS by itself
+  results should be identical to running this example with MDI
+
+% lmp_mpi < in.aimd.alone
+
+With MDI, the driver prints the QM and Total energies.  These should
+match the PotEng and TotEng output of the in.aimd.alone script.
+
+---
+
+Run with TCP: 1 proc each
+
+% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
+
+% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
+
+% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
+
+---
+
+Run with TCP: 2 procs + 2 procs + 3 procs
+
+% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
+
+% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
+
+% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
+
+---
+
+Run with MPI: 1 proc each
+
+% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
+
+---
+
+Run with MPI: 2 procs + 2 procs + 3 procs
+
+% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm

examples/mdi/aimd_driver.py

@@ -0,0 +1,255 @@
+# MDI driver to perform an AIMD simulation
+# using one instance of LAMMPS as the MD timestepper
+# using second instance of LAMMPS as a QM surrogate to compute forces
+
+# NOTE: this script is derived from the MDI_AIMD_Driver.cpp code
+#       included in the MDI distribution
+#  it alters the timestepping to match a velocity Verlet algorithm
+#    forces are computed once before timestepping beings
+#  both the @COORDS and @FORCES nodes are triggered in the MM code
+#    as the appropriate places to extract COORDS and provide FORCES
+
+# Syntax: python3 aimd_driver.py switch arg switch arg ...
+#   possible switches:
+#   -mdi "-role DRIVER ..."
+#     required switch
+#     example for stand-alone mode:
+#       -mdi "-role DRIVER -name sequence -method TCP -port 8021"
+#     example for plugin mode:
+#       -mdi "-role DRIVER -name sequemce -method LINK
+#             -plugin_path /home/sjplimp/lammps/src/"
+#   -plugin name
+#     name of plugin library, only when using plugin mode
+#   -plugin_args arglist
+#     args to add when launching plugin library, only when using plugin mode
+#     enclose arglist in quotes if multiple words
+#   -nsteps 5
+#     number of timesteps, default = 5
+
+import sys,math,random
+import mdi
+import numpy as np
+from mpi4py import MPI
+
+# error message
+
+def error(txt=None):
+  if txt: raise Exception(txt)
+  raise Exception("Syntax: python3 aimd_driver.py switch arg switch arg ...")
+
+# run an AIMD simulation
+
+def perform_aimd(world,mm_comm,qm_comm):
+
+  me = world.Get_rank()
+  nprocs = world.Get_size()
+
+  # receive number of atoms from the MM engine
+  
+  mdi.MDI_Send_command("<NATOMS",mm_comm)
+  natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mm_comm)
+  natoms = world.bcast(natoms,root=0)
+
+  # allocate arrays for coordinates and forces
+
+  coords = np.zeros(3*natoms,dtype=np.float64)
+  forces = np.zeros(3*natoms,dtype=np.float64)
+
+  # MM engine initializes a new MD simulation
+  
+  mdi.MDI_Send_command("@INIT_MD",mm_comm)
+  
+  # -----------------
+  # compute initial forces for Verlet timestepping
+  #   and initial energy for output on step 0
+  # -----------------
+  
+  # MM engine proceeds to @FORCES node in setup()
+  
+  mdi.MDI_Send_command("@FORCES",mm_comm)
+
+  # get coords from MM engine
+    
+  mdi.MDI_Send_command("<COORDS",mm_comm)
+  mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
+  world.Bcast(coords,root=0)
+
+  # send coords to QM engine
+  
+  mdi.MDI_Send_command(">COORDS",qm_comm)
+  mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
+
+  # get QM potential energy
+    
+  mdi.MDI_Send_command("<PE",qm_comm)
+  qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
+  qm_pe = world.bcast(qm_pe,root=0)
+  
+  # get forces from QM engine
+    
+  mdi.MDI_Send_command("<FORCES",qm_comm)
+  mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
+  world.Bcast(forces,root=0)
+
+  # send forces to MM engine
+  
+  mdi.MDI_Send_command(">FORCES",mm_comm)
+  mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
+
+  # get MM kinetic energy
+  
+  mdi.MDI_Send_command("<KE",mm_comm)
+  mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
+  mm_ke = world.bcast(mm_ke,root=0)
+
+  # output by driver
+  # normalize energies by atom count
+    
+  if me == 0:
+    print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
+          (0,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
+
+  # -----------------
+  # timestepping loop
+  # -----------------
+
+  for istep in range(nsteps):
+
+    # MM engine proceeds to @FORCES node
+    
+    mdi.MDI_Send_command("@FORCES",mm_comm)
+
+    # get coords from MM engine
+    
+    mdi.MDI_Send_command("<COORDS",mm_comm)
+    mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
+    world.Bcast(coords,root=0)
+
+    # send coords to QM engine
+    
+    mdi.MDI_Send_command(">COORDS",qm_comm)
+    mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
+
+    # get QM potential energy
+    
+    mdi.MDI_Send_command("<PE",qm_comm)
+    qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
+    qm_pe = world.bcast(qm_pe,root=0)
+
+    # get forces from QM engine
+    
+    mdi.MDI_Send_command("<FORCES",qm_comm)
+    mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
+    world.Bcast(forces,root=0)
+
+    # send forces to MM engine
+    
+    mdi.MDI_Send_command(">FORCES",mm_comm)
+    mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
+
+    # MM engine proceeds to @ENDSTEP node
+    # so that KE will be for fully updated velocity
+    
+    mdi.MDI_Send_command("@ENDSTEP",mm_comm)
+
+    # get MM kinetic energy
+    
+    mdi.MDI_Send_command("<KE",mm_comm)
+    mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
+    mm_ke = world.bcast(mm_ke,root=0)
+
+    # output by driver
+    # normalize energies by atom count
+    
+    if me == 0:
+      print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
+            (istep+1,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
+
+  #  send EXIT to each engine
+
+  mdi.MDI_Send_command("EXIT",mm_comm)
+  mdi.MDI_Send_command("EXIT",qm_comm)
+
+# ------------------------
+# main program
+# ------------------------
+
+args = sys.argv[1:]
+narg = len(args)
+
+# defaults for command-line args
+
+mdiarg = ""
+plugin = ""
+plugin_args = ""
+
+nsteps = 5
+
+# parse command-line args
+
+iarg = 0
+while iarg < narg:
+  if args[iarg] == "-mdi": 
+    if iarg+2 > narg: error()
+    mdiarg = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-plugin": 
+    if iarg+2 > narg: error()
+    plugin = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-plugin_args": 
+    if iarg+2 > narg: error()
+    plugin_args = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-nsteps":
+    if iarg+2 > narg: error()
+    nsteps = int(args[iarg+1])
+    if nsteps < 0: error()
+    iarg += 2 
+  else: error()
+
+if not mdiarg: error()
+
+# LAMMPS engines are stand-alone codes
+# world = MPI communicator for just this driver
+# invoke perform_tasks() directly
+
+if not plugin:
+  mdi.MDI_Init(mdiarg)
+  world = mdi.MDI_MPI_get_world_comm()
+  
+  # connect to 2 engines, determine which is MM vs QM
+
+  mdicomm1 = mdi.MDI_Accept_Communicator()
+  mdicomm2 = mdi.MDI_Accept_Communicator()
+
+  mdi.MDI_Send_command("<NAME",mdicomm1)
+  name1 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm1)
+  name1 = world.bcast(name1,root=0)
+  mdi.MDI_Send_command("<NAME",mdicomm2)
+  name2 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm2)
+  name2 = world.bcast(name2,root=0)
+
+  if name1 == "MM" and name2 == "QM":
+    mm_comm = mdicomm1
+    qm_comm = mdicomm2
+  elif name1 == "QM" and name2 == "MM":
+    mm_comm = mdicomm2
+    qm_comm = mdicomm1
+  else: error("Two engines have invalid names")
+    
+  perform_aimd(world,mm_comm,qm_comm)
+
+# LAMMPS engines are plugin libraries
+# launch plugins
+# NOTE: need to run driver on 2 or more procs
+#       partition driver into 2 MPI comms
+#       launch one plugin on each partition
+#       each with their own callback function
+
+if plugin:
+  error("Cannot yet run in plugin mode")
+  mdi.MDI_Init(mdiarg)
+  world = MPI.COMM_WORLD
+  plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
+  mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)

examples/mdi/in.aimd.alone

@@ -0,0 +1,32 @@
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5

examples/mdi/in.aimd.driver

@@ -0,0 +1,32 @@
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5

examples/mdi/in.aimd.driver.plugin

@@ -0,0 +1,34 @@
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd plugin
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+mdi             plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
+                infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
+                command "run 5"

examples/mdi/in.aimd.engine

@@ -0,0 +1,22 @@
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine

examples/mdi/in.aimd.mm

@@ -0,0 +1,23 @@
+# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+mdi             engine

examples/mdi/in.aimd.qm

@@ -0,0 +1,22 @@
+# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine

examples/mdi/in.sequence

@@ -0,0 +1,21 @@
+# MDI engine script to process a series of evaulate, run, minimize commands
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 1 0 1 0 1
+create_box	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             1 all nve
+
+thermo          10
+
+mdi             engine

examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1

@@ -0,0 +1,90 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
+
+Performance: 505739.085 tau/day, 1170.692 timesteps/s
+73.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0038665  | 0.0038665  | 0.0038665  |   0.0 | 90.53
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0001297  | 0.0001297  | 0.0001297  |   0.0 |  3.04
+Output  | 0.00014902 | 0.00014902 | 0.00014902 |   0.0 |  3.49
+Modify  | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 |   0.0 |  1.53
+Other   |            | 6.054e-05  |            |       |  1.42
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1956 ave        1956 max        1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          19500 ave       19500 max       19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1

@@ -0,0 +1,79 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms
+
+Performance: 731582.413 tau/day, 1693.478 timesteps/s
+99.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 |   0.0 |  0.43
+Output  | 0.00010561 | 0.00010561 | 0.00010561 |   0.0 |  3.58
+Modify  | 0.0028043  | 0.0028043  | 0.0028043  |   0.0 | 94.98
+Other   |            | 3e-05      |            |       |  1.02
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            166 ave         166 max         166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -1
+Ave neighs/atom = -0.002
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3

@@ -0,0 +1,79 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 3 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms
+
+Performance: 684416.574 tau/day, 1584.298 timesteps/s
+99.5% CPU use with 3 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.769e-05  | 3.7059e-05 | 4.7808e-05 |   0.0 |  1.17
+Output  | 0.00011556 | 0.00015516 | 0.00021954 |   0.0 |  4.92
+Modify  | 0.002819   | 0.0028366  | 0.0028599  |   0.0 | 89.88
+Other   |            | 0.0001272  |            |       |  4.03
+
+Nlocal:        166.667 ave         200 max         150 min
+Histogram: 2 0 0 0 0 0 0 0 0 1
+Nghost:        55.3333 ave          92 max          32 min
+Histogram: 1 1 0 0 0 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -3
+Ave neighs/atom = -0.006
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1

@@ -0,0 +1,80 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd plugin
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+mdi             plugin lammps mdi "-role ENGINE -name lammps -method LINK"                 infile in.aimd.engine extra "-log log.aimd.engine.plugin"                 command "run 5"
+run 5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms
+
+Performance: 544685.246 tau/day, 1260.845 timesteps/s
+98.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 |   0.0 |  0.40
+Output  | 0.00011527 | 0.00011527 | 0.00011527 |   0.0 |  2.91
+Modify  | 0.0038025  | 0.0038025  | 0.0038025  |   0.0 | 95.89
+Other   |            | 3.184e-05  |            |       |  0.80
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            166 ave         166 max         166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -1
+Ave neighs/atom = -0.002
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3

@@ -0,0 +1,80 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 3 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd plugin
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+mdi             plugin lammps mdi "-role ENGINE -name lammps -method LINK"                 infile in.aimd.engine extra "-log log.aimd.engine.plugin"                 command "run 5"
+run 5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms
+
+Performance: 752045.581 tau/day, 1740.846 timesteps/s
+99.1% CPU use with 3 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 |   0.0 |  1.36
+Output  | 9.6932e-05 | 0.00012081 | 0.00016442 |   0.0 |  4.21
+Modify  | 0.0026109  | 0.0026258  | 0.0026494  |   0.0 | 91.42
+Other   |            | 8.637e-05  |            |       |  3.01
+
+Nlocal:        166.667 ave         200 max         150 min
+Histogram: 2 0 0 0 0 0 0 0 0 1
+Nghost:        55.3333 ave          92 max          32 min
+Histogram: 1 1 0 0 0 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -3
+Ave neighs/atom = -0.006
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1

@@ -0,0 +1,79 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms
+
+Performance: 1792.736 tau/day, 4.150 timesteps/s
+0.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 |   0.0 |  0.00
+Output  | 0.00026499 | 0.00026499 | 0.00026499 |   0.0 |  0.02
+Modify  | 1.2045     | 1.2045     | 1.2045     |   0.0 | 99.97
+Other   |            | 6.184e-05  |            |       |  0.01
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            166 ave         166 max         166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -1
+Ave neighs/atom = -0.002
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:08

examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3

@@ -0,0 +1,79 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI driver script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 3 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+# NVE
+fix		1 all nve
+# NPT
+#fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
+
+fix             2 all mdi/aimd
+fix_modify      2 energy yes virial yes
+
+thermo_style    custom step temp pe etotal press vol
+thermo          1
+
+run             5
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0         1.44   -6.7733681   -4.6176881   -5.0221006    592.27671 
+       1    1.4377309   -6.7699814   -4.6176981   -5.0007431    592.27671 
+       2     1.430825   -6.7596844   -4.6177394   -4.9363501    592.27671 
+       3    1.4189655   -6.7420029   -4.6178116   -4.8276957    592.27671 
+       4    1.4016029   -6.7161132   -4.6179137   -4.6726332    592.27671 
+       5    1.3779738   -6.6808361   -4.6180094    -4.468186    592.27671 
+Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms
+
+Performance: 1800.259 tau/day, 4.167 timesteps/s
+66.7% CPU use with 3 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 4.604e-06  | 4.8462e-05 | 7.527e-05  |   0.0 |  0.00
+Output  | 0.00015266 | 0.00020593 | 0.00031177 |   0.0 |  0.02
+Modify  | 1.1993     | 1.1994     | 1.1994     |   0.0 | 99.96
+Other   |            | 0.0002123  |            |       |  0.02
+
+Nlocal:        166.667 ave         200 max         150 min
+Histogram: 2 0 0 0 0 0 0 0 0 1
+Nghost:        55.3333 ave          92 max          32 min
+Histogram: 1 1 0 0 0 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = -3
+Ave neighs/atom = -0.006
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:08

examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 3 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:01

examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - MDI engine script
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:01

examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1

@@ -0,0 +1,5 @@
+Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
+Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
+Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
+Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
+Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2

@@ -0,0 +1,5 @@
+Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
+Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
+Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
+Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
+Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1

@@ -0,0 +1,6 @@
+Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
+Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
+Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
+Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
+Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
+Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2

@@ -0,0 +1,6 @@
+Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
+Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
+Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
+Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
+Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
+Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1

@@ -0,0 +1,44 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+mdi             engine
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44            0            0      2.15568    1.2132167 
+       1    1.4377309            0            0    2.1522832     1.211305 
+       2     1.430825            0            0     2.141945    1.2054866 
+       3    1.4189655            0            0    2.1241913    1.1954949 
+       4    1.4016029            0            0    2.0981995    1.1808667 
+       5    1.3779738            0            0    2.0628267    1.1609589 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2

@@ -0,0 +1,44 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+mdi             engine
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44            0            0      2.15568    1.2132167 
+       1    1.4377309            0            0    2.1522832     1.211305 
+       2     1.430825            0            0     2.141945    1.2054866 
+       3    1.4189655            0            0    2.1241913    1.1954949 
+       4    1.4016029            0            0    2.0981995    1.1808667 
+       5    1.3779738            0            0    2.0628267    1.1609589 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1

@@ -0,0 +1,44 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+mdi             engine
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44            0            0      2.15568    1.2132167 
+       1    1.4377309            0            0    2.1522832     1.211305 
+       2     1.430825            0            0     2.141945    1.2054866 
+       3    1.4189655            0            0    2.1241913    1.1954949 
+       4    1.4016029            0            0    2.0981995    1.1808667 
+       5    1.3779738            0            0    2.0628267    1.1609589 
+Total wall time: 0:00:11

examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2

@@ -0,0 +1,44 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+mdi             engine
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
+Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44            0            0      2.15568    1.2132167 
+       1    1.4377309            0            0    2.1522832     1.211305 
+       2     1.430825            0            0     2.141945    1.2054866 
+       3    1.4189655            0            0    2.1241913    1.1954949 
+       4    1.4016029            0            0    2.0981995    1.1808667 
+       5    1.3779738            0            0    2.0628267    1.1609589 
+Total wall time: 0:00:11

examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 3 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:00

examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1

@@ -0,0 +1,55 @@
+LAMMPS (17 Feb 2022)
+# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
+  create_atoms CPU = 0.001 seconds
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+mdi             engine
+WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.7733681            0   -6.7733681   -6.2353173 
+       1            0   -6.7699814            0   -6.7699814   -6.2120481 
+       2            0   -6.7596844            0   -6.7596844   -6.1418368 
+       3            0   -6.7420029            0   -6.7420029   -6.0231905 
+       4            0   -6.7161132            0   -6.7161132   -5.8534999 
+       5            0   -6.6808361            0   -6.6808361   -5.6291449 
+Total wall time: 0:00:01