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Merge branch 'develop' into remove-message-package

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This commit is contained in:
Axel Kohlmeyer
2022-04-09 00:25:11 -04:00
parent 521d45dcc6 8b53ff9383
commit 674d2a6788
213 changed files with 21808 additions and 8033 deletions
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4
bench/README
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@ -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

4
cmake/Modules/Packages/GPU.cmake
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@ -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)

4
cmake/Modules/Packages/MDI.cmake
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@ -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_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum 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 "8a8da217148bd9b700083b67d795af5e" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)

1
doc/src/Commands_compute.rst
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@ -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>`

2
doc/src/Commands_fix.rst
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@ -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>`

8
doc/src/Commands_pair.rst
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@ -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/tstat <pair_dpd_ext>`
* :doc:`dpd/ext (k) <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>`

21
doc/src/Developer_plugins.rst
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@ -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.

2
doc/src/Examples.rst
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@ -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 |

27
doc/src/Howto_couple.rst
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@ -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
this scenario, LAMMPS is the driver code. During timestepping,
1. Define a new :doc:`fix <fix>` command that calls the other code.
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>`_
to compute forces, is hooked to LAMMPS.
See the :doc:`fix latte <fix_latte>` command for more details.
Also see the :doc:`Modify <Modify>` doc pages for info on how to
add a new fix to LAMMPS.
tight-binding calculations using the `LATTE software
<https://github.com/lanl/LATTE>`_ to compute forces, is hooked to
LAMMPS. See the :doc:`fix latte <fix_latte>` command for more
details. Also see the :doc:`Modify <Modify>` doc pages for info on
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
described on the :doc:`Howto MDI library coupling <Howto_mdi>` page.
4. Couple LAMMPS with another code in a client/server fashion, using
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.

211
doc/src/Howto_mdi.rst
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@ -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"
and sends request messages (data) to a "server" code. The server
responds to each request with a reply message. This enables the two
codes to work in tandem to perform a simulation. LAMMPS can act as
either a client or server code; it does this by using the `MolSSI
Driver Interface (MDI) library
Client/server coupling of two (or more) codes is where one code is the
"client" and sends request messages (data) to one (or more) "server"
code(s). A server responds to each request with a reply message
(data). This enables two (or more) codes to work in tandem to perform
a simulation. LAMMPS can act as either a client or server code; it
does this by using the `MolSSI Driver Interface (MDI) library
<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
to run the two codes on different numbers of processors. If a message
protocol (format and content) is defined for a particular kind of
simulation, then in principle any code which implements the client-side
protocol can be used in tandem with any code which implements the
server-side protocol. Neither code needs to know what specific other
code it is working with.
neither code needs to have a library interface. This also makes it
easy to run the two codes on different numbers of processors. If a
message protocol (format and content) is defined for a particular kind
of simulation, then in principle any code which implements the
client-side protocol can be used in tandem with any code which
implements the server-side protocol. Neither code needs to know what
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
stand-alone executables, MDI also enables a server code to be a
"plugin" to the client code. In this scenario, server code(s) are
compiled as shared libraries, and one (or more) instances of the
server are instantiated by the driver code. If the driver code runs
in parallel, it can split its MPI communicator into multiple
sub-communicators, and launch each plugin engine instance on a
sub-communicator. Driver processors in that sub-communicator exchange
messages with that engine instance, and can also send MPI messages to
other processors in the driver. The driver code can also destroy
engine instances and re-instantiate them.
In addition to allowing driver and engine(s) to run as stand-alone
executables, MDI also enables an engine to be a *plugin* to the client
code. In this scenario, server code(s) are compiled as shared
libraries, and one (or more) instances of the server are instantiated
by the driver code. If the driver code runs in parallel, it can split
its MPI communicator into multiple sub-communicators, and launch each
plugin engine instance on a sub-communicator. Driver processors
within that sub-communicator exchange messages with the corresponding
engine instance, and can also send MPI messages to other processors in
the driver. The driver code can also destroy engine instances and
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
MDI_Send() and MDI_Recv() calls, which are conceptually similar to
MPI_Send() and MPI_Recv() calls. Each send or receive has a string
which identifies the command name, and optionally some data, which can
be a single value or vector of values of any data type. Inside the
MDI library, data is exchanged between the driver and engine via MPI
calls or sockets. This a run-time choice by the user.
The way in which an MDI driver communicates with an MDI engine is by
making MDI_Send() and MDI_Recv() calls, which are conceptually similar
to MPI_Send() and MPI_Recv() calls. Each send or receive operation
uses a string to identify the command name, and optionally some data,
which can be a single value or vector of values of any data type.
Inside the MDI library, data is exchanged between the driver and
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
suite of quantum DFT codes), can work together via the MDI library to
perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
simulation and sends a message each timestep to ``pw.x`` asking it to
compute quantum forces on the current configuration of atoms. Here is
how the 2 codes are launched to communicate by MPI:
Currently there are two quantum DFT codes which have direct MDI
support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also
several QM codes which have indirect support through QCEngine or i-PI.
The former means they require a wrapper program (QCEngine) with MDI
support which writes/read files to pass data to the quantum code
itself. The list of QCEngine-supported and i-PI-supported quantum
codes is on the `MDI webpage
<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" \
-in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
% 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
processors.
Here is how the 2 codes are launched to communicate by sockets:
Here is how to build QE as a shared library which can be used in plugin mode,
which results in a libqemdi.so file in <base_path>/q-e/MDI/src:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
% 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
machine. Or in the same window, if the first command is ended with
"&" so as to run in the background. If "localhost" is replaced by an
IP address, ``pw.x`` could be run on another machine on the same network, or
even on another machine across the country.
INQ cannot be built as a stand-alone code; it is by design a library.
Here is how to build INQ as a shared library which can be used in
plugin mode, which results in a libinqmdi.so file in
<base_path>/inq/build/examples:
After both codes initialize themselves to model the same system, this is
what occurs each timestep:
.. code-block:: bash
* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
* LAMMPS receives the forces and time integrates to complete a single timestep
-------------
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
% git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
% cd <base_path>/inq
% mkdir -p build
% cd build
% ../configure --prefix=<install_path>/install
% make -j 4
% make install

6
doc/src/Howto_structured_data.rst
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@ -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])

15
doc/src/Packages_details.rst
View File

@ -1395,17 +1395,24 @@ MDI package
**Contents:**
A LAMMPS command and fix to allow client-server coupling of LAMMPS to
other atomic or molecular simulation codes via the `MolSSI Driver Interface
A LAMMPS command and fixes to allow client-server coupling of LAMMPS
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>`
* :doc:`fix mdi/engine <fix_mdi_engine>`
* lib/mdi/README
* :doc:`Howto MDI <Howto_mdi>`
* :doc:`mdi <mdi>`
* :doc:`fix mdi/aimd <fix_mdi_aimd>`
* examples/PACKAGES/mdi
----------

2
doc/src/Packages_list.rst
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@ -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

3
doc/src/compute.rst
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@ -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>` -

99
doc/src/compute_fep_ta.rst Normal file
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@ -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)

79
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@ -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
support parallel I/O for output. This option is not available for the
*dcd*, *xtc*, and *xyz* styles.
files and can be a fast mode of output on parallel machines that support
parallel I/O for output. This option is **not** available for the *dcd*,
*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
are only enabled if LAMMPS was built with that package. See the
The *xtc*, *dcd* and *yaml* styles are part of the EXTRA-DUMP package.
They are only enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands

36
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@ -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
triggers writing of :doc:`thermo <thermo>` information to the dump file
The *thermo* keyword only applies the dump styles *netcdf* and *yaml*.
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>`.

2
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@ -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

103
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@ -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

59
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@ -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

19
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@ -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
away from) the target configuration. The parameter "rho" is
monotonically decreased (or increased) from its initial value to
rho_final at the end of the run.
holonomic constraint is used to force the atoms to move towards (or away
from) the target configuration. The parameter "rho" is monotonically
decreased (or increased) from its initial value to rho_final at the end
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
included, the first 3 lines should not appear. The 3 lines contain the
first 3 lo/hi lines **must** appear in the file. If image flags are not
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.

8
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@ -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/
Every line with the odd number is considered as a comment and
The fix ttm/mod parameter file *init_file* has the following syntax.
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::

312
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@ -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

88
doc/src/mdi_engine.rst
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@ -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

19
doc/src/package.rst
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@ -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
signicant.
therefore doubles the memory overhead of the neighbor list, which can
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
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
kokkos command allows it to be set from the command line. 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
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 kokkos command allows it to be set from the command line.
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

6
doc/src/pair_dpd.rst
View File

@ -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
""""""

10
doc/src/pair_dpd_ext.rst
View File

@ -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**\ :

9
doc/src/plugin.rst
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@ -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.
See the :doc:`Build package <Build_package>` page for
more info. Plugins are not available on Windows.
only enabled if LAMMPS was built with that package. See
the :doc:`Build package <Build_package>` page for more info.
If plugins access functions or classes from a package, LAMMPS must
have been compiled with that package included.
If plugins access functions or classes from a package,
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

43
doc/src/thermo_modify.rst
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@ -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
which is used for the Mth value output in each line, e.g. the fifth
column is output in high precision for "format 5 %20.15g".
output. The setting for *ID string* also takes a single format argument
which is used for the indexed value in each line. The interpretation is
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

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -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

20
examples/PACKAGES/dpd-basic/README
View File

@ -1,10 +1,16 @@
Examples for Extended Dissipative Particle Dynamics (DPD)
---------------------------------------------------------
This directory contains examples for extended DPD simulations
Examples for Basic Dissipative Particle Dynamics (DPD)
------------------------------------------------------
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
configuration (dpdext.data)
1) 'dpd' - simple example (DPD fluid) for 'dpd' pair style (in.dpd)
2) 'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style
(in.cg_spce), an initial configuration (dpdext.data) and tabulated potential
2) 'dpd_tstat' - coarse-grained SPC/E water example for 'dpd/tstat' pair style
(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.

43
examples/PACKAGES/dpd-basic/dpd/in.dpd Normal file
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@ -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

154
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@ -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

154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4 Normal file
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@ -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

2
examples/PACKAGES/dpd-basic/dpdext/dpdext.data → examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce.data
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@ -1,4 +1,4 @@
DPD Fluid
Coarse-Grained SPC/E Water
2180 atoms

354
examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot Normal file
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@ -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
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

31
examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat Normal file
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@ -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

106
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@ -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

106
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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

10
examples/PACKAGES/dpd-basic/dpdext/in.dpdext
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@ -16,9 +16,8 @@ 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 132456 simBox
create_atoms 2 random 100 132456 simBox
create_atoms 1 random 100 12456 simBox
create_atoms 2 random 100 13245 simBox
mass 1 1.0
mass 2 2.0
###
@ -35,10 +34,9 @@ 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

153
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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

153
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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

2196
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data
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354
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot
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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

1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot Symbolic link
View File

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

6
examples/PACKAGES/dpd-basic/dpdext_tstat/in.cg_spce → examples/PACKAGES/dpd-basic/dpdext_tstat/in.dpdext_tstat
View File

@ -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

293
examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1
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@ -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

293
examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4
View File

@ -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

106
examples/PACKAGES/dpd-basic/dpdext_tstat/log.5Apr22.dpdext_tstat.g++.1 Normal file
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@ -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

106
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@ -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

2
examples/PACKAGES/fep/README.md
View File

@ -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.

6174
examples/PACKAGES/fep/ta/data.spce Normal file
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File diff suppressed because it is too large Load Diff

49
examples/PACKAGES/fep/ta/in.spce.lmp Normal file
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@ -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

689
examples/PACKAGES/fep/ta/log.spce Normal file
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@ -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
80000 296.17928 -360.65589 -8679.0048 -11390.25 0.68794433 0.31538684 0.45
85000 303.90294 488.01134 -8643.2028 -11425.151 0.41330713 0.49993365 0.45
90000 296.49425 14.901201 -8636.0539 -11350.182 -0.21538319 1.4351695 0.45
95000 308.63505 137.10659 -8570.395 -11395.661 0.51407684 0.42218544 0.45
100000 302.56638 -402.80803 -8635.0157 -11404.729 0.1552006 0.77079493 0.45
105000 293.79289 -417.74599 -8626.2538 -11315.654 -0.13491963 1.253969 0.45
110000 293.52504 -808.94658 -8684.9259 -11371.874 0.20573374 0.70815164 0.45
115000 307.6821 132.78071 -8639.817 -11456.36 -0.67060193 3.0798018 0.45
120000 303.22974 121.87128 -8714.7295 -11490.515 0.3675961 0.5397742 0.45
125000 303.8202 -34.518279 -8625.1384 -11406.329 0.17151619 0.74998608 0.45
130000 294.5718 -508.86133 -8684.9608 -11381.491 0.23323323 0.67622827 0.45
135000 302.79866 -445.99091 -8627.6163 -11399.456 0.3300839 0.57482965 0.45
140000 297.84052 -78.442467 -8621.5234 -11347.976 0.39157424 0.51849484 0.45
145000 303.64247 463.89678 -8673.8591 -11453.423 0.39692857 0.51385891 0.45
150000 288.38239 28.567607 -8789.6464 -11429.518 -0.045509865 1.0793274 0.45
155000 296.02581 -111.35664 -8674.295 -11384.135 0.23313764 0.67633671 0.45
160000 307.72004 -410.73956 -8578.8169 -11395.707 0.28485416 0.62013794 0.45
165000 300.42279 -483.56039 -8598.0354 -11348.126 0.38342507 0.52563101 0.45
170000 302.51326 -150.99512 -8626.2426 -11395.469 0.2439355 0.66419697 0.45
175000 295.41161 -554.9058 -8760.0201 -11464.238 0.38186652 0.52700696 0.45
180000 296.21987 -194.97724 -8645.4143 -11357.031 0.098453456 0.84777037 0.45
185000 296.52352 -186.85833 -8690.0538 -11404.45 0.6348999 0.34473516 0.45
190000 304.72799 -60.2868 -8667.2005 -11456.701 0.1885985 0.72880108 0.45
195000 306.65221 -871.17267 -8679.3434 -11486.458 0.56138735 0.38997638 0.45
200000 301.07509 362.96369 -8616.9867 -11373.048 -0.53126323 2.4379049 0.45
205000 303.65587 -216.8767 -8564.3182 -11344.005 0.11046546 0.83085967 0.45
210000 296.20891 -474.08356 -8698.3778 -11409.894 -0.11237476 1.2074335 0.45
215000 295.37276 422.46284 -8714.4636 -11418.326 0.042757549 0.93079022 0.45
220000 301.20663 -202.20616 -8577.1827 -11334.449 0.30387837 0.60066105 0.45
225000 306.20481 -90.566175 -8503.5134 -11306.533 0.29188403 0.6128683 0.45
230000 303.54253 -24.255163 -8641.8724 -11420.521 -0.38522168 1.9082173 0.45
235000 300.29265 -572.08074 -8664.2779 -11413.177 0.48055356 0.44660587 0.45
240000 302.90712 -226.88617 -8636.6962 -11409.528 -0.15295452 1.2924832 0.45
245000 305.05222 -68.241521 -8591.0885 -11383.557 -0.19850824 1.3951152 0.45
250000 300.27784 -46.680162 -8746.7288 -11495.492 -0.0098493376 1.0166585 0.45
255000 308.23091 -424.64171 -8573.7405 -11395.307 0.1366107 0.79520901 0.45
260000 296.11619 4.6901264 -8742.1916 -11452.859 -0.12450429 1.2322516 0.45
265000 301.62359 134.42152 -8565.5323 -11326.615 -0.028534957 1.0490284 0.45
270000 306.71999 -62.484213 -8690.7983 -11498.534 0.28432443 0.62068922 0.45
275000 292.91982 532.15442 -8779.2684 -11460.676 -0.40898808 1.9858264 0.45
280000 306.88024 -339.05165 -8557.2761 -11366.479 0.12573772 0.80984534 0.45
285000 303.38798 617.66326 -8630.5787 -11407.813 -0.1310487 1.2458532 0.45
290000 299.66094 302.90333 -8692.267 -11435.383 0.65063395 0.33575584 0.45
295000 304.49009 656.72392 -8710.7918 -11498.115 -0.16849302 1.3266137 0.45
300000 303.80861 -221.66912 -8688.9465 -11470.031 -0.24985266 1.5205954 0.45
305000 300.67136 -498.92059 -8669.6648 -11422.031 0.19219443 0.72441833 0.45
310000 305.7021 -521.59218 -8505.6751 -11304.093 0.52013748 0.4179152 0.45
315000 302.66313 -359.25677 -8682.4925 -11453.091 -0.26135382 1.5502155 0.45
320000 304.5646 441.04962 -8610.9569 -11398.962 0.41662005 0.49716319 0.45
325000 300.04934 -142.59053 -8698.3246 -11444.997 -0.23029219 1.4715132 0.45
330000 305.55522 -212.47771 -8576.3678 -11373.441 0.091594168 0.85758093 0.45
335000 294.79439 -151.62761 -8762.4565 -11461.024 0.14345357 0.78613362 0.45
340000 302.4373 463.41717 -8643.2588 -11411.79 0.36279978 0.54413438 0.45
345000 295.91624 -272.3623 -8678.9725 -11387.81 0.1032874 0.84092407 0.45
350000 300.60829 62.418773 -8633.2343 -11385.023 -0.040578988 1.0704371 0.45
355000 301.41802 -860.82496 -8573.5867 -11332.788 0.04947461 0.9203617 0.45
360000 298.03103 -265.05516 -8619.4232 -11347.619 -0.20903224 1.4199617 0.45
365000 298.08727 -359.76277 -8612.4898 -11341.201 0.040109682 0.93493354 0.45
370000 301.55162 -339.05976 -8687.3746 -11447.799 0.1705358 0.75122045 0.45
375000 299.3933 -290.38029 -8723.9515 -11464.618 -0.1476 1.2809266 0.45
380000 303.02442 -1104.7914 -8626.7252 -11400.631 0.3211992 0.58346059 0.45
385000 301.49421 -613.53228 -8662.2479 -11422.146 -0.42642873 2.0447796 0.45
390000 302.01134 -351.23257 -8662.4664 -11427.099 0.23747904 0.67142935 0.45
395000 307.32962 -443.86959 -8624.8646 -11438.181 0.17359502 0.74737541 0.45
400000 301.67955 -253.92045 -8690.6143 -11452.209 -0.43779134 2.0841261 0.45
405000 302.60773 -97.544471 -8646.8281 -11416.92 0.071259831 0.88733652 0.45
410000 302.48853 -630.99507 -8710.4497 -11479.45 0.28763517 0.61725182 0.45
415000 296.46562 -443.33457 -8763.0661 -11476.932 0.088532948 0.86199583 0.45
420000 295.37803 -70.515081 -8720.0027 -11423.913 0.06359365 0.89882065 0.45
425000 299.31069 -48.284153 -8678.6115 -11418.522 0.063520704 0.89893064 0.45
430000 296.37918 -651.48627 -8784.4246 -11497.5 -0.0094249768 1.0159351 0.45
435000 303.07145 -284.10404 -8558.3149 -11332.651 0.034731239 0.94340646 0.45
440000 293.1823 -280.18182 -8707.2432 -11391.054 0.14151034 0.78870025 0.45
445000 305.55617 -286.4858 -8646.9315 -11444.013 0.26166889 0.64473078 0.45
450000 300.67206 102.89156 -8705.2376 -11457.61 0.88202179 0.2277515 0.45
455000 304.23258 9.5792632 -8571.8771 -11356.843 -0.42835558 2.0513992 0.45
460000 292.30355 265.8009 -8707.4453 -11383.212 0.20592758 0.70792142 0.45
465000 297.62746 193.66269 -8716.5132 -11441.015 0.36938368 0.53815813 0.45
470000 292.53483 -75.549804 -8728.3188 -11406.202 0.49993961 0.43231669 0.45
475000 296.10181 -202.26042 -8657.5804 -11368.116 -0.29829888 1.6493239 0.45
480000 300.24953 249.20038 -8688.6705 -11437.175 0.4372485 0.48025452 0.45
485000 296.41241 -73.46156 -8558.9344 -11272.314 -0.15947631 1.3067001 0.45
490000 302.51379 -654.60188 -8571.28 -11340.512 0.36608136 0.54114742 0.45
495000 300.50497 -127.55361 -8724.7069 -11475.55 0.029571506 0.95160701 0.45
500000 303.60879 183.79306 -8568.3539 -11347.609 0.050255275 0.91915729 0.45
505000 303.19721 -181.45226 -8614.403 -11389.891 0.32941264 0.57547725 0.45
510000 296.74554 -22.844257 -8659.5977 -11376.026 0.017555998 0.97098101 0.45
515000 304.94785 184.89151 -8657.5502 -11449.063 0.36892431 0.53857296 0.45
520000 297.55996 -618.66865 -8737.5039 -11461.388 0.0057510291 0.99039963 0.45
525000 301.79028 298.59479 -8629.0889 -11391.698 0.34316268 0.56235619 0.45
530000 309.73127 127.43322 -8551.5448 -11386.846 0.76278829 0.27817682 0.45
535000 296.10155 231.50902 -8700.9183 -11411.452 0.44398766 0.47485618 0.45
540000 299.71005 -102.1096 -8655.905 -11399.471 0.76085637 0.27907974 0.45
545000 300.14982 -206.19313 -8714.8486 -11462.44 0.22627441 0.68416793 0.45
550000 294.79885 -643.7432 -8605.2486 -11303.857 -0.057557071 1.1013603 0.45
555000 294.17638 -19.930168 -8726.0381 -11418.949 0.40954478 0.50309869 0.45
560000 297.03199 -369.45853 -8470.404 -11189.455 -0.6540448 2.9954437 0.45
565000 291.48707 -349.3956 -8714.1576 -11382.45 0.16175418 0.76236802 0.45
570000 310.66906 -63.356318 -8637.4971 -11481.383 0.025729917 0.95775884 0.45
575000 300.62447 -741.10788 -8620.5725 -11372.509 0.16003059 0.76457532 0.45
580000 303.7169 -69.625554 -8649.3106 -11429.556 0.13011667 0.80391862 0.45
585000 296.8583 22.033506 -8781.0388 -11498.5 0.05826221 0.9068948 0.45
590000 295.12104 251.36802 -8661.2354 -11362.793 0.0042041083 0.99297285 0.45
595000 291.91551 264.01646 -8784.286 -11456.5 -0.3176707 1.7037977 0.45
600000 299.51751 -425.6209 -8680.4016 -11422.205 0.063170047 0.89945954 0.45
605000 296.04489 -702.56187 -8648.8336 -11358.848 0.44150563 0.47683729 0.45
610000 293.08062 387.21018 -8636.9022 -11319.782 0.430424 0.48578377 0.45
615000 300.1062 -406.07366 -8651.5383 -11398.731 0.16393273 0.75958719 0.45
620000 304.45492 -717.77411 -8466.6335 -11253.634 0.14754207 0.78076073 0.45
625000 300.25467 394.44177 -8545.7468 -11294.298 -0.098814662 1.1802796 0.45
630000 301.25687 315.97468 -8555.4413 -11313.167 -0.30209606 1.6598626 0.45
635000 296.62552 -313.8236 -8661.4264 -11376.756 0.82351209 0.25123759 0.45
640000 300.49659 458.65236 -8648.2545 -11399.021 -0.2575 1.5402266 0.45
645000 299.08458 -40.905776 -8589.4621 -11327.303 0.07180479 0.88652576 0.45
650000 299.78807 286.71966 -8663.8862 -11408.166 -0.10586303 1.1943167 0.45
655000 300.2646 175.76273 -8685.9588 -11434.601 -0.4131303 1.9996722 0.45
660000 296.01304 69.482635 -8722.0849 -11431.808 0.65234529 0.33479341 0.45
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1730000 302.58784 590.55523 -8670.9964 -11440.906 -0.28655798 1.6171597 0.45
1735000 295.17235 -60.036989 -8631.671 -11333.699 0.72231294 0.29771902 0.45
1740000 290.06228 -254.79282 -8715.6619 -11370.912 0.35583392 0.55052961 0.45
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

22
examples/PACKAGES/fep/ta/spce.fep.ta Normal file
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# 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

1
examples/PACKAGES/tmd/data.peptide Symbolic link
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../../peptide/data.peptide

45
examples/PACKAGES/tmd/in.tmd Normal file
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# 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

210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 Normal file
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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

210
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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

4
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# 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

4
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# 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

13
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# 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

2
examples/README
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@ -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:

99
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##########################################
# 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()

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# 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()

54
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#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);
}

228
examples/mdi/README Normal file
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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

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# 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)

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# 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

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# 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

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# 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"

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# 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

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# 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

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# 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

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# 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

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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

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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

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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

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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

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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

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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

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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

55
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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

55
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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

55
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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

55
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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

55
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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

55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 Normal file
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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

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 Normal file
View File

@ -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

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 Normal file
View File

@ -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

6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 Normal file
View File

@ -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

6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 Normal file
View File

@ -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

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 Normal file
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@ -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

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 Normal file
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@ -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

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 Normal file
View File

@ -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

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 Normal file
View File

@ -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

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 Normal file
View File

@ -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

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 Normal file
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@ -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

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 Normal file
View File

@ -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

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