Fix merge conflicts
This commit is contained in:
rohskopf
@ -6,6 +6,9 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
"Please remove CMakeCache.txt and CMakeFiles first.")
|
||||
endif()
|
||||
|
||||
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
|
||||
CACHE STRING "URL for thirdparty package downloads")
|
||||
|
||||
# global LAMMPS/plugin build settings
|
||||
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
|
||||
if(NOT LAMMPS_SOURCE_DIR)
|
||||
@ -78,6 +81,13 @@ function(get_newest_file path variable)
|
||||
set(${variable} ${_bestfile} PARENT_SCOPE)
|
||||
endfunction()
|
||||
|
||||
# get LAMMPS version date
|
||||
function(get_lammps_version version_header variable)
|
||||
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
|
||||
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}")
|
||||
set(${variable} "${date}" PARENT_SCOPE)
|
||||
endfunction()
|
||||
|
||||
#################################################################################
|
||||
# LAMMPS C++ interface. We only need the header related parts except on windows.
|
||||
add_library(lammps INTERFACE)
|
||||
@ -89,6 +99,7 @@ endif()
|
||||
################################################################################
|
||||
# MPI configuration
|
||||
if(NOT CMAKE_CROSSCOMPILING)
|
||||
set(MPI_CXX_SKIP_MPICXX TRUE)
|
||||
find_package(MPI QUIET)
|
||||
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
|
||||
else()
|
||||
|
||||
@ -47,8 +47,8 @@ if(DOWNLOAD_KOKKOS)
|
||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
|
||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
||||
include(ExternalProject)
|
||||
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
|
||||
set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" CACHE STRING "MD5 checksum of KOKKOS tarball")
|
||||
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
|
||||
set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball")
|
||||
mark_as_advanced(KOKKOS_URL)
|
||||
mark_as_advanced(KOKKOS_MD5)
|
||||
ExternalProject_Add(kokkos_build
|
||||
@ -72,7 +72,7 @@ if(DOWNLOAD_KOKKOS)
|
||||
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
|
||||
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
|
||||
elseif(EXTERNAL_KOKKOS)
|
||||
find_package(Kokkos 3.6.00 REQUIRED CONFIG)
|
||||
find_package(Kokkos 3.6.01 REQUIRED CONFIG)
|
||||
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
||||
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
|
||||
else()
|
||||
|
||||
@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
|
||||
|
||||
if(DOWNLOAD_MDI)
|
||||
message(STATUS "MDI download requested - we will build our own")
|
||||
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
|
||||
set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
|
||||
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball")
|
||||
set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball")
|
||||
mark_as_advanced(MDI_URL)
|
||||
mark_as_advanced(MDI_MD5)
|
||||
enable_language(C)
|
||||
@ -44,7 +44,7 @@ if(DOWNLOAD_MDI)
|
||||
ExternalProject_Add(mdi_build
|
||||
URL ${MDI_URL}
|
||||
URL_MD5 ${MDI_MD5}
|
||||
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
|
||||
CMAKE_ARGS
|
||||
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
|
||||
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
|
||||
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
|
||||
@ -54,6 +54,7 @@ if(DOWNLOAD_MDI)
|
||||
-Dlanguage=C
|
||||
-Dlibtype=STATIC
|
||||
-Dmpi=${MDI_USE_MPI}
|
||||
-Dplugins=ON
|
||||
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
|
||||
UPDATE_COMMAND ""
|
||||
INSTALL_COMMAND ""
|
||||
|
||||
@ -44,7 +44,9 @@ if(DOWNLOAD_N2P2)
|
||||
else()
|
||||
# get path to MPI include directory
|
||||
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
|
||||
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
|
||||
foreach (_INCL ${N2P2_MPI_INCLUDE})
|
||||
set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -I${_INCL}")
|
||||
endforeach()
|
||||
endif()
|
||||
|
||||
# prefer GNU make, if available. N2P2 lib seems to need it.
|
||||
@ -75,7 +77,7 @@ if(DOWNLOAD_N2P2)
|
||||
UPDATE_COMMAND ""
|
||||
CONFIGURE_COMMAND ""
|
||||
PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
|
||||
BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
|
||||
BUILD_COMMAND ${N2P2_MAKE} -C <SOURCE_DIR>/src -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
|
||||
BUILD_ALWAYS YES
|
||||
INSTALL_COMMAND ""
|
||||
BUILD_IN_SOURCE 1
|
||||
|
||||
@ -138,6 +138,8 @@ KOKKOS, o = OPENMP, t = OPT.
|
||||
* :doc:`smd/vol <compute_smd_vol>`
|
||||
* :doc:`snap <compute_sna_atom>`
|
||||
* :doc:`sna/atom <compute_sna_atom>`
|
||||
* :doc:`sna/grid <compute_sna_atom>`
|
||||
* :doc:`sna/grid/local <compute_sna_atom>`
|
||||
* :doc:`snad/atom <compute_sna_atom>`
|
||||
* :doc:`snav/atom <compute_sna_atom>`
|
||||
* :doc:`sph/e/atom <compute_sph_e_atom>`
|
||||
|
||||
@ -103,7 +103,7 @@ OPT.
|
||||
* :doc:`lb/viscous <fix_lb_viscous>`
|
||||
* :doc:`lineforce <fix_lineforce>`
|
||||
* :doc:`manifoldforce <fix_manifoldforce>`
|
||||
* :doc:`mdi/aimd <fix_mdi_aimd>`
|
||||
* :doc:`mdi/qm <fix_mdi_qm>`
|
||||
* :doc:`meso/move <fix_meso_move>`
|
||||
* :doc:`mol/swap <fix_mol_swap>`
|
||||
* :doc:`momentum (k) <fix_momentum>`
|
||||
|
||||
@ -194,7 +194,7 @@ OPT.
|
||||
* :doc:`lubricateU/poly <pair_lubricateU>`
|
||||
* :doc:`mdpd <pair_mesodpd>`
|
||||
* :doc:`mdpd/rhosum <pair_mesodpd>`
|
||||
* :doc:`meam <pair_meam>`
|
||||
* :doc:`meam (k) <pair_meam>`
|
||||
* :doc:`meam/spline (o) <pair_meam_spline>`
|
||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
|
||||
* :doc:`mesocnt <pair_mesocnt>`
|
||||
|
||||
@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
|
||||
*More than one compute sna/atom*
|
||||
Self-explanatory.
|
||||
|
||||
*More than one compute sna/grid*
|
||||
Self-explanatory.
|
||||
|
||||
*More than one compute sna/grid/local*
|
||||
Self-explanatory.
|
||||
|
||||
*More than one compute snad/atom*
|
||||
Self-explanatory.
|
||||
|
||||
|
||||
@ -5,9 +5,9 @@ Client/server coupling of two (or more) codes is where one code is the
|
||||
"client" and sends request messages (data) to one (or more) "server"
|
||||
code(s). A server responds to each request with a reply message
|
||||
(data). This enables two (or more) codes to work in tandem to perform
|
||||
a simulation. LAMMPS can act as either a client or server code; it
|
||||
does this by using the `MolSSI Driver Interface (MDI) library
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
|
||||
a simulation. In this context, LAMMPS can act as either a client or
|
||||
server code. It does this by using the `MolSSI Driver Interface (MDI)
|
||||
library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
|
||||
developed by the `Molecular Sciences Software Institute (MolSSI)
|
||||
<https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
|
||||
package.
|
||||
@ -63,22 +63,39 @@ 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 package also has a `fix mdi/qm <fix_mdi_qm>` command in which
|
||||
LAMMPS operates as an MDI driver in conjunction with a quantum
|
||||
mechanics code as an MDI engine. The post_force() method of the
|
||||
fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
|
||||
code. This command can be used to couple to an MDI engine which is
|
||||
either a stand-alone code or a plugin library.
|
||||
|
||||
As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
|
||||
be used to perform *ab initio* MD simulations or energy minimizations,
|
||||
or to evaluate the quantum energy and forces for a series of
|
||||
independent systems. The examples/mdi directory has example input
|
||||
scripts for all of these use cases.
|
||||
|
||||
----------
|
||||
|
||||
The examples/mdi directory contains Python scripts and LAMMPS input
|
||||
script which use LAMMPS as either an MDI driver or engine or both.
|
||||
Three example use cases are provided:
|
||||
Currently, 5 example use cases are provided:
|
||||
|
||||
* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
|
||||
and one as an engine. As an engine, LAMMPS is a surrogate for a
|
||||
quantum code.
|
||||
* Run ab initio MD (AIMD) using 2 instances of LAMMPS. As a driver
|
||||
LAMMPS performs the timestepping in either NVE or NPT mode. As an
|
||||
engine, LAMMPS computes forces and is a surrogate for a quantum
|
||||
code.
|
||||
|
||||
* As a driver, LAMMPS runs an MD simulation. Every N steps it passes
|
||||
the current snapshot to an MDI engine to evaluate the energy,
|
||||
virial, and peratom forces. As the engine LAMMPS is a surrogate for
|
||||
a quantum code.
|
||||
|
||||
* As a driver, LAMMPS loops over a series of data files and passes the
|
||||
configuration to an MDI engine to evaluate the energy, virial, and
|
||||
peratom forces. As the engine LAMMPS is a surrogate for a quantum
|
||||
code.
|
||||
|
||||
* A Python script driver invokes a sequence of unrelated LAMMPS
|
||||
calculations. Calculations can be single-point energy/force
|
||||
@ -91,20 +108,22 @@ Three example use cases are provided:
|
||||
|
||||
Note that in any of these example where LAMMPS is used as an engine,
|
||||
an actual QM code (which supports MDI) could be used in its place,
|
||||
without modifying other code or scripts, except to specify the name of
|
||||
the QM code.
|
||||
without modifying the input scripts or launch commands, except to
|
||||
specify the name of the QM code.
|
||||
|
||||
The examples/mdi/README file explains how to launch both driver and
|
||||
The examples/mdi/Run.sh file illustrates how to launch both driver and
|
||||
engine codes so that they communicate using the MDI library via either
|
||||
MPI or sockets.
|
||||
MPI or sockets. Or using the engine as a stand-alone code or plugin
|
||||
library.
|
||||
|
||||
-------------
|
||||
|
||||
Currently there are two quantum DFT codes which have direct MDI
|
||||
support, `Quantum ESPRESSO (QE) <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
|
||||
Currently there are at least 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
|
||||
|
||||
@ -68,7 +68,8 @@ liquid Ar via the GK formalism:
|
||||
# Sample LAMMPS input script for viscosity of liquid Ar
|
||||
|
||||
units real
|
||||
variable T equal 86.4956
|
||||
variable T equal 200.0 # run temperature
|
||||
variable Tinit equal 250.0 # equilibration temperature
|
||||
variable V equal vol
|
||||
variable dt equal 4.0
|
||||
variable p equal 400 # correlation length
|
||||
@ -99,12 +100,14 @@ liquid Ar via the GK formalism:
|
||||
|
||||
# equilibration and thermalization
|
||||
|
||||
velocity all create $T 102486 mom yes rot yes dist gaussian
|
||||
fix NVT all nvt temp $T $T 10 drag 0.2
|
||||
velocity all create ${Tinit} 102486 mom yes rot yes dist gaussian
|
||||
fix NVT all nvt temp ${Tinit} ${Tinit} 10 drag 0.2
|
||||
run 8000
|
||||
|
||||
# viscosity calculation, switch to NVE if desired
|
||||
|
||||
velocity all create $T 102486 mom yes rot yes dist gaussian
|
||||
fix NVT all nvt temp $T $T 10 drag 0.2
|
||||
#unfix NVT
|
||||
#fix NVE all nve
|
||||
|
||||
@ -122,7 +125,7 @@ liquid Ar via the GK formalism:
|
||||
run 100000
|
||||
variable v equal (v_v11+v_v22+v_v33)/3.0
|
||||
variable ndens equal count(all)/vol
|
||||
print "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3"
|
||||
print "average viscosity: $v [Pa.s] @ $T K, ${ndens} atoms/A^3"
|
||||
|
||||
The fifth method is related to the above Green-Kubo method,
|
||||
but uses the Einstein formulation, analogous to the Einstein
|
||||
@ -131,9 +134,9 @@ time-integrated momentum fluxes play the role of Cartesian
|
||||
coordinates, whose mean-square displacement increases linearly
|
||||
with time at sufficiently long times.
|
||||
|
||||
The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
|
||||
However, instead of measure the momentum flux in response of applied velocity gradient,
|
||||
it measures the velocity profile in response of applied stress.
|
||||
The sixth is the periodic perturbation method, which is also a non-equilibrium MD method.
|
||||
However, instead of measuring the momentum flux in response to an applied velocity gradient,
|
||||
it measures the velocity profile in response to applied stress.
|
||||
A cosine-shaped periodic acceleration is added to the system via the
|
||||
:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
|
||||
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the
|
||||
|
||||
@ -1479,7 +1479,7 @@ the :doc:`Build extras <Build_extras>` page.
|
||||
* lib/mdi/README
|
||||
* :doc:`Howto MDI <Howto_mdi>`
|
||||
* :doc:`mdi <mdi>`
|
||||
* :doc:`fix mdi/aimd <fix_mdi_aimd>`
|
||||
* :doc:`fix mdi/qm <fix_mdi_qm>`
|
||||
* examples/PACKAGES/mdi
|
||||
|
||||
----------
|
||||
@ -1801,6 +1801,8 @@ computes which analyze attributes of the potential.
|
||||
* src/ML-SNAP: filenames -> commands
|
||||
* :doc:`pair_style snap <pair_snap>`
|
||||
* :doc:`compute sna/atom <compute_sna_atom>`
|
||||
* :doc:`compute sna/grid <compute_sna_atom>`
|
||||
* :doc:`compute sna/grid/local <compute_sna_atom>`
|
||||
* :doc:`compute snad/atom <compute_sna_atom>`
|
||||
* :doc:`compute snav/atom <compute_sna_atom>`
|
||||
* examples/snap
|
||||
|
||||
@ -284,6 +284,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
||||
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
|
||||
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
|
||||
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
|
||||
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
|
||||
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
|
||||
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
|
||||
* :doc:`sph/e/atom <compute_sph_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
|
||||
|
||||
@ -2,6 +2,8 @@
|
||||
.. index:: compute snad/atom
|
||||
.. index:: compute snav/atom
|
||||
.. index:: compute snap
|
||||
.. index:: compute sna/grid
|
||||
.. index:: compute sna/grid/local
|
||||
|
||||
compute sna/atom command
|
||||
========================
|
||||
@ -15,6 +17,12 @@ compute snav/atom command
|
||||
compute snap command
|
||||
====================
|
||||
|
||||
compute sna/grid command
|
||||
========================
|
||||
|
||||
compute sna/grid/local command
|
||||
==============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -24,6 +32,9 @@ Syntax
|
||||
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID sna/grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID sna/grid/local nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* sna/atom = style name of this compute command
|
||||
@ -32,6 +43,7 @@ Syntax
|
||||
* twojmax = band limit for bispectrum components (non-negative integer)
|
||||
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
|
||||
* w_1, w_2,... = list of neighbor weights, one for each type
|
||||
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag*
|
||||
|
||||
@ -81,6 +93,7 @@ Examples
|
||||
compute snap all snap 1.4 0.95 6 2.0 1.0
|
||||
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
|
||||
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
|
||||
compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -215,6 +228,46 @@ command:
|
||||
See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
The compute *sna/grid* and *sna/grid/local* commands calculate
|
||||
bispectrum components for a regular grid of points.
|
||||
These are calculated from the local density of nearby atoms *i'*
|
||||
around each grid point, as if there was a central atom *i*
|
||||
at the grid point. This is useful for characterizing fine-scale
|
||||
structure in a configuration of atoms, and it is used
|
||||
in the `MALA package <https://github.com/casus/mala>`_
|
||||
to build machine-learning surrogates for finite-temperature Kohn-Sham
|
||||
density functional theory (:ref:`Ellis et al. <Ellis2021>`)
|
||||
Neighbor atoms not in the group do not contribute to the
|
||||
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
|
||||
assumes that *i* has the same type as the neighbor atom *i'*.
|
||||
|
||||
Compute *sna/grid* calculates a global array containing bispectrum
|
||||
components for a regular grid of points.
|
||||
The grid is aligned with the current box dimensions, with the
|
||||
first point at the box origin, and forming a regular 3d array with
|
||||
*nx*, *ny*, and *nz* points in the x, y, and z directions. For triclinic
|
||||
boxes, the array is congruent with the periodic lattice vectors
|
||||
a, b, and c. The array contains one row for each of the
|
||||
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
|
||||
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
|
||||
and *z* coordinates of the grid point, followed by the bispectrum
|
||||
components. See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
Compute *sna/grid/local* calculates bispectrum components of a regular
|
||||
grid of points similarly to compute *sna/grid* described above.
|
||||
However, because the array is local, it contains only rows for grid points
|
||||
that are local to the processor sub-domain. The global grid
|
||||
of :math:`nx \times ny \times nz` points is still laid out in space the same as for *sna/grid*,
|
||||
but grid points are strictly partitioned, so that every grid point appears in
|
||||
one and only one local array. The array contains one row for each of the
|
||||
local grid points, looping over the global index *ix* fastest,
|
||||
then *iy*, and *iz* slowest. Each row of the array contains
|
||||
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
|
||||
and *z* coordinates of the grid point, followed by the bispectrum
|
||||
components. See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
The value of all bispectrum components will be zero for atoms not in
|
||||
the group. Neighbor atoms not in the group do not contribute to the
|
||||
bispectrum of atoms in the group.
|
||||
@ -428,6 +481,21 @@ number of columns in the global array generated by *snap* are 31, and
|
||||
931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N*
|
||||
is the total number of atoms.
|
||||
|
||||
Compute *sna/grid* evaluates a global array.
|
||||
The array contains one row for each of the
|
||||
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
|
||||
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
|
||||
and *z* coordinates of the grid point, followed by the bispectrum
|
||||
components.
|
||||
|
||||
Compute *sna/grid/local* evaluates a local array.
|
||||
The array contains one row for each of the
|
||||
local grid points, looping over the global index *ix* fastest,
|
||||
then *iy*, and *iz* slowest. Each row of the array contains
|
||||
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
|
||||
and *z* coordinates of the grid point, followed by the bispectrum
|
||||
components.
|
||||
|
||||
If the *quadratic* keyword value is set to 1, then additional columns
|
||||
are generated, corresponding to the products of all distinct pairs of
|
||||
bispectrum components. If the number of bispectrum components is *K*,
|
||||
@ -509,8 +577,7 @@ The optional keyword defaults are *rmin0* = 0,
|
||||
|
||||
.. _Thompson20141:
|
||||
|
||||
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
|
||||
available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
|
||||
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316, (2015).
|
||||
|
||||
.. _Bartok20101:
|
||||
|
||||
@ -531,4 +598,8 @@ of Angular Momentum, World Scientific, Singapore (1987).
|
||||
|
||||
.. _Cusentino2020:
|
||||
|
||||
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
|
||||
**(Cusentino)** Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
|
||||
|
||||
.. _Ellis2021:
|
||||
|
||||
**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
|
||||
|
||||
@ -27,6 +27,9 @@ dump command
|
||||
:doc:`dump custom/adios <dump_adios>` command
|
||||
=============================================
|
||||
|
||||
:doc:`dump cfg/uef <dump_cfg_uef>` command
|
||||
==========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -36,7 +39,7 @@ Syntax
|
||||
|
||||
* ID = user-assigned name for the dump
|
||||
* group-ID = ID of the group of atoms to be dumped
|
||||
* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
|
||||
* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
|
||||
* N = dump every this many timesteps
|
||||
* file = name of file to write dump info to
|
||||
* args = list of arguments for a particular style
|
||||
@ -47,22 +50,23 @@ Syntax
|
||||
*atom/gz* args = none
|
||||
*atom/zstd* args = none
|
||||
*atom/mpiio* args = none
|
||||
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` doc page
|
||||
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
|
||||
*cfg* args = same as *custom* args, see below
|
||||
*cfg/gz* args = same as *custom* args, see below
|
||||
*cfg/zstd* args = same as *custom* args, see below
|
||||
*cfg/mpiio* args = same as *custom* args, see below
|
||||
*cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
|
||||
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below
|
||||
*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` doc page
|
||||
*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` page
|
||||
*dcd* args = none
|
||||
*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` doc page
|
||||
*image* args = discussed on :doc:`dump image <dump_image>` doc page
|
||||
*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` page
|
||||
*image* args = discussed on :doc:`dump image <dump_image>` page
|
||||
*local*, *local/gz*, *local/zstd* args = see below
|
||||
*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` doc page
|
||||
*movie* args = discussed on :doc:`dump image <dump_image>` doc page
|
||||
*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
|
||||
*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
|
||||
*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` doc page
|
||||
*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` page
|
||||
*movie* args = discussed on :doc:`dump image <dump_image>` page
|
||||
*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
|
||||
*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
|
||||
*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` page
|
||||
*xtc* args = none
|
||||
*xyz* args = none
|
||||
*xyz/gz* args = none
|
||||
@ -155,7 +159,7 @@ timesteps in one of several styles. The *image* and *movie* styles are
|
||||
the exception: the *image* style renders a JPG, PNG, or PPM image file
|
||||
of the atom configuration every N timesteps while the *movie* style
|
||||
combines and compresses them into a movie file; both are discussed in
|
||||
detail on the :doc:`dump image <dump_image>` doc page. The timesteps on
|
||||
detail on the :doc:`dump image <dump_image>` page. The timesteps on
|
||||
which dump output is written can also be controlled by a variable.
|
||||
See the :doc:`dump_modify every <dump_modify>` command.
|
||||
|
||||
@ -194,7 +198,7 @@ or multiple smaller files).
|
||||
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
|
||||
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
|
||||
by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
|
||||
doc page for details.
|
||||
page for details.
|
||||
|
||||
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
|
||||
are identical in command syntax to the corresponding styles without
|
||||
@ -204,7 +208,7 @@ alternative approach to writing compressed files via a pipe, as done
|
||||
by the regular dump styles, which may be required on clusters where
|
||||
the interface to the high-speed network disallows using the fork()
|
||||
library call (which is needed for a pipe). For the remainder of this
|
||||
doc page, you should thus consider the *atom* and *atom/gz* styles
|
||||
page, you should thus consider the *atom* and *atom/gz* styles
|
||||
(etc) to be inter-changeable, with the exception of the required
|
||||
filename suffix.
|
||||
|
||||
@ -218,7 +222,7 @@ As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
|
||||
*xyz/mpiio* styles are identical in command syntax and in the format
|
||||
of the dump files they create, to the corresponding styles without
|
||||
"mpiio", except the single dump file they produce is written in
|
||||
parallel via the MPI-IO library. For the remainder of this doc page,
|
||||
parallel via the MPI-IO library. For the remainder of this page,
|
||||
you should thus consider the *atom* and *atom/mpiio* styles (etc) to
|
||||
be inter-changeable. The one exception is how the filename is
|
||||
specified for the MPI-IO styles, as explained below.
|
||||
@ -664,7 +668,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
|
||||
(tilted), then all atom coords will still be between 0.0 and 1.0.
|
||||
I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are
|
||||
the non-orthogonal vectors of the simulation box edges, as discussed
|
||||
on the :doc:`Howto triclinic <Howto_triclinic>` doc page.
|
||||
on the :doc:`Howto triclinic <Howto_triclinic>` page.
|
||||
|
||||
Use *xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the
|
||||
image flags for each atom. Unwrapped means that if the atom has
|
||||
@ -787,7 +791,7 @@ more info.
|
||||
The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles
|
||||
are part of the MPIIO package. They are only enabled if LAMMPS was
|
||||
built with that package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
page for more info.
|
||||
|
||||
The *xtc*, *dcd* and *yaml* styles are part of the EXTRA-DUMP package.
|
||||
They are only enabled if LAMMPS was built with that package. See the
|
||||
@ -797,12 +801,12 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
|
||||
:doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
|
||||
:doc:`dump molfile <dump_molfile>`, :doc:`dump_modify <dump_modify>`,
|
||||
:doc:`undump <undump>`
|
||||
:doc:`dump cfg/uef <dump_cfg_uef>`, :doc:`dump h5md <dump_h5md>`,
|
||||
:doc:`dump image <dump_image>`, :doc:`dump molfile <dump_molfile>`,
|
||||
:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`, :doc:`write_dump <write_dump>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The defaults for the *image* and *movie* styles are listed on the
|
||||
:doc:`dump image <dump_image>` doc page.
|
||||
:doc:`dump image <dump_image>` page.
|
||||
|
||||
@ -246,7 +246,7 @@ 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/aimd <fix_mdi_aimd>` - LAMMPS operates as driver for ab initio MD (AIMD) via the MolSSI Driver Interface (MDI)
|
||||
* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as driver for a quantum code 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
|
||||
|
||||
@ -116,13 +116,6 @@ potential energy of the system as part of :doc:`thermodynamic output
|
||||
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
|
||||
energy yes <fix_modify>`.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||
this fix to add the contribution compute by LATTE to the global
|
||||
pressure of the system via the :doc:`compute pressure
|
||||
<compute_pressure>` command. This can be accessed by
|
||||
:doc:`thermodynamic output <thermo_style>`. The default setting for
|
||||
this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||
this fix to add the contribution computed by LATTE to the global
|
||||
pressure of the system as part of :doc:`thermodynamic output
|
||||
@ -137,7 +130,7 @@ energy discussed above. The scalar value calculated by this fix is
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
The DFTB forces computed by LATTE via this fix are imposed during an
|
||||
The DFTB forces computed by LATTE via this fix are used during an
|
||||
energy minimization, invoked by the :doc:`minimize <minimize>`
|
||||
command.
|
||||
|
||||
|
||||
@ -1,93 +0,0 @@
|
||||
.. index:: fix mdi/aimd
|
||||
|
||||
fix mdi/aimd command
|
||||
======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID mdi/aimd keyword
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* mdi/aimd = style name of this fix command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all mdi/aimd
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command enables LAMMPS to act as a client with another server
|
||||
code to couple the two codes together to perform ab initio MD (AIMD)
|
||||
simulations.
|
||||
|
||||
More specifically, this command causes LAMMPS to begin using the `MDI
|
||||
Library <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.
|
||||
|
||||
----------
|
||||
|
||||
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
|
||||
276
doc/src/fix_mdi_qm.rst
Normal file
276
doc/src/fix_mdi_qm.rst
Normal file
@ -0,0 +1,276 @@
|
||||
.. index:: fix mdi/qm
|
||||
|
||||
fix mdi/qm command
|
||||
======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID mdi/qm keyword
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* mdi/qm = style name of this fix command
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *virial* or *add* or *every* or *connect* or *elements*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*virial* args = *yes* or *no*
|
||||
yes = request virial tensor from server code
|
||||
no = do not request virial tensor from server code
|
||||
*add* args = *yes* or *no*
|
||||
yes = add returned value from server code to LAMMPS quantities
|
||||
no = do not add returned values to LAMMPS quantities
|
||||
*every* args = Nevery
|
||||
Nevery = request values from server code once every Nevery steps
|
||||
*connect* args = *yes* or *no*
|
||||
yes = perform a one-time connection to the MDI engine code
|
||||
no = do not perform the connection operation
|
||||
*elements* args = N_1 N_2 ... N_ntypes
|
||||
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all mdi/qm
|
||||
fix 1 all mdi/qm virial yes
|
||||
fix 1 all mdi/qm add no every 100 elements 13 29
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command enables LAMMPS to act as a client with another server
|
||||
code that will compute the total energy, per-atom forces, and total
|
||||
virial for atom conformations and simulation box size/shapes that
|
||||
LAMMPS sends it.
|
||||
|
||||
Typically the server code will be a quantum mechanics (QM) code, hence
|
||||
the name of the fix. However this is not required, the server code
|
||||
could be another classical molecular dynamics code or LAMMPS itself.
|
||||
The server code must support use of the `MDI Library
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
||||
explained below.
|
||||
|
||||
These are example use cases for this fix, discussed further below:
|
||||
|
||||
* perform an ab initio MD (AIMD) simulation with quantum forces
|
||||
* perform an energy minimization with quantum forces
|
||||
* perform a nudged elastic band (NEB) calculation with quantum forces
|
||||
* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
|
||||
|
||||
The code coupling performed by this command is done via the `MDI
|
||||
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
||||
LAMMPS runs as an MDI driver (client), and sends MDI commands to an
|
||||
external MDI engine code (server), e.g. a QM code which has support
|
||||
for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
|
||||
information about how LAMMPS can operate as either an MDI driver or
|
||||
engine.
|
||||
|
||||
The examples/mdi directory contains input scripts using this fix in
|
||||
the various use cases discussed below. In each case, two instances of
|
||||
LAMMPS are used, once as an MDI driver, once as an MDI engine
|
||||
(surrogate for a QM code). The examples/mdi/README file explains how
|
||||
to launch two codes so that they communicate via the MDI library using
|
||||
either MPI or sockets. Any QM code that supports MDI could be used in
|
||||
place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi
|
||||
<Howto_mdi>` page for a current list (March 2022) of such QM codes.
|
||||
|
||||
Note that an engine code can support MDI in either or both of two
|
||||
modes. It can be used as a stand-alone code, launched at the same
|
||||
time as LAMMPS. Or it can be used as a plugin library, which LAMMPS
|
||||
loads. See the :doc:`mdi plugin <mdi>` command for how to trigger
|
||||
LAMMPS to load a plugin library. The examples/mdi/README file
|
||||
explains how to launch the two codes in either mode.
|
||||
|
||||
----------
|
||||
|
||||
The *virial* keyword setting of yes or no determines whether
|
||||
LAMMPS will request the QM code to also compute and return
|
||||
a 6-element symmetric virial tensor for the system.
|
||||
|
||||
The *add* keyword setting of *yes* or *no* determines whether the
|
||||
energy and forces and virial returned by the QM code will be added to
|
||||
the LAMMPS internal energy and forces and virial or not. If the
|
||||
setting is *no* then the default :doc:`fix_modify energy <fix_modify>`
|
||||
and :doc:`fix_modify virial <fix_modify>` settings are also set to
|
||||
*no* and your input scripts should not set them to yes. See more
|
||||
details on these fix_modify settings below.
|
||||
|
||||
Whatever the setting for the *add* keyword, the QM energy, forces, and
|
||||
virial will be stored by the fix, so they can be accessed by other
|
||||
commands. See details below.
|
||||
|
||||
The *every* keyword determines how often the QM code will be invoked
|
||||
during a dynamics run with the current LAMMPS simulation box and
|
||||
configuration of atoms. The QM code will be called once every
|
||||
*Nevery* timesteps.
|
||||
|
||||
The *connect* keyword determines whether this fix performs a one-time
|
||||
connection to the QM code. The default is *yes*. The only time a
|
||||
*no* is needed is if this command is used multiple times in an input
|
||||
script. E.g. if it used inside a loop which also uses the :doc:`clear
|
||||
<clear>` command to destroy the system (including any defined fixes).
|
||||
See the examples/mdi/in.series.driver script as an example of this,
|
||||
where LAMMPS is using the QM code to compute energy and forces for a
|
||||
series of system configurations. In this use case *connect no*
|
||||
is used along with the :doc:`mdi connect and exit <mdi>` command
|
||||
to one-time initiate/terminate the connection outside the loop.
|
||||
|
||||
The *elements* keyword allows specification of what element each
|
||||
LAMMPS atom type corresponds to. This is specified by the atomic
|
||||
number of the element, e.g. 13 for Al. An atomic number must be
|
||||
specified for each of the ntypes LAMMPS atom types. Ntypes is
|
||||
typically specified via the create_box command or in the data file
|
||||
read by the read_data command. If this keyword is not specified, then
|
||||
this fix will send the LAMMPS atom type for each atom to the MDI
|
||||
engine. If both the LAMMPS driver and the MDI engine are initialized
|
||||
so that atom type values are consistent in both codes, then the
|
||||
*elements* keyword is not needed. Otherwise the keyword can be used
|
||||
to insure the two codes are consistent in their definition of atomic
|
||||
species.
|
||||
|
||||
----------
|
||||
|
||||
The following 3 example use cases are illustrated in the examples/mdi
|
||||
directory. See its README file for more details.
|
||||
|
||||
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
|
||||
minimization with QM forces, or a multi-replica NEB calculation, use
|
||||
*add yes* and *every 1* (the defaults). This is so that every time
|
||||
LAMMPS needs energy and forces, the QM code will be invoked.
|
||||
|
||||
Both LAMMPS and the QM code should define the same system (simulation
|
||||
box, atoms and their types) in their respective input scripts. Note
|
||||
that on this scenario, it may not be necessary for LAMMPS to define a
|
||||
pair style or use a neighbor list.
|
||||
|
||||
LAMMPS will then perform the timestepping or minimization iterations
|
||||
for the simulation. At the point in each timestep or iteration when
|
||||
LAMMPS needs the force on each atom, it communicates with the engine
|
||||
code. It sends the current simulation box size and shape (if they
|
||||
change dynamically, e.g. during an NPT simulation), and the current
|
||||
atom coordinates. The engine code computes quantum forces on each
|
||||
atom and the total energy of the system and returns them to LAMMPS.
|
||||
|
||||
Note that if the AIMD simulation is an NPT or NPH model, or the energy
|
||||
minimization includes :doc:`fix box relax <fix_box_relax>` to
|
||||
equilibrate the box size/shape, then LAMMPS computes a pressure. This
|
||||
means the *virial* keyword should be set to *yes* so that the QM
|
||||
contribution to the pressure can be included.
|
||||
|
||||
(2) To run dynamics with a LAMMPS interatomic potential, and evaluate
|
||||
the QM energy and forces once every 1000 steps, use *add no* and
|
||||
*every 1000*. This could be useful for using an MD run to generate
|
||||
randomized configurations which are then passed to the QM code to
|
||||
produce training data for a machine learning potential. A :doc:`dump
|
||||
custom <dump>` command could be invoked every 1000 steps to dump the
|
||||
atom coordinates and QM forces to a file. Likewise the QM energy and
|
||||
virial could be output with the :doc:`thermo_style custom
|
||||
<thermo_style>` command.
|
||||
|
||||
(3) To do a QM evaluation of energy and forces for a series of *N*
|
||||
independent systems (simulation box and atoms), use *add no* and
|
||||
*every 1*. Write a LAMMPS input script which loops over the *N*
|
||||
systems. See the :doc:`Howto multiple <Howto_multiple>` doc page for
|
||||
details on looping and removing old systems. The series of systems
|
||||
could be initialized by reading them from data files with
|
||||
:doc:`read_data <read_data>` commands. Or, for example, by using the
|
||||
:doc:`lattice <lattice>` , :doc:`create_atoms <create_atoms>`,
|
||||
:doc:`delete_atoms <delete_atoms>`, and/or :doc:`displace_atoms
|
||||
random <displace_atoms>` commands to generate a series of different
|
||||
systems. At the end of the loop perform :doc:`run 0 <run>` and
|
||||
:doc:`write_dump <write_dump>` commands to invoke the QM code and
|
||||
output the QM energy and forces. As in (2) this be useful to produce
|
||||
QM data for training a machine learning potential.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
|
||||
this fix to add the potential energy computed by the QM code to the
|
||||
global potential energy of the system as part of :doc:`thermodynamic
|
||||
output <thermo_style>`. The default setting for this fix is
|
||||
:doc:`fix_modify energy yes <fix_modify>`, unless the *add* keyword is
|
||||
set to *no*, in which case the default setting is *no*.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||
this fix to add the contribution computed by the QM code to the global
|
||||
pressure of the system as part of :doc:`thermodynamic output
|
||||
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
|
||||
virial yes <fix_modify>`, unless the *add* keyword is set to *no*, in
|
||||
which case the default setting is *no*.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the energy
|
||||
returned by the QM code. The scalar value calculated by this fix is
|
||||
"extensive".
|
||||
|
||||
This fix also computes a global vector with of length 6 which contains
|
||||
the symmetric virial tensor values returned by the QM code. It can
|
||||
likewise be accessed by various :doc:`output commands <Howto_output>`.
|
||||
|
||||
The ordering of values in the symmetric virial tensor is as follows:
|
||||
vxx, vyy, vzz, vxy, vxz, vyz. The values will be in pressure
|
||||
:doc:`units <units>`.
|
||||
|
||||
This fix also computes a peratom array with 3 columns which contains
|
||||
the peratom forces returned by the QM code. It can likewise be
|
||||
accessed by various :doc:`output commands <Howto_output>`.
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
Assuming the *add* keyword is set to *yes* (the default), the forces
|
||||
computed by the QM code are used during an energy minimization,
|
||||
invoked by the :doc:`minimize <minimize>` command.
|
||||
|
||||
.. note::
|
||||
|
||||
If you want the potential energy associated with the QM forces to
|
||||
be included in the total potential energy of the system (the
|
||||
quantity being minimized), you MUST not disable the
|
||||
:doc:`fix_modify <fix_modify>` *energy* option for this fix, which
|
||||
means the *add* keyword should also be set to *yes* (the default).
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the MDI package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
The QM code does not currently compute and return per-atom energy or
|
||||
per-atom virial contributions. So they will not show up as part of
|
||||
the calculations performed by the :doc:`compute pe/atom
|
||||
<compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>`
|
||||
commands.
|
||||
|
||||
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
||||
codes (MD or QM codes), the :doc:`units <units>` command should be
|
||||
used to specify *real* or *metal* units. This will ensure the correct
|
||||
unit conversions between LAMMPS and MDI units. The other code will
|
||||
also perform similar unit conversions into its preferred units.
|
||||
|
||||
LAMMPS can also be used as an MDI driver in other unit choices it
|
||||
supports, e.g. *lj*, but then no unit conversion is performed.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`mdi plugin <mdi>`, :doc:`mdi engine <mdi>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default for the optional keywords are virial = no, add = yes,
|
||||
every = 1, connect = yes.
|
||||
@ -156,27 +156,28 @@ and Boolean operators:
|
||||
Each A and B is a number or string or a variable reference like $a or
|
||||
${abc}, or A or B can be another Boolean expression.
|
||||
|
||||
If a variable is used it can produce a number when evaluated, like an
|
||||
:doc:`equal-style variable <variable>`. Or it can produce a string,
|
||||
like an :doc:`index-style variable <variable>`. For an individual
|
||||
Boolean operator, A and B must both be numbers or must both be
|
||||
strings. You cannot compare a number to a string.
|
||||
Note that all variables used will be substituted for before the
|
||||
Boolean expression in evaluated. A variable can produce a number,
|
||||
like an :doc:`equal-style variable <variable>`. Or it can produce a
|
||||
string, like an :doc:`index-style variable <variable>`.
|
||||
|
||||
The Boolean operators "==" and "!=" can operate on a pair or strings
|
||||
or numbers. They cannot compare a number to a string. All the other
|
||||
Boolean operations can only operate on numbers.
|
||||
|
||||
Expressions are evaluated left to right and have the usual C-style
|
||||
precedence: the unary logical NOT operator "!" has the highest
|
||||
precedence, the 4 relational operators "<", "<=", ">", and ">=" are
|
||||
next; the two remaining relational operators "==" and "!=" are next;
|
||||
then the logical AND operator "&&"; and finally the logical OR
|
||||
operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have the
|
||||
lowest precedence. Parenthesis can be used to group one or more
|
||||
operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have
|
||||
the lowest precedence. Parenthesis can be used to group one or more
|
||||
portions of an expression and/or enforce a different order of
|
||||
evaluation than what would occur with the default precedence.
|
||||
|
||||
When the 6 relational operators (first 6 in list above) compare 2
|
||||
numbers, they return either a 1.0 or 0.0 depending on whether the
|
||||
relationship between A and B is TRUE or FALSE. When the 6 relational
|
||||
operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or
|
||||
FALSE, but the comparison is done by the C function strcmp().
|
||||
relationship between A and B is TRUE or FALSE.
|
||||
|
||||
When the 3 logical operators (last 3 in list above) compare 2 numbers,
|
||||
they also return either a 1.0 or 0.0 depending on whether the
|
||||
@ -190,8 +191,16 @@ returns 1.0 if its argument is 0.0, else it returns 0.0. The 3
|
||||
logical operators can only be used to operate on numbers, not on
|
||||
strings.
|
||||
|
||||
The overall Boolean expression produces a TRUE result if the result is
|
||||
non-zero. If the result is zero, the expression result is FALSE.
|
||||
The overall Boolean expression produces a TRUE result if the numeric
|
||||
result is non-zero. If the result is zero, the expression result is
|
||||
FALSE.
|
||||
|
||||
.. note::
|
||||
|
||||
If the Boolean expression is a single numeric value with no Boolean
|
||||
operators, it will be FALSE if the value = 0.0, otherwise TRUE. If
|
||||
the Boolean expression is a single string, an error message will be
|
||||
issued.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
113
doc/src/mdi.rst
113
doc/src/mdi.rst
@ -8,21 +8,26 @@ Syntax
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
mdi mode args
|
||||
mdi option args
|
||||
|
||||
* mode = *engine* or *plugin*
|
||||
* option = *engine* or *plugin* or *connect* or *exit*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*engine* args = none
|
||||
*plugin* args = name keyword value keyword value
|
||||
*engine* args = zero or more keyword arg pairs
|
||||
keywords = *elements*
|
||||
*elements* args = N_1 N_2 ... N_ntypes
|
||||
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
||||
*plugin* args = name keyword value keyword value ...
|
||||
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
|
||||
keyword/value pairs in any order, some are required, some are optional
|
||||
keywords = *mdi* or *infile* or *extra* or *command*
|
||||
*mdi* value = args passed to MDI for driver to operate with plugins
|
||||
*infile* value = filename the engine will read at start-up
|
||||
*mdi* value = args passed to MDI for driver to operate with plugins (required)
|
||||
*infile* value = filename the engine will read at start-up (optional)
|
||||
*extra* value = aditional command-line args to pass to engine library when loaded
|
||||
*command* value = a LAMMPS input script command to execute
|
||||
|
||||
*command* value = a LAMMPS input script command to execute (required)
|
||||
*connect* args = none
|
||||
*exit* args = none
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -30,26 +35,19 @@ Examples
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
mdi engine
|
||||
mdi engine elements 13 29
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||
command "run 5"
|
||||
mdi connect
|
||||
mdi exit
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command implements two high-level operations within LAMMPS to use
|
||||
the `MDI Library
|
||||
<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.
|
||||
This command implements 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.
|
||||
|
||||
See the Howto MDI doc page for a discussion of all the different ways
|
||||
2 or more codes can interact via MDI.
|
||||
@ -61,6 +59,22 @@ stand-alone code or as a plugin. The README file in that directory
|
||||
shows how to launch and couple codes for all the 4 usage modes, and so
|
||||
they communicate via the MDI library using either MPI or sockets.
|
||||
|
||||
The scripts in that directory illustrate the use of all the options
|
||||
for this command.
|
||||
|
||||
The *engine* option enables LAMMPS to act as an MDI engine (server),
|
||||
responding to requests from an MDI driver (client) code.
|
||||
|
||||
The *plugin* option enables LAMMPS to act as an MDI driver (client),
|
||||
and load the MDI engine (server) code as a library plugin. In this
|
||||
case the MDI engine is a library plugin. An MDI engine can also be a
|
||||
stand-alone code, launched separately from LAMMPS, in which case the
|
||||
mdi plugin command is not used.
|
||||
|
||||
The *connect* and *exit* options are only used when LAMMPS is acting
|
||||
as an MDI driver. As explained below, these options are normally not
|
||||
needed, except for a specific kind of use case.
|
||||
|
||||
----------
|
||||
|
||||
The *mdi engine* command is used to make LAMMPS operate as an MDI
|
||||
@ -100,6 +114,8 @@ commands, which are described further below.
|
||||
- Send/request charge on each atom (N values)
|
||||
* - >COORDS or <COORDS
|
||||
- Send/request coordinates of each atom (3N values)
|
||||
* - >ELEMENTS
|
||||
- Send elements (atomic numbers) for each atom (N values)
|
||||
* - <ENERGY
|
||||
- Request total energy (potential + kinetic) of the system (1 value)
|
||||
* - >FORCES or <FORCES
|
||||
@ -121,11 +137,11 @@ commands, which are described further below.
|
||||
* - <PE
|
||||
- Request potential energy of the system (1 value)
|
||||
* - <STRESS
|
||||
- Request stress tensor (virial) of the system (6 values)
|
||||
- Request symmetric stress tensor (virial) of the system (9 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)
|
||||
- Send/request the LAMMPS atom type for each atom (N values)
|
||||
* - >VELOCITIES or <VELOCITIES
|
||||
- Send/request the velocity of each atom (3N values)
|
||||
* - @INIT_MD or @INIT_OPTG
|
||||
@ -145,9 +161,25 @@ commands, which are described further below.
|
||||
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.
|
||||
re-neighbor. If the >NATOMS or >TYPES or >ELEMENTS commands have
|
||||
been sent (since the previous >COORDS command), then LAMMPS assumes
|
||||
the system is new and re-initializes an entirely new simulation.
|
||||
|
||||
.. note::
|
||||
|
||||
The >TYPES or >ELEMENTS commands are how the MDI driver tells the
|
||||
LAMMPS engine which LAMMPS atom type to assign to each atom. If
|
||||
both the MDI driver and the LAMMPS engine are initialized so that
|
||||
atom type values are consistent in both codes, then the >TYPES
|
||||
command can be used. If not, the optional *elements* keyword can
|
||||
be used to specify what element each LAMMPS atom type corresponds
|
||||
to. This is specified by the atomic number of the element, e.g. 13
|
||||
for Al. An atomic number must be specified for each of the ntypes
|
||||
LAMMPS atom types. Ntypes is typically specified via the
|
||||
create_box command or in the data file read by the read_data
|
||||
command. In this has been done, the MDI driver can send an
|
||||
>ELEMENTS command to the LAMMPS driver with the atomic number of
|
||||
each atom.
|
||||
|
||||
The MD and OPTG commands perform an entire MD simulation or energy
|
||||
minimization (to convergence) with no communication from the driver
|
||||
@ -270,7 +302,7 @@ The *command* keyword is required. It specifies a LAMMPS input script
|
||||
command (as a single argument in quotes if it is multiple words).
|
||||
Once the plugin library is launched, LAMMPS will execute this command.
|
||||
Other previously-defined commands in the input script, such as the
|
||||
:doc:`fix mdi/aimd <fix_mdi_aimd>` command, should perform MDI
|
||||
:doc:`fix mdi/qm <fix_mdi_qm>` 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.
|
||||
@ -284,6 +316,31 @@ could specify a filename with multiple LAMMPS commands.
|
||||
"mdi plugin" command could then load the same library plugin or
|
||||
a different one if desired.
|
||||
|
||||
----------
|
||||
|
||||
The *mdi connect* and *mdi exit* commands are only used when LAMMPS is
|
||||
operating as an MDI driver. And when other LAMMPS command(s) which
|
||||
send MDI commands and associated data to/from the MDI engine are not
|
||||
able to initiate and terminate the connection to the engine code.
|
||||
|
||||
The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm
|
||||
<fix_mdi_qm>` command. If it is only used once in an input script
|
||||
then it can initiate and terminate the connection. But if it is being
|
||||
issued multiple times, e.g. in a loop that issues a :doc:`clear
|
||||
<clear>` command, then it cannot initiate or terminate the connection
|
||||
multiple times. Instead, the *mdi connect* and *mdi exit* commands
|
||||
should be used outside the loop to initiate or terminate the connection.
|
||||
|
||||
See the examples/mdi/in.series.driver script for an example of how
|
||||
this is done. The LOOP in that script is reading a series of data
|
||||
file configurations and passing them to an MDI engine (e.g. quantum
|
||||
code) for energy and force evaluation. A *clear* command inside the
|
||||
loop wipes out the current system so a new one can be defined. This
|
||||
operation also destroys all fixes. So the :doc:`fix mdi/qm
|
||||
<fix_mdi_qm>` command is issued once per loop iteration. Note that it
|
||||
includes a "connect no" option which disables the initiate/terminate
|
||||
logic within that fix.
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
@ -304,7 +361,7 @@ supports, e.g. *lj*, but then no unit conversion is performed.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix mdi/aimd <fix_mdi_aimd>`
|
||||
:doc:`fix mdi/qm <fix_mdi_qm>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -71,7 +71,7 @@ Syntax
|
||||
*no_affinity* values = none
|
||||
*kokkos* args = keyword value ...
|
||||
zero or more keyword/value pairs may be appended
|
||||
keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *gpu/aware* or *pair/only*
|
||||
keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only*
|
||||
*neigh* value = *full* or *half*
|
||||
full = full neighbor list
|
||||
half = half neighbor list built in thread-safe manner
|
||||
@ -96,6 +96,7 @@ Syntax
|
||||
*comm/pair/forward* value = *no* or *device*
|
||||
*comm/fix/forward* value = *no* or *device*
|
||||
*comm/reverse* value = *no* or *host* or *device*
|
||||
*comm/pair/reverse* value = *no* or *device*
|
||||
no = perform communication pack/unpack in non-KOKKOS mode
|
||||
host = perform pack/unpack on host (e.g. with OpenMP threading)
|
||||
device = perform pack/unpack on device (e.g. on GPU)
|
||||
@ -500,7 +501,7 @@ rule of thumb may give too large a binsize and the default should be
|
||||
overridden with a smaller value.
|
||||
|
||||
The *comm* and *comm/exchange* and *comm/forward* and *comm/pair/forward*
|
||||
and *comm/fix/forward* and comm/reverse*
|
||||
and *comm/fix/forward* and *comm/reverse* and *comm/pair/reverse*
|
||||
keywords determine whether the host or device performs the packing and
|
||||
unpacking of data when communicating per-atom data between processors.
|
||||
"Exchange" communication happens only on timesteps that neighbor lists
|
||||
@ -521,9 +522,16 @@ packing/unpacking data for the communication. A value of *host* means to
|
||||
use the host, typically a multi-core CPU, and perform the
|
||||
packing/unpacking in parallel with threads. A value of *device* means to
|
||||
use the device, typically a GPU, to perform the packing/unpacking
|
||||
operation. If a value of *host* is used for the *comm/pair/forward* or
|
||||
*comm/fix/forward* keyword, it will be automatically be changed to *no*
|
||||
since these keywords don't support *host* mode.
|
||||
operation.
|
||||
|
||||
For the *comm/pair/forward* or *comm/fix/forward* or *comm/pair/reverse*
|
||||
keywords, if a value of *host* is used it will be automatically
|
||||
be changed to *no* since these keywords don't support *host* mode. The
|
||||
value of *no* will also always be used when running on the CPU, i.e. setting
|
||||
the value to *device* will have no effect if the pair/fix style is
|
||||
running on the CPU. For the *comm/fix/forward* or *comm/pair/reverse*
|
||||
keywords, not all styles support *device* mode and in that case will run
|
||||
in *no* mode instead.
|
||||
|
||||
The optimal choice for these keywords depends on the input script and
|
||||
the hardware used. The *no* value is useful for verifying that the
|
||||
|
||||
@ -1,8 +1,11 @@
|
||||
.. index:: pair_style meam
|
||||
.. index:: pair_style meam/kk
|
||||
|
||||
pair_style meam command
|
||||
=========================
|
||||
|
||||
Accelerator Variants: *meam/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -347,6 +350,12 @@ Most published MEAM parameter sets use the default values *attrac* = *repulse* =
|
||||
Setting *repuls* = *attrac* = *delta* corresponds to the form used in several
|
||||
recent published MEAM parameter sets, such as :ref:`(Valone) <Valone>`
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
.. note::
|
||||
|
||||
The default form of the *erose* expression in LAMMPS was corrected
|
||||
|
||||
@ -373,6 +373,7 @@ Caltech
|
||||
Camilloni
|
||||
Camiloni
|
||||
Campana
|
||||
Cangi
|
||||
Cao
|
||||
Capolungo
|
||||
Caro
|
||||
@ -2681,6 +2682,7 @@ polyhedra
|
||||
Polym
|
||||
polymorphism
|
||||
popen
|
||||
Popoola
|
||||
Popov
|
||||
popstore
|
||||
Poresag
|
||||
@ -2824,6 +2826,7 @@ radians
|
||||
Rafferty
|
||||
rahman
|
||||
Rahman
|
||||
Rajamanickam
|
||||
Ralf
|
||||
Raman
|
||||
ramped
|
||||
@ -3676,13 +3679,19 @@ vx
|
||||
Vx
|
||||
vxcm
|
||||
vxmu
|
||||
vxx
|
||||
vxy
|
||||
vxz
|
||||
vy
|
||||
Vy
|
||||
vycm
|
||||
vyy
|
||||
vyz
|
||||
vz
|
||||
Vz
|
||||
vzcm
|
||||
vzi
|
||||
vzz
|
||||
Waals
|
||||
Wadley
|
||||
wallstyle
|
||||
|
||||
@ -31,6 +31,23 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
|
||||
if(CMAKE_CROSSCOMPILING)
|
||||
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
|
||||
endif()
|
||||
|
||||
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
|
||||
find_program(MAKENSIS_PATH makensis)
|
||||
if(MAKENSIS_PATH)
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
|
||||
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR})
|
||||
if(BUILD_MPI)
|
||||
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis
|
||||
DEPENDS paceplugin
|
||||
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe)
|
||||
else()
|
||||
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis
|
||||
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
|
||||
DEPENDS paceplugin lammps.ico lammps-text-logo-wide.bmp paceplugin.nsis
|
||||
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}.exe)
|
||||
endif()
|
||||
endif()
|
||||
else()
|
||||
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic")
|
||||
endif()
|
||||
|
||||
@ -2,10 +2,11 @@ These are examples that work the MDI package in LAMMPS which uses the
|
||||
MolSSI MDI library for coupling codes together and communicating
|
||||
between them with MDI messages.
|
||||
|
||||
In MDI lingo, one code is the driver and another code is the engine.
|
||||
The 2 codes can be written in any language; C++ (LAMMPS) and Python
|
||||
are illustrated here. The 2 codes can each be stand-alone codes, in
|
||||
which case they can be run on different numbers of processors. The 2
|
||||
Within the MDI context, one code is the driver and another code is
|
||||
the engine. The 2 codes can be written in any language; C++ (LAMMPS)
|
||||
and Python are illustrated here. The 2 codes can each be stand-alone
|
||||
codes, in which case they can be run on different numbers of processors.
|
||||
The 2
|
||||
codes can communicate either via TCP (sockets) or via MPI. For the
|
||||
TCP case, the driver and engine need to be launched separately,
|
||||
e.g. in 2 windows on your desktop machine. For the MPI case, a single
|
||||
@ -19,87 +20,99 @@ LAMMPS supports operating in all these MDI modes. It can be an engine
|
||||
operating either as a stand-alone code or as a plugin. It can also be
|
||||
a driver and couple to an engine that is either a stand-alone code or
|
||||
a plugin. Examples for all these use cases are in this directory.
|
||||
The example commands below illustrate how to run all the variants.
|
||||
The Run.sh file shows how run in all the modes. Type "sh Run.sh"
|
||||
to try them all out.
|
||||
|
||||
To use LAMMPS as a plugin engine, you must build it as a shared library.
|
||||
Something like this, which also builds the normal LAMMPS executable
|
||||
lmp_mpi:
|
||||
To use LAMMPS as a plugin engine, you must build it as a shared
|
||||
library. Something like this with make, which also builds the normal
|
||||
LAMMPS executable lmp_mpi:
|
||||
|
||||
cd src
|
||||
make yes-mdi
|
||||
make mode=shlib mpi
|
||||
|
||||
To use the serial_driver.py example you will need Python 3 with Numpy
|
||||
and mpi4py available in your Python. Make sure LAMMPS and Python are
|
||||
using same the same version of MPI.
|
||||
-------------------------------------------------
|
||||
|
||||
Examples 4 and 5 use Python scripts as MDI drivers. For this you will
|
||||
need Python 3 with Numpy and mpi4py installed. Make sure LAMMPS and
|
||||
Python/mpi4py are using same the same version of MPI.
|
||||
|
||||
You will also need MDI installed in your Python. You cannot use the
|
||||
LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a
|
||||
static library, not shared, which Python requires.
|
||||
|
||||
You can install MDI in your Python via conda:
|
||||
|
||||
% conda install -c conda-forge pymdi=1.4.1
|
||||
|
||||
or via pip:
|
||||
|
||||
% pip install pymdi==1.4.1
|
||||
|
||||
It is likely fine to leave off the version number, to get the latest
|
||||
MDI version. But to be safe, 1.4.1 is the version LAMMPS is currently
|
||||
using.
|
||||
|
||||
-------------------------------------------------
|
||||
|
||||
5 example use-cases are explained below.
|
||||
|
||||
In the first 3 examples, results running with MDI should be identical
|
||||
to running without MDI (alone log files). Example #4 has no non-MDI
|
||||
run. Example #5 results should match the non-MDI run of example #1.
|
||||
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #1 = run ab initio MD (AIMD)
|
||||
|
||||
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||
LAMMPS is a surrogate for a quantum code.
|
||||
|
||||
You can compare the thermo output in log.aimd.alone.1 to the thermo output in
|
||||
any of the log.aimd.driver* files. It should be identical.
|
||||
|
||||
Note that the "alone" and "driver" input scripts have options for
|
||||
running in NVE vs NPT Comment in/out the appropriate line to make
|
||||
change. Nothing needs to be changed in the "engine" scripts.
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #1 = run ab inito MD (AIMD)
|
||||
Two instances of LAMMPS operate as a driver and engine
|
||||
As an engine, LAMMPS is a surrogate for a quantum code
|
||||
* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
|
||||
|
||||
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
|
||||
have an option for running in NVE vs NPT mode. Comment in/out
|
||||
the appropriate line to change modes. Nothing needs to be
|
||||
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
|
||||
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||
LAMMPS is a surrogate for a quantum code
|
||||
|
||||
---
|
||||
You can compare the thermo output in log.snapshot.alone.1 to the
|
||||
thermo output in any of the log.snapshot.driver* files. It should be
|
||||
identical.
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the thermo output of the driver should match the thermo
|
||||
output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
You can compare the dumped forces in dump.snapshot.alone.1 to the
|
||||
forces in any of the dump.snapshot.* files. They should be identical,
|
||||
although at step 0 the forces are "zero" and may be epsilon different.
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||
Each calculation can be a single-point evaluation, MD run, or minimization
|
||||
* Example #3 = run LAMMPS, compute QM forces on series of independent systems
|
||||
|
||||
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||
LAMMPS is a surrogate for a quantum code
|
||||
|
||||
You can compare the thermo output in log.series.alone.1 to the thermo
|
||||
output in any of the log.series.driver* files. It should be
|
||||
identical.
|
||||
|
||||
You can compare the dumped forces in dump.series.alone.1 to the forces
|
||||
in any of the dump.series.* files. They should be identical,
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||
|
||||
Each calculation can be a single-point evaluation, MD run, or
|
||||
minimization
|
||||
|
||||
The sequence_driver.py code allows for optional switches in addition
|
||||
to -mdi (required) and the -plugin and -plugin_args switches which are
|
||||
@ -128,101 +141,31 @@ copied here:
|
||||
# -seed 12345
|
||||
# random number seed > 0, default = 12345
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 proc + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
You can compare the thermo output in any of the log.sequence.engine.*
|
||||
files. It should be identical.
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||
First LAMMPS instance performs the MD timestepping
|
||||
Second LAMMPS instance is surrogate QM = computes forces
|
||||
* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||
|
||||
First LAMMPS instance performs the MD timestepping. Second LAMMPS
|
||||
instance is surrogate QM to compute forces.
|
||||
|
||||
The aimd_driver.py code allows for an optional switch in addition to
|
||||
-mdi (required) and the -plugin and -plugin_args swiches which are
|
||||
used to link to the 2 engines as a plugin libraries. The example run
|
||||
commands below use the default values of the optional switch. The
|
||||
switch is also explained the top of the file; the info is copied
|
||||
here:
|
||||
switch is also explained the top of the file; the info is copied here:
|
||||
|
||||
# -nsteps 5
|
||||
# number of timesteps in dynamics runs, default = 5
|
||||
# -nsteps 10
|
||||
# number of timesteps in dynamics runs, default = 10
|
||||
|
||||
---
|
||||
This calculation is the same as Example #1 with a LAMMPS driver and a
|
||||
LAMMPS engine. Now there is a Python driver and two LAMMPS engines.
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
You can compare the thermo output in log.aimd.alone.1 output to the
|
||||
thermo output is any of the log.sequence.engine.* files. It should be
|
||||
identical for the Total Energy printed out by the Python driver script.
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the driver prints the QM and Total energies. These should
|
||||
match the PotEng and TotEng output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
E.g. Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||
|
||||
256
examples/mdi/Run.sh
Normal file
256
examples/mdi/Run.sh
Normal file
@ -0,0 +1,256 @@
|
||||
# Run all the examples
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 1 = run ab initio MD (AIMD)
|
||||
|
||||
# ---
|
||||
|
||||
# Run without MDI
|
||||
|
||||
lmp_mpi -log log.aimd.alone.1 < in.aimd.alone
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver &
|
||||
|
||||
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin
|
||||
mv log.aimd.engine.plugin log.aimd.engine.plugin.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin
|
||||
mv log.aimd.engine.plugin log.aimd.engine.plugin.3
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 2 = run LAMMPS, compute QM forces on snapshots from a long run
|
||||
|
||||
# ---
|
||||
|
||||
# Run without MDI
|
||||
|
||||
lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone
|
||||
mv dump.snapshot.alone dump.snapshot.alone.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver &
|
||||
|
||||
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.tcp.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.tcp.4
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.mpi.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.mpi.4
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin
|
||||
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1
|
||||
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin
|
||||
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3
|
||||
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 3 = run LAMMPS, compute QM forces on series of independent systems
|
||||
|
||||
# ---
|
||||
|
||||
# Run without MDI
|
||||
|
||||
lmp_mpi -log log.series.alone.1 < in.series.alone
|
||||
mv dump.series.alone dump.series.alone.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver &
|
||||
|
||||
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.tcp.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.tcp.4
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.mpi.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.mpi.4
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin
|
||||
mv log.series.engine.plugin log.series.engine.plugin.1
|
||||
mv dump.series.driver.plugin dump.series.driver.plugin.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin
|
||||
mv log.series.engine.plugin log.series.engine.plugin.3
|
||||
mv dump.series.driver.plugin dump.series.driver.plugin.3
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 4 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 2 proc + 4 procs
|
||||
|
||||
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 2 procs + 4 procs
|
||||
|
||||
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.1 &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimdpy.mm &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimdpy.qm
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 2 procs + 2 procs + 3 procs
|
||||
|
||||
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.2 &
|
||||
|
||||
mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.2 -in in.aimdpy.mm &
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.3 -in in.aimdpy.qm
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.1 -in in.aimdpy.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.1 -in in.aimdpy.qm > log.aimdpy.driver.mpi.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 2 procs + 2 procs + 3 procs
|
||||
|
||||
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.2 -in in.aimdpy.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.3 -in in.aimdpy.qm > log.aimdpy.driver.mpi.2
|
||||
@ -23,8 +23,8 @@
|
||||
# -plugin_args arglist
|
||||
# args to add when launching plugin library, only when using plugin mode
|
||||
# enclose arglist in quotes if multiple words
|
||||
# -nsteps 5
|
||||
# number of timesteps, default = 5
|
||||
# -nsteps 10
|
||||
# number of timesteps, default = 10
|
||||
|
||||
import sys
|
||||
import mdi
|
||||
@ -182,7 +182,7 @@ mdiarg = ""
|
||||
plugin = ""
|
||||
plugin_args = ""
|
||||
|
||||
nsteps = 5
|
||||
nsteps = 10
|
||||
|
||||
# parse command-line args
|
||||
|
||||
|
||||
1018
examples/mdi/data.series.0.7
Normal file
1018
examples/mdi/data.series.0.7
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.series.0.8
Normal file
1018
examples/mdi/data.series.0.8
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.series.0.9
Normal file
1018
examples/mdi/data.series.0.9
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.snapshot
Normal file
1018
examples/mdi/data.snapshot
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.alone.1
Normal file
1527
examples/mdi/dump.17Jun22.series.alone.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.plugin.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.alone.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.alone.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -29,4 +29,4 @@ fix 1 all nve
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
run 10
|
||||
|
||||
@ -23,10 +23,9 @@ fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
run 10
|
||||
|
||||
@ -23,12 +23,11 @@ fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||
command "run 5"
|
||||
command "run 10"
|
||||
|
||||
@ -1,16 +1,11 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
lattice fcc 1.0
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
@ -19,4 +14,7 @@ pair_coeff 1 1 1.0 1.0 2.5
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
|
||||
@ -19,3 +19,4 @@ fix 1 all nve
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
|
||||
37
examples/mdi/in.series.alone
Normal file
37
examples/mdi/in.series.alone
Normal file
@ -0,0 +1,37 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
run 0
|
||||
|
||||
write_dump all custom dump.series.alone &
|
||||
id type x y z fx fy fz modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
39
examples/mdi/in.series.driver
Normal file
39
examples/mdi/in.series.driver
Normal file
@ -0,0 +1,39 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
|
||||
write_dump all custom dump.series.driver &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
38
examples/mdi/in.series.driver.plugin
Normal file
38
examples/mdi/in.series.driver.plugin
Normal file
@ -0,0 +1,38 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||
infile in.series.engine &
|
||||
extra "-log log.series.engine.plugin" &
|
||||
command "run 0"
|
||||
|
||||
write_dump all custom dump.series.driver.plugin &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
17
examples/mdi/in.series.engine
Normal file
17
examples/mdi/in.series.engine
Normal file
@ -0,0 +1,17 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
28
examples/mdi/in.snapshot.alone
Normal file
28
examples/mdi/in.snapshot.alone
Normal file
@ -0,0 +1,28 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.snapshot
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all custom 100 dump.snapshot.alone &
|
||||
id type x y z fx fy fz
|
||||
dump_modify 1 sort id
|
||||
|
||||
run 300
|
||||
33
examples/mdi/in.snapshot.driver
Normal file
33
examples/mdi/in.snapshot.driver
Normal file
@ -0,0 +1,33 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.snapshot
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm add no every 100 virial yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all custom 100 dump.snapshot.driver &
|
||||
id type x y z f_2[1] f_2[2] f_2[3]
|
||||
dump_modify 1 sort id
|
||||
|
||||
run 300 pre no post no every 100 &
|
||||
"print 'QM eng = $(f_2/atoms)'" &
|
||||
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||
42
examples/mdi/in.snapshot.driver.plugin
Normal file
42
examples/mdi/in.snapshot.driver.plugin
Normal file
@ -0,0 +1,42 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.snapshot
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm add no every 100 virial yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all custom 100 dump.snapshot.driver.plugin &
|
||||
id type x y z f_2[1] f_2[2] f_2[3]
|
||||
dump_modify 1 sort id
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||
infile in.snapshot.engine &
|
||||
extra "-log log.snapshot.engine.plugin" &
|
||||
command """
|
||||
run 300 pre no post no every 100
|
||||
"print 'QM eng = $(f_2/atoms)'"
|
||||
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||
"""
|
||||
17
examples/mdi/in.snapshot.engine
Normal file
17
examples/mdi/in.snapshot.engine
Normal file
@ -0,0 +1,17 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
@ -39,8 +39,8 @@ fix 1 all nve
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
run 10
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -61,30 +61,35 @@ Step Temp PotEng TotEng Press Volume
|
||||
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
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 0.00919691 on 1 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 505739.085 tau/day, 1170.692 timesteps/s
|
||||
73.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 469723.136 tau/day, 1087.322 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
|
||||
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
|
||||
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
|
||||
Other | | 6.054e-05 | | | 1.42
|
||||
Pair | 0.0066536 | 0.0066536 | 0.0066536 | 0.0 | 72.35
|
||||
Neigh | 0.0017906 | 0.0017906 | 0.0017906 | 0.0 | 19.47
|
||||
Comm | 0.0002554 | 0.0002554 | 0.0002554 | 0.0 | 2.78
|
||||
Output | 0.00029976 | 0.00029976 | 0.00029976 | 0.0 | 3.26
|
||||
Modify | 9.8718e-05 | 9.8718e-05 | 9.8718e-05 | 0.0 | 1.07
|
||||
Other | | 9.887e-05 | | | 1.08
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Neighs: 19396 ave 19396 max 19396 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Total # of neighbors = 19396
|
||||
Ave neighs/atom = 38.792
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
Normal file
@ -0,0 +1,83 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 0.0078442 on 1 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 550725.026 tau/day, 1274.826 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.592e-06 | 1.592e-06 | 1.592e-06 | 0.0 | 0.02
|
||||
Comm | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.34
|
||||
Output | 0.00021168 | 0.00021168 | 0.00021168 | 0.0 | 2.70
|
||||
Modify | 0.0075488 | 0.0075488 | 0.0075488 | 0.0 | 96.23
|
||||
Other | | 5.544e-05 | | | 0.71
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
@ -0,0 +1,83 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 0.00523112 on 3 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 825827.658 tau/day, 1911.638 timesteps/s
|
||||
98.8% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 5.95e-07 | 1.7073e-06 | 3.907e-06 | 0.0 | 0.03
|
||||
Comm | 3.8259e-05 | 6.2707e-05 | 7.5974e-05 | 0.0 | 1.20
|
||||
Output | 0.00017543 | 0.00021238 | 0.00028075 | 0.0 | 4.06
|
||||
Modify | 0.004815 | 0.0048289 | 0.0048521 | 0.0 | 92.31
|
||||
Other | | 0.0001254 | | | 2.40
|
||||
|
||||
Nlocal: 166.667 ave 176 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
@ -0,0 +1,84 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 0.00940117 on 1 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 459517.175 tau/day, 1063.697 timesteps/s
|
||||
96.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.9e-06 | 1.9e-06 | 1.9e-06 | 0.0 | 0.02
|
||||
Comm | 3.0131e-05 | 3.0131e-05 | 3.0131e-05 | 0.0 | 0.32
|
||||
Output | 0.00030359 | 0.00030359 | 0.00030359 | 0.0 | 3.23
|
||||
Modify | 0.0090041 | 0.0090041 | 0.0090041 | 0.0 | 95.78
|
||||
Other | | 6.144e-05 | | | 0.65
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
@ -0,0 +1,84 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 0.00613177 on 3 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 704527.327 tau/day, 1630.850 timesteps/s
|
||||
99.2% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 7.93e-07 | 1.8723e-06 | 3.996e-06 | 0.0 | 0.03
|
||||
Comm | 4.4254e-05 | 7.4628e-05 | 9.321e-05 | 0.0 | 1.22
|
||||
Output | 0.00019476 | 0.00024309 | 0.00032745 | 0.0 | 3.96
|
||||
Modify | 0.005637 | 0.0056559 | 0.0056903 | 0.0 | 92.24
|
||||
Other | | 0.0001563 | | | 2.55
|
||||
|
||||
Nlocal: 166.667 ave 176 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
@ -0,0 +1,83 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 2.41182 on 1 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 1791.180 tau/day, 4.146 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 2.596e-06 | 2.596e-06 | 2.596e-06 | 0.0 | 0.00
|
||||
Comm | 4.9627e-05 | 4.9627e-05 | 4.9627e-05 | 0.0 | 0.00
|
||||
Output | 0.00063707 | 0.00063707 | 0.00063707 | 0.0 | 0.03
|
||||
Modify | 2.411 | 2.411 | 2.411 | 0.0 | 99.97
|
||||
Other | | 0.0001146 | | | 0.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
@ -0,0 +1,83 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/qm virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 10
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||
Loop time of 2.39983 on 3 procs for 10 steps with 500 atoms
|
||||
|
||||
Performance: 1800.127 tau/day, 4.167 timesteps/s
|
||||
66.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.75e-07 | 1.3583e-06 | 2.574e-06 | 0.0 | 0.00
|
||||
Comm | 5.4167e-05 | 0.00010938 | 0.00015338 | 0.0 | 0.00
|
||||
Output | 0.00030885 | 0.00042099 | 0.00064497 | 0.0 | 0.02
|
||||
Modify | 2.3988 | 2.3989 | 2.3989 | 0.0 | 99.96
|
||||
Other | | 0.0004276 | | | 0.02
|
||||
|
||||
Nlocal: 166.667 ave 176 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:02
|
||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||
Total wall time: 0:00:02
|
||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:00
|
||||
Total wall time: 0:00:00
|
||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:00
|
||||
Total wall time: 0:00:00
|
||||
@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||
@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
@ -0,0 +1,49 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:00
|
||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
@ -0,0 +1,49 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:00
|
||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
@ -0,0 +1,49 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:02
|
||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
@ -0,0 +1,49 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
6 1.3471497 0 0 2.016683 1.1349892
|
||||
7 1.3081237 0 0 1.9582612 1.1021094
|
||||
8 1.2599751 0 0 1.8861828 1.0615437
|
||||
9 1.2021373 0 0 1.7995995 1.0128146
|
||||
10 1.1347688 0 0 1.6987489 0.95605588
|
||||
Total wall time: 0:00:02
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
@ -20,7 +20,7 @@ Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -52,4 +52,9 @@ Step Temp E_pair E_mol TotEng Press
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -52,4 +52,9 @@ Step Temp E_pair E_mol TotEng Press
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -52,4 +52,9 @@ Step Temp E_pair E_mol TotEng Press
|
||||
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
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Total wall time: 0:00:02
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -52,4 +52,9 @@ Step Temp E_pair E_mol TotEng Press
|
||||
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
|
||||
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||
Total wall time: 0:00:02
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
3 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
|
||||
Total wall time: 0:00:00
|
||||
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
@ -0,0 +1,248 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 2.729e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
109.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.729e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 15687 ave 15687 max 15687 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15687
|
||||
Ave neighs/atom = 31.374
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.135 | 3.135 | 3.135 Mbytes
|
||||
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 1.434e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
139.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.434e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18734 ave 18734 max 18734 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18734
|
||||
Ave neighs/atom = 37.468
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
compute 1 all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
|
||||
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 1.483e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
134.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.483e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 20023 ave 20023 max 20023 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 20023
|
||||
Ave neighs/atom = 40.046
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
Total wall time: 0:00:00
|
||||
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
@ -0,0 +1,213 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 1.919e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.919e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 1.141e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
87.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.141e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 1.019e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
98.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.019e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:00
|
||||
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
@ -0,0 +1,213 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 4.00933e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
91.5% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 4.009e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 177 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 3.11833e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
117.6% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.118e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 178 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
3 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 2.85467e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
140.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.855e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 181 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:00
|
||||
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 2.359e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
127.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.359e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 1.468e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
204.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.468e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 1.378e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
145.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.378e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
Total wall time: 0:00:00
|
||||
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 3.50867e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
114.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.509e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 177 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 3.225e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
82.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.225e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 178 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
3 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 2.713e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
98.3% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.713e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 181 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
Total wall time: 0:00:00
|
||||
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
@ -0,0 +1,213 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 3.017e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.017e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 1.977e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
101.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.977e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 2.042e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
97.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.042e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:00
|
||||
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
@ -0,0 +1,213 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.7
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||
Loop time of 9.08933e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
95.3% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.089e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 177 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.8
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||
Loop time of 3.63567e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
100.9% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.636e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 178 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data data.series.${rho}
|
||||
read_data data.series.0.9
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||
3 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 48294
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||
Loop time of 3.806e-06 on 3 procs for 0 steps with 500 atoms
|
||||
|
||||
105.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.806e-06 | | |100.00
|
||||
|
||||
Nlocal: 166.667 ave 181 max 150 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:00
|
||||
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
@ -0,0 +1,58 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||
delete_atoms group all
|
||||
Deleted 500 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||
delete_atoms group all
|
||||
Deleted 500 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||
Total wall time: 0:00:00
|
||||
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
@ -0,0 +1,58 @@
|
||||
LAMMPS (2 Jun 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||
delete_atoms group all
|
||||
Deleted 500 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||
delete_atoms group all
|
||||
Deleted 500 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||
Total wall time: 0:00:00
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user