Merge branch 'develop' into type-labels-for-pair_style_commands
This commit is contained in:
Axel Kohlmeyer
@ -510,6 +510,14 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
|
|||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
|
find_package(CURL QUIET COMPONENTS HTTP HTTPS)
|
||||||
|
option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
|
||||||
|
if(WITH_CURL)
|
||||||
|
find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
|
||||||
|
target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
|
||||||
|
target_link_libraries(lammps PRIVATE CURL::libcurl)
|
||||||
|
endif()
|
||||||
|
|
||||||
# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
|
# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
|
||||||
set(JPEG_NAMES libjpeg libjpeg-62)
|
set(JPEG_NAMES libjpeg libjpeg-62)
|
||||||
find_package(JPEG QUIET)
|
find_package(JPEG QUIET)
|
||||||
|
|||||||
@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
|
|||||||
target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
|
target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
|
||||||
target_link_libraries(lammps PRIVATE colvars)
|
target_link_libraries(lammps PRIVATE colvars)
|
||||||
|
|
||||||
|
if(BUILD_OMP)
|
||||||
|
# Enable OpenMP for Colvars as well
|
||||||
|
target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
|
||||||
|
target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
|
||||||
|
endif()
|
||||||
|
|
||||||
if(COLVARS_DEBUG)
|
if(COLVARS_DEBUG)
|
||||||
# Need to export the define publicly to be valid in interface code
|
# Need to export the define publicly to be valid in interface code
|
||||||
target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
|
target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
|
||||||
|
|||||||
@ -2,9 +2,10 @@
|
|||||||
|
|
||||||
APP_NAME=lammps-gui
|
APP_NAME=lammps-gui
|
||||||
DESTDIR=${PWD}/../LAMMPS_GUI
|
DESTDIR=${PWD}/../LAMMPS_GUI
|
||||||
|
VERSION="$1"
|
||||||
|
|
||||||
echo "Delete old files, if they exist"
|
echo "Delete old files, if they exist"
|
||||||
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
|
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
|
||||||
|
|
||||||
echo "Create staging area for deployment and populate"
|
echo "Create staging area for deployment and populate"
|
||||||
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
|
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
|
||||||
@ -71,7 +72,7 @@ do \
|
|||||||
done
|
done
|
||||||
|
|
||||||
pushd ..
|
pushd ..
|
||||||
tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
|
tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
|
||||||
popd
|
popd
|
||||||
|
|
||||||
echo "Cleanup dir"
|
echo "Cleanup dir"
|
||||||
|
|||||||
@ -1,9 +1,10 @@
|
|||||||
#!/bin/bash
|
#!/bin/bash
|
||||||
|
|
||||||
APP_NAME=lammps-gui
|
APP_NAME=lammps-gui
|
||||||
|
VERSION="$1"
|
||||||
|
|
||||||
echo "Delete old files, if they exist"
|
echo "Delete old files, if they exist"
|
||||||
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
|
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
|
||||||
|
|
||||||
echo "Create initial dmg file with macdeployqt"
|
echo "Create initial dmg file with macdeployqt"
|
||||||
macdeployqt lammps-gui.app -dmg
|
macdeployqt lammps-gui.app -dmg
|
||||||
@ -96,12 +97,12 @@ sync
|
|||||||
|
|
||||||
echo "Unmount modified disk image and convert to compressed read-only image"
|
echo "Unmount modified disk image and convert to compressed read-only image"
|
||||||
hdiutil detach "${DEVICE}"
|
hdiutil detach "${DEVICE}"
|
||||||
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
|
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
|
||||||
|
|
||||||
echo "Attach icon to .dmg file"
|
echo "Attach icon to .dmg file"
|
||||||
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
|
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
|
||||||
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
|
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
|
||||||
SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
|
SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
|
||||||
rm icon.rsrc
|
rm icon.rsrc
|
||||||
|
|
||||||
echo "Delete temporary disk images"
|
echo "Delete temporary disk images"
|
||||||
|
|||||||
@ -3,9 +3,10 @@
|
|||||||
APP_NAME=lammps-gui
|
APP_NAME=lammps-gui
|
||||||
DESTDIR=${PWD}/LAMMPS_GUI
|
DESTDIR=${PWD}/LAMMPS_GUI
|
||||||
SYSROOT="$1"
|
SYSROOT="$1"
|
||||||
|
VERSION="$2"
|
||||||
|
|
||||||
echo "Delete old files, if they exist"
|
echo "Delete old files, if they exist"
|
||||||
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
|
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
|
||||||
|
|
||||||
echo "Create staging area for deployment and populate"
|
echo "Create staging area for deployment and populate"
|
||||||
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
|
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
|
||||||
@ -60,5 +61,5 @@ cat > ${DESTDIR}/bin/qt.conf <<EOF
|
|||||||
[Paths]
|
[Paths]
|
||||||
Plugins = ../qt5plugins
|
Plugins = ../qt5plugins
|
||||||
EOF
|
EOF
|
||||||
zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
|
zip -9rvD LAMMPS-Win10-amd64-${VERSION}.zip LAMMPS_GUI
|
||||||
|
|
||||||
|
|||||||
14
doc/lammps.1
14
doc/lammps.1
@ -226,6 +226,20 @@ arguments of the "dump" command. See the
|
|||||||
.B LAMMPS
|
.B LAMMPS
|
||||||
manual for details on either of the two commands.
|
manual for details on either of the two commands.
|
||||||
.TP
|
.TP
|
||||||
|
\fB\-r2info <restart file> <keyword> ...\fR or
|
||||||
|
\fB\-restart2info <restart file> <keyword> ...\fR
|
||||||
|
Write information about the <restart file> previously written by
|
||||||
|
.B LAMMPS
|
||||||
|
to the screen and immediately exit. Following <restart file>
|
||||||
|
argument, additional keywords for the
|
||||||
|
.B LAMMPS
|
||||||
|
"info" command may be added to increase the amount of information
|
||||||
|
written. By default "system" "group" "fix" "compute" are already
|
||||||
|
set. See the
|
||||||
|
.B LAMMPS
|
||||||
|
manual for details on the "info" command.
|
||||||
|
.TP
|
||||||
|
.TP
|
||||||
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
|
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
|
||||||
Specify a file for
|
Specify a file for
|
||||||
.B LAMMPS
|
.B LAMMPS
|
||||||
|
|||||||
@ -153,7 +153,12 @@ development headers to compile (if those are not found locally a recent
|
|||||||
version of that library will be downloaded and compiled along with
|
version of that library will be downloaded and compiled along with
|
||||||
LAMMPS and the test programs) and will download and compile a specific
|
LAMMPS and the test programs) and will download and compile a specific
|
||||||
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
|
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
|
||||||
test framework that is used to implement the tests.
|
test framework that is used to implement the tests. Those unit tests
|
||||||
|
may be combined with memory access and leak checking with valgrind
|
||||||
|
(see below for how to enable it). In that case, running so-called
|
||||||
|
death tests will create a lot of false positives and thus they can be
|
||||||
|
disabled by configuring compilation with the additional setting
|
||||||
|
``-D SKIP_DEATH_TESTS=on``.
|
||||||
|
|
||||||
.. admonition:: Software version and LAMMPS configuration requirements
|
.. admonition:: Software version and LAMMPS configuration requirements
|
||||||
:class: note
|
:class: note
|
||||||
|
|||||||
@ -8,7 +8,8 @@ explains how to do this for building both with CMake and make.
|
|||||||
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
|
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
|
||||||
* `Size of LAMMPS integer types and size limits`_
|
* `Size of LAMMPS integer types and size limits`_
|
||||||
* `Read or write compressed files`_
|
* `Read or write compressed files`_
|
||||||
* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
|
* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
|
||||||
|
* `Support for downloading files`_
|
||||||
* `Memory allocation alignment`_
|
* `Memory allocation alignment`_
|
||||||
* `Workaround for long long integers`_
|
* `Workaround for long long integers`_
|
||||||
* `Exception handling when using LAMMPS as a library`_ to capture errors
|
* `Exception handling when using LAMMPS as a library`_ to capture errors
|
||||||
@ -19,7 +20,7 @@ explains how to do this for building both with CMake and make.
|
|||||||
.. _cxx11:
|
.. _cxx11:
|
||||||
|
|
||||||
C++11 standard compliance
|
C++11 standard compliance
|
||||||
------------------------------------------
|
-------------------------
|
||||||
|
|
||||||
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
|
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
|
||||||
LAMMPS version 3 March 2020 is the last version compatible with the previous
|
LAMMPS version 3 March 2020 is the last version compatible with the previous
|
||||||
@ -31,12 +32,16 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
|
|||||||
|
|
||||||
CCFLAGS = -g -O3 -std=c++11
|
CCFLAGS = -g -O3 -std=c++11
|
||||||
|
|
||||||
|
Individual packages may require compliance with a later C++ standard
|
||||||
|
like C++14 or C++17. These requirements will be documented with the
|
||||||
|
:doc:`individual packages <Packages_details>`.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _fft:
|
.. _fft:
|
||||||
|
|
||||||
FFT library
|
FFT library
|
||||||
---------------------
|
-----------
|
||||||
|
|
||||||
When the KSPACE package is included in a LAMMPS build, the
|
When the KSPACE package is included in a LAMMPS build, the
|
||||||
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
|
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
|
||||||
@ -341,8 +346,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
|
|||||||
|
|
||||||
.. _graphics:
|
.. _graphics:
|
||||||
|
|
||||||
Output of JPG, PNG, and movie files
|
Output of JPEG, PNG, and movie files
|
||||||
--------------------------------------------------
|
------------------------------------
|
||||||
|
|
||||||
The :doc:`dump image <dump_image>` command has options to output JPEG or
|
The :doc:`dump image <dump_image>` command has options to output JPEG or
|
||||||
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
|
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
|
||||||
@ -356,9 +361,9 @@ requires the following settings:
|
|||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
-D WITH_JPEG=value # yes or no
|
-D WITH_JPEG=value # yes or no
|
||||||
# default = yes if CMake finds JPEG files, else no
|
# default = yes if CMake finds JPEG development files, else no
|
||||||
-D WITH_PNG=value # yes or no
|
-D WITH_PNG=value # yes or no
|
||||||
# default = yes if CMake finds PNG and ZLIB files, else no
|
# default = yes if CMake finds PNG and ZLIB development files, else no
|
||||||
-D WITH_FFMPEG=value # yes or no
|
-D WITH_FFMPEG=value # yes or no
|
||||||
# default = yes if CMake can find ffmpeg, else no
|
# default = yes if CMake can find ffmpeg, else no
|
||||||
|
|
||||||
@ -446,12 +451,58 @@ during a run.
|
|||||||
available using a compression library instead, which is what the
|
available using a compression library instead, which is what the
|
||||||
:ref:`COMPRESS package <PKG-COMPRESS>` enables.
|
:ref:`COMPRESS package <PKG-COMPRESS>` enables.
|
||||||
|
|
||||||
|
--------------------------------------------------
|
||||||
|
|
||||||
|
.. _libcurl:
|
||||||
|
|
||||||
|
Support for downloading files
|
||||||
|
-----------------------------
|
||||||
|
|
||||||
|
.. versionadded:: TBD
|
||||||
|
|
||||||
|
The :doc:`geturl command <geturl>` command uses the `the libcurl library
|
||||||
|
<https://curl.se/libcurl/>`_ to download files. This requires that
|
||||||
|
LAMMPS is compiled accordingly which needs the following settings:
|
||||||
|
|
||||||
|
.. tabs::
|
||||||
|
|
||||||
|
.. tab:: CMake build
|
||||||
|
|
||||||
|
.. code-block:: bash
|
||||||
|
|
||||||
|
-D WITH_CURL=value # yes or no
|
||||||
|
# default = yes if CMake finds CURL development files, else no
|
||||||
|
|
||||||
|
Usually these settings are all that is needed. If CMake cannot
|
||||||
|
find the graphics header, library, executable files, you can set
|
||||||
|
these variables:
|
||||||
|
|
||||||
|
.. code-block:: bash
|
||||||
|
|
||||||
|
-D CURL_INCLUDE_DIR=path # path to folder which contains curl.h header file
|
||||||
|
-D CURL_LIBRARY=path # path to libcurls.a (.so) file
|
||||||
|
|
||||||
|
.. tab:: Traditional make
|
||||||
|
|
||||||
|
.. code-block:: make
|
||||||
|
|
||||||
|
LMP_INC = -DLAMMPS_CURL <other LMP_INC settings>
|
||||||
|
|
||||||
|
CURL_INC = -I/usr/local/include # path to curl folder with curl.h
|
||||||
|
CURL_PATH = -L/usr/lib # paths to libcurl.a(.so) if make cannot find it
|
||||||
|
CURL_LIB = -lcurl # library names
|
||||||
|
|
||||||
|
As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
|
||||||
|
if make can find the libcurl header and library files in their
|
||||||
|
default system locations. You must specify ``CURL_LIB`` with a
|
||||||
|
paths or linker flags to link to libcurl.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _align:
|
.. _align:
|
||||||
|
|
||||||
Memory allocation alignment
|
Memory allocation alignment
|
||||||
---------------------------------------
|
---------------------------
|
||||||
|
|
||||||
This setting enables the use of the "posix_memalign()" call instead of
|
This setting enables the use of the "posix_memalign()" call instead of
|
||||||
"malloc()" when LAMMPS allocates large chunks of memory. Vector
|
"malloc()" when LAMMPS allocates large chunks of memory. Vector
|
||||||
|
|||||||
@ -54,6 +54,7 @@ table above.
|
|||||||
* :doc:`echo <echo>`
|
* :doc:`echo <echo>`
|
||||||
* :doc:`fix <fix>`
|
* :doc:`fix <fix>`
|
||||||
* :doc:`fix_modify <fix_modify>`
|
* :doc:`fix_modify <fix_modify>`
|
||||||
|
* :doc:`geturl <geturl>`
|
||||||
* :doc:`group <group>`
|
* :doc:`group <group>`
|
||||||
* :doc:`if <if>`
|
* :doc:`if <if>`
|
||||||
* :doc:`improper_coeff <improper_coeff>`
|
* :doc:`improper_coeff <improper_coeff>`
|
||||||
|
|||||||
@ -98,10 +98,26 @@ get access to the other included executables.
|
|||||||
Linux on x86\_64
|
Linux on x86\_64
|
||||||
^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
After downloading and unpacking the
|
For Linux with x86\_64 CPU there are currently two variants. The first
|
||||||
|
is compiled on Ubuntu 20.04LTS, is using some wrapper scripts, and
|
||||||
|
should be compatible with more recent Linux distributions. After
|
||||||
|
downloading and unpacking the
|
||||||
``LAMMPS-Linux-x86_64-GUI-<version>.tar.gz`` package. You can switch
|
``LAMMPS-Linux-x86_64-GUI-<version>.tar.gz`` package. You can switch
|
||||||
into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
|
into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
|
||||||
|
|
||||||
|
The second variant uses `flatpak <https://www.flatpak.org>`_ and
|
||||||
|
requires the flatpak management and runtime software to be installed.
|
||||||
|
After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
|
||||||
|
flatpak bundle, you can install it with ``flatpak install --user
|
||||||
|
LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``. After installation,
|
||||||
|
LAMMPS-GUI should be integrated into your desktop environment under
|
||||||
|
"Applications > Science" but also can be launched from the console with
|
||||||
|
``flatpak run org.lammps.lammps-gui``. The flatpak bundle also includes
|
||||||
|
the console LAMMPS executable ``lmp`` which can be launched to run
|
||||||
|
simulations with, for example: ``flatpak run --command=lmp
|
||||||
|
org.lammps.lammps-gui -in in.melt``.
|
||||||
|
|
||||||
|
|
||||||
Compiling from Source
|
Compiling from Source
|
||||||
^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
@ -371,6 +387,8 @@ record a separate log for each run attempt by using the command
|
|||||||
at the beginning of an input file. That would record logs to files
|
at the beginning of an input file. That would record logs to files
|
||||||
``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
|
``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
|
||||||
|
|
||||||
|
.. _snapshot_viewer:
|
||||||
|
|
||||||
Snapshot Image Viewer
|
Snapshot Image Viewer
|
||||||
---------------------
|
---------------------
|
||||||
|
|
||||||
@ -400,10 +418,16 @@ Otherwise the default sequence of colors of the :doc:`dump image
|
|||||||
<dump_image>` command is assigned to the different atom types and the
|
<dump_image>` command is assigned to the different atom types and the
|
||||||
diameters are all the same.
|
diameters are all the same.
|
||||||
|
|
||||||
.. image:: JPG/lammps-gui-image.png
|
.. figure:: JPG/lammps-gui-image.png
|
||||||
:align: center
|
:align: center
|
||||||
:scale: 50%
|
:scale: 50%
|
||||||
|
|
||||||
|
Visualization of LAMMPS "peptide" example
|
||||||
|
|
||||||
|
.. versionchanged:: 1.6
|
||||||
|
|
||||||
|
Buttons for toggling shininess and re-centering were added.
|
||||||
|
|
||||||
The default image size, some default image quality settings, the view
|
The default image size, some default image quality settings, the view
|
||||||
style and some colors can be changed in the ``Preferences`` dialog
|
style and some colors can be changed in the ``Preferences`` dialog
|
||||||
window. From the image viewer window further adjustments can be made:
|
window. From the image viewer window further adjustments can be made:
|
||||||
@ -442,6 +466,12 @@ Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
|
|||||||
dialog will pop up asking whether to cancel the exit operation, or to
|
dialog will pop up asking whether to cancel the exit operation, or to
|
||||||
save or not save the buffer contents to a file.
|
save or not save the buffer contents to a file.
|
||||||
|
|
||||||
|
.. versionadded:: 1.6
|
||||||
|
|
||||||
|
The editor has an auto-save mode that can be enabled or disabled in the
|
||||||
|
``Preferences`` dialog. In auto-save mode, the editor buffer is
|
||||||
|
automatically saved before running LAMMPS or before exiting LAMMPS-GUI.
|
||||||
|
|
||||||
Context Specific Word Completion
|
Context Specific Word Completion
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
@ -471,11 +501,12 @@ Line Reformatting
|
|||||||
The editor supports reformatting lines according to the syntax in order
|
The editor supports reformatting lines according to the syntax in order
|
||||||
to have consistently aligned lines. This primarily means adding
|
to have consistently aligned lines. This primarily means adding
|
||||||
whitespace padding to commands, type specifiers, IDs and names. This
|
whitespace padding to commands, type specifiers, IDs and names. This
|
||||||
reformatting is performed by default when hitting the 'Enter' key to
|
reformatting is performed manually by hitting the 'Tab' key. It is
|
||||||
start a new line. This feature can be turned on or off in the
|
also possible to have this done automatically when hitting the 'Enter'
|
||||||
``Preferences`` dialog, but it can still be manually performed by
|
key to start a new line. This feature can be turned on or off in the
|
||||||
hitting the 'TAB' key. The amount of padding can be adjusted in the
|
``Preferences`` dialog for ``Editor Settings`` with the
|
||||||
``Preferences`` dialog for the *Editor*.
|
"Reformat with 'Enter'" checkbox. The amount of padding for multiple
|
||||||
|
categories can be adjusted in the same dialog.
|
||||||
|
|
||||||
Internally this functionality is achieved by splitting the line into
|
Internally this functionality is achieved by splitting the line into
|
||||||
"words" and then putting it back together with padding added where the
|
"words" and then putting it back together with padding added where the
|
||||||
@ -504,13 +535,40 @@ keyboard, the first of those entries is chosen.
|
|||||||
|
|
||||||
If the word under the cursor is a file, then additionally the context
|
If the word under the cursor is a file, then additionally the context
|
||||||
menu has an entry to open the file in a read-only text viewer window.
|
menu has an entry to open the file in a read-only text viewer window.
|
||||||
This is a convenient way to view the contents of files that are
|
If the file is a LAMMPS restart file, instead the menu entry offers to
|
||||||
referenced in the input. The file viewer also supports on-the-fly
|
:ref:`inspect the restart <inspect_restart>`.
|
||||||
|
|
||||||
|
The text viewer is a convenient way to view the contents of files that
|
||||||
|
are referenced in the input. The file viewer also supports on-the-fly
|
||||||
decompression based on the file name suffix in a :ref:`similar fashion
|
decompression based on the file name suffix in a :ref:`similar fashion
|
||||||
as available with LAMMPS <gzip>`. If the necessary decompression
|
as available with LAMMPS <gzip>`. If the necessary decompression
|
||||||
program is missing or the file cannot be decompressed, the viewer window
|
program is missing or the file cannot be decompressed, the viewer window
|
||||||
will contain a corresponding message.
|
will contain a corresponding message.
|
||||||
|
|
||||||
|
.. _inspect_restart:
|
||||||
|
|
||||||
|
Inspecting a Restart file
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
.. versionadded:: 1.6
|
||||||
|
|
||||||
|
When LAMMPS-GUI is asked to "Inspect a Restart", it will read the
|
||||||
|
restart file into a LAMMPS instance and then open three different
|
||||||
|
windows. The first window is a text viewer with the output of an
|
||||||
|
:doc:`info command <info>` with system information stored in the
|
||||||
|
restart. The second window is text viewer containing a data file
|
||||||
|
generated with a :doc:`write_data command <write_data>`. The third
|
||||||
|
window is a :ref:`Snapshot Image Viewer <snapshot_viewer>` containing a
|
||||||
|
visualization of the system in the restart.
|
||||||
|
|
||||||
|
If the restart file is larger than 250 MBytes, a dialog will ask
|
||||||
|
for confirmation before continuing, since large restart files
|
||||||
|
may require large amounts of RAM since the entire system must
|
||||||
|
be read into RAM. Thus restart file for large simulations that
|
||||||
|
have been run on an HPC cluster may overload a laptop or local
|
||||||
|
workstation. The ``Show Details...`` button will display a rough
|
||||||
|
estimate of the additional memory required.
|
||||||
|
|
||||||
Menu
|
Menu
|
||||||
----
|
----
|
||||||
|
|
||||||
@ -530,6 +588,7 @@ The ``File`` menu offers the usual options:
|
|||||||
- ``New`` clears the current buffer and resets the file name to ``*unknown*``
|
- ``New`` clears the current buffer and resets the file name to ``*unknown*``
|
||||||
- ``Open`` opens a dialog to select a new file for editing in the *Editor*
|
- ``Open`` opens a dialog to select a new file for editing in the *Editor*
|
||||||
- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only) with support for on-the-fly decompression as explained above.
|
- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only) with support for on-the-fly decompression as explained above.
|
||||||
|
- ``Inspect restart`` opens a dialog to select a file. If that file is a :doc:`LAMMPS restart <write_restart>` three windows with :ref:`information about the file are opened <inspect_restart>`.
|
||||||
- ``Save`` saves the current file; if the file name is ``*unknown*``
|
- ``Save`` saves the current file; if the file name is ``*unknown*``
|
||||||
a dialog will open to select a new file name
|
a dialog will open to select a new file name
|
||||||
- ``Save As`` opens a dialog to select and new file name (and folder, if
|
- ``Save As`` opens a dialog to select and new file name (and folder, if
|
||||||
@ -696,13 +755,15 @@ General Settings:
|
|||||||
log) of the application can be set.
|
log) of the application can be set.
|
||||||
- *Select Text Font:* Opens a font selection dialog where the type and
|
- *Select Text Font:* Opens a font selection dialog where the type and
|
||||||
size for the text editor and log font of the application can be set.
|
size for the text editor and log font of the application can be set.
|
||||||
- *GUI update interval:* Allows to set the time interval between GUI
|
- *GUI update interval:* Allows to set the time interval between GUI and
|
||||||
and data updates during a LAMMPS run in milliseconds. The default is
|
data updates during a LAMMPS run in milliseconds. The default is to
|
||||||
to update the GUI every 10 milliseconds. This is good for most cases.
|
update the GUI every 10 milliseconds. This is good for many cases.
|
||||||
For LAMMPS runs that run *very* fast, however, data may be missed and
|
Set this to 100 milliseconds or more if LAMMPS-GUI consumes too many
|
||||||
through lowering this interval, this can be corrected. However, this
|
resources during a run. For LAMMPS runs that run *very* fast (for
|
||||||
will make the GUI use more resources, which may be a problem on some
|
example in tutorial examples), however, data may be missed and through
|
||||||
computers with slower CPUs and a small number of CPU cores. This
|
lowering this interval, this can be corrected. However, this will
|
||||||
|
make the GUI use more resources, which may be a problem on some
|
||||||
|
computers with slower CPUs and a small number of CPU cores. This
|
||||||
setting may be changed to a value between 1 and 1000 milliseconds.
|
setting may be changed to a value between 1 and 1000 milliseconds.
|
||||||
|
|
||||||
Accelerators:
|
Accelerators:
|
||||||
@ -719,18 +780,23 @@ Snapshot Image:
|
|||||||
^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
This tab allows setting defaults for the snapshot images displayed in
|
This tab allows setting defaults for the snapshot images displayed in
|
||||||
the ``Image Viewer`` window, such as its dimensions and the zoom
|
the ``Image Viewer`` window, such as its dimensions and the zoom factor
|
||||||
factor applied. The *Antialias* switch will render images with twice
|
applied. The *Antialias* switch will render images with twice the
|
||||||
the number of pixels for width and height and then smoothly scale the
|
number of pixels for width and height and then smoothly scale the image
|
||||||
image back to the requested size. This produces higher quality images
|
back to the requested size. This produces higher quality images with
|
||||||
with smoother edges at the expense of requiring more CPU time to
|
smoother edges at the expense of requiring more CPU time to render the
|
||||||
render the image. The *HQ Image mode* option turns on screen space
|
image. The *HQ Image mode* option turns on screen space ambient
|
||||||
ambient occlusion (SSAO) mode when rendering images. This is also
|
occlusion (SSAO) mode when rendering images. This is also more time
|
||||||
more time consuming, but produces a more 'spatial' representation of
|
consuming, but produces a more 'spatial' representation of the system
|
||||||
the system shading of atoms by their depth. The *VDW Style* checkbox
|
shading of atoms by their depth. The *Shiny Image mode* option will
|
||||||
selects whether atoms are represented by space filling spheres when
|
render objects with a shiny surface when enabled. Otherwise the
|
||||||
checked or by smaller spheres and sticks. Finally there are a couple
|
surfaces will be matted. The *Show Box* option selects whether the
|
||||||
of drop down lists to select the background and box colors.
|
system box is drawn as a colored set of sticks. Similarly, the *Show
|
||||||
|
Axes* option selects whether a representation of the three system axes
|
||||||
|
will be drawn as colored sticks. The *VDW Style* checkbox selects
|
||||||
|
whether atoms are represented by space filling spheres when checked or
|
||||||
|
by smaller spheres and sticks. Finally there are a couple of drop down
|
||||||
|
lists to select the background and box colors.
|
||||||
|
|
||||||
Editor Settings:
|
Editor Settings:
|
||||||
^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^
|
||||||
@ -741,9 +807,11 @@ ranges, IDs (e.g. for fixes), and names (e.g. for groups). The value
|
|||||||
set is the minimum width for the text element and it can be chosen in
|
set is the minimum width for the text element and it can be chosen in
|
||||||
the range between 1 and 32.
|
the range between 1 and 32.
|
||||||
|
|
||||||
The two settings which follow enable or disable the automatic
|
The three settings which follow enable or disable the automatic
|
||||||
reformatting when hitting the 'Enter' key and the automatic display of
|
reformatting when hitting the 'Enter' key, the automatic display of
|
||||||
the completion pop-up window.
|
the completion pop-up window, and whether auto-save mode is enabled.
|
||||||
|
In auto-save mode the editor buffer is saved before a run or before
|
||||||
|
exiting LAMMPS-GUI.
|
||||||
|
|
||||||
-----------
|
-----------
|
||||||
|
|
||||||
|
|||||||
@ -14,7 +14,13 @@ choices among them.
|
|||||||
|
|
||||||
The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
|
The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
|
||||||
styles can output internally rendered images or convert them to a movie
|
styles can output internally rendered images or convert them to a movie
|
||||||
during the MD run.
|
during the MD run. It is also possible to create visualizations from
|
||||||
|
LAMMPS inputs or restart file with the :doc:`LAMMPS-GUI
|
||||||
|
<Howto_lammps_gui>`, which uses the :doc:`dump image <dump_image>`
|
||||||
|
command internally. The ``Snapshot Image Viewer`` can be used to
|
||||||
|
adjust the visualization of the system interactively and then export
|
||||||
|
the corresponding LAMMPS commands to the clipboard to be inserted
|
||||||
|
into input files.
|
||||||
|
|
||||||
Programs included with LAMMPS as auxiliary tools can convert
|
Programs included with LAMMPS as auxiliary tools can convert
|
||||||
between LAMMPS format files and other formats. See the :doc:`Tools
|
between LAMMPS format files and other formats. See the :doc:`Tools
|
||||||
|
|||||||
Binary file not shown.
|
Before Width: | Height: | Size: 145 KiB After Width: | Height: | Size: 115 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 33 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 44 KiB After Width: | Height: | Size: 41 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 81 KiB After Width: | Height: | Size: 60 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 50 KiB After Width: | Height: | Size: 46 KiB |
Binary file not shown.
@ -22,6 +22,7 @@ letter abbreviation can be used:
|
|||||||
* :ref:`-ro or -reorder <reorder>`
|
* :ref:`-ro or -reorder <reorder>`
|
||||||
* :ref:`-r2data or -restart2data <restart2data>`
|
* :ref:`-r2data or -restart2data <restart2data>`
|
||||||
* :ref:`-r2dump or -restart2dump <restart2dump>`
|
* :ref:`-r2dump or -restart2dump <restart2dump>`
|
||||||
|
* :ref:`-r2info or -restart2info <restart2info>`
|
||||||
* :ref:`-sc or -screen <screen>`
|
* :ref:`-sc or -screen <screen>`
|
||||||
* :ref:`-sr or skiprun <skiprun>`
|
* :ref:`-sr or skiprun <skiprun>`
|
||||||
* :ref:`-sf or -suffix <suffix>`
|
* :ref:`-sf or -suffix <suffix>`
|
||||||
@ -503,6 +504,37 @@ e.g. the *nfile* and *fileper* keywords. See the
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
.. _restart2info:
|
||||||
|
|
||||||
|
**-restart2info restartfile keyword ...**
|
||||||
|
|
||||||
|
.. versionadded:: TBD
|
||||||
|
|
||||||
|
Write out some info about the restart file and and immediately exit.
|
||||||
|
This is the same operation as if the following 2-line input script were
|
||||||
|
run:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
read_restart restartfile
|
||||||
|
info system group computes fixes
|
||||||
|
|
||||||
|
The specified restartfile name may contain the wild-card character "\*".
|
||||||
|
The restartfile name may also contain the wild-card character "%". The
|
||||||
|
meaning of these characters is explained on the :doc:`read_restart
|
||||||
|
<read_restart>` documentation. The use of "%" means that a parallel
|
||||||
|
restart file can be read. Note that a filename such as file.\* may need
|
||||||
|
to be enclosed in quotes or the "\*" character prefixed with a backslash
|
||||||
|
("\") to avoid shell expansion of the "\*" character.
|
||||||
|
|
||||||
|
Optional keywords may follow the restartfile argument. These must be
|
||||||
|
valid keywords for the :doc:`info command <info>`. The most useful
|
||||||
|
ones - *system*, *group*, *computes*, and *fixes* - are already applied.
|
||||||
|
Appending keywords like *coeffs* or *communication* may provide
|
||||||
|
additional useful information stored in the restart file.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
.. _screen:
|
.. _screen:
|
||||||
|
|
||||||
**-screen file**
|
**-screen file**
|
||||||
|
|||||||
@ -92,7 +92,7 @@ Miscellaneous tools
|
|||||||
* :ref:`emacs <emacs>`
|
* :ref:`emacs <emacs>`
|
||||||
* :ref:`i-PI <ipi>`
|
* :ref:`i-PI <ipi>`
|
||||||
* :ref:`kate <kate>`
|
* :ref:`kate <kate>`
|
||||||
* :ref:`LAMMPS GUI <lammps_gui>`
|
* :ref:`LAMMPS-GUI <lammps_gui>`
|
||||||
* :ref:`LAMMPS magic patterns for file(1) <magic>`
|
* :ref:`LAMMPS magic patterns for file(1) <magic>`
|
||||||
* :ref:`Offline build tool <offline>`
|
* :ref:`Offline build tool <offline>`
|
||||||
* :ref:`singularity/apptainer <singularity_tool>`
|
* :ref:`singularity/apptainer <singularity_tool>`
|
||||||
@ -524,6 +524,7 @@ The LAMMPS-GUI has been successfully compiled and tested on:
|
|||||||
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
|
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
|
||||||
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
|
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
|
||||||
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
|
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
|
||||||
|
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.40, Qt version 6.7
|
||||||
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
|
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
|
||||||
|
|
||||||
.. _lammps_gui_install:
|
.. _lammps_gui_install:
|
||||||
@ -532,14 +533,28 @@ The LAMMPS-GUI has been successfully compiled and tested on:
|
|||||||
Pre-compiled executables
|
Pre-compiled executables
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
Pre-compiled LAMMPS executable packages that include the GUI are currently
|
Pre-compiled LAMMPS executable packages that include the GUI are
|
||||||
available from https://download.lammps.org/static or
|
currently available from https://download.lammps.org/static or
|
||||||
https://github.com/lammps/lammps/releases. You can unpack the archives
|
https://github.com/lammps/lammps/releases. For Windows, you need to
|
||||||
(or mount the macOS disk image) and run the GUI directly in place. The
|
download and then run the application installer. For macOS you download
|
||||||
folder may also be moved around and added to the ``PATH`` environment
|
and mount the disk image and then drag the application bundle to the
|
||||||
variable so the executables will be found automatically. The LAMMPS-GUI
|
Applications folder. For Linux (x86_64) you currently have two
|
||||||
executable is called ``lammps-gui`` and either takes no arguments or
|
options: 1) you can download the tar.gz archive, unpack it and run the
|
||||||
attempts to load the first argument as LAMMPS input file.
|
GUI directly in place. The ``LAMMPS_GUI`` folder may also be moved
|
||||||
|
around and added to the ``PATH`` environment variable so the executables
|
||||||
|
will be found automatically. 2) you can download the `Flatpak file
|
||||||
|
<https://www.flatpak.org/>`_ and then install it locally with the
|
||||||
|
*flatpak* command: ``flatpak install --user
|
||||||
|
LAMMPS-Linux-x86_64-GUI-<version>.flatpak`` and run it with ``flatpak
|
||||||
|
run org.lammps.lammps-gui``. The flatpak bundle also includes the
|
||||||
|
command line version of LAMMPS and some LAMMPS tools like msi2lmp. The
|
||||||
|
can be launched by using the ``--command`` flag. For example to run
|
||||||
|
LAMMPS directly on the ``in.lj`` benchmark input you would type in the
|
||||||
|
``bench`` folder: ``flatpak run --command=lmp -in in.lj`` The flatpak
|
||||||
|
version should also appear in the applications menu of standard desktop
|
||||||
|
environments. The LAMMPS-GUI executable is called ``lammps-gui`` and
|
||||||
|
either takes no arguments or attempts to load the first argument as
|
||||||
|
LAMMPS input file.
|
||||||
|
|
||||||
.. _lammps_gui_compilation:
|
.. _lammps_gui_compilation:
|
||||||
|
|
||||||
@ -1107,13 +1122,13 @@ necessary development headers and libraries are present.
|
|||||||
|
|
||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
-D WITH_SWIG=on # to enable building any SWIG wrapper
|
-D WITH_SWIG=on # to enable building any SWIG wrapper
|
||||||
-D BUILD_SWIG_JAVA=on # to enable building the Java wrapper
|
-D BUILD_SWIG_JAVA=on # to enable building the Java wrapper
|
||||||
-D BUILD_SWIG_LUA=on # to enable building the Lua wrapper
|
-D BUILD_SWIG_LUA=on # to enable building the Lua wrapper
|
||||||
-D BUILD_SWIG_PERL5=on # to enable building the Perl 5.x wrapper
|
-D BUILD_SWIG_PERL5=on # to enable building the Perl 5.x wrapper
|
||||||
-D BUILD_SWIG_PYTHON=on # to enable building the Python wrapper
|
-D BUILD_SWIG_PYTHON=on # to enable building the Python wrapper
|
||||||
-D BUILD_SWIG_RUBY=on # to enable building the Ruby wrapper
|
-D BUILD_SWIG_RUBY=on # to enable building the Ruby wrapper
|
||||||
-D BUILD_SWIG_TCL=on # to enable building the Tcl wrapper
|
-D BUILD_SWIG_TCL=on # to enable building the Tcl wrapper
|
||||||
|
|
||||||
|
|
||||||
Manual building allows a little more flexibility. E.g. one can choose
|
Manual building allows a little more flexibility. E.g. one can choose
|
||||||
|
|||||||
@ -45,6 +45,7 @@ Commands
|
|||||||
fix
|
fix
|
||||||
fix_modify
|
fix_modify
|
||||||
fitpod_command
|
fitpod_command
|
||||||
|
geturl
|
||||||
group
|
group
|
||||||
group2ndx
|
group2ndx
|
||||||
hyper
|
hyper
|
||||||
|
|||||||
@ -12,10 +12,10 @@ Syntax
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
|
fix ID group-ID style Nevery itype jtype Rmin bondtype keyword values ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* bond/create = style name of this fix command
|
* style = *bond/create* or *bond/create/angle*
|
||||||
* Nevery = attempt bond creation every this many steps
|
* Nevery = attempt bond creation every this many steps
|
||||||
* itype,jtype = atoms of itype can bond to atoms of jtype (1-Ntypes or type label)
|
* itype,jtype = atoms of itype can bond to atoms of jtype (1-Ntypes or type label)
|
||||||
* Rmin = 2 atoms separated by less than Rmin can bond (distance units)
|
* Rmin = 2 atoms separated by less than Rmin can bond (distance units)
|
||||||
|
|||||||
@ -8,151 +8,232 @@ Syntax
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix ID group-ID colvars configfile keyword values ...
|
fix ID group-ID colvars *configfile* keyword value ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* *ID*, *group-ID* are documented in :doc:`fix <fix>` command
|
||||||
* colvars = style name of this fix command
|
* "colvars" = style name of this fix command
|
||||||
* configfile = the configuration file for the colvars module
|
* *configfile* = configuration file for Colvars (use "*none*" to provide it inline)
|
||||||
* keyword = *input* or *output* or *seed* or *unwrap* or *tstat*
|
* keyword = *output* or *input* or *unwrap* or *tstat* or *seed*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
*output* value = state filename/prefix for Colvars (default: "out")
|
||||||
*input* arg = colvars.state file name or prefix or NULL (default: NULL)
|
*input* value = input state filename/prefix for Colvars (optional, default: "NULL")
|
||||||
*output* arg = output filename prefix (default: out)
|
*unwrap* value = "yes" or "no" (default: "yes")
|
||||||
*seed* arg = seed for random number generator (default: 1966)
|
*tstat* value = fix ID of thermostat applied to relevant atoms (default: "NULL")
|
||||||
*unwrap* arg = *yes* or *no*
|
*seed* value = seed for random number generator (default: 1966)
|
||||||
use unwrapped coordinates in collective variables (default: yes)
|
|
||||||
*tstat* arg = fix id of a thermostat or NULL (default: NULL)
|
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
|
# Create the fix using a config file, set prefix for its output files
|
||||||
fix abf all colvars colvars.inp tstat 1
|
fix Colvars all colvars colvars.inp output ${JOB}
|
||||||
|
|
||||||
|
# Communicate the LAMMPS target temperature to the Colvars module
|
||||||
|
fix_modify Colvars tstat NPT
|
||||||
|
|
||||||
|
# Add a new restraint specific to this LAMMPS run
|
||||||
|
fix_modify Colvars config """
|
||||||
|
harmonic {
|
||||||
|
name restraint
|
||||||
|
colvars distance1 distance2
|
||||||
|
centers ${ref1} ${ref2}
|
||||||
|
forceConstant ${kappa}
|
||||||
|
}"""
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This fix interfaces LAMMPS to the collective variables (Colvars)
|
This fix interfaces LAMMPS to the collective variables `Colvars
|
||||||
library, which allows to calculate potentials of mean force (PMFs) for
|
<https://colvars.github.io>`_ library, which allows to accelerate sampling of
|
||||||
any set of colvars, using sampling methods, including but not limited to
|
rare events and the computation of free energy surfaces and potentials of
|
||||||
Adaptive Biasing Force (ABF), metadynamics (MtD), Steered Molecular
|
mean force (PMFs) for any set of collective variables using a variety of
|
||||||
Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic
|
sampling methods (e.g. umbrella-sampling, metadynamics, ABF...).
|
||||||
restraint bias.
|
|
||||||
|
|
||||||
This documentation describes only the ``fix colvars`` command itself in
|
This documentation describes only the "fix colvars" command itself in
|
||||||
a LAMMPS script. The Colvars library is documented via the included
|
a LAMMPS script. The Colvars library is fully documented in the included
|
||||||
`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or at the webpage
|
`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or in the webpage
|
||||||
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
|
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
|
||||||
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.
|
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.
|
||||||
|
|
||||||
The Colvars library is developed at `https://github.com/Colvars/colvars
|
The Colvars library is developed at `https://github.com/Colvars/colvars
|
||||||
<https://github.com/Colvars/colvars>`_ A detailed discussion of its
|
<https://github.com/colvars/colvars>`_ A detailed discussion of its
|
||||||
implementation is in :ref:`(Fiorin) <Fiorin>`; additional references are
|
implementation is in :ref:`(Fiorin) <Fiorin>`; additional citations for
|
||||||
printed at runtime based on specific features being used.
|
specific features are printed at runtime if these features are used.
|
||||||
|
|
||||||
There are some example scripts for using this package with LAMMPS in the
|
There are example scripts on the `Colvars website <https://colvars.github.io>`_
|
||||||
``examples/PACKAGES/colvars`` directory.
|
as well as in the ``examples/PACKAGES/colvars`` directory in the LAMMPS
|
||||||
|
source tree.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The only required argument to ``fix colvars`` is the filename to the
|
The only required argument to the fix is the name of the Colvars
|
||||||
Colvars configuration file that contains the definition of the variables
|
configuration file. The contents of this file are independent from the
|
||||||
and any biasing methods applied to them. from the MD program in which
|
MD engine in which the Colvars library has been integrated, save for the
|
||||||
the colvars library has been integrated.
|
units that are specific to each engine. In LAMMPS, the units used by
|
||||||
|
Colvars are consistent with those specified by the :doc:`units <units>`
|
||||||
|
command.
|
||||||
|
|
||||||
The *group-ID* entry is ignored. ``fix colvars`` will always apply to
|
.. versionadded:: Colvars_2023-06-04 The special value "*none*"
|
||||||
|
(lowercase) initializes an empty Colvars module, which
|
||||||
|
allows loading configuration dynamically using
|
||||||
|
:doc:`fix_modify <fix_modify>` (see below).
|
||||||
|
|
||||||
|
The *group-ID* entry is ignored. "fix colvars" will always apply to
|
||||||
the entire system, but specific atoms will be selected based on
|
the entire system, but specific atoms will be selected based on
|
||||||
selection keywords in the Colvars configuration file or files. There is
|
selection keywords in the Colvars configuration file or files. There is
|
||||||
no need to define multiple ``fix colvars`` instances and it is not
|
no need to define multiple "fix colvars" instances and it is not
|
||||||
allowed.
|
allowed.
|
||||||
|
|
||||||
The *output* keyword allows to specify the prefix of output files
|
The "output" keyword allows to specify the prefix of output files generated
|
||||||
generated by Colvars, for example ``output.colvars.traj`` or
|
by Colvars, for example "*output*.colvars.traj" or "output.pmf". Supplying
|
||||||
``output.pmf``.
|
an empty string suppresses any file output from Colvars to file, except for
|
||||||
|
data saved into the LAMMPS :doc:`binary restart <restart>` files.
|
||||||
|
|
||||||
The *input* keyword allows to specify an optional state file that
|
The "input" keyword allows to specify an optional state file that contains
|
||||||
contains the restart information needed to continue a previous
|
the restart information needed to continue a previous simulation state.
|
||||||
simulation state. Note, however, that ``fix colvars`` records its state
|
However, because "fix colvars" records its state in LAMMPS :doc:`binary
|
||||||
in :doc:`binary restart <restart>` files, so when using the
|
restart <restart>` files, this is usually not needed when using the
|
||||||
:doc:`read_restart <read_restart>` command, this is usually not needed.
|
:doc:`read_restart <read_restart>` command.
|
||||||
|
|
||||||
The *seed* keyword contains the seed for the random number generator
|
The *unwrap* keyword controls whether wrapped or unwrapped coordinates are
|
||||||
used by Colvars.
|
passed to the Colvars library for calculation of the collective variables and
|
||||||
|
the resulting forces. The default is *yes*, i.e. the image flags are used to
|
||||||
The *unwrap* keyword controls whether wrapped or unwrapped coordinates
|
reconstruct the absolute atom positions. Setting this to *no* will use the
|
||||||
are passed to the Colvars library for calculation of the collective
|
current local coordinates that are wrapped back into the simulation cell at
|
||||||
variables and the resulting forces. The default is *yes*, i.e. to use
|
each re-neighboring step instead. For information about when and how this
|
||||||
the image flags to reconstruct the absolute atom positions. Setting
|
affects results, please see
|
||||||
this to *no* will use the current local coordinates that are wrapped
|
|
||||||
back into the simulation cell at each re-neighboring instead. For
|
|
||||||
information about when and how this affects results, please see
|
|
||||||
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping
|
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping
|
||||||
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.
|
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.
|
||||||
|
|
||||||
The *tstat* keyword can be either NULL or the label of a thermostatting
|
The *tstat* keyword can be either "NULL" or the label of a thermostatting
|
||||||
fix that thermostats all atoms in the fix colvars group. This will be
|
fix that thermostats all atoms in the fix colvars group. This will be
|
||||||
used to let Colvars know what is the current thermostat target
|
used to provide the colvars module with the current thermostat target
|
||||||
temperature.
|
temperature.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
The *seed* keyword contains the seed for the random number generator
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
that will be used in the colvars module.
|
||||||
|
|
||||||
This fix writes the current status of the colvars module into
|
|
||||||
:doc:`binary restart files <restart>`. This is in addition to the text
|
|
||||||
mode ``.colvars.state`` written by Colvars itself and the information in
|
|
||||||
both files is identical.
|
|
||||||
|
|
||||||
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
|
Restarting
|
||||||
fix to add the energy change from the biasing force added by Colvars 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 no <fix_modify>`.
|
|
||||||
|
|
||||||
The *fix_modify configfile <config file>* option loads Colvars
|
This fix writes the current state of the Colvars module into :doc:`binary
|
||||||
configuration from an additional file. This option can only be used,
|
restart files <restart>`. This is in addition to the text-mode
|
||||||
after the system has been initialized with a :doc:`run <run>` command.
|
".colvars.state" state file that is written by the Colvars module itself.
|
||||||
|
The information contained in both files is identical, and the binary LAMMPS
|
||||||
|
restart file is also used by fix colvars when :doc:`read_restart
|
||||||
|
<read_restart>` is called in a LAMMPS script. In that case, there is
|
||||||
|
typically no need to specify the *input* keyword.
|
||||||
|
|
||||||
The *fix_modify config <quoted string>* option allows to add settings
|
As long as LAMMPS binary restarts will be used to continue a simulation, it
|
||||||
from inline strings. Those have to fit on a single line when enclosed in
|
is safe to delete the ".colvars.state" files to save space. However, when a
|
||||||
a pair of double quotes ("), or can span multiple lines when bracketed
|
LAMMPS simulation is restarted using :doc:`read_data <read_data>`, the
|
||||||
by a pair of triple double quotes (""", like Python embedded
|
Colvars state file must be available and loaded via the "input" keyword or
|
||||||
documentation).
|
via a "fix_modify Colvars load" command (see below).
|
||||||
|
|
||||||
|
When restarting, the fix and the Colvars module should be created and
|
||||||
|
configured using either the original configuration file(s).
|
||||||
|
|
||||||
|
|
||||||
|
Output
|
||||||
|
""""""
|
||||||
|
|
||||||
This fix computes a global scalar which can be accessed by various
|
This fix computes a global scalar which can be accessed by various
|
||||||
:doc:`output commands <Howto_output>`. The scalar is the Colvars energy
|
:doc:`output commands <Howto_output>`. The scalar is the energy due to all
|
||||||
mentioned above. The scalar value calculated by this fix is
|
external potentials defined in the Colvars configuration. The scalar value
|
||||||
"extensive".
|
calculated by this fix is "extensive".
|
||||||
|
|
||||||
|
Aside from the state information in a ".colvars.state" file, other
|
||||||
|
`output files <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_output>`_
|
||||||
|
are produced by Colvars depending on the type of simulation.
|
||||||
|
For this reason, the "output" keyword is required for fix colvars.
|
||||||
|
|
||||||
|
|
||||||
|
Controlling Colvars via `fix_modify`
|
||||||
|
""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: Colvars_2023-06-04
|
||||||
|
|
||||||
|
The :doc:`fix_modify <fix_modify>` command may be used on "fix colvars" in
|
||||||
|
either one of two ways:
|
||||||
|
|
||||||
|
(1) Provide updated values for the fix parameters, such as *output*, *input*,
|
||||||
|
*unwrap*, *tstat* and *seed*. Additionally, the :doc:`fix_modify
|
||||||
|
<fix_modify>` *energy* keyword is supported by this fix to add the energy
|
||||||
|
change from the biasing force added by Colvars to the global potential
|
||||||
|
energy of the system as part of :doc:`thermodynamic output <thermo_style>`
|
||||||
|
(the default is :doc:`fix_modify energy no <fix_modify>`).
|
||||||
|
For example, in a multi-step LAMMPS script involving multiple thermostats
|
||||||
|
(e.g. fix nvt followed by fix npt), Colvars can read a new thermostat's
|
||||||
|
target temperature like this:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix NVT all nvt ...
|
||||||
|
fix Colvars all colvars <configfile> output equil1 tstat NVT
|
||||||
|
run <NUMSTEPS>
|
||||||
|
unfix nvt
|
||||||
|
fix NPT all n ...
|
||||||
|
fix_modify Colvars tstat NPT
|
||||||
|
fix_modify Colvars output equil2
|
||||||
|
|
||||||
|
|
||||||
|
(2) Call one of the scripting functions provided by the Colvars module
|
||||||
|
itself (a full list is available in the Colvars doc). The arguments
|
||||||
|
to these functions are provided as strings and passed to Colvars.
|
||||||
|
|
||||||
|
LAMMPS variables referenced by their string representation
|
||||||
|
"${variable}" will be expanded immediately. Note also that this
|
||||||
|
variable expansion *will also happen within quotes*, similar to what the
|
||||||
|
:doc:`mdi <mdi>` command provides. This feature makes it possible to use
|
||||||
|
the values of certain LAMMPS variables in Colvars configuration strings.
|
||||||
|
For example, to synchronize the LAMMPS and Colvars dump frequencies:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
variable freq index 10000
|
||||||
|
dump myDump all atom/zstd ${freq} dump.atom.zstd
|
||||||
|
fix_modify Colvars config "colvarsTrajFrequency ${freq}"
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
Although it is possible to use :doc:`fix_modify <fix_modify>` at any time,
|
||||||
|
its results will only reflect the state of the Colvars module at the end
|
||||||
|
of the most recent "run" or "minimize" command. Any new configuration
|
||||||
|
added via "fix_modify Colvars configfile" or "fix_modify Colvars config"
|
||||||
|
will only be loaded when the simulation resumes. Configuration files or
|
||||||
|
strings will be parsed in the same sequence as they were provided in the
|
||||||
|
LAMMPS script.
|
||||||
|
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
``fix colvars`` is provided by the COLVARS package and is only available
|
This fix is provided by the COLVARS package and is only available if LAMMPS
|
||||||
if LAMMPS was built with that package. Some of the features also
|
was built with that package (default in most builds). Some of the features
|
||||||
require code available from the LEPTON package. See the :doc:`Build
|
also require code available from the LEPTON package. See the :doc:`Build
|
||||||
package <Build_package>` page for more info.
|
package <Build_package>` page for more info.
|
||||||
|
|
||||||
There can only be one Colvars instance defined at a time. Since the
|
There can only be one Colvars instance defined at a time. Since the
|
||||||
interface communicates only the minimum amount of information and the
|
interface communicates only the minimum required amount of information, and
|
||||||
Colvars module itself can handle an arbitrary number of collective
|
the Colvars module itself can handle an arbitrary number of collective
|
||||||
variables, this is not a limitation of functionality.
|
variables, this is not a limitation of functionality.
|
||||||
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`fix smd <fix_smd>`, :doc:`fix spring <fix_spring>`,
|
:doc:`fix smd <fix_smd>`, :doc:`fix spring <fix_spring>`,
|
||||||
:doc:`fix plumed <fix_plumed>`
|
:doc:`fix plumed <fix_plumed>`
|
||||||
|
|
||||||
Default
|
|
||||||
"""""""
|
|
||||||
|
|
||||||
The default options are input = NULL, output = out, seed = 1966, unwrap yes,
|
|
||||||
and tstat = NULL.
|
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _Fiorin:
|
.. _Fiorin:
|
||||||
|
|
||||||
**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
|
**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys. 111, 3345 (2013) https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
|
||||||
|
.. _Colvars_LAMMPS_doc:
|
||||||
|
|
||||||
|
https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
|
||||||
|
|||||||
82
doc/src/geturl.rst
Normal file
82
doc/src/geturl.rst
Normal file
@ -0,0 +1,82 @@
|
|||||||
|
.. index:: geturl
|
||||||
|
|
||||||
|
geturl command
|
||||||
|
==============
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
geturl url keyword args ...
|
||||||
|
|
||||||
|
* url = URL of the file to download
|
||||||
|
* zero or more keyword argument pairs may be provided
|
||||||
|
* keyword = *output* or *verify* or *overwrite* or *verbose*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
*output* filename = write to *filename* instead of inferring the name from the URL
|
||||||
|
*verify* yes/no = verify SSL certificate and hostname if *yes*, do not if *no*
|
||||||
|
*overwrite* yes/no = if *yes* overwrite the output file in case it exists, do not if *no*
|
||||||
|
*verbose* yes/no = if *yes* write verbose debug output from libcurl to screen, do not if *no*
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
geturl https://www.ctcms.nist.gov/potentials/Download/1990--Ackland-G-J-Vitek-V--Cu/2/Cu2.eam.fs
|
||||||
|
geturl https://github.com/lammps/lammps/blob/develop/bench/in.lj output in.bench-lj
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: TBD
|
||||||
|
|
||||||
|
Download a file from an URL to the local disk. This is implemented with
|
||||||
|
the `libcurl library <https:://curl.se/libcurl/>`_ which supports a
|
||||||
|
large variety of protocols including "http", "https", "ftp", "scp",
|
||||||
|
"sftp", "file". The transfer will only be performed on MPI rank 0.
|
||||||
|
|
||||||
|
The *output* keyword can be used to set the filename. By default, the last part
|
||||||
|
of the URL is used.
|
||||||
|
|
||||||
|
The *verify* keyword determines whether ``libcurl`` will validate the
|
||||||
|
SSL certificate and hostname for encrypted connections. Turning this
|
||||||
|
off may be required when using a proxy or connecting to a server with a
|
||||||
|
self-signed SSL certificate.
|
||||||
|
|
||||||
|
The *overwrite* keyword determines whether a file should be overwritten if it
|
||||||
|
already exists. If the argument is *no*, then the download will be skipped
|
||||||
|
if the file exists.
|
||||||
|
|
||||||
|
The *verbose* keyword determines whether a detailed protocol of the steps
|
||||||
|
performed by libcurl is written to the screen. Using the argument *yes*
|
||||||
|
can be used to debug connection issues when the *geturl* command does not
|
||||||
|
behave as expected. If the argument is *no*, geturl will operate silently
|
||||||
|
and only report the error status number provided by libcurl, in case of a
|
||||||
|
failure.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This command is part of the EXTRA-COMMAND package. It is only enabled
|
||||||
|
if LAMMPS was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info. It also requires that LAMMPS was
|
||||||
|
built with support for `the libcurl library
|
||||||
|
<https://curl.se/libcurl/>`_. See the page about :ref:`Compiling LAMMPS
|
||||||
|
with libcurl support <libcurl>` for further info. If support for
|
||||||
|
libcurl is not included, using *geturl* will trigger an error.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`shell <shell>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
*verify* = yes, *overwrite* = yes
|
||||||
@ -24,15 +24,18 @@ Examples
|
|||||||
info all out log
|
info all out log
|
||||||
info all out append info.txt
|
info all out append info.txt
|
||||||
info styles all
|
info styles all
|
||||||
info styles atom
|
info styles atom styles command
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
Print out information about the current internal state of the running
|
Print out information about the current internal state of the running
|
||||||
LAMMPS process. This can be helpful when debugging or validating
|
LAMMPS process. This can be helpful when debugging or validating complex
|
||||||
complex input scripts. Several output categories are available and
|
input scripts. Several output categories are available and one or more
|
||||||
one or more output category may be requested.
|
output categories may be requested. All category keywords take no
|
||||||
|
arguments, only *out* and *styles* take arguments as shown below. The
|
||||||
|
keywords are cumulative, may be abbreviated, and unknown keywords are
|
||||||
|
ignored.
|
||||||
|
|
||||||
The *out* flag controls where the output is sent. It can only be sent
|
The *out* flag controls where the output is sent. It can only be sent
|
||||||
to one target. By default this is the screen, if it is active. The
|
to one target. By default this is the screen, if it is active. The
|
||||||
@ -99,9 +102,12 @@ support. This lists the 3d-FFT engine, FFT precision, FFT library
|
|||||||
used by the FFT engine. If the KOKKOS package is included, the settings
|
used by the FFT engine. If the KOKKOS package is included, the settings
|
||||||
used for the KOKKOS package are displayed as well.
|
used for the KOKKOS package are displayed as well.
|
||||||
|
|
||||||
The *styles* category prints the list of styles available in the
|
The *styles* category prints the list of styles available in the current
|
||||||
current LAMMPS binary. It supports one of the following options
|
LAMMPS binary. The *styles* keyword without option is the same as using
|
||||||
to control which category of styles is printed out:
|
the "all" option. One of the following options may be used to control
|
||||||
|
which category of styles is printed out. To select multiple categories,
|
||||||
|
the styles keyword needs to be used multiple times with the desired
|
||||||
|
categories:
|
||||||
|
|
||||||
* all
|
* all
|
||||||
* angle
|
* angle
|
||||||
|
|||||||
@ -426,8 +426,8 @@ The *meam* and *meam/ms* pair styles are provided in the MEAM
|
|||||||
package. They are only enabled if LAMMPS was built with that package.
|
package. They are only enabled if LAMMPS was built with that package.
|
||||||
See the :doc:`Build package <Build_package>` page for more info.
|
See the :doc:`Build package <Build_package>` page for more info.
|
||||||
|
|
||||||
The maximum number of elements, that can be read from the MEAM library
|
The maximum number of elements that can be read from the MEAM library
|
||||||
file, is determined at compile time. The default is 8. If you need
|
file is determined at compile time. The default is 8. If you need
|
||||||
support for more elements, you have to change the the constant 'MAXELT'
|
support for more elements, you have to change the the constant 'MAXELT'
|
||||||
at the beginning of the file ``src/MEAM/meam.h`` and update/recompile
|
at the beginning of the file ``src/MEAM/meam.h`` and update/recompile
|
||||||
LAMMPS. There is no limit on the number of atoms types.
|
LAMMPS. There is no limit on the number of atoms types.
|
||||||
|
|||||||
@ -47,6 +47,12 @@ Restart files are saved in binary format to enable exact restarts,
|
|||||||
meaning that the trajectories of a restarted run will precisely match
|
meaning that the trajectories of a restarted run will precisely match
|
||||||
those produced by the original run had it continued on.
|
those produced by the original run had it continued on.
|
||||||
|
|
||||||
|
Some information about a restart file can be gathered directly from the
|
||||||
|
command line when using LAMMPS with the :ref:`-restart2info
|
||||||
|
<restart2info>` command line flag. On Unix-like operating systems (like
|
||||||
|
Linux or macOS), one can also :ref:`configure the "file" command line
|
||||||
|
program <magic>` to display basic information about a restart file
|
||||||
|
|
||||||
The binary restart file format was not designed with backward, forward,
|
The binary restart file format was not designed with backward, forward,
|
||||||
or cross-platform compatibility in mind, so the files are only expected
|
or cross-platform compatibility in mind, so the files are only expected
|
||||||
to be read correctly by the same LAMMPS executable on the same platform.
|
to be read correctly by the same LAMMPS executable on the same platform.
|
||||||
@ -130,7 +136,7 @@ these settings after the restart file is read.
|
|||||||
* :doc:`newton bond <newton>` (see discussion of newton command below)
|
* :doc:`newton bond <newton>` (see discussion of newton command below)
|
||||||
* :doc:`atom style <atom_style>` and :doc:`atom_modify <atom_modify>` settings id, map, sort
|
* :doc:`atom style <atom_style>` and :doc:`atom_modify <atom_modify>` settings id, map, sort
|
||||||
* :doc:`comm style <comm_style>` and :doc:`comm_modify <comm_modify>` settings mode, cutoff, vel
|
* :doc:`comm style <comm_style>` and :doc:`comm_modify <comm_modify>` settings mode, cutoff, vel
|
||||||
* :doc:`timestep <timestep>`
|
* :doc:`timestep size <timestep>` and :doc:`timestep number <reset_timestep>`
|
||||||
* simulation box size and shape and :doc:`boundary <boundary>` settings
|
* simulation box size and shape and :doc:`boundary <boundary>` settings
|
||||||
* atom :doc:`group <group>` definitions
|
* atom :doc:`group <group>` definitions
|
||||||
* per-type atom settings such as :doc:`mass <mass>`
|
* per-type atom settings such as :doc:`mass <mass>`
|
||||||
|
|||||||
@ -1186,6 +1186,7 @@ flaglog
|
|||||||
flagN
|
flagN
|
||||||
flagVF
|
flagVF
|
||||||
flang
|
flang
|
||||||
|
flatpak
|
||||||
fld
|
fld
|
||||||
floralwhite
|
floralwhite
|
||||||
Florez
|
Florez
|
||||||
@ -1297,6 +1298,7 @@ Gershgorin
|
|||||||
getrusage
|
getrusage
|
||||||
getter
|
getter
|
||||||
gettimeofday
|
gettimeofday
|
||||||
|
geturl
|
||||||
gewald
|
gewald
|
||||||
Gezelter
|
Gezelter
|
||||||
Gflop
|
Gflop
|
||||||
@ -1491,6 +1493,8 @@ hplanck
|
|||||||
Hs
|
Hs
|
||||||
hstyle
|
hstyle
|
||||||
html
|
html
|
||||||
|
http
|
||||||
|
https
|
||||||
hTST
|
hTST
|
||||||
https
|
https
|
||||||
hu
|
hu
|
||||||
@ -2902,6 +2906,7 @@ plumedfile
|
|||||||
pmb
|
pmb
|
||||||
pmcmoves
|
pmcmoves
|
||||||
pme
|
pme
|
||||||
|
pmf
|
||||||
Pmolrotate
|
Pmolrotate
|
||||||
Pmoltrans
|
Pmoltrans
|
||||||
pN
|
pN
|
||||||
@ -3348,6 +3353,7 @@ Schunk
|
|||||||
Schuring
|
Schuring
|
||||||
Schwen
|
Schwen
|
||||||
Sci
|
Sci
|
||||||
|
scp
|
||||||
screenshot
|
screenshot
|
||||||
screenshots
|
screenshots
|
||||||
Scripps
|
Scripps
|
||||||
@ -3388,6 +3394,7 @@ setvel
|
|||||||
sevenbody
|
sevenbody
|
||||||
sfftw
|
sfftw
|
||||||
sfree
|
sfree
|
||||||
|
sftp
|
||||||
Sg
|
Sg
|
||||||
sgcmc
|
sgcmc
|
||||||
Shan
|
Shan
|
||||||
@ -3902,6 +3909,7 @@ upenn
|
|||||||
upto
|
upto
|
||||||
Urbakh
|
Urbakh
|
||||||
Urbana
|
Urbana
|
||||||
|
url
|
||||||
UreyBradley
|
UreyBradley
|
||||||
Usabiaga
|
Usabiaga
|
||||||
usec
|
usec
|
||||||
|
|||||||
@ -150,6 +150,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
|||||||
ADDSYM(config_has_png_support);
|
ADDSYM(config_has_png_support);
|
||||||
ADDSYM(config_has_jpeg_support);
|
ADDSYM(config_has_jpeg_support);
|
||||||
ADDSYM(config_has_ffmpeg_support);
|
ADDSYM(config_has_ffmpeg_support);
|
||||||
|
ADDSYM(config_has_curl_support);
|
||||||
ADDSYM(config_has_exceptions);
|
ADDSYM(config_has_exceptions);
|
||||||
|
|
||||||
ADDSYM(config_has_package);
|
ADDSYM(config_has_package);
|
||||||
|
|||||||
@ -203,6 +203,7 @@ struct _liblammpsplugin {
|
|||||||
int (*config_has_png_support)();
|
int (*config_has_png_support)();
|
||||||
int (*config_has_jpeg_support)();
|
int (*config_has_jpeg_support)();
|
||||||
int (*config_has_ffmpeg_support)();
|
int (*config_has_ffmpeg_support)();
|
||||||
|
int (*config_has_curl_support)();
|
||||||
int (*config_has_exceptions)();
|
int (*config_has_exceptions)();
|
||||||
|
|
||||||
int (*config_has_package)(const char *);
|
int (*config_has_package)(const char *);
|
||||||
|
|||||||
@ -1,629 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
shell "rm -f out*.colvars.*"
|
|
||||||
fix 2 all colvars peptide.colvars
|
|
||||||
fix 2a ref setforce 0.0 0.0 0.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "two"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 2 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one, two }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
|
||||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
|
||||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
|
||||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
|
||||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
|
||||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
|
||||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
|
||||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
|
||||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
|
||||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
|
||||||
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
|
||||||
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
|
||||||
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
|
||||||
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
|
||||||
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
|
||||||
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
|
||||||
Other | | 0.001615 | | | 0.07
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11124 ave 11124 max 11124 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708237 ave 708237 max 708237 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708237
|
|
||||||
Ave neighs/atom = 353.412
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 12
|
|
||||||
Dangerous builds = 2
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
|
||||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
|
||||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
|
||||||
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
|
||||||
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
|
||||||
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
|
||||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
|
||||||
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
|
||||||
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.81266e-06
|
|
||||||
6 0.997 7.79424e-07
|
|
||||||
8 1.08 1.08903e-06
|
|
||||||
10 1.111 2.96503e-07
|
|
||||||
12 1.08 4.69038e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76471e-06
|
|
||||||
31 104.52 0.000411055
|
|
||||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
|
||||||
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
|
||||||
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
|
||||||
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
|
||||||
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
|
||||||
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
|
||||||
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
|
||||||
Other | | 0.001596 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11159 ave 11159 max 11159 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708083 ave 708083 max 708083 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708083
|
|
||||||
Ave neighs/atom = 353.335
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 7
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "two"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 2 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one, two }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Restarting from file "out.colvars.state".
|
|
||||||
colvars: Restarting collective variable "one" from value: 10.0128
|
|
||||||
colvars: Restarting collective variable "two" from value: 9.62236
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
|
||||||
colvars: Setting initial step number from LAMMPS: 200
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.81266e-06
|
|
||||||
6 0.997 7.79424e-07
|
|
||||||
8 1.08 1.08903e-06
|
|
||||||
10 1.111 2.96503e-07
|
|
||||||
12 1.08 4.69038e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76471e-06
|
|
||||||
31 104.52 0.000411055
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
|
||||||
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
|
||||||
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
|
||||||
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
|
||||||
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
|
||||||
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
|
||||||
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
|
||||||
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
|
||||||
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
|
||||||
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
|
||||||
SHAKE stats (type/ave/delta) on step 300
|
|
||||||
4 1.111 1.79792e-05
|
|
||||||
6 0.997005 1.02512e-05
|
|
||||||
8 1.08 1.85102e-05
|
|
||||||
10 1.111 9.98839e-06
|
|
||||||
12 1.08 8.84111e-06
|
|
||||||
14 0.960008 0
|
|
||||||
18 0.957203 1.8445e-05
|
|
||||||
31 104.52 0.00168383
|
|
||||||
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
|
|
||||||
colvars: Saving collective variables state to "out2.colvars.state".
|
|
||||||
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
|
||||||
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
|
||||||
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
|
||||||
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
|
||||||
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
|
||||||
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
|
||||||
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
|
||||||
Other | | 0.001731 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11296 ave 11296 max 11296 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708152 ave 708152 max 708152 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708152
|
|
||||||
Ave neighs/atom = 353.369
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:06
|
|
||||||
@ -1,629 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
shell "rm -f out*.colvars.*"
|
|
||||||
fix 2 all colvars peptide.colvars
|
|
||||||
fix 2a ref setforce 0.0 0.0 0.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "two"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 2 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one, two }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
|
||||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
|
||||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
|
||||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
|
||||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
|
||||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
|
||||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
|
||||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
|
||||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
|
||||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
|
|
||||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
|
|
||||||
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
|
|
||||||
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
|
|
||||||
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
|
|
||||||
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
|
|
||||||
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
|
|
||||||
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
|
|
||||||
Other | | 0.001141 | | | 0.19
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 489 min
|
|
||||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
|
||||||
Nghost: 6563.25 ave 6596 max 6519 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
||||||
Neighs: 177059 ave 181742 max 172942 min
|
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708237
|
|
||||||
Ave neighs/atom = 353.412
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 12
|
|
||||||
Dangerous builds = 2
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
|
||||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
|
||||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
|
||||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
|
||||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
|
||||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
|
||||||
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
|
|
||||||
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
|
|
||||||
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.81266e-06
|
|
||||||
6 0.997 7.79424e-07
|
|
||||||
8 1.08 1.08903e-06
|
|
||||||
10 1.111 2.96503e-07
|
|
||||||
12 1.08 4.69038e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76471e-06
|
|
||||||
31 104.52 0.000411055
|
|
||||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
|
|
||||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
|
|
||||||
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
|
|
||||||
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
|
|
||||||
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
|
|
||||||
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
|
|
||||||
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
|
|
||||||
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
|
|
||||||
Other | | 0.001623 | | | 0.28
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 481 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
|
||||||
Nghost: 6556.5 ave 6608 max 6514 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
||||||
Neighs: 177021 ave 182259 max 172089 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708083
|
|
||||||
Ave neighs/atom = 353.335
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 7
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "two"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 2 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one, two }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Restarting from file "out.colvars.state".
|
|
||||||
colvars: Restarting collective variable "one" from value: 10.0128
|
|
||||||
colvars: Restarting collective variable "two" from value: 9.62236
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
|
||||||
colvars: Setting initial step number from LAMMPS: 200
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.81266e-06
|
|
||||||
6 0.997 7.79424e-07
|
|
||||||
8 1.08 1.08903e-06
|
|
||||||
10 1.111 2.96503e-07
|
|
||||||
12 1.08 4.69038e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76471e-06
|
|
||||||
31 104.52 0.000411055
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
|
||||||
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
|
||||||
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
|
||||||
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
|
||||||
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
|
||||||
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
|
||||||
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
|
||||||
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
|
||||||
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
|
||||||
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
|
||||||
SHAKE stats (type/ave/delta) on step 300
|
|
||||||
4 1.111 1.79792e-05
|
|
||||||
6 0.997005 1.02512e-05
|
|
||||||
8 1.08 1.85102e-05
|
|
||||||
10 1.111 9.98838e-06
|
|
||||||
12 1.08 8.84113e-06
|
|
||||||
14 0.960008 0
|
|
||||||
18 0.957203 1.8445e-05
|
|
||||||
31 104.52 0.00168382
|
|
||||||
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
|
||||||
colvars: Saving collective variables state to "out2.colvars.state".
|
|
||||||
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
|
||||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
|
||||||
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
|
||||||
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
|
||||||
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
|
||||||
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
|
||||||
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
|
||||||
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
|
||||||
Other | | 0.001705 | | | 0.29
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 472 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
|
||||||
Nghost: 6612.75 ave 6681 max 6561 min
|
|
||||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
|
||||||
Neighs: 177038 ave 180136 max 170218 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 708152
|
|
||||||
Ave neighs/atom = 353.369
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
@ -1,260 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
shell "rm -f peptide2.colvars.*"
|
|
||||||
fix 2 all colvars peptide.colvars2 output peptide2
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars2":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10 }
|
|
||||||
colvars: # targetCenters = { 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "peptide2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
|
||||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
|
||||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
|
||||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
|
||||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
|
||||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
|
||||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
|
||||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
|
||||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
|
||||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191462
|
|
||||||
6 0.996989 3.55508e-05
|
|
||||||
8 1.08 9.0997e-06
|
|
||||||
10 1.111 1.58544e-05
|
|
||||||
12 1.08 5.80604e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92445e-05
|
|
||||||
31 104.52 0.00239923
|
|
||||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
|
||||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
|
||||||
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
|
||||||
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
|
||||||
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
|
||||||
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
|
||||||
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
|
||||||
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
|
||||||
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
|
||||||
Other | | 0.001465 | | | 0.06
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11143 ave 11143 max 11143 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708234 ave 708234 max 708234 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708234
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:02
|
|
||||||
@ -1,260 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
shell "rm -f peptide2.colvars.*"
|
|
||||||
fix 2 all colvars peptide.colvars2 output peptide2
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
colvars: Creating proxy instance
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
||||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
||||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
|
||||||
colvars: in any publication based on this calculation.
|
|
||||||
colvars: SMP parallelism is available.
|
|
||||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Reading new configuration from file "peptide.colvars2":
|
|
||||||
colvars: # smp = on [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # scriptedColvarForces = off [default]
|
|
||||||
colvars: # scriptingAfterBiases = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = "one"
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # scalable = on [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: # name = "" [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # atomsOfGroup = "" [default]
|
|
||||||
colvars: # indexGroup = "" [default]
|
|
||||||
colvars: # psfSegID = [default]
|
|
||||||
colvars: # atomsFile = "" [default]
|
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
||||||
colvars: # enableForces = on [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
|
||||||
colvars: # printAtomIDs = off [default]
|
|
||||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: # oneSiteTotalForce = off [default]
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputTotalForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: # subtractAppliedForce = off [default]
|
|
||||||
colvars: # runAve = off [default]
|
|
||||||
colvars: # corrFunc = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new "harmonic" instance.
|
|
||||||
colvars: # name = "h_pot"
|
|
||||||
colvars: # colvars = { one }
|
|
||||||
colvars: # outputEnergy = off [default]
|
|
||||||
colvars: # timeStepFactor = 1 [default]
|
|
||||||
colvars: # writeTISamples = off [default]
|
|
||||||
colvars: # writeTIPMF = off [default]
|
|
||||||
colvars: # centers = { 10 }
|
|
||||||
colvars: # targetCenters = { 10 } [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
|
||||||
colvars: # forceConstant = 100
|
|
||||||
colvars: # targetForceConstant = -1 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module (re)initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "peptide2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
|
||||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
|
||||||
colvars: Performing analysis.
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
|
||||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
|
||||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
|
||||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
|
||||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
|
||||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
|
||||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
|
||||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
|
||||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
|
||||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191462
|
|
||||||
6 0.996989 3.55508e-05
|
|
||||||
8 1.08 9.0997e-06
|
|
||||||
10 1.111 1.58544e-05
|
|
||||||
12 1.08 5.80604e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92445e-05
|
|
||||||
31 104.52 0.00239923
|
|
||||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
|
||||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
|
||||||
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
|
|
||||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
|
|
||||||
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
|
|
||||||
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
|
|
||||||
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
|
|
||||||
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
|
|
||||||
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
|
|
||||||
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
|
|
||||||
Other | | 0.001264 | | | 0.20
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 494 min
|
|
||||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
|
||||||
Nghost: 6572.5 ave 6593 max 6548 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
||||||
Neighs: 177058 ave 181778 max 174301 min
|
|
||||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708234
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
colvars: Resetting the Collective Variables module.
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,163 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
|
||||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
|
||||||
|
|
||||||
fix 2a ref setforce 0.0 0.0 0.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
variable sp equal f_3a+f_3b
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
|
||||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
|
||||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
|
||||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
|
||||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
|
||||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
|
||||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
|
||||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
|
||||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
|
||||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s
|
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
|
|
||||||
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
|
|
||||||
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
|
|
||||||
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
|
|
||||||
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
|
|
||||||
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
|
|
||||||
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
|
|
||||||
Other | | 0.001613 | | | 0.07
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11124 ave 11124 max 11124 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708237 ave 708237 max 708237 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708237
|
|
||||||
Ave neighs/atom = 353.412
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 12
|
|
||||||
Dangerous builds = 2
|
|
||||||
Total wall time: 0:00:02
|
|
||||||
@ -1,163 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
|
||||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
|
||||||
|
|
||||||
fix 2a ref setforce 0.0 0.0 0.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
variable sp equal f_3a+f_3b
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
|
||||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
|
||||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
|
||||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
|
||||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
|
||||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
|
||||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
|
||||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
|
||||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
|
||||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97155e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84253e-05
|
|
||||||
12 1.08 7.2713e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36079e-05
|
|
||||||
31 104.52 0.0030599
|
|
||||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
|
||||||
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
|
|
||||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
|
|
||||||
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
|
|
||||||
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
|
|
||||||
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
|
|
||||||
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
|
|
||||||
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
|
|
||||||
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
|
|
||||||
Other | | 0.001274 | | | 0.21
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 489 min
|
|
||||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
|
||||||
Nghost: 6563.25 ave 6596 max 6519 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
||||||
Neighs: 177059 ave 181742 max 172942 min
|
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708237
|
|
||||||
Ave neighs/atom = 353.412
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 12
|
|
||||||
Dangerous builds = 2
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,158 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 10648 3375
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
|
||||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
|
||||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
|
||||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
|
||||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
|
||||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
|
||||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
|
||||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
|
||||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
|
||||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191462
|
|
||||||
6 0.996989 3.55508e-05
|
|
||||||
8 1.08 9.0997e-06
|
|
||||||
10 1.111 1.58544e-05
|
|
||||||
12 1.08 5.80604e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92445e-05
|
|
||||||
31 104.52 0.00239923
|
|
||||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
|
||||||
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s
|
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
|
|
||||||
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
|
|
||||||
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
|
|
||||||
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
|
|
||||||
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
|
|
||||||
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
|
|
||||||
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
|
|
||||||
Other | | 0.001546 | | | 0.07
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11143 ave 11143 max 11143 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708234 ave 708234 max 708234 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708234
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
Total wall time: 0:00:02
|
|
||||||
@ -1,158 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Solvated 5-mer peptide
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
kspace_style pppm 0.0001
|
|
||||||
|
|
||||||
read_data data.peptide
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
2004 atoms
|
|
||||||
reading velocities ...
|
|
||||||
2004 velocities
|
|
||||||
scanning bonds ...
|
|
||||||
3 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
1365 bonds
|
|
||||||
reading angles ...
|
|
||||||
786 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
207 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
12 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
14 = max # of 1-4 neighbors
|
|
||||||
18 = max # of special neighbors
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 5
|
|
||||||
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
group peptide type <= 12
|
|
||||||
84 atoms in group peptide
|
|
||||||
group one id 2 4 5 6
|
|
||||||
4 atoms in group one
|
|
||||||
group two id 80 82 83 84
|
|
||||||
4 atoms in group two
|
|
||||||
group ref id 37
|
|
||||||
1 atoms in group ref
|
|
||||||
group colvar union one two ref
|
|
||||||
9 atoms in group colvar
|
|
||||||
|
|
||||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
||||||
|
|
||||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
|
||||||
|
|
||||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
||||||
19 = # of size 2 clusters
|
|
||||||
6 = # of size 3 clusters
|
|
||||||
3 = # of size 4 clusters
|
|
||||||
640 = # of frozen angles
|
|
||||||
|
|
||||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
||||||
G vector (1/distance) = 0.268725
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
|
||||||
estimated relative force accuracy = 6.87243e-05
|
|
||||||
using double precision FFTs
|
|
||||||
3d grid and FFT values/proc = 4312 960
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/charmm/coul/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
SHAKE stats (type/ave/delta) on step 0
|
|
||||||
4 1.111 1.44264e-05
|
|
||||||
6 0.996998 7.26967e-06
|
|
||||||
8 1.08 1.32536e-05
|
|
||||||
10 1.111 1.22749e-05
|
|
||||||
12 1.08 1.11767e-05
|
|
||||||
14 0.96 0
|
|
||||||
18 0.957206 4.37979e-05
|
|
||||||
31 104.519 0.00396029
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
|
||||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
|
||||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
|
||||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
|
||||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
|
||||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
|
||||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
|
||||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
|
||||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
|
||||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191462
|
|
||||||
6 0.996989 3.55508e-05
|
|
||||||
8 1.08 9.0997e-06
|
|
||||||
10 1.111 1.58544e-05
|
|
||||||
12 1.08 5.80604e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92445e-05
|
|
||||||
31 104.52 0.00239923
|
|
||||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
|
||||||
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
|
|
||||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
|
|
||||||
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
|
|
||||||
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
|
|
||||||
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
|
|
||||||
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
|
|
||||||
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
|
|
||||||
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
|
|
||||||
Other | | 0.001239 | | | 0.20
|
|
||||||
|
|
||||||
Nlocal: 501 ave 513 max 494 min
|
|
||||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
|
||||||
Nghost: 6572.5 ave 6593 max 6548 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
||||||
Neighs: 177058 ave 181778 max 174301 min
|
|
||||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708234
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
@ -0,0 +1,732 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.012 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
shell "rm -f out*.colvars.*"
|
||||||
|
fix 2 all colvars peptide.colvars
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
fix 2a ref setforce 0.0 0.0 0.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "two"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 2 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one, two }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10, 10 }
|
||||||
|
# targetCenters = { 10, 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
The final output state file will be "out.colvars.state".
|
||||||
|
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||||
|
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||||
|
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||||
|
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||||
|
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||||
|
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||||
|
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||||
|
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||||
|
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||||
|
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
Saving collective variables state to "out.colvars.state".
|
||||||
|
Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47
|
||||||
|
Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14
|
||||||
|
Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60
|
||||||
|
Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23
|
||||||
|
Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37
|
||||||
|
Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02
|
||||||
|
Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11
|
||||||
|
Other | | 0.0004941 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11124 ave 11124 max 11124 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708237 ave 708237 max 708237 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708237
|
||||||
|
Ave neighs/atom = 353.41168
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 12
|
||||||
|
Dangerous builds = 2
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||||
|
|
||||||
|
|
||||||
|
% Colvars module:
|
||||||
|
% Colvars-LAMMPS interface:
|
||||||
|
% Harmonic colvar bias implementation:
|
||||||
|
% Optimal rotation via flexible fitting:
|
||||||
|
% distance colvar component:
|
||||||
|
|
||||||
|
@article{Fiorin2013,
|
||||||
|
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||||
|
title = {Using collective variables to drive molecular dynamics simulations},
|
||||||
|
journal = {Mol. Phys.},
|
||||||
|
year = {2013},
|
||||||
|
volume = {111},
|
||||||
|
number = {22-23},
|
||||||
|
pages = {3345--3362},
|
||||||
|
publisher = {Taylor & Francis},
|
||||||
|
doi = {10.1080/00268976.2013.813594},
|
||||||
|
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
% LAMMPS engine:
|
||||||
|
|
||||||
|
@article{Thompson2022,
|
||||||
|
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||||
|
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||||
|
journal = {Comp. Phys. Comm.},
|
||||||
|
volume = {271},
|
||||||
|
pages = {108171},
|
||||||
|
year = {2022},
|
||||||
|
doi = {10.1016/j.cpc.2021.108171},
|
||||||
|
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||||
|
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||||
|
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||||
|
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||||
|
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||||
|
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679
|
||||||
|
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||||
|
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037
|
||||||
|
190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 4 1.111 1.81266e-06 9
|
||||||
|
Bond: 6 0.997 7.79424e-07 6
|
||||||
|
Bond: 8 1.08 1.08903e-06 7
|
||||||
|
Bond: 10 1.111 2.96503e-07 8
|
||||||
|
Bond: 12 1.08 4.69038e-07 9
|
||||||
|
Bond: 14 0.960001 0 1
|
||||||
|
Bond: 18 0.957201 3.76471e-06 1280
|
||||||
|
Angle: 31 104.52 0.000411055 640
|
||||||
|
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||||
|
Saving collective variables state to "out.colvars.state".
|
||||||
|
Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15
|
||||||
|
Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15
|
||||||
|
Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01
|
||||||
|
Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14
|
||||||
|
Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34
|
||||||
|
Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02
|
||||||
|
Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14
|
||||||
|
Other | | 0.0004882 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11159 ave 11159 max 11159 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708083 ave 708083 max 708083 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708083
|
||||||
|
Ave neighs/atom = 353.33483
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 7
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
Setting initial step number from MD engine: 200
|
||||||
|
|
||||||
|
run 100
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "two"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 2 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one, two }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10, 10 }
|
||||||
|
# targetCenters = { 10, 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Loading state from text file "out.colvars.state".
|
||||||
|
Restarting collective variable "one" from value: 10.0128
|
||||||
|
Restarting collective variable "two" from value: 9.62236
|
||||||
|
Restarted harmonic bias "h_pot" with step number 200.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
The final output state file will be "out2.colvars.state".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 4 1.111 1.81266e-06 9
|
||||||
|
Bond: 6 0.997 7.79424e-07 6
|
||||||
|
Bond: 8 1.08 1.08903e-06 7
|
||||||
|
Bond: 10 1.111 2.96503e-07 8
|
||||||
|
Bond: 12 1.08 4.69038e-07 9
|
||||||
|
Bond: 14 0.960001 0 1
|
||||||
|
Bond: 18 0.957201 3.76471e-06 1280
|
||||||
|
Angle: 31 104.52 0.000411055 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||||
|
210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488
|
||||||
|
220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387
|
||||||
|
230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256
|
||||||
|
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815
|
||||||
|
250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023
|
||||||
|
260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102
|
||||||
|
270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||||
|
280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492
|
||||||
|
290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 300
|
||||||
|
Bond: 4 1.111 1.79793e-05 9
|
||||||
|
Bond: 6 0.997005 1.02512e-05 6
|
||||||
|
Bond: 8 1.08 1.85103e-05 7
|
||||||
|
Bond: 10 1.111 9.9884e-06 8
|
||||||
|
Bond: 12 1.08 8.84114e-06 9
|
||||||
|
Bond: 14 0.960008 0 1
|
||||||
|
Bond: 18 0.957203 1.8445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00168383 640
|
||||||
|
300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427
|
||||||
|
Saving collective variables state to "out2.colvars.state".
|
||||||
|
Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70
|
||||||
|
Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15
|
||||||
|
Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79
|
||||||
|
Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82
|
||||||
|
Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35
|
||||||
|
Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02
|
||||||
|
Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13
|
||||||
|
Other | | 0.0004882 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11296 ave 11296 max 11296 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708152 ave 708152 max 708152 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708152
|
||||||
|
Ave neighs/atom = 353.36926
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 8
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:02
|
||||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
@ -0,0 +1,732 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.011 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
shell "rm -f out*.colvars.*"
|
||||||
|
fix 2 all colvars peptide.colvars
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
fix 2a ref setforce 0.0 0.0 0.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "two"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 2 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one, two }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10, 10 }
|
||||||
|
# targetCenters = { 10, 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
The final output state file will be "out.colvars.state".
|
||||||
|
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||||
|
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||||
|
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||||
|
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||||
|
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||||
|
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||||
|
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||||
|
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||||
|
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||||
|
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
Saving collective variables state to "out.colvars.state".
|
||||||
|
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42
|
||||||
|
Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18
|
||||||
|
Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30
|
||||||
|
Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07
|
||||||
|
Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38
|
||||||
|
Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06
|
||||||
|
Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44
|
||||||
|
Other | | 0.0003631 | | | 0.15
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 489 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Nghost: 6563.25 ave 6596 max 6519 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 177059 ave 181742 max 172942 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 708237
|
||||||
|
Ave neighs/atom = 353.41168
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 12
|
||||||
|
Dangerous builds = 2
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||||
|
|
||||||
|
|
||||||
|
% Colvars module:
|
||||||
|
% Colvars-LAMMPS interface:
|
||||||
|
% Harmonic colvar bias implementation:
|
||||||
|
% Optimal rotation via flexible fitting:
|
||||||
|
% distance colvar component:
|
||||||
|
|
||||||
|
@article{Fiorin2013,
|
||||||
|
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||||
|
title = {Using collective variables to drive molecular dynamics simulations},
|
||||||
|
journal = {Mol. Phys.},
|
||||||
|
year = {2013},
|
||||||
|
volume = {111},
|
||||||
|
number = {22-23},
|
||||||
|
pages = {3345--3362},
|
||||||
|
publisher = {Taylor & Francis},
|
||||||
|
doi = {10.1080/00268976.2013.813594},
|
||||||
|
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
% LAMMPS engine:
|
||||||
|
|
||||||
|
@article{Thompson2022,
|
||||||
|
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||||
|
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||||
|
journal = {Comp. Phys. Comm.},
|
||||||
|
volume = {271},
|
||||||
|
pages = {108171},
|
||||||
|
year = {2022},
|
||||||
|
doi = {10.1016/j.cpc.2021.108171},
|
||||||
|
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||||
|
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||||
|
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||||
|
140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||||
|
150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008
|
||||||
|
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||||
|
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||||
|
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036
|
||||||
|
190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 4 1.111 1.81266e-06 9
|
||||||
|
Bond: 6 0.997 7.79424e-07 6
|
||||||
|
Bond: 8 1.08 1.08903e-06 7
|
||||||
|
Bond: 10 1.111 2.96503e-07 8
|
||||||
|
Bond: 12 1.08 4.69038e-07 9
|
||||||
|
Bond: 14 0.960001 0 1
|
||||||
|
Bond: 18 0.957201 3.76471e-06 1280
|
||||||
|
Angle: 31 104.52 0.000411055 640
|
||||||
|
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||||
|
Saving collective variables state to "out.colvars.state".
|
||||||
|
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s
|
||||||
|
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32
|
||||||
|
Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19
|
||||||
|
Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43
|
||||||
|
Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88
|
||||||
|
Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33
|
||||||
|
Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06
|
||||||
|
Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63
|
||||||
|
Other | | 0.0004069 | | | 0.17
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 481 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
|
Nghost: 6556.5 ave 6608 max 6514 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Neighs: 177021 ave 182259 max 172089 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 708083
|
||||||
|
Ave neighs/atom = 353.33483
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 7
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
Setting initial step number from MD engine: 200
|
||||||
|
|
||||||
|
run 100
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "two"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 1 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 2 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one, two }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10, 10 }
|
||||||
|
# targetCenters = { 10, 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Loading state from text file "out.colvars.state".
|
||||||
|
Restarting collective variable "one" from value: 10.0128
|
||||||
|
Restarting collective variable "two" from value: 9.62236
|
||||||
|
Restarted harmonic bias "h_pot" with step number 200.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
The final output state file will be "out2.colvars.state".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 4 1.111 1.81266e-06 9
|
||||||
|
Bond: 6 0.997 7.79424e-07 6
|
||||||
|
Bond: 8 1.08 1.08903e-06 7
|
||||||
|
Bond: 10 1.111 2.96503e-07 8
|
||||||
|
Bond: 12 1.08 4.69038e-07 9
|
||||||
|
Bond: 14 0.960001 0 1
|
||||||
|
Bond: 18 0.957201 3.76471e-06 1280
|
||||||
|
Angle: 31 104.52 0.000411055 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||||
|
210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488
|
||||||
|
220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387
|
||||||
|
230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559
|
||||||
|
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815
|
||||||
|
250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023
|
||||||
|
260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104
|
||||||
|
270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||||
|
280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
|
||||||
|
290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 300
|
||||||
|
Bond: 4 1.111 1.79793e-05 9
|
||||||
|
Bond: 6 0.997005 1.02512e-05 6
|
||||||
|
Bond: 8 1.08 1.85103e-05 7
|
||||||
|
Bond: 10 1.111 9.9884e-06 8
|
||||||
|
Bond: 12 1.08 8.84114e-06 9
|
||||||
|
Bond: 14 0.960008 0 1
|
||||||
|
Bond: 18 0.957203 1.8445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00168383 640
|
||||||
|
300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428
|
||||||
|
Saving collective variables state to "out2.colvars.state".
|
||||||
|
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90
|
||||||
|
Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20
|
||||||
|
Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42
|
||||||
|
Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02
|
||||||
|
Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46
|
||||||
|
Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06
|
||||||
|
Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74
|
||||||
|
Other | | 0.0004738 | | | 0.19
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 472 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Nghost: 6612.75 ave 6681 max 6561 min
|
||||||
|
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||||
|
Neighs: 177038 ave 180136 max 170218 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 708152
|
||||||
|
Ave neighs/atom = 353.36926
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 8
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
@ -0,0 +1,344 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.012 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
shell "rm -f peptide2.colvars.*"
|
||||||
|
fix 2 all colvars peptide.colvars2 output peptide2
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars2":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 4 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10 }
|
||||||
|
# targetCenters = { 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
The final output state file will be "peptide2.colvars.state".
|
||||||
|
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||||
|
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||||
|
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||||
|
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||||
|
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||||
|
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||||
|
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||||
|
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||||
|
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||||
|
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11096 0.000191462 9
|
||||||
|
Bond: 6 0.996989 3.55508e-05 6
|
||||||
|
Bond: 8 1.08 9.0997e-06 7
|
||||||
|
Bond: 10 1.111 1.58544e-05 8
|
||||||
|
Bond: 12 1.08 5.80604e-06 9
|
||||||
|
Bond: 14 0.959997 0 1
|
||||||
|
Bond: 18 0.957198 2.92445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00239923 640
|
||||||
|
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||||
|
Saving collective variables state to "peptide2.colvars.state".
|
||||||
|
Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
|
||||||
|
Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
|
||||||
|
Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
|
||||||
|
Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
|
||||||
|
Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
|
||||||
|
Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
|
||||||
|
Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
|
||||||
|
Other | | 0.0004888 | | | 0.05
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11143 ave 11143 max 11143 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708234 ave 708234 max 708234 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708234
|
||||||
|
Ave neighs/atom = 353.41018
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 13
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||||
|
|
||||||
|
|
||||||
|
% Colvars module:
|
||||||
|
% Colvars-LAMMPS interface:
|
||||||
|
% Harmonic colvar bias implementation:
|
||||||
|
% Optimal rotation via flexible fitting:
|
||||||
|
% distance colvar component:
|
||||||
|
|
||||||
|
@article{Fiorin2013,
|
||||||
|
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||||
|
title = {Using collective variables to drive molecular dynamics simulations},
|
||||||
|
journal = {Mol. Phys.},
|
||||||
|
year = {2013},
|
||||||
|
volume = {111},
|
||||||
|
number = {22-23},
|
||||||
|
pages = {3345--3362},
|
||||||
|
publisher = {Taylor & Francis},
|
||||||
|
doi = {10.1080/00268976.2013.813594},
|
||||||
|
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
% LAMMPS engine:
|
||||||
|
|
||||||
|
@article{Thompson2022,
|
||||||
|
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||||
|
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||||
|
journal = {Comp. Phys. Comm.},
|
||||||
|
volume = {271},
|
||||||
|
pages = {108171},
|
||||||
|
year = {2022},
|
||||||
|
doi = {10.1016/j.cpc.2021.108171},
|
||||||
|
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
@ -0,0 +1,344 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.011 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
shell "rm -f peptide2.colvars.*"
|
||||||
|
fix 2 all colvars peptide.colvars2 output peptide2
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing the collective variables module, version 2024-06-04.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
Please cite Fiorin et al, Mol Phys 2013:
|
||||||
|
https://doi.org/10.1080/00268976.2013.813594
|
||||||
|
as well as all other papers listed below for individual features used.
|
||||||
|
This version was built with the C++11 standard or higher.
|
||||||
|
Summary of compile-time features available in this build:
|
||||||
|
- SMP parallelism: enabled (num. threads = 1)
|
||||||
|
- Lepton custom functions: available
|
||||||
|
- Tcl interpreter: not available
|
||||||
|
Using LAMMPS interface, version "2024-07-05".
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Reading new configuration from file "peptide.colvars2":
|
||||||
|
# units = "" [default]
|
||||||
|
# smp = on [default]
|
||||||
|
# colvarsTrajFrequency = 1
|
||||||
|
# colvarsRestartFrequency = 1000
|
||||||
|
# scriptedColvarForces = off [default]
|
||||||
|
# scriptingAfterBiases = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new collective variable.
|
||||||
|
# name = "one"
|
||||||
|
Initializing a new "distance" component.
|
||||||
|
# name = "" [default]
|
||||||
|
# componentCoeff = 1 [default]
|
||||||
|
# componentExp = 1 [default]
|
||||||
|
# period = 0 [default]
|
||||||
|
# wrapAround = 0 [default]
|
||||||
|
# forceNoPBC = off [default]
|
||||||
|
# scalable = on [default]
|
||||||
|
Initializing atom group "group1".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group1" defined with 4 atoms requested.
|
||||||
|
Initializing atom group "group2".
|
||||||
|
# name = "" [default]
|
||||||
|
# centerToOrigin = off [default]
|
||||||
|
# centerToReference = off [default]
|
||||||
|
# rotateToReference = off [default]
|
||||||
|
# atomsOfGroup = "" [default]
|
||||||
|
# indexGroup = "" [default]
|
||||||
|
# psfSegID = [default]
|
||||||
|
# atomsFile = "" [default]
|
||||||
|
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
|
# enableFitGradients = on [default]
|
||||||
|
# printAtomIDs = off [default]
|
||||||
|
Atom group "group2" defined with 4 atoms requested.
|
||||||
|
# oneSiteSystemForce = off [default]
|
||||||
|
# oneSiteTotalForce = off [default]
|
||||||
|
All components initialized.
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# width = 1 [default]
|
||||||
|
# lowerBoundary = 0 [default]
|
||||||
|
# upperBoundary = 1 [default]
|
||||||
|
# hardLowerBoundary = on [default]
|
||||||
|
# hardUpperBoundary = off [default]
|
||||||
|
# expandBoundaries = off [default]
|
||||||
|
# extendedLagrangian = off [default]
|
||||||
|
# outputValue = on [default]
|
||||||
|
# outputVelocity = off [default]
|
||||||
|
# outputTotalForce = off [default]
|
||||||
|
# outputAppliedForce = off [default]
|
||||||
|
# subtractAppliedForce = off [default]
|
||||||
|
# runAve = off [default]
|
||||||
|
# corrFunc = off [default]
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Initializing a new "harmonic" instance.
|
||||||
|
# name = "h_pot"
|
||||||
|
# colvars = { one }
|
||||||
|
# stepZeroData = off [default]
|
||||||
|
# outputEnergy = off [default]
|
||||||
|
# outputFreq = 1000 [default]
|
||||||
|
# timeStepFactor = 1 [default]
|
||||||
|
# writeTISamples = off [default]
|
||||||
|
# writeTIPMF = off [default]
|
||||||
|
# centers = { 10 }
|
||||||
|
# targetCenters = { 10 } [default]
|
||||||
|
# outputCenters = off [default]
|
||||||
|
# forceConstant = 100
|
||||||
|
# decoupling = off [default]
|
||||||
|
# targetForceConstant = -1 [default]
|
||||||
|
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables biases initialized, 1 in total.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Collective variables module (re)initialized.
|
||||||
|
----------------------------------------------------------------------
|
||||||
|
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||||
|
Updating atomic parameters (masses, charges, etc).
|
||||||
|
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||||
|
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||||
|
The final output state file will be "peptide2.colvars.state".
|
||||||
|
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||||
|
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||||
|
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||||
|
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||||
|
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||||
|
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||||
|
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||||
|
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||||
|
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||||
|
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11096 0.000191462 9
|
||||||
|
Bond: 6 0.996989 3.55508e-05 6
|
||||||
|
Bond: 8 1.08 9.0997e-06 7
|
||||||
|
Bond: 10 1.111 1.58544e-05 8
|
||||||
|
Bond: 12 1.08 5.80604e-06 9
|
||||||
|
Bond: 14 0.959997 0 1
|
||||||
|
Bond: 18 0.957198 2.92445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00239923 640
|
||||||
|
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||||
|
Saving collective variables state to "peptide2.colvars.state".
|
||||||
|
Loop time of 0.253421 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76
|
||||||
|
Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22
|
||||||
|
Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46
|
||||||
|
Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01
|
||||||
|
Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57
|
||||||
|
Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05
|
||||||
|
Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74
|
||||||
|
Other | | 0.0004667 | | | 0.18
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 494 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 6572.5 ave 6593 max 6548 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 177058 ave 181778 max 174301 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 708234
|
||||||
|
Ave neighs/atom = 353.41018
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 13
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||||
|
|
||||||
|
|
||||||
|
% Colvars module:
|
||||||
|
% Colvars-LAMMPS interface:
|
||||||
|
% Harmonic colvar bias implementation:
|
||||||
|
% Optimal rotation via flexible fitting:
|
||||||
|
% distance colvar component:
|
||||||
|
|
||||||
|
@article{Fiorin2013,
|
||||||
|
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||||
|
title = {Using collective variables to drive molecular dynamics simulations},
|
||||||
|
journal = {Mol. Phys.},
|
||||||
|
year = {2013},
|
||||||
|
volume = {111},
|
||||||
|
number = {22-23},
|
||||||
|
pages = {3345--3362},
|
||||||
|
publisher = {Taylor & Francis},
|
||||||
|
doi = {10.1080/00268976.2013.813594},
|
||||||
|
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
% LAMMPS engine:
|
||||||
|
|
||||||
|
@article{Thompson2022,
|
||||||
|
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||||
|
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||||
|
journal = {Comp. Phys. Comm.},
|
||||||
|
volume = {271},
|
||||||
|
pages = {108171},
|
||||||
|
year = {2022},
|
||||||
|
doi = {10.1016/j.cpc.2021.108171},
|
||||||
|
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
@ -0,0 +1,194 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.012 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||||
|
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||||
|
|
||||||
|
fix 2a ref setforce 0.0 0.0 0.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
variable sp equal f_3a+f_3b
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||||
|
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||||
|
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||||
|
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||||
|
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||||
|
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||||
|
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||||
|
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||||
|
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||||
|
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58
|
||||||
|
Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14
|
||||||
|
Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69
|
||||||
|
Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03
|
||||||
|
Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37
|
||||||
|
Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02
|
||||||
|
Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11
|
||||||
|
Other | | 0.0005014 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11124 ave 11124 max 11124 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708237 ave 708237 max 708237 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708237
|
||||||
|
Ave neighs/atom = 353.41168
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 12
|
||||||
|
Dangerous builds = 2
|
||||||
|
Total wall time: 0:00:00
|
||||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
@ -0,0 +1,194 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.010 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||||
|
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||||
|
|
||||||
|
fix 2a ref setforce 0.0 0.0 0.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
variable sp equal f_3a+f_3b
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||||
|
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||||
|
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||||
|
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||||
|
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||||
|
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||||
|
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||||
|
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||||
|
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||||
|
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11098 8.97155e-05 9
|
||||||
|
Bond: 6 0.996996 1.00568e-05 6
|
||||||
|
Bond: 8 1.08 6.02345e-06 7
|
||||||
|
Bond: 10 1.111 1.84253e-05 8
|
||||||
|
Bond: 12 1.08 7.2713e-06 9
|
||||||
|
Bond: 14 0.959996 0 1
|
||||||
|
Bond: 18 0.957198 3.36079e-05 1280
|
||||||
|
Angle: 31 104.52 0.0030599 640
|
||||||
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
|
Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
|
||||||
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
|
||||||
|
Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
|
||||||
|
Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
|
||||||
|
Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
|
||||||
|
Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
|
||||||
|
Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
|
||||||
|
Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
|
||||||
|
Other | | 0.0004289 | | | 0.17
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 489 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Nghost: 6563.25 ave 6596 max 6519 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 177059 ave 181742 max 172942 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 708237
|
||||||
|
Ave neighs/atom = 353.41168
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 12
|
||||||
|
Dangerous builds = 2
|
||||||
|
Total wall time: 0:00:00
|
||||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
@ -0,0 +1,189 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.012 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 10648 3375
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||||
|
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||||
|
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||||
|
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||||
|
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||||
|
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||||
|
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||||
|
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||||
|
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||||
|
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11096 0.000191462 9
|
||||||
|
Bond: 6 0.996989 3.55508e-05 6
|
||||||
|
Bond: 8 1.08 9.0997e-06 7
|
||||||
|
Bond: 10 1.111 1.58544e-05 8
|
||||||
|
Bond: 12 1.08 5.80604e-06 9
|
||||||
|
Bond: 14 0.959997 0 1
|
||||||
|
Bond: 18 0.957198 2.92445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00239923 640
|
||||||
|
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||||
|
Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/s
|
||||||
|
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77
|
||||||
|
Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14
|
||||||
|
Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66
|
||||||
|
Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82
|
||||||
|
Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40
|
||||||
|
Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02
|
||||||
|
Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13
|
||||||
|
Other | | 0.0005695 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11143 ave 11143 max 11143 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 708234 ave 708234 max 708234 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 708234
|
||||||
|
Ave neighs/atom = 353.41018
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 13
|
||||||
|
Dangerous builds = 1
|
||||||
|
Total wall time: 0:00:00
|
||||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
@ -0,0 +1,189 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style charmm
|
||||||
|
dihedral_style charmm
|
||||||
|
improper_style harmonic
|
||||||
|
kspace_style pppm 0.0001
|
||||||
|
|
||||||
|
read_data data.peptide
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2004 atoms
|
||||||
|
reading velocities ...
|
||||||
|
2004 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
3 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
14 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
1 = max impropers/atom
|
||||||
|
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading bonds ...
|
||||||
|
1365 bonds
|
||||||
|
reading angles ...
|
||||||
|
786 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
207 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
12 impropers
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
4 = max # of 1-2 neighbors
|
||||||
|
7 = max # of 1-3 neighbors
|
||||||
|
14 = max # of 1-4 neighbors
|
||||||
|
18 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.011 seconds
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
group peptide type <= 12
|
||||||
|
84 atoms in group peptide
|
||||||
|
group one id 2 4 5 6
|
||||||
|
4 atoms in group one
|
||||||
|
group two id 80 82 83 84
|
||||||
|
4 atoms in group two
|
||||||
|
group ref id 37
|
||||||
|
1 atoms in group ref
|
||||||
|
group colvar union one two ref
|
||||||
|
9 atoms in group colvar
|
||||||
|
|
||||||
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||||
|
|
||||||
|
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||||
|
|
||||||
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||||
|
Finding SHAKE clusters ...
|
||||||
|
19 = # of size 2 clusters
|
||||||
|
6 = # of size 3 clusters
|
||||||
|
3 = # of size 4 clusters
|
||||||
|
640 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000 seconds
|
||||||
|
|
||||||
|
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 sort id
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.26872465
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.022820853
|
||||||
|
estimated relative force accuracy = 6.872432e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 4312 960
|
||||||
|
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 5 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 5 5 5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/charmm/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 4 1.111 1.44264e-05 9
|
||||||
|
Bond: 6 0.996998 7.26967e-06 6
|
||||||
|
Bond: 8 1.08 1.32536e-05 7
|
||||||
|
Bond: 10 1.111 1.22749e-05 8
|
||||||
|
Bond: 12 1.08 1.11767e-05 9
|
||||||
|
Bond: 14 0.96 0 1
|
||||||
|
Bond: 18 0.957206 4.37979e-05 1280
|
||||||
|
Angle: 31 104.519 0.00396029 640
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||||
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||||
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||||
|
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||||
|
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||||
|
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||||
|
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||||
|
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||||
|
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||||
|
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||||
|
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||||
|
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 4 1.11096 0.000191462 9
|
||||||
|
Bond: 6 0.996989 3.55508e-05 6
|
||||||
|
Bond: 8 1.08 9.0997e-06 7
|
||||||
|
Bond: 10 1.111 1.58544e-05 8
|
||||||
|
Bond: 12 1.08 5.80604e-06 9
|
||||||
|
Bond: 14 0.959997 0 1
|
||||||
|
Bond: 18 0.957198 2.92445e-05 1280
|
||||||
|
Angle: 31 104.52 0.00239923 640
|
||||||
|
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||||
|
Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms
|
||||||
|
|
||||||
|
Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35
|
||||||
|
Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18
|
||||||
|
Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44
|
||||||
|
Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35
|
||||||
|
Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34
|
||||||
|
Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06
|
||||||
|
Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12
|
||||||
|
Other | | 0.0004197 | | | 0.17
|
||||||
|
|
||||||
|
Nlocal: 501 ave 513 max 494 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 6572.5 ave 6593 max 6548 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 177058 ave 181778 max 174301 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 708234
|
||||||
|
Ave neighs/atom = 353.41018
|
||||||
|
Ave special neighs/atom = 2.3403194
|
||||||
|
Neighbor list builds = 13
|
||||||
|
Dangerous builds = 1
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -1,17 +1,17 @@
|
|||||||
configuration {
|
configuration {
|
||||||
step 200
|
step 200
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
version 2020-07-07
|
version 2024-06-04
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 1.00127732034965e+01
|
x 10.012773203962
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name two
|
name two
|
||||||
x 9.62235997490241e+00
|
x 9.6223599748448
|
||||||
}
|
}
|
||||||
|
|
||||||
restraint {
|
restraint {
|
||||||
|
|||||||
@ -1,17 +1,17 @@
|
|||||||
configuration {
|
configuration {
|
||||||
step 100
|
step 100
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
version 2020-07-07
|
version 2024-06-04
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 1.00136989326255e+01
|
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|||||||
@ -13,191 +13,191 @@
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141 1.00644400705403e+01 9.95041823460627e+00
|
||||||
142 1.00541501159131e+01 9.92180857541951e+00
|
142 1.00541501157683e+01 9.92180857562118e+00
|
||||||
143 1.00436834569978e+01 9.89050941872713e+00
|
143 1.00436834568360e+01 9.89050941892251e+00
|
||||||
144 1.00330649757401e+01 9.85603943350860e+00
|
144 1.00330649755670e+01 9.85603943369589e+00
|
||||||
145 1.00223855042347e+01 9.81818968302844e+00
|
145 1.00223855041248e+01 9.81818968320503e+00
|
||||||
146 1.00118066120717e+01 9.77759398920638e+00
|
146 1.00118066120332e+01 9.77759398937178e+00
|
||||||
147 1.00015635423691e+01 9.73590632972306e+00
|
147 1.00015635424482e+01 9.73590632987673e+00
|
||||||
148 9.99195808427061e+00 9.69551862637489e+00
|
148 9.99195808450856e+00 9.69551862651774e+00
|
||||||
149 9.98332973799261e+00 9.65911623085002e+00
|
149 9.98332973840472e+00 9.65911623099469e+00
|
||||||
150 9.97599905761175e+00 9.62915505877515e+00
|
150 9.97599905822999e+00 9.62915505892649e+00
|
||||||
151 9.97019367767784e+00 9.60716909686955e+00
|
151 9.97019367845638e+00 9.60716909703526e+00
|
||||||
152 9.96598267281873e+00 9.59318709200410e+00
|
152 9.96598267372795e+00 9.59318709218540e+00
|
||||||
153 9.96324605944343e+00 9.58559881047527e+00
|
153 9.96324606044969e+00 9.58559881066392e+00
|
||||||
154 9.96169276126796e+00 9.58153758556819e+00
|
154 9.96169276237047e+00 9.58153758575953e+00
|
||||||
155 9.96092625032814e+00 9.57763829311044e+00
|
155 9.96092625152242e+00 9.57763829328116e+00
|
||||||
156 9.96054315607791e+00 9.57093750799266e+00
|
156 9.96054315740228e+00 9.57093750810941e+00
|
||||||
157 9.96023482227745e+00 9.55965895377840e+00
|
157 9.96023482376251e+00 9.55965895382487e+00
|
||||||
158 9.95985352165466e+00 9.54367776307569e+00
|
158 9.95985352333786e+00 9.54367776304373e+00
|
||||||
159 9.95942460039566e+00 9.52452561463833e+00
|
159 9.95942460236116e+00 9.52452561453112e+00
|
||||||
160 9.95911205589222e+00 9.50490226824346e+00
|
160 9.95911205820184e+00 9.50490226807002e+00
|
||||||
161 9.95914975443396e+00 9.48781410600212e+00
|
161 9.95914975712190e+00 9.48781410580017e+00
|
||||||
162 9.95975278911406e+00 9.47562429341561e+00
|
162 9.95975279219164e+00 9.47562429324685e+00
|
||||||
163 9.96103890040379e+00 9.46939719079233e+00
|
163 9.96103890394426e+00 9.46939719071147e+00
|
||||||
164 9.96299147170478e+00 9.46883821286236e+00
|
164 9.96299147570651e+00 9.46883821294305e+00
|
||||||
165 9.96547099380307e+00 9.47284423942468e+00
|
165 9.96547099819345e+00 9.47284423972085e+00
|
||||||
166 9.96826097146115e+00 9.48031949605208e+00
|
166 9.96826097616579e+00 9.48031949660299e+00
|
||||||
167 9.97113131026389e+00 9.49080246783928e+00
|
167 9.97113131520360e+00 9.49080246868345e+00
|
||||||
168 9.97390346515378e+00 9.50467508257787e+00
|
168 9.97390347029220e+00 9.50467508368792e+00
|
||||||
169 9.97650055807565e+00 9.52297045210046e+00
|
169 9.97650056337441e+00 9.52297045344289e+00
|
||||||
170 9.97896696852481e+00 9.54683120799382e+00
|
170 9.97896697398981e+00 9.54683120949238e+00
|
||||||
171 9.98144993167344e+00 9.57673108800475e+00
|
171 9.98144993724280e+00 9.57673108957231e+00
|
||||||
172 9.98414386605973e+00 9.61177309775590e+00
|
172 9.98414387172420e+00 9.61177309931033e+00
|
||||||
173 9.98721435874383e+00 9.64941604907962e+00
|
173 9.98721436449207e+00 9.64941605055506e+00
|
||||||
174 9.99072987081047e+00 9.68581828149366e+00
|
174 9.99072987660973e+00 9.68581828287900e+00
|
||||||
175 9.99462784290560e+00 9.71674849920838e+00
|
175 9.99462784873357e+00 9.71674850053884e+00
|
||||||
176 9.99872910050856e+00 9.73876571566039e+00
|
176 9.99872910630021e+00 9.73876571701760e+00
|
||||||
177 1.00027910094647e+01 9.75024496509227e+00
|
177 1.00027910151196e+01 9.75024496660445e+00
|
||||||
178 1.00065753933095e+01 9.75188677631197e+00
|
178 1.00065753987481e+01 9.75188677811518e+00
|
||||||
179 1.00099096736715e+01 9.74652424002240e+00
|
179 1.00099096788152e+01 9.74652424221370e+00
|
||||||
180 1.00127256239536e+01 9.73825559652692e+00
|
180 1.00127256286803e+01 9.73825559920752e+00
|
||||||
181 1.00150707323506e+01 9.73120003142692e+00
|
181 1.00150707365928e+01 9.73120003464725e+00
|
||||||
182 1.00170870650914e+01 9.72835138795971e+00
|
182 1.00170870688102e+01 9.72835139174119e+00
|
||||||
183 1.00189588719574e+01 9.73088542644806e+00
|
183 1.00189588750915e+01 9.73088543078432e+00
|
||||||
184 1.00208370553711e+01 9.73798855694274e+00
|
184 1.00208370578559e+01 9.73798856175907e+00
|
||||||
185 1.00227676206971e+01 9.74722630488312e+00
|
185 1.00227676225361e+01 9.74722631009118e+00
|
||||||
186 1.00246552838286e+01 9.75544013816019e+00
|
186 1.00246552850623e+01 9.75544014363497e+00
|
||||||
187 1.00262844434324e+01 9.75985859738447e+00
|
187 1.00262844441069e+01 9.75985860295140e+00
|
||||||
188 1.00273887691195e+01 9.75895345517658e+00
|
188 1.00273887692830e+01 9.75895346064793e+00
|
||||||
189 1.00277400472209e+01 9.75275536148299e+00
|
189 1.00277400469004e+01 9.75275536661271e+00
|
||||||
190 1.00272200725279e+01 9.74261382746486e+00
|
190 1.00272200717913e+01 9.74261383198996e+00
|
||||||
191 1.00258549688160e+01 9.73056754269459e+00
|
191 1.00258549677417e+01 9.73056754639127e+00
|
||||||
192 1.00238089567536e+01 9.71853980670345e+00
|
192 1.00238089554369e+01 9.71853980943337e+00
|
||||||
193 1.00213474465750e+01 9.70762043885231e+00
|
193 1.00213474450786e+01 9.70762044056817e+00
|
||||||
194 1.00187805230869e+01 9.69773175124558e+00
|
194 1.00187805216026e+01 9.69773175201182e+00
|
||||||
195 1.00164016154513e+01 9.68784935173366e+00
|
195 1.00164016141049e+01 9.68784935170505e+00
|
||||||
196 1.00144402674219e+01 9.67667427007303e+00
|
196 1.00144402663323e+01 9.67667426952134e+00
|
||||||
197 1.00130444574495e+01 9.66343938720852e+00
|
197 1.00130444566844e+01 9.66343938641739e+00
|
||||||
198 1.00122912607270e+01 9.64854739476250e+00
|
198 1.00122912603524e+01 9.64854739402150e+00
|
||||||
199 1.00122066750836e+01 9.63383866331536e+00
|
199 1.00122066751424e+01 9.63383866285097e+00
|
||||||
200 1.00127732034965e+01 9.62235997490241e+00
|
200 1.00127732039621e+01 9.62235997484479e+00
|
||||||
|
|||||||
@ -1,17 +1,17 @@
|
|||||||
configuration {
|
configuration {
|
||||||
step 300
|
step 300
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
version 2020-07-07
|
version 2024-06-04
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 9.95315918568411e+00
|
x 9.9531592295885
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name two
|
name two
|
||||||
x 9.79318883680258e+00
|
x 9.7931889789213
|
||||||
}
|
}
|
||||||
|
|
||||||
restraint {
|
restraint {
|
||||||
|
|||||||
@ -1,102 +1,102 @@
|
|||||||
# step one two
|
# step one two
|
||||||
200 1.00127732034965e+01 9.62235997490241e+00
|
200 1.00127732039621e+01 9.62235997484479e+00
|
||||||
201 1.00139198864982e+01 9.61766167925624e+00
|
201 1.00139198873142e+01 9.61766167960114e+00
|
||||||
202 1.00155004339120e+01 9.62284272858813e+00
|
202 1.00155004349735e+01 9.62284272927993e+00
|
||||||
203 1.00172741972246e+01 9.63964899323068e+00
|
203 1.00172741984288e+01 9.63964899413135e+00
|
||||||
204 1.00189052021826e+01 9.66786718571673e+00
|
204 1.00189052034286e+01 9.66786718668113e+00
|
||||||
205 1.00199887119842e+01 9.70521202056400e+00
|
205 1.00199887131237e+01 9.70521202139326e+00
|
||||||
206 1.00201070660155e+01 9.74782380666112e+00
|
206 1.00201070669505e+01 9.74782380717117e+00
|
||||||
207 1.00189089093749e+01 9.79114913038349e+00
|
207 1.00189089099933e+01 9.79114913037297e+00
|
||||||
208 1.00162005540278e+01 9.83091553260188e+00
|
208 1.00162005542527e+01 9.83091553193592e+00
|
||||||
209 1.00120316562035e+01 9.86409994884863e+00
|
209 1.00120316559893e+01 9.86409994753053e+00
|
||||||
210 1.00067394529596e+01 9.88955328455197e+00
|
210 1.00067394522266e+01 9.88955328278264e+00
|
||||||
211 1.00009200584653e+01 9.90798080826055e+00
|
211 1.00009200570685e+01 9.90798080630807e+00
|
||||||
212 9.99531475905311e+00 9.92127385542524e+00
|
212 9.99531475670037e+00 9.92127385350745e+00
|
||||||
213 9.99063400342297e+00 9.93157198661852e+00
|
213 9.99063399978946e+00 9.93157198491364e+00
|
||||||
214 9.98737188807678e+00 9.94051482696048e+00
|
214 9.98737188290188e+00 9.94051482558046e+00
|
||||||
215 9.98567127567181e+00 9.94885527957784e+00
|
215 9.98567126870035e+00 9.94885527853167e+00
|
||||||
216 9.98528704043382e+00 9.95646746111755e+00
|
216 9.98528703143402e+00 9.95646746044078e+00
|
||||||
217 9.98565832937415e+00 9.96275739929720e+00
|
217 9.98565831825084e+00 9.96275739920543e+00
|
||||||
218 9.98606724184677e+00 9.96730423246689e+00
|
218 9.98606722850532e+00 9.96730423316541e+00
|
||||||
219 9.98583582550472e+00 9.97036378703713e+00
|
219 9.98583581006681e+00 9.97036378874527e+00
|
||||||
220 9.98451001643477e+00 9.97292736129215e+00
|
220 9.98450999905139e+00 9.97292736402649e+00
|
||||||
221 9.98198434901656e+00 9.97627439806637e+00
|
221 9.98198432974296e+00 9.97627440161597e+00
|
||||||
222 9.97853678731273e+00 9.98127100659218e+00
|
222 9.97853676608100e+00 9.98127101043889e+00
|
||||||
223 9.97475984191141e+00 9.98785371236258e+00
|
223 9.97475981847134e+00 9.98785371579891e+00
|
||||||
224 9.97140286510626e+00 9.99492286335624e+00
|
224 9.97140283904510e+00 9.99492286559338e+00
|
||||||
225 9.96917137580259e+00 1.00005443231922e+01
|
225 9.96917134637541e+00 1.00005443234936e+01
|
||||||
226 9.96854523900174e+00 1.00023222923235e+01
|
226 9.96854520536988e+00 1.00023222900809e+01
|
||||||
227 9.96967375964547e+00 9.99790273206806e+00
|
227 9.96967372102824e+00 9.99790272698630e+00
|
||||||
228 9.97237636771905e+00 9.98555960216881e+00
|
228 9.97237632329275e+00 9.98555959429830e+00
|
||||||
229 9.97624253505807e+00 9.96473792067690e+00
|
229 9.97624248419111e+00 9.96473791046628e+00
|
||||||
230 9.98078777310055e+00 9.93636511602182e+00
|
230 9.98078771543058e+00 9.93636510426670e+00
|
||||||
231 9.98560846780419e+00 9.90275990393703e+00
|
231 9.98560840329183e+00 9.90275989164257e+00
|
||||||
232 9.99048787217569e+00 9.86710855077386e+00
|
232 9.99048780094848e+00 9.86710853890991e+00
|
||||||
233 9.99543040822038e+00 9.83269539984149e+00
|
233 9.99543033063032e+00 9.83269538913306e+00
|
||||||
234 1.00006246021103e+01 9.80221208335553e+00
|
234 1.00006245185513e+01 9.80221207423406e+00
|
||||||
235 1.00063530848982e+01 9.77738136586701e+00
|
235 1.00063529959328e+01 9.77738135842695e+00
|
||||||
236 1.00128741709083e+01 9.75887400813685e+00
|
236 1.00128740773079e+01 9.75887400220566e+00
|
||||||
237 1.00203106975850e+01 9.74632163179798e+00
|
237 1.00203106003782e+01 9.74632162713091e+00
|
||||||
238 1.00285805371730e+01 9.73844350416337e+00
|
238 1.00285804376080e+01 9.73844350045589e+00
|
||||||
239 1.00373945897865e+01 9.73349215182819e+00
|
239 1.00373944894039e+01 9.73349214878674e+00
|
||||||
240 1.00463194539327e+01 9.72980720779576e+00
|
240 1.00463193546284e+01 9.72980720512224e+00
|
||||||
241 1.00548770491533e+01 9.72611599020063e+00
|
241 1.00548769529672e+01 9.72611598750665e+00
|
||||||
242 1.00626421174965e+01 9.72152572108181e+00
|
242 1.00626420263492e+01 9.72152571786963e+00
|
||||||
243 1.00693109823863e+01 9.71531423107737e+00
|
243 1.00693108979996e+01 9.71531422666390e+00
|
||||||
244 1.00747300690509e+01 9.70668632474813e+00
|
244 1.00747299927796e+01 9.70668631833486e+00
|
||||||
245 1.00788811512303e+01 9.69472082245661e+00
|
245 1.00788810840328e+01 9.69472081315003e+00
|
||||||
246 1.00818281591535e+01 9.67872530149764e+00
|
246 1.00818281015229e+01 9.67872528846535e+00
|
||||||
247 1.00836382918008e+01 9.65899116363609e+00
|
247 1.00836382438846e+01 9.65899114629446e+00
|
||||||
248 1.00843077585461e+01 9.63702967428387e+00
|
248 1.00843077202414e+01 9.63702965268533e+00
|
||||||
249 1.00837304601058e+01 9.61431312359133e+00
|
249 1.00837304312378e+01 9.61431309843794e+00
|
||||||
250 1.00817369874724e+01 9.59193249256670e+00
|
250 1.00817369677632e+01 9.59193246490958e+00
|
||||||
251 1.00781951382998e+01 9.57162234547176e+00
|
251 1.00781951275561e+01 9.57162231665577e+00
|
||||||
252 1.00731274409141e+01 9.55557274350384e+00
|
252 1.00731274389447e+01 9.55557271498134e+00
|
||||||
253 1.00667870632608e+01 9.54560001126946e+00
|
253 1.00667870699195e+01 9.54559998431332e+00
|
||||||
254 1.00596598859158e+01 9.54253147668434e+00
|
254 1.00596599010604e+01 9.54253145213164e+00
|
||||||
255 1.00523956909045e+01 9.54593692832520e+00
|
255 1.00523957143832e+01 9.54593690642836e+00
|
||||||
256 1.00457028282132e+01 9.55423082330650e+00
|
256 1.00457028598538e+01 9.55423080384305e+00
|
||||||
257 1.00402418669526e+01 9.56514761944992e+00
|
257 1.00402419064054e+01 9.56514760196478e+00
|
||||||
258 1.00365397691695e+01 9.57641296971103e+00
|
258 1.00365398159221e+01 9.57641295373454e+00
|
||||||
259 1.00349276270394e+01 9.58620624196598e+00
|
259 1.00349276804438e+01 9.58620622717253e+00
|
||||||
260 1.00355019919770e+01 9.59332346959128e+00
|
260 1.00355020510841e+01 9.59332345585722e+00
|
||||||
261 1.00381137097146e+01 9.59732188686984e+00
|
261 1.00381137733017e+01 9.59732187421620e+00
|
||||||
262 1.00423905760179e+01 9.59837618250971e+00
|
262 1.00423906427137e+01 9.59837617102817e+00
|
||||||
263 1.00477959188736e+01 9.59679324477687e+00
|
263 1.00477959872900e+01 9.59679323453788e+00
|
||||||
264 1.00537068007149e+01 9.59269523141530e+00
|
264 1.00537068694862e+01 9.59269522224878e+00
|
||||||
265 1.00594937260641e+01 9.58610120816249e+00
|
265 1.00594937939774e+01 9.58610119961332e+00
|
||||||
266 1.00645870781682e+01 9.57722117048002e+00
|
266 1.00645871442695e+01 9.57722116190429e+00
|
||||||
267 1.00685316571224e+01 9.56668493985151e+00
|
267 1.00685317208695e+01 9.56668493059359e+00
|
||||||
268 1.00710357823615e+01 9.55556251047062e+00
|
268 1.00710358435525e+01 9.55556250017823e+00
|
||||||
269 1.00720144042107e+01 9.54520978473172e+00
|
269 1.00720144628669e+01 9.54520977349603e+00
|
||||||
270 1.00716144493745e+01 9.53703781183182e+00
|
270 1.00716145056864e+01 9.53703780013997e+00
|
||||||
271 1.00701992199135e+01 9.53227489206590e+00
|
271 1.00701992741473e+01 9.53227488069496e+00
|
||||||
272 1.00682808706064e+01 9.53173333554826e+00
|
272 1.00682809229059e+01 9.53173332532930e+00
|
||||||
273 1.00663988075209e+01 9.53554943194497e+00
|
273 1.00663988579612e+01 9.53554942356440e+00
|
||||||
274 1.00649733063520e+01 9.54299862049767e+00
|
274 1.00649733547668e+01 9.54299861430164e+00
|
||||||
275 1.00641836485840e+01 9.55262143610080e+00
|
275 1.00641836945973e+01 9.55262143202964e+00
|
||||||
276 1.00639178664285e+01 9.56271517955029e+00
|
276 1.00639179095174e+01 9.56271517715327e+00
|
||||||
277 1.00638153921535e+01 9.57192148747872e+00
|
277 1.00638154316074e+01 9.57192148613520e+00
|
||||||
278 1.00633853985923e+01 9.57957875475062e+00
|
278 1.00633854335686e+01 9.57957875400668e+00
|
||||||
279 1.00621626720543e+01 9.58572327394556e+00
|
279 1.00621627016565e+01 9.58572327370357e+00
|
||||||
280 1.00598570838615e+01 9.59085686511578e+00
|
280 1.00598571070638e+01 9.59085686592320e+00
|
||||||
281 1.00564566071967e+01 9.59567423393283e+00
|
281 1.00564566229803e+01 9.59567423699651e+00
|
||||||
282 1.00522576614697e+01 9.60085550637412e+00
|
282 1.00522576689401e+01 9.60085551333600e+00
|
||||||
283 1.00478091897332e+01 9.60690040068280e+00
|
283 1.00478091881844e+01 9.60690041329352e+00
|
||||||
284 1.00437767664032e+01 9.61396708331890e+00
|
284 1.00437767554115e+01 9.61396710318380e+00
|
||||||
285 1.00407546813490e+01 9.62178118810825e+00
|
285 1.00407546608873e+01 9.62178121653831e+00
|
||||||
286 1.00390773261870e+01 9.62975547860500e+00
|
286 1.00390772967935e+01 9.62975551670189e+00
|
||||||
287 1.00386906040191e+01 9.63733595704590e+00
|
287 1.00386905666453e+01 9.63733600598964e+00
|
||||||
288 1.00391292740982e+01 9.64435229335154e+00
|
288 1.00391292301728e+01 9.64435235461356e+00
|
||||||
289 1.00396077171765e+01 9.65114124926381e+00
|
289 1.00396076684883e+01 9.65114132457984e+00
|
||||||
290 1.00391967746350e+01 9.65843904962787e+00
|
290 1.00391967232973e+01 9.65843914091158e+00
|
||||||
291 1.00370409303829e+01 9.66713735495098e+00
|
291 1.00370408787737e+01 9.66713746391752e+00
|
||||||
292 1.00325613495850e+01 9.67798035621834e+00
|
292 1.00325613002434e+01 9.67798048381559e+00
|
||||||
293 1.00255913568518e+01 9.69130440474672e+00
|
293 1.00255913122523e+01 9.69130455064462e+00
|
||||||
294 1.00164044158125e+01 9.70689841022156e+00
|
294 1.00164043783898e+01 9.70689857240811e+00
|
||||||
295 1.00056261321876e+01 9.72399810930261e+00
|
295 1.00056261042358e+01 9.72399828398139e+00
|
||||||
296 9.99406221883501e+00 9.74140402524052e+00
|
296 9.99406220236070e+00 9.74140420689973e+00
|
||||||
297 9.98250803362175e+00 9.75776438941627e+00
|
297 9.98250803047048e+00 9.75776457125789e+00
|
||||||
298 9.97160202027972e+00 9.77203069297329e+00
|
298 9.97160203186903e+00 9.77203086770013e+00
|
||||||
299 9.96175637151037e+00 9.78379375044905e+00
|
299 9.96175639897897e+00 9.78379391142304e+00
|
||||||
300 9.95315918568411e+00 9.79318883680258e+00
|
300 9.95315922958854e+00 9.79318897892133e+00
|
||||||
|
|||||||
@ -1,12 +1,12 @@
|
|||||||
configuration {
|
configuration {
|
||||||
step 100
|
step 100
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
version 2020-07-07
|
version 2024-06-04
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 1.00387423506482e+01
|
x 10.038742350674
|
||||||
}
|
}
|
||||||
|
|
||||||
restraint {
|
restraint {
|
||||||
|
|||||||
@ -20,16 +20,16 @@
|
|||||||
18 9.41602481112176e+00
|
18 9.41602481112176e+00
|
||||||
19 9.44413580740584e+00
|
19 9.44413580740584e+00
|
||||||
20 9.49001346044027e+00
|
20 9.49001346044027e+00
|
||||||
21 9.55036359015270e+00
|
21 9.55036359015271e+00
|
||||||
22 9.62258602486444e+00
|
22 9.62258602486445e+00
|
||||||
23 9.70460545744668e+00
|
23 9.70460545744666e+00
|
||||||
24 9.79475465622561e+00
|
24 9.79475465622561e+00
|
||||||
25 9.89135302429916e+00
|
25 9.89135302429913e+00
|
||||||
26 9.99213332770717e+00
|
26 9.99213332770716e+00
|
||||||
27 1.00938522423366e+01
|
27 1.00938522423366e+01
|
||||||
28 1.01925371414626e+01
|
28 1.01925371414626e+01
|
||||||
29 1.02845129002944e+01
|
29 1.02845129002944e+01
|
||||||
30 1.03676671987640e+01
|
30 1.03676671987639e+01
|
||||||
31 1.04416385355998e+01
|
31 1.04416385355998e+01
|
||||||
32 1.05071349561950e+01
|
32 1.05071349561950e+01
|
||||||
33 1.05650463398331e+01
|
33 1.05650463398331e+01
|
||||||
@ -41,39 +41,39 @@
|
|||||||
39 1.07331870068021e+01
|
39 1.07331870068021e+01
|
||||||
40 1.07158913924701e+01
|
40 1.07158913924701e+01
|
||||||
41 1.06789115566470e+01
|
41 1.06789115566470e+01
|
||||||
42 1.06198840652253e+01
|
42 1.06198840652254e+01
|
||||||
43 1.05380097743725e+01
|
43 1.05380097743725e+01
|
||||||
44 1.04346581978275e+01
|
44 1.04346581978275e+01
|
||||||
45 1.03132910149185e+01
|
45 1.03132910149185e+01
|
||||||
46 1.01792819503691e+01
|
46 1.01792819503692e+01
|
||||||
47 1.00398949454818e+01
|
47 1.00398949454818e+01
|
||||||
48 9.90373650268307e+00
|
48 9.90373650268307e+00
|
||||||
49 9.77934647164350e+00
|
49 9.77934647164349e+00
|
||||||
50 9.67343955381284e+00
|
50 9.67343955381283e+00
|
||||||
51 9.58957255517495e+00
|
51 9.58957255517494e+00
|
||||||
52 9.52771577288560e+00
|
52 9.52771577288559e+00
|
||||||
53 9.48463495848957e+00
|
53 9.48463495848955e+00
|
||||||
54 9.45495747488851e+00
|
54 9.45495747488850e+00
|
||||||
55 9.43277083061229e+00
|
55 9.43277083061230e+00
|
||||||
56 9.41329510571902e+00
|
56 9.41329510571900e+00
|
||||||
57 9.39417852043035e+00
|
57 9.39417852043034e+00
|
||||||
58 9.37607916767444e+00
|
58 9.37607916767444e+00
|
||||||
59 9.36243879601093e+00
|
59 9.36243879601092e+00
|
||||||
60 9.35853234890725e+00
|
60 9.35853234890724e+00
|
||||||
61 9.36993739187210e+00
|
61 9.36993739187209e+00
|
||||||
62 9.40084256925489e+00
|
62 9.40084256925487e+00
|
||||||
63 9.45286356660258e+00
|
63 9.45286356660258e+00
|
||||||
64 9.52464585631223e+00
|
64 9.52464585631223e+00
|
||||||
65 9.61230948096192e+00
|
65 9.61230948096192e+00
|
||||||
66 9.71074418990813e+00
|
66 9.71074418990814e+00
|
||||||
67 9.81507236552599e+00
|
67 9.81507236552600e+00
|
||||||
68 9.92117974657176e+00
|
68 9.92117974657179e+00
|
||||||
69 1.00244259961919e+01
|
69 1.00244259961920e+01
|
||||||
70 1.01178306268727e+01
|
70 1.01178306268727e+01
|
||||||
71 1.01986985644537e+01
|
71 1.01986985644538e+01
|
||||||
72 1.02671003889995e+01
|
72 1.02671003889995e+01
|
||||||
73 1.03213098011429e+01
|
73 1.03213098011430e+01
|
||||||
74 1.03597236984298e+01
|
74 1.03597236984299e+01
|
||||||
75 1.03817789163109e+01
|
75 1.03817789163109e+01
|
||||||
76 1.03880650963390e+01
|
76 1.03880650963390e+01
|
||||||
77 1.03809140245635e+01
|
77 1.03809140245635e+01
|
||||||
@ -82,21 +82,21 @@
|
|||||||
80 1.03243676495902e+01
|
80 1.03243676495902e+01
|
||||||
81 1.03082131278348e+01
|
81 1.03082131278348e+01
|
||||||
82 1.02961310659179e+01
|
82 1.02961310659179e+01
|
||||||
83 1.02862115513553e+01
|
83 1.02862115513552e+01
|
||||||
84 1.02756073299153e+01
|
84 1.02756073299153e+01
|
||||||
85 1.02618115461408e+01
|
85 1.02618115461408e+01
|
||||||
86 1.02435127550163e+01
|
86 1.02435127550163e+01
|
||||||
87 1.02212112849545e+01
|
87 1.02212112849545e+01
|
||||||
88 1.01972788307491e+01
|
88 1.01972788307491e+01
|
||||||
89 1.01743918261207e+01
|
89 1.01743918261206e+01
|
||||||
90 1.01538328424605e+01
|
90 1.01538328424605e+01
|
||||||
91 1.01363005552771e+01
|
91 1.01363005552771e+01
|
||||||
92 1.01223066231827e+01
|
92 1.01223066231826e+01
|
||||||
93 1.01118037967830e+01
|
93 1.01118037967829e+01
|
||||||
94 1.01038502876980e+01
|
94 1.01038502876980e+01
|
||||||
95 1.00967012947728e+01
|
95 1.00967012947726e+01
|
||||||
96 1.00885779123137e+01
|
96 1.00885779123133e+01
|
||||||
97 1.00784256309007e+01
|
97 1.00784256308996e+01
|
||||||
98 1.00661429612272e+01
|
98 1.00661429612359e+01
|
||||||
99 1.00524913461711e+01
|
99 1.00524913461887e+01
|
||||||
100 1.00387423506482e+01
|
100 1.00387423506735e+01
|
||||||
|
|||||||
@ -16,7 +16,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
|||||||
variable dt equal 1e-3 # timestep microseconds
|
variable dt equal 1e-3 # timestep microseconds
|
||||||
variable skin equal 0.2*$h
|
variable skin equal 0.2*$h
|
||||||
|
|
||||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
region box block -${Lb} ${Lb} -${Lb} ${Lb} -0.5 0.5 units box
|
||||||
create_box 4 box
|
create_box 4 box
|
||||||
lattice sq $a
|
lattice sq $a
|
||||||
|
|
||||||
|
|||||||
@ -14,7 +14,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
|||||||
variable dt equal 1e-3 # timestep microseconds
|
variable dt equal 1e-3 # timestep microseconds
|
||||||
variable skin equal 0.2*$h
|
variable skin equal 0.2*$h
|
||||||
|
|
||||||
region box block -$L $L -$L $L 0 $a units box
|
region box block -$L $L -$L $L -0.5 0.5 units box
|
||||||
create_box 2 box
|
create_box 2 box
|
||||||
lattice sq $a
|
lattice sq $a
|
||||||
|
|
||||||
|
|||||||
@ -1,40 +1,40 @@
|
|||||||
variable sname index ch4
|
variable sname index ch4
|
||||||
|
|
||||||
units electron
|
units electron
|
||||||
newton on
|
newton on
|
||||||
boundary f f f
|
boundary f f f
|
||||||
|
|
||||||
atom_style electron
|
atom_style electron
|
||||||
|
|
||||||
read_data data.${sname}
|
read_data data.${sname}
|
||||||
|
|
||||||
pair_style eff/cut 100.0
|
pair_style eff/cut 100.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
comm_modify vel yes
|
comm_modify vel yes
|
||||||
|
|
||||||
# Minimize
|
# Minimize
|
||||||
min_style cg
|
min_style cg
|
||||||
compute 1 all property/atom spin eradius
|
compute 1 all property/atom spin eradius
|
||||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
#dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
min_modify line quadratic dmax 0.1
|
min_modify line quadratic dmax 0.1
|
||||||
minimize 0 1.0e-6 1000 10000
|
minimize 0 1.0e-6 1000 10000
|
||||||
|
|
||||||
# Dynamics
|
# Dynamics
|
||||||
|
|
||||||
compute effTemp all temp/eff
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
thermo 1000
|
thermo 1000
|
||||||
thermo_style custom step pe temp press
|
thermo_style custom step pe temp press
|
||||||
thermo_modify temp effTemp
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||||
|
|
||||||
timestep 0.005
|
timestep 0.005
|
||||||
fix 1 all nve/eff
|
fix 1 all nve/eff
|
||||||
|
|
||||||
# the custom dump includes the radii
|
# the custom dump includes the radii
|
||||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
#dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
#dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||||
|
|
||||||
run 100000
|
run 100000
|
||||||
|
|||||||
@ -1,17 +1,17 @@
|
|||||||
variable sname index ch4
|
variable sname index ch4
|
||||||
|
|
||||||
units electron
|
units electron
|
||||||
newton on
|
newton on
|
||||||
boundary f f f
|
boundary f f f
|
||||||
|
|
||||||
atom_style electron
|
atom_style electron
|
||||||
|
|
||||||
read_data data.${sname}
|
read_data data.${sname}
|
||||||
|
|
||||||
pair_style eff/cut 100.0
|
pair_style eff/cut 100.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
comm_modify vel yes
|
comm_modify vel yes
|
||||||
|
|
||||||
compute effTemp all temp/eff
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
@ -24,8 +24,8 @@ variable erres equal c_energies[4]
|
|||||||
thermo 1
|
thermo 1
|
||||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
||||||
|
|
||||||
min_style cg
|
min_style cg
|
||||||
compute 1 all property/atom spin eradius erforce
|
compute 1 all property/atom spin eradius erforce
|
||||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
minimize 0 1e-6 2000 4000
|
minimize 0 1e-6 2000 4000
|
||||||
|
|
||||||
|
|||||||
@ -1,17 +1,17 @@
|
|||||||
variable sname index ch4_ionized
|
variable sname index ch4_ionized
|
||||||
|
|
||||||
units electron
|
units electron
|
||||||
newton on
|
newton on
|
||||||
boundary f f f
|
boundary f f f
|
||||||
|
|
||||||
atom_style electron
|
atom_style electron
|
||||||
|
|
||||||
read_data data.${sname}
|
read_data data.${sname}
|
||||||
|
|
||||||
pair_style eff/cut 5000.0 0 0
|
pair_style eff/cut 5000.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
comm_modify vel yes
|
comm_modify vel yes
|
||||||
|
|
||||||
# minimize
|
# minimize
|
||||||
|
|
||||||
@ -20,23 +20,23 @@ min_modify line quadratic
|
|||||||
minimize 0 1.0e-6 10000 100000
|
minimize 0 1.0e-6 10000 100000
|
||||||
|
|
||||||
# dynamics
|
# dynamics
|
||||||
compute effTemp all temp/eff
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
thermo 100
|
thermo 100
|
||||||
thermo_style custom step etotal pe ke temp press
|
thermo_style custom step etotal pe ke temp press
|
||||||
thermo_modify temp effTemp
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
# equilibrate
|
# equilibrate
|
||||||
timestep 0.001
|
timestep 0.001
|
||||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||||
|
|
||||||
# the custom dump includes the radii
|
# the custom dump includes the radii
|
||||||
compute 1 all property/atom spin eradius
|
compute 1 all property/atom spin eradius
|
||||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
#dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
#dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||||
|
|
||||||
run 1000000
|
run 1000000
|
||||||
|
|
||||||
fix 2 all nve/eff
|
fix 2 all nve/eff
|
||||||
|
|
||||||
run 1000000
|
run 1000000
|
||||||
|
|||||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
@ -0,0 +1,266 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index ch4
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary f f f
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.ch4
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
15 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 100.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
# Minimize
|
||||||
|
min_style cg
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
min_modify line quadratic dmax 0.1
|
||||||
|
minimize 0 1.0e-6 1000 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
|
||||||
|
@Article{Jaramillo-Botero11,
|
||||||
|
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||||
|
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||||
|
journal = {J.~Comp.\ Chem.},
|
||||||
|
year = 2011,
|
||||||
|
volume = 32,
|
||||||
|
number = 3,
|
||||||
|
pages = {497--512}
|
||||||
|
}
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 102
|
||||||
|
ghost atom cutoff = 102
|
||||||
|
binsize = 51, bins = 20 20 20
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/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) = 5.405 | 5.405 | 5.405 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -27.314082 0 -27.314082 -56588.53
|
||||||
|
1000 0 -34.07448 0 -34.07448 1.3464499
|
||||||
|
Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms
|
||||||
|
|
||||||
|
88.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max iterations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-27.3140820331247 -34.0744796893375 -34.0744796893447
|
||||||
|
Force two-norm initial, final = 10.728716 0.00017815706
|
||||||
|
Force max component initial, final = 6.1727999 8.2675815e-05
|
||||||
|
Final line search alpha, max atom move = 1 8.2675815e-05
|
||||||
|
Iterations, force evaluations = 1000 1943
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40
|
||||||
|
Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.001604 | | | 5.20
|
||||||
|
|
||||||
|
Nlocal: 15 ave 15 max 15 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: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 105
|
||||||
|
Ave neighs/atom = 7
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Dynamics
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
thermo_style custom step pe temp press
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
fix 1 all nve/eff
|
||||||
|
|
||||||
|
# the custom dump includes the radii
|
||||||
|
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||||
|
dump 3 all xyz 1000 ch4.nve.xyz
|
||||||
|
|
||||||
|
run 100000
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
1000 -34.07448 1050 392.66426
|
||||||
|
2000 -34.065618 583.71716 -618.55027
|
||||||
|
3000 -34.063563 475.54605 661.95076
|
||||||
|
4000 -34.06119 350.76183 -449.64687
|
||||||
|
5000 -34.0652 561.71223 -131.2575
|
||||||
|
6000 -34.065798 593.21728 754.38406
|
||||||
|
7000 -34.067408 677.86019 -409.21139
|
||||||
|
8000 -34.065663 586.03411 446.32573
|
||||||
|
9000 -34.06294 442.71136 414.41408
|
||||||
|
10000 -34.060101 293.33406 -1203.0131
|
||||||
|
11000 -34.064946 548.39598 345.29601
|
||||||
|
12000 -34.067323 673.49043 444.55927
|
||||||
|
13000 -34.063275 460.43973 -854.83884
|
||||||
|
14000 -34.064666 533.57265 1542.0127
|
||||||
|
15000 -34.063343 463.97449 -778.73252
|
||||||
|
16000 -34.064462 522.77625 -1.5339614
|
||||||
|
17000 -34.061203 351.37068 -148.19163
|
||||||
|
18000 -34.066534 631.87837 -237.0746
|
||||||
|
19000 -34.065169 560.16772 1360.7348
|
||||||
|
20000 -34.063042 448.13104 -664.72128
|
||||||
|
21000 -34.060696 324.68723 -167.83333
|
||||||
|
22000 -34.065376 570.90279 -831.73853
|
||||||
|
23000 -34.063127 452.61143 766.59984
|
||||||
|
24000 -34.064572 528.62282 -107.80755
|
||||||
|
25000 -34.06584 595.42175 610.33075
|
||||||
|
26000 -34.066886 650.43579 -894.20521
|
||||||
|
27000 -34.062035 395.20224 1754.7666
|
||||||
|
28000 -34.060696 324.66878 -2622.013
|
||||||
|
29000 -34.066777 644.66282 1551.3147
|
||||||
|
30000 -34.066421 625.94614 -507.44173
|
||||||
|
31000 -34.066163 612.36658 610.11907
|
||||||
|
32000 -34.063109 451.70185 -47.463209
|
||||||
|
33000 -34.062833 437.16794 -607.25848
|
||||||
|
34000 -34.061657 375.30056 -158.28097
|
||||||
|
35000 -34.064937 547.86519 272.75585
|
||||||
|
36000 -34.067509 683.23088 359.91072
|
||||||
|
37000 -34.067582 686.96461 -384.97405
|
||||||
|
38000 -34.063213 457.13191 411.86349
|
||||||
|
39000 -34.06272 431.13187 -594.23723
|
||||||
|
40000 -34.062286 408.41212 456.09079
|
||||||
|
41000 -34.064078 502.64096 -1149.8496
|
||||||
|
42000 -34.066408 625.33334 1403.4937
|
||||||
|
43000 -34.065948 601.03876 -773.40678
|
||||||
|
44000 -34.064113 504.49498 179.93456
|
||||||
|
45000 -34.060573 318.11433 223.38679
|
||||||
|
46000 -34.063614 478.24588 -409.99081
|
||||||
|
47000 -34.064814 541.38544 614.25246
|
||||||
|
48000 -34.065602 582.87984 -743.92184
|
||||||
|
49000 -34.063923 494.52673 474.88127
|
||||||
|
50000 -34.064616 530.94533 288.81199
|
||||||
|
51000 -34.062038 395.2991 -480.07513
|
||||||
|
52000 -34.06497 549.5123 -305.53764
|
||||||
|
53000 -34.065578 581.59919 964.80956
|
||||||
|
54000 -34.06766 691.12707 -437.99603
|
||||||
|
55000 -34.064707 535.85658 1058.6734
|
||||||
|
56000 -34.062481 418.58003 -1011.5341
|
||||||
|
57000 -34.064997 551.06731 -32.91724
|
||||||
|
58000 -34.064281 513.25358 374.91628
|
||||||
|
59000 -34.066177 613.1188 -464.85124
|
||||||
|
60000 -34.064718 536.29803 1011.6698
|
||||||
|
61000 -34.065746 590.46955 -1057.9241
|
||||||
|
62000 -34.063253 459.23293 1526.2698
|
||||||
|
63000 -34.062261 407.08636 -1743.6652
|
||||||
|
64000 -34.063835 489.88286 761.60266
|
||||||
|
65000 -34.069569 791.614 323.26812
|
||||||
|
66000 -34.065557 580.45685 874.52459
|
||||||
|
67000 -34.064917 546.77223 -1349.3606
|
||||||
|
68000 -34.062963 443.96697 1178.4319
|
||||||
|
69000 -34.063063 449.26418 -1660.686
|
||||||
|
70000 -34.063597 477.39716 1323.13
|
||||||
|
71000 -34.065424 573.47914 -131.55428
|
||||||
|
72000 -34.065211 562.31067 -415.56361
|
||||||
|
73000 -34.06339 466.38097 724.92885
|
||||||
|
74000 -34.062286 408.34027 -1094.3845
|
||||||
|
75000 -34.065545 579.79767 587.58121
|
||||||
|
76000 -34.066774 644.61685 -357.22241
|
||||||
|
77000 -34.064479 523.74831 1545.6628
|
||||||
|
78000 -34.065506 577.88405 -1013.2409
|
||||||
|
79000 -34.062874 439.24856 240.66725
|
||||||
|
80000 -34.06306 449.09678 -799.14252
|
||||||
|
81000 -34.063338 463.66067 1528.3351
|
||||||
|
82000 -34.066812 646.52985 -1351.1758
|
||||||
|
83000 -34.064724 536.65114 1338.595
|
||||||
|
84000 -34.063774 486.67172 -876.0475
|
||||||
|
85000 -34.06156 370.19256 617.89915
|
||||||
|
86000 -34.063628 478.95398 -134.40164
|
||||||
|
87000 -34.065141 558.60424 -758.03942
|
||||||
|
88000 -34.066732 642.27865 1159.5992
|
||||||
|
89000 -34.067349 674.83453 -301.45201
|
||||||
|
90000 -34.063623 478.69626 386.87752
|
||||||
|
91000 -34.061885 387.30728 -774.32296
|
||||||
|
92000 -34.061363 359.77745 500.06117
|
||||||
|
93000 -34.065724 589.32209 -469.10399
|
||||||
|
94000 -34.065006 551.42796 818.92294
|
||||||
|
95000 -34.06541 572.75191 -677.20865
|
||||||
|
96000 -34.062331 410.64868 1383.8935
|
||||||
|
97000 -34.061499 366.95753 -1715.2058
|
||||||
|
98000 -34.061153 348.68703 353.63545
|
||||||
|
99000 -34.066217 615.27816 193.79593
|
||||||
|
100000 -34.067739 695.36238 205.35389
|
||||||
|
101000 -34.067314 672.94727 929.41223
|
||||||
|
Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms
|
||||||
|
|
||||||
|
Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s
|
||||||
|
85.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28
|
||||||
|
Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62
|
||||||
|
Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80
|
||||||
|
Other | | 0.01755 | | | 0.79
|
||||||
|
|
||||||
|
Nlocal: 15 ave 15 max 15 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: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 105
|
||||||
|
Ave neighs/atom = 7
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
@ -0,0 +1,266 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index ch4
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary f f f
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.ch4
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
15 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 100.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
# Minimize
|
||||||
|
min_style cg
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
min_modify line quadratic dmax 0.1
|
||||||
|
minimize 0 1.0e-6 1000 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
|
||||||
|
@Article{Jaramillo-Botero11,
|
||||||
|
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||||
|
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||||
|
journal = {J.~Comp.\ Chem.},
|
||||||
|
year = 2011,
|
||||||
|
volume = 32,
|
||||||
|
number = 3,
|
||||||
|
pages = {497--512}
|
||||||
|
}
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 102
|
||||||
|
ghost atom cutoff = 102
|
||||||
|
binsize = 51, bins = 20 20 20
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/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) = 5.385 | 5.385 | 5.385 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -27.314082 0 -27.314082 -56588.53
|
||||||
|
1000 0 -34.07448 0 -34.07448 0.39495391
|
||||||
|
Loop time of 0.0230482 on 4 procs for 1000 steps with 15 atoms
|
||||||
|
|
||||||
|
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max iterations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-27.3140820331249 -34.0744796901924 -34.0744796901707
|
||||||
|
Force two-norm initial, final = 10.728716 0.00024139276
|
||||||
|
Force max component initial, final = 6.1727999 0.00017091779
|
||||||
|
Final line search alpha, max atom move = 1 0.00017091779
|
||||||
|
Iterations, force evaluations = 1000 1946
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0015331 | 0.0032095 | 0.0046681 | 2.0 | 13.93
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0037211 | 0.0053887 | 0.0069902 | 1.6 | 23.38
|
||||||
|
Output | 0.0062087 | 0.0079064 | 0.011172 | 2.2 | 34.30
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.006544 | | | 28.39
|
||||||
|
|
||||||
|
Nlocal: 3.75 ave 6 max 3 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 11.25 ave 12 max 9 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 26.25 ave 39 max 12 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 105
|
||||||
|
Ave neighs/atom = 7
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Dynamics
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
thermo_style custom step pe temp press
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
fix 1 all nve/eff
|
||||||
|
|
||||||
|
# the custom dump includes the radii
|
||||||
|
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||||
|
dump 3 all xyz 1000 ch4.nve.xyz
|
||||||
|
|
||||||
|
run 100000
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
1000 -34.07448 1050 391.71277
|
||||||
|
2000 -34.065618 583.70724 -617.78946
|
||||||
|
3000 -34.063563 475.53779 661.75865
|
||||||
|
4000 -34.06119 350.74901 -449.8917
|
||||||
|
5000 -34.065201 561.76559 -130.73147
|
||||||
|
6000 -34.065798 593.21893 753.94281
|
||||||
|
7000 -34.067408 677.86552 -409.14034
|
||||||
|
8000 -34.065662 586.02658 446.74947
|
||||||
|
9000 -34.062939 442.6953 413.93386
|
||||||
|
10000 -34.060101 293.35262 -1202.4169
|
||||||
|
11000 -34.064946 548.37877 344.89658
|
||||||
|
12000 -34.067324 673.52389 444.40605
|
||||||
|
13000 -34.063275 460.44923 -854.41022
|
||||||
|
14000 -34.064667 533.59655 1541.2922
|
||||||
|
15000 -34.063344 464.01572 -777.83895
|
||||||
|
16000 -34.064461 522.76554 -2.2050586
|
||||||
|
17000 -34.061202 351.31261 -148.09486
|
||||||
|
18000 -34.066534 631.89021 -236.72076
|
||||||
|
19000 -34.065169 560.16576 1359.8928
|
||||||
|
20000 -34.063042 448.14707 -663.76152
|
||||||
|
21000 -34.060695 324.66945 -168.3252
|
||||||
|
22000 -34.065376 570.90677 -831.8481
|
||||||
|
23000 -34.063127 452.62391 767.31463
|
||||||
|
24000 -34.064572 528.62018 -108.63204
|
||||||
|
25000 -34.06584 595.41818 610.87995
|
||||||
|
26000 -34.066885 650.4263 -894.11862
|
||||||
|
27000 -34.062035 395.1876 1754.1737
|
||||||
|
28000 -34.060697 324.71187 -2621.333
|
||||||
|
29000 -34.066777 644.68166 1550.7046
|
||||||
|
30000 -34.066421 625.9368 -507.12512
|
||||||
|
31000 -34.066163 612.3605 610.12993
|
||||||
|
32000 -34.063108 451.66459 -48.049967
|
||||||
|
33000 -34.062834 437.21062 -606.58502
|
||||||
|
34000 -34.061656 375.26971 -158.76936
|
||||||
|
35000 -34.064938 547.90576 273.26572
|
||||||
|
36000 -34.067508 683.20936 360.05973
|
||||||
|
37000 -34.067582 686.96938 -385.62265
|
||||||
|
38000 -34.063213 457.13708 412.74004
|
||||||
|
39000 -34.06272 431.16474 -595.05437
|
||||||
|
40000 -34.062285 408.38247 456.29631
|
||||||
|
41000 -34.064078 502.65934 -1149.196
|
||||||
|
42000 -34.066408 625.33356 1402.5676
|
||||||
|
43000 -34.065948 601.04311 -772.96544
|
||||||
|
44000 -34.064113 504.47553 179.83988
|
||||||
|
45000 -34.060572 318.08821 222.85125
|
||||||
|
46000 -34.063614 478.25613 -409.06152
|
||||||
|
47000 -34.064813 541.37361 613.37159
|
||||||
|
48000 -34.065602 582.88704 -743.72019
|
||||||
|
49000 -34.063922 494.52189 475.22811
|
||||||
|
50000 -34.064616 530.95516 288.46302
|
||||||
|
51000 -34.062038 395.30091 -479.68548
|
||||||
|
52000 -34.06497 549.50477 -305.82851
|
||||||
|
53000 -34.065577 581.56927 964.95886
|
||||||
|
54000 -34.06766 691.14533 -437.95563
|
||||||
|
55000 -34.064707 535.85441 1058.0886
|
||||||
|
56000 -34.062481 418.62259 -1010.5517
|
||||||
|
57000 -34.064996 551.02074 -33.54291
|
||||||
|
58000 -34.064281 513.27818 375.07194
|
||||||
|
59000 -34.066177 613.11494 -464.71576
|
||||||
|
60000 -34.064718 536.306 1010.9545
|
||||||
|
61000 -34.065746 590.47317 -1056.9192
|
||||||
|
62000 -34.063252 459.22005 1525.6789
|
||||||
|
63000 -34.06226 407.05859 -1743.9974
|
||||||
|
64000 -34.063836 489.91026 762.61836
|
||||||
|
65000 -34.069569 791.63831 322.35333
|
||||||
|
66000 -34.065557 580.46799 875.11714
|
||||||
|
67000 -34.064916 546.74052 -1349.5741
|
||||||
|
68000 -34.062962 443.93438 1178.1978
|
||||||
|
69000 -34.063064 449.3052 -1659.8695
|
||||||
|
70000 -34.063596 477.36452 1322.0559
|
||||||
|
71000 -34.065424 573.49586 -131.11749
|
||||||
|
72000 -34.06521 562.24612 -415.25895
|
||||||
|
73000 -34.06339 466.38351 724.08642
|
||||||
|
74000 -34.062286 408.37673 -1093.6751
|
||||||
|
75000 -34.065545 579.81257 586.8907
|
||||||
|
76000 -34.066774 644.62609 -356.7044
|
||||||
|
77000 -34.064479 523.75235 1545.8498
|
||||||
|
78000 -34.065506 577.88123 -1014.0878
|
||||||
|
79000 -34.062875 439.30997 241.55748
|
||||||
|
80000 -34.06306 449.06553 -799.58139
|
||||||
|
81000 -34.063338 463.64261 1528.4412
|
||||||
|
82000 -34.066812 646.55603 -1350.9377
|
||||||
|
83000 -34.064724 536.63793 1338.2148
|
||||||
|
84000 -34.063774 486.717 -875.60363
|
||||||
|
85000 -34.06156 370.19433 617.85579
|
||||||
|
86000 -34.063628 478.9961 -135.13703
|
||||||
|
87000 -34.065141 558.62541 -756.91518
|
||||||
|
88000 -34.066732 642.27743 1158.5797
|
||||||
|
89000 -34.067351 674.92164 -300.79164
|
||||||
|
90000 -34.063624 478.70378 386.44004
|
||||||
|
91000 -34.061884 387.27577 -774.22945
|
||||||
|
92000 -34.061364 359.79856 500.36442
|
||||||
|
93000 -34.065723 589.31234 -469.57015
|
||||||
|
94000 -34.065006 551.46665 819.01826
|
||||||
|
95000 -34.065409 572.7351 -676.74519
|
||||||
|
96000 -34.06233 410.60509 1382.9732
|
||||||
|
97000 -34.0615 366.99019 -1714.2302
|
||||||
|
98000 -34.061152 348.67783 352.89211
|
||||||
|
99000 -34.066217 615.29222 193.8722
|
||||||
|
100000 -34.067739 695.32836 206.03841
|
||||||
|
101000 -34.067313 672.90918 928.0541
|
||||||
|
Loop time of 1.62544 on 4 procs for 100000 steps with 15 atoms
|
||||||
|
|
||||||
|
Performance: 26577371.575 fs/day, 0.000 hours/fs, 61521.693 timesteps/s, 922.825 katom-step/s
|
||||||
|
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.066581 | 0.15332 | 0.25928 | 21.7 | 9.43
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.18521 | 0.29733 | 0.3879 | 16.1 | 18.29
|
||||||
|
Output | 0.66513 | 0.81838 | 1.1333 | 20.4 | 50.35
|
||||||
|
Modify | 0.01285 | 0.014237 | 0.016092 | 1.0 | 0.88
|
||||||
|
Other | | 0.3422 | | | 21.05
|
||||||
|
|
||||||
|
Nlocal: 3.75 ave 5 max 3 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
Nghost: 11.25 ave 12 max 10 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
Neighs: 26.25 ave 47 max 10 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 105
|
||||||
|
Ave neighs/atom = 7
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -3,12 +3,11 @@
|
|||||||
|
|
||||||
# General parameters
|
# General parameters
|
||||||
|
|
||||||
variable sname index Si2H6
|
variable sname index Si2H6
|
||||||
log ${sname}.log
|
|
||||||
|
|
||||||
units electron
|
units electron
|
||||||
newton on
|
newton on
|
||||||
boundary f f f
|
boundary f f f
|
||||||
|
|
||||||
atom_style electron
|
atom_style electron
|
||||||
|
|
||||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
|||||||
variable estatics equal c_energies[3]
|
variable estatics equal c_energies[3]
|
||||||
variable errestrain equal c_energies[4]
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
comm_modify vel yes
|
comm_modify vel yes
|
||||||
|
|
||||||
compute peratom all stress/atom NULL
|
compute peratom all stress/atom NULL
|
||||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
@ -39,12 +38,12 @@ thermo_modify temp effTemp press effPress
|
|||||||
# Minimization
|
# Minimization
|
||||||
|
|
||||||
min_style cg
|
min_style cg
|
||||||
dump 1 all xyz 2 ${sname}.min.xyz
|
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||||
compute 1 all property/atom spin eradius erforce
|
compute 1 all property/atom spin eradius erforce
|
||||||
dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
min_modify line quadratic
|
min_modify line quadratic
|
||||||
minimize 0 1.0e-5 1000 10000
|
minimize 0 1.0e-5 1000 10000
|
||||||
|
|
||||||
undump 1
|
#undump 1
|
||||||
undump 2
|
#undump 2
|
||||||
|
|
||||||
|
|||||||
@ -3,18 +3,17 @@
|
|||||||
|
|
||||||
# General parameters
|
# General parameters
|
||||||
|
|
||||||
variable sname index Si2H6.ang
|
variable sname index Si2H6.ang
|
||||||
log ${sname}.log
|
|
||||||
|
|
||||||
units real
|
units real
|
||||||
newton on
|
newton on
|
||||||
boundary f f f
|
boundary f f f
|
||||||
|
|
||||||
atom_style electron
|
atom_style electron
|
||||||
|
|
||||||
read_data data.${sname}
|
read_data data.${sname}
|
||||||
|
|
||||||
pair_style eff/cut 529.177249
|
pair_style eff/cut 529.177249 ecp 1 Si
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
compute energies all pair eff/cut
|
compute energies all pair eff/cut
|
||||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
|||||||
variable estatics equal c_energies[3]
|
variable estatics equal c_energies[3]
|
||||||
variable errestrain equal c_energies[4]
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
comm_modify vel yes
|
comm_modify vel yes
|
||||||
|
|
||||||
compute peratom all stress/atom NULL
|
compute peratom all stress/atom NULL
|
||||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
@ -39,21 +38,21 @@ thermo_modify temp effTemp press effPress
|
|||||||
# Minimization
|
# Minimization
|
||||||
|
|
||||||
min_style cg
|
min_style cg
|
||||||
dump 1 all xyz 10 ${sname}.min.xyz
|
#dump 1 all xyz 10 ${sname}.min.xyz
|
||||||
compute 1 all property/atom spin eradius erforce
|
compute 1 all property/atom spin eradius erforce
|
||||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
min_modify line quadratic
|
min_modify line quadratic
|
||||||
minimize 0 1.0e-6 2000 10000
|
minimize 0 1.0e-6 2000 10000
|
||||||
|
|
||||||
undump 1
|
#undump 1
|
||||||
undump 2
|
#undump 2
|
||||||
|
|
||||||
# Equilibrate at 300K
|
# Equilibrate at 300K
|
||||||
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
||||||
|
|
||||||
timestep 0.001
|
timestep 0.001
|
||||||
|
|
||||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
#dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||||
|
|
||||||
|
|||||||
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
@ -0,0 +1,185 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
# Created 2011-01-07
|
||||||
|
|
||||||
|
# General parameters
|
||||||
|
|
||||||
|
variable sname index Si2H6
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary f f f
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Si2H6
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
22 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1000.0 ecp 1 Si
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 2
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
# Minimization
|
||||||
|
|
||||||
|
min_style cg
|
||||||
|
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||||
|
compute 1 all property/atom spin eradius erforce
|
||||||
|
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize 0 1.0e-5 1000 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
|
||||||
|
@Article{Jaramillo-Botero11,
|
||||||
|
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||||
|
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||||
|
journal = {J.~Comp.\ Chem.},
|
||||||
|
year = 2011,
|
||||||
|
volume = 32,
|
||||||
|
number = 3,
|
||||||
|
pages = {497--512}
|
||||||
|
}
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1002
|
||||||
|
ghost atom cutoff = 1002
|
||||||
|
binsize = 501, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/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) = 6.098 | 6.098 | 6.098 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||||
|
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||||
|
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||||
|
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||||
|
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||||
|
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||||
|
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||||
|
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||||
|
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||||
|
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||||
|
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||||
|
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||||
|
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||||
|
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||||
|
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||||
|
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||||
|
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||||
|
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||||
|
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||||
|
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||||
|
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||||
|
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||||
|
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||||
|
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||||
|
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||||
|
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||||
|
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311526 -15.311526
|
||||||
|
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.10049441 -0.10049441
|
||||||
|
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138433 -0.12138433
|
||||||
|
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175181 -1.2175181
|
||||||
|
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979907 -0.80979907
|
||||||
|
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945578 -0.85945578
|
||||||
|
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534716 -0.95534716
|
||||||
|
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220676 -0.89220676
|
||||||
|
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44630696 -0.44630696
|
||||||
|
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919073 -0.72919073
|
||||||
|
72 -10.459539 -10.459539 0 6.3202928 0.66056004 -17.440392 0 0 -0.049410442 -0.049410442
|
||||||
|
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025063323 -0.025063323
|
||||||
|
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010779864 -0.010779864
|
||||||
|
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087251782 0.087251782
|
||||||
|
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822668 -0.13822668
|
||||||
|
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043786214 -0.043786214
|
||||||
|
84 -10.459539 -10.459539 0 6.32037 0.66054938 -17.440458 0 0 -0.10833476 -0.10833476
|
||||||
|
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.04772439 -0.04772439
|
||||||
|
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055815521 -0.055815521
|
||||||
|
Loop time of 0.00236996 on 1 procs for 88 steps with 22 atoms
|
||||||
|
|
||||||
|
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = force tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-8.50109938620961 -10.4595390706544 -10.459539070672
|
||||||
|
Force two-norm initial, final = 3.2945156 4.8001667e-06
|
||||||
|
Force max component initial, final = 1.8019385 2.1391495e-06
|
||||||
|
Final line search alpha, max atom move = 1 2.1391495e-06
|
||||||
|
Iterations, force evaluations = 88 127
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0019013 | 0.0019013 | 0.0019013 | 0.0 | 80.23
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 7.926e-06 | 7.926e-06 | 7.926e-06 | 0.0 | 0.33
|
||||||
|
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 11.64
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0001848 | | | 7.80
|
||||||
|
|
||||||
|
Nlocal: 22 ave 22 max 22 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: 231 ave 231 max 231 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 231
|
||||||
|
Ave neighs/atom = 10.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#undump 1
|
||||||
|
#undump 2
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
@ -0,0 +1,185 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
# Created 2011-01-07
|
||||||
|
|
||||||
|
# General parameters
|
||||||
|
|
||||||
|
variable sname index Si2H6
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary f f f
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Si2H6
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
22 atoms
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1000.0 ecp 1 Si
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 2
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
# Minimization
|
||||||
|
|
||||||
|
min_style cg
|
||||||
|
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||||
|
compute 1 all property/atom spin eradius erforce
|
||||||
|
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize 0 1.0e-5 1000 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
|
||||||
|
@Article{Jaramillo-Botero11,
|
||||||
|
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||||
|
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||||
|
journal = {J.~Comp.\ Chem.},
|
||||||
|
year = 2011,
|
||||||
|
volume = 32,
|
||||||
|
number = 3,
|
||||||
|
pages = {497--512}
|
||||||
|
}
|
||||||
|
|
||||||
|
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||||
|
|
||||||
|
@Article{Gissinger24,
|
||||||
|
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||||
|
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||||
|
journal = {J. Phys. Chem. B},
|
||||||
|
year = 2024,
|
||||||
|
volume = 128,
|
||||||
|
number = 13,
|
||||||
|
pages = {3282–-3297}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1002
|
||||||
|
ghost atom cutoff = 1002
|
||||||
|
binsize = 501, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/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) = 6.113 | 6.113 | 6.113 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||||
|
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||||
|
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||||
|
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||||
|
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||||
|
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||||
|
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||||
|
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||||
|
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||||
|
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||||
|
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||||
|
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||||
|
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||||
|
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||||
|
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||||
|
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||||
|
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||||
|
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||||
|
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||||
|
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||||
|
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||||
|
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||||
|
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||||
|
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||||
|
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||||
|
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||||
|
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311525 -15.311525
|
||||||
|
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.1004938 -0.1004938
|
||||||
|
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138436 -0.12138436
|
||||||
|
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175176 -1.2175176
|
||||||
|
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979946 -0.80979946
|
||||||
|
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945162 -0.85945162
|
||||||
|
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534903 -0.95534903
|
||||||
|
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220297 -0.89220297
|
||||||
|
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44631358 -0.44631358
|
||||||
|
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919322 -0.72919322
|
||||||
|
72 -10.459539 -10.459539 0 6.3202928 0.66056005 -17.440392 0 0 -0.049401694 -0.049401694
|
||||||
|
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025056381 -0.025056381
|
||||||
|
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010774653 -0.010774653
|
||||||
|
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087250755 0.087250755
|
||||||
|
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822694 -0.13822694
|
||||||
|
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043784806 -0.043784806
|
||||||
|
84 -10.459539 -10.459539 0 6.32037 0.66054937 -17.440458 0 0 -0.10833935 -0.10833935
|
||||||
|
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.047719128 -0.047719128
|
||||||
|
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055818341 -0.055818341
|
||||||
|
Loop time of 0.00213866 on 4 procs for 88 steps with 22 atoms
|
||||||
|
|
||||||
|
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = force tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-8.50109938620958 -10.4595390706543 -10.459539070672
|
||||||
|
Force two-norm initial, final = 3.2945156 4.7997573e-06
|
||||||
|
Force max component initial, final = 1.8019385 2.1386971e-06
|
||||||
|
Final line search alpha, max atom move = 1 2.1386971e-06
|
||||||
|
Iterations, force evaluations = 88 127
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00027642 | 0.00052972 | 0.00096856 | 0.0 | 24.77
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00035997 | 0.00081245 | 0.0010746 | 0.0 | 37.99
|
||||||
|
Output | 0.00037064 | 0.00039193 | 0.00045231 | 0.0 | 18.33
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0004046 | | | 18.92
|
||||||
|
|
||||||
|
Nlocal: 5.5 ave 7 max 3 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||||
|
Nghost: 16.5 ave 19 max 15 min
|
||||||
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||||
|
Neighs: 57.75 ave 109 max 29 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 231
|
||||||
|
Ave neighs/atom = 10.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#undump 1
|
||||||
|
#undump 2
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../potentials/AlCu.eam.alloy
|
||||||
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../potentials/SiC.tersoff.zbl
|
||||||
@ -12,8 +12,8 @@ region box block -10 10 -10 10 -10 10
|
|||||||
create_box 2 box
|
create_box 2 box
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
|
|
||||||
pair_style eam/alloy
|
pair_style eam/alloy
|
||||||
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
|
pair_coeff * * AlCu.eam.alloy Al Cu
|
||||||
|
|
||||||
mass 1 26.982
|
mass 1 26.982
|
||||||
mass 2 63.546
|
mass 2 63.546
|
||||||
|
|||||||
@ -13,7 +13,7 @@ create_box 1 box
|
|||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
|
|
||||||
pair_style tersoff/zbl
|
pair_style tersoff/zbl
|
||||||
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
|
pair_coeff * * SiC.tersoff.zbl Si
|
||||||
|
|
||||||
mass 1 28.0855
|
mass 1 28.0855
|
||||||
|
|
||||||
|
|||||||
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../../potentials/COH.DMC.aip.water.2dm
|
||||||
@ -4,26 +4,26 @@ boundary p p p
|
|||||||
atom_style full
|
atom_style full
|
||||||
processors * * 1 # domain decomposition over x and y
|
processors * * 1 # domain decomposition over x and y
|
||||||
read_data ./gra_water.data
|
read_data ./gra_water.data
|
||||||
mass 1 12.0107 # carbon mass (g/mole)
|
mass 1 12.0107 # carbon mass (g/mole)
|
||||||
mass 2 15.9994 # oxygen mass (g/mole)
|
mass 2 15.9994 # oxygen mass (g/mole)
|
||||||
mass 3 1.008 # hydrogen mass (g/mole)
|
mass 3 1.008 # hydrogen mass (g/mole)
|
||||||
# Separate atom groups
|
# Separate atom groups
|
||||||
group gr molecule 1
|
group gr molecule 1
|
||||||
group water molecule 2
|
group water molecule 2
|
||||||
######################## Potential defition ##############################
|
######################## Potential defition ##############################
|
||||||
# Interlayer potential
|
# Interlayer potential
|
||||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||||
####################################################################
|
####################################################################
|
||||||
pair_coeff 1 1 none
|
pair_coeff 1 1 none
|
||||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
pair_coeff * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||||
# bond and angle
|
# bond and angle
|
||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
bond_coeff 1 0.0 0.9572
|
bond_coeff 1 0.0 0.9572
|
||||||
angle_style harmonic
|
angle_style harmonic
|
||||||
angle_coeff 1 0.0 104.52
|
angle_coeff 1 0.0 104.52
|
||||||
# define kspace calculation
|
# define kspace calculation
|
||||||
kspace_style pppm/tip4p 1E-5
|
kspace_style pppm/tip4p 1E-5
|
||||||
# Neighbor update settings
|
# Neighbor update settings
|
||||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
|||||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||||
####################################################################
|
####################################################################
|
||||||
# Calculate pair energy
|
# Calculate pair energy
|
||||||
compute 1 all pair lj/cut/tip4p/long
|
compute 1 all pair lj/cut/tip4p/long
|
||||||
compute 2 all pair aip/water/2dm
|
compute 2 all pair aip/water/2dm
|
||||||
compute wt water temp
|
compute wt water temp
|
||||||
variable TIP4P equal c_1
|
variable TIP4P equal c_1
|
||||||
variable EILP equal c_2 # total interlayer energy
|
variable EILP equal c_2 # total interlayer energy
|
||||||
variable temp_wt equal c_wt
|
variable temp_wt equal c_wt
|
||||||
############# Output ##############
|
############# Output ##############
|
||||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||||
thermo 100
|
thermo 100
|
||||||
thermo_modify lost error
|
thermo_modify lost error
|
||||||
|
|
||||||
fix subf gr setforce 0.0 0.0 0.0
|
fix subf gr setforce 0.0 0.0 0.0
|
||||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||||
|
|
||||||
timestep 1e-3
|
timestep 1e-3
|
||||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||||
fix 2 water nve
|
fix 2 water nve
|
||||||
run 1000
|
run 1000
|
||||||
|
|||||||
@ -4,26 +4,26 @@ boundary p p p
|
|||||||
atom_style full
|
atom_style full
|
||||||
processors * * 1 # domain decomposition over x and y
|
processors * * 1 # domain decomposition over x and y
|
||||||
read_data ./gra_water.data
|
read_data ./gra_water.data
|
||||||
mass 1 12.0107 # carbon mass (g/mole)
|
mass 1 12.0107 # carbon mass (g/mole)
|
||||||
mass 2 15.9994 # oxygen mass (g/mole)
|
mass 2 15.9994 # oxygen mass (g/mole)
|
||||||
mass 3 1.008 # hydrogen mass (g/mole)
|
mass 3 1.008 # hydrogen mass (g/mole)
|
||||||
# Separate atom groups
|
# Separate atom groups
|
||||||
group gr molecule 1
|
group gr molecule 1
|
||||||
group water molecule 2
|
group water molecule 2
|
||||||
######################## Potential defition ##############################
|
######################## Potential defition ##############################
|
||||||
# Interlayer potential
|
# Interlayer potential
|
||||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||||
####################################################################
|
####################################################################
|
||||||
pair_coeff 1 1 none
|
pair_coeff 1 1 none
|
||||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
pair_coeff * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||||
# bond and angle
|
# bond and angle
|
||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
bond_coeff 1 0.0 0.9572
|
bond_coeff 1 0.0 0.9572
|
||||||
angle_style harmonic
|
angle_style harmonic
|
||||||
angle_coeff 1 0.0 104.52
|
angle_coeff 1 0.0 104.52
|
||||||
# define kspace calculation
|
# define kspace calculation
|
||||||
kspace_style pppm/tip4p 1E-5
|
kspace_style pppm/tip4p 1E-5
|
||||||
# Neighbor update settings
|
# Neighbor update settings
|
||||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
|||||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||||
####################################################################
|
####################################################################
|
||||||
# Calculate pair energy
|
# Calculate pair energy
|
||||||
compute 1 all pair lj/cut/tip4p/long
|
compute 1 all pair lj/cut/tip4p/long
|
||||||
compute 2 all pair aip/water/2dm/opt
|
compute 2 all pair aip/water/2dm/opt
|
||||||
compute wt water temp
|
compute wt water temp
|
||||||
variable TIP4P equal c_1
|
variable TIP4P equal c_1
|
||||||
variable EILP equal c_2 # total interlayer energy
|
variable EILP equal c_2 # total interlayer energy
|
||||||
variable temp_wt equal c_wt
|
variable temp_wt equal c_wt
|
||||||
############# Output ##############
|
############# Output ##############
|
||||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||||
thermo 100
|
thermo 100
|
||||||
thermo_modify lost error
|
thermo_modify lost error
|
||||||
|
|
||||||
fix subf gr setforce 0.0 0.0 0.0
|
fix subf gr setforce 0.0 0.0 0.0
|
||||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||||
|
|
||||||
timestep 1e-3
|
timestep 1e-3
|
||||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||||
fix 2 water nve
|
fix 2 water nve
|
||||||
run 1000
|
run 1000
|
||||||
|
|||||||
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../potentials/Fe_mm.eam.fs
|
||||||
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../potentials/Cu_mishin1.eam.alloy
|
||||||
@ -5,7 +5,7 @@ LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000
|
|||||||
|
|
||||||
9.95143358025075 331.8139610404791 xlo xhi
|
9.95143358025075 331.8139610404791 xlo xhi
|
||||||
9.95143358025075 331.8139610404791 ylo yhi
|
9.95143358025075 331.8139610404791 ylo yhi
|
||||||
0 1 zlo zhi
|
-0.5 0.5 zlo zhi
|
||||||
0 0 0 xy xz yz
|
0 0 0 xy xz yz
|
||||||
|
|
||||||
Atoms # sphere
|
Atoms # sphere
|
||||||
|
|||||||
@ -1,6 +1,12 @@
|
|||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
# part 3: continuing from restart file
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.molecular-mix
|
||||||
|
write_restart molecular-mix.restart
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
molecule cychex cyclohexane.mol
|
molecule cychex cyclohexane.mol
|
||||||
read_restart molecular-mix.restart
|
read_restart molecular-mix.restart
|
||||||
|
|
||||||
@ -9,3 +15,6 @@ thermo 100
|
|||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
run 2000
|
run 2000
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm molecular-mix.restart
|
||||||
|
|||||||
@ -1,6 +1,12 @@
|
|||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
# part 3: continuing from restart file
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.template-mix
|
||||||
|
write_restart template-mix.restart
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
molecule cychex cyclohexane.mol
|
molecule cychex cyclohexane.mol
|
||||||
read_restart template-mix.restart
|
read_restart template-mix.restart
|
||||||
|
|
||||||
@ -9,3 +15,6 @@ thermo 100
|
|||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
run 2000
|
run 2000
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm template-mix.restart
|
||||||
|
|||||||
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
@ -0,0 +1,302 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.molecular-mix
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
atom_style molecular
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style harmonic
|
||||||
|
|
||||||
|
lattice sc 6.0
|
||||||
|
Lattice spacing in x,y,z = 6 6 6
|
||||||
|
variable boxlen index 4.0
|
||||||
|
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||||
|
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
create_atoms 0 box mol cychex 734594
|
||||||
|
Created 3072 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.004 seconds
|
||||||
|
create_atoms 2 random 800 495437 box
|
||||||
|
Created 800 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 14.027
|
||||||
|
mass 2 16.043
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.1180 3.905
|
||||||
|
pair_coeff 2 2 0.2940 3.730
|
||||||
|
|
||||||
|
bond_coeff 1 260.00 1.5260
|
||||||
|
angle_coeff 1 63.0 112.40
|
||||||
|
dihedral_coeff 1 2.0 1 3
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
minimize 0.001 0.001 500 1000
|
||||||
|
Generated 1 of 1 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 = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||||
|
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||||
|
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
|
||||||
|
Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms
|
||||||
|
|
||||||
|
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
43897850768892.8 -5729.17409504969 -5734.20694761353
|
||||||
|
Force two-norm initial, final = 1.1080994e+15 72.745546
|
||||||
|
Force max component initial, final = 4.6607099e+14 17.390179
|
||||||
|
Final line search alpha, max atom move = 0.0041638487 0.072410076
|
||||||
|
Iterations, force evaluations = 190 297
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19
|
||||||
|
Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75
|
||||||
|
Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22
|
||||||
|
Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47
|
||||||
|
Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.03504 | | | 1.37
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 12122 ave 12122 max 12122 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 774375 ave 774375 max 774375 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 774375
|
||||||
|
Ave neighs/atom = 199.99354
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 14
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
velocity all create 100.0 6234235
|
||||||
|
fix 1 all nvt temp 100.0 300.0 1.0
|
||||||
|
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||||
|
run 2500
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 100 -6191.8196 457.61266 -4580.3354 4842.371
|
||||||
|
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
|
||||||
|
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
|
||||||
|
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
|
||||||
|
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
|
||||||
|
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
|
||||||
|
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
|
||||||
|
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
|
||||||
|
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
|
||||||
|
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
|
||||||
|
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
|
||||||
|
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
|
||||||
|
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
|
||||||
|
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
|
||||||
|
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
|
||||||
|
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
|
||||||
|
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
|
||||||
|
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
|
||||||
|
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
|
||||||
|
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
|
||||||
|
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
|
||||||
|
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
|
||||||
|
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
|
||||||
|
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
|
||||||
|
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
|
||||||
|
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||||
|
Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s
|
||||||
|
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 15.936 | 15.936 | 15.936 | 0.0 | 92.46
|
||||||
|
Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27
|
||||||
|
Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97
|
||||||
|
Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57
|
||||||
|
Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00
|
||||||
|
Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59
|
||||||
|
Other | | 0.02248 | | | 0.13
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11821 ave 11821 max 11821 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 770416 ave 770416 max 770416 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 770416
|
||||||
|
Ave neighs/atom = 198.97107
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_data molecular-mix.data
|
||||||
|
#write_restart molecular-mix.restart
|
||||||
|
write_restart molecular-mix.restart
|
||||||
|
System init for write_restart ...
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
read_restart molecular-mix.restart
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||||
|
restoring atom style molecular from restart
|
||||||
|
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
restoring pair style lj/cut from restart
|
||||||
|
restoring bond style harmonic from restart
|
||||||
|
restoring angle style harmonic from restart
|
||||||
|
restoring dihedral style harmonic from restart
|
||||||
|
3872 atoms
|
||||||
|
3072 bonds
|
||||||
|
3072 angles
|
||||||
|
3072 dihedrals
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.001 seconds
|
||||||
|
read_restart CPU = 0.003 seconds
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
|
run 2000
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||||
|
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
|
||||||
|
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
|
||||||
|
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
|
||||||
|
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
|
||||||
|
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
|
||||||
|
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
|
||||||
|
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
|
||||||
|
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
|
||||||
|
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
|
||||||
|
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
|
||||||
|
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
|
||||||
|
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
|
||||||
|
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
|
||||||
|
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
|
||||||
|
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
|
||||||
|
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
|
||||||
|
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
|
||||||
|
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
|
||||||
|
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
|
||||||
|
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
|
||||||
|
Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 12.191 | 12.191 | 12.191 | 0.0 | 91.74
|
||||||
|
Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18
|
||||||
|
Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83
|
||||||
|
Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55
|
||||||
|
Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00
|
||||||
|
Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59
|
||||||
|
Other | | 0.01451 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11685 ave 11685 max 11685 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 770346 ave 770346 max 770346 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 770346
|
||||||
|
Ave neighs/atom = 198.953
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm molecular-mix.restart
|
||||||
|
Total wall time: 0:00:33
|
||||||
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
@ -0,0 +1,303 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.molecular-mix
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
atom_style molecular
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style harmonic
|
||||||
|
|
||||||
|
lattice sc 6.0
|
||||||
|
Lattice spacing in x,y,z = 6 6 6
|
||||||
|
variable boxlen index 4.0
|
||||||
|
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||||
|
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
|
||||||
|
create_atoms 0 box mol cychex 734594
|
||||||
|
Created 3072 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
create_atoms 2 random 800 495437 box
|
||||||
|
Created 800 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 14.027
|
||||||
|
mass 2 16.043
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.1180 3.905
|
||||||
|
pair_coeff 2 2 0.2940 3.730
|
||||||
|
|
||||||
|
bond_coeff 1 260.00 1.5260
|
||||||
|
angle_coeff 1 63.0 112.40
|
||||||
|
dihedral_coeff 1 2.0 1 3
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
minimize 0.001 0.001 500 1000
|
||||||
|
Generated 1 of 1 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 = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||||
|
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||||
|
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||||
|
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
|
||||||
|
Loop time of 0.719327 on 4 procs for 204 steps with 3872 atoms
|
||||||
|
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
|
||||||
|
Force two-norm initial, final = 8.7430661e+18 74.636836
|
||||||
|
Force max component initial, final = 4.1468626e+18 8.680078
|
||||||
|
Final line search alpha, max atom move = 0.0032186724 0.027938327
|
||||||
|
Iterations, force evaluations = 204 328
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.60273 | 0.60882 | 0.61181 | 0.5 | 84.64
|
||||||
|
Bond | 0.018965 | 0.019154 | 0.019363 | 0.1 | 2.66
|
||||||
|
Neigh | 0.054004 | 0.054008 | 0.054012 | 0.0 | 7.51
|
||||||
|
Comm | 0.022945 | 0.026108 | 0.032071 | 2.2 | 3.63
|
||||||
|
Output | 3.4085e-05 | 3.6968e-05 | 4.5055e-05 | 0.0 | 0.01
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0112 | | | 1.56
|
||||||
|
|
||||||
|
Nlocal: 968 ave 980 max 954 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 6630 ave 6644 max 6616 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 193550 ave 195957 max 191376 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 774200
|
||||||
|
Ave neighs/atom = 199.94835
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 14
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
velocity all create 100.0 6234235
|
||||||
|
fix 1 all nvt temp 100.0 300.0 1.0
|
||||||
|
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||||
|
run 2500
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
|
||||||
|
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
|
||||||
|
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
|
||||||
|
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
|
||||||
|
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
|
||||||
|
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
|
||||||
|
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
|
||||||
|
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
|
||||||
|
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
|
||||||
|
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
|
||||||
|
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
|
||||||
|
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
|
||||||
|
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
|
||||||
|
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
|
||||||
|
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
|
||||||
|
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
|
||||||
|
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
|
||||||
|
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
|
||||||
|
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
|
||||||
|
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
|
||||||
|
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
|
||||||
|
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
|
||||||
|
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
|
||||||
|
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
|
||||||
|
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
|
||||||
|
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||||
|
Loop time of 4.32954 on 4 procs for 2500 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 49.890 ns/day, 0.481 hours/ns, 577.429 timesteps/s, 2.236 Matom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.8113 | 3.8529 | 3.8893 | 1.7 | 88.99
|
||||||
|
Bond | 0.13153 | 0.13433 | 0.13718 | 0.7 | 3.10
|
||||||
|
Neigh | 0.13036 | 0.13039 | 0.13042 | 0.0 | 3.01
|
||||||
|
Comm | 0.13688 | 0.1751 | 0.21857 | 8.4 | 4.04
|
||||||
|
Output | 0.00032606 | 0.00035873 | 0.00045009 | 0.0 | 0.01
|
||||||
|
Modify | 0.027754 | 0.028116 | 0.028735 | 0.2 | 0.65
|
||||||
|
Other | | 0.008382 | | | 0.19
|
||||||
|
|
||||||
|
Nlocal: 968 ave 986 max 944 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||||
|
Nghost: 6379.75 ave 6407 max 6352 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 192584 ave 196718 max 188693 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 770338
|
||||||
|
Ave neighs/atom = 198.95093
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_data molecular-mix.data
|
||||||
|
#write_restart molecular-mix.restart
|
||||||
|
write_restart molecular-mix.restart
|
||||||
|
System init for write_restart ...
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
read_restart molecular-mix.restart
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||||
|
restoring atom style molecular from restart
|
||||||
|
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
restoring pair style lj/cut from restart
|
||||||
|
restoring bond style harmonic from restart
|
||||||
|
restoring angle style harmonic from restart
|
||||||
|
restoring dihedral style harmonic from restart
|
||||||
|
3872 atoms
|
||||||
|
3072 bonds
|
||||||
|
3072 angles
|
||||||
|
3072 dihedrals
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_restart CPU = 0.004 seconds
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
|
run 2000
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.475 | 8.571 | 8.857 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||||
|
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
|
||||||
|
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
|
||||||
|
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
|
||||||
|
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
|
||||||
|
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
|
||||||
|
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
|
||||||
|
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
|
||||||
|
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
|
||||||
|
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
|
||||||
|
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
|
||||||
|
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
|
||||||
|
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
|
||||||
|
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
|
||||||
|
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
|
||||||
|
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
|
||||||
|
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
|
||||||
|
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
|
||||||
|
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
|
||||||
|
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
|
||||||
|
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
|
||||||
|
Loop time of 3.58588 on 4 procs for 2000 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 48.189 ns/day, 0.498 hours/ns, 557.743 timesteps/s, 2.160 Matom-step/s
|
||||||
|
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.0873 | 3.1383 | 3.2136 | 2.7 | 87.52
|
||||||
|
Bond | 0.10381 | 0.10769 | 0.11168 | 0.9 | 3.00
|
||||||
|
Neigh | 0.13651 | 0.13652 | 0.13654 | 0.0 | 3.81
|
||||||
|
Comm | 0.094882 | 0.1741 | 0.22894 | 12.3 | 4.86
|
||||||
|
Output | 0.00024683 | 0.00028387 | 0.00038642 | 0.0 | 0.01
|
||||||
|
Modify | 0.021974 | 0.022331 | 0.022623 | 0.2 | 0.62
|
||||||
|
Other | | 0.006685 | | | 0.19
|
||||||
|
|
||||||
|
Nlocal: 968 ave 984 max 948 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Nghost: 6349.5 ave 6370 max 6330 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 192457 ave 196654 max 187154 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 769828
|
||||||
|
Ave neighs/atom = 198.81921
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 35
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm molecular-mix.restart
|
||||||
|
Total wall time: 0:00:08
|
||||||
295
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
295
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
@ -0,0 +1,295 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.template-mix
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 1: creating system with create_atoms
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
atom_style template cychex
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style harmonic
|
||||||
|
|
||||||
|
lattice sc 6.0
|
||||||
|
Lattice spacing in x,y,z = 6 6 6
|
||||||
|
variable boxlen index 4.0
|
||||||
|
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||||
|
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
create_atoms 0 box mol cychex 734594
|
||||||
|
Created 3072 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 2 random 800 495437 box
|
||||||
|
Created 800 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 14.027
|
||||||
|
mass 2 16.043
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.1180 3.905
|
||||||
|
pair_coeff 2 2 0.2940 3.730
|
||||||
|
|
||||||
|
bond_coeff 1 260.00 1.5260
|
||||||
|
angle_coeff 1 63.0 112.40
|
||||||
|
dihedral_coeff 1 2.0 1 3
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
minimize 0.001 0.001 500 1000
|
||||||
|
Generated 1 of 1 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 = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.05 | 8.05 | 8.05 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||||
|
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||||
|
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
|
||||||
|
Loop time of 2.46574 on 1 procs for 190 steps with 3872 atoms
|
||||||
|
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
43897850768892.8 -5729.17409504969 -5734.20694761353
|
||||||
|
Force two-norm initial, final = 1.1080994e+15 72.745546
|
||||||
|
Force max component initial, final = 4.6607099e+14 17.390179
|
||||||
|
Final line search alpha, max atom move = 0.0041638487 0.072410076
|
||||||
|
Iterations, force evaluations = 190 297
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.1376 | 2.1376 | 2.1376 | 0.0 | 86.69
|
||||||
|
Bond | 0.068456 | 0.068456 | 0.068456 | 0.0 | 2.78
|
||||||
|
Neigh | 0.21212 | 0.21212 | 0.21212 | 0.0 | 8.60
|
||||||
|
Comm | 0.012436 | 0.012436 | 0.012436 | 0.0 | 0.50
|
||||||
|
Output | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.03511 | | | 1.42
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 12122 ave 12122 max 12122 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 774375 ave 774375 max 774375 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 774375
|
||||||
|
Ave neighs/atom = 199.99354
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 14
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
velocity all create 100.0 6234235
|
||||||
|
fix 1 all nvt temp 100.0 300.0 1.0
|
||||||
|
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||||
|
run 2500
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 100 -6191.8196 457.61266 -4580.3354 4842.371
|
||||||
|
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
|
||||||
|
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
|
||||||
|
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
|
||||||
|
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
|
||||||
|
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
|
||||||
|
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
|
||||||
|
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
|
||||||
|
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
|
||||||
|
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
|
||||||
|
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
|
||||||
|
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
|
||||||
|
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
|
||||||
|
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
|
||||||
|
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
|
||||||
|
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
|
||||||
|
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
|
||||||
|
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
|
||||||
|
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
|
||||||
|
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
|
||||||
|
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
|
||||||
|
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
|
||||||
|
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
|
||||||
|
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
|
||||||
|
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
|
||||||
|
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||||
|
Loop time of 16.1773 on 1 procs for 2500 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 14.927 | 14.927 | 14.927 | 0.0 | 92.27
|
||||||
|
Bond | 0.52161 | 0.52161 | 0.52161 | 0.0 | 3.22
|
||||||
|
Neigh | 0.52299 | 0.52299 | 0.52299 | 0.0 | 3.23
|
||||||
|
Comm | 0.090871 | 0.090871 | 0.090871 | 0.0 | 0.56
|
||||||
|
Output | 0.00059782 | 0.00059782 | 0.00059782 | 0.0 | 0.00
|
||||||
|
Modify | 0.096104 | 0.096104 | 0.096104 | 0.0 | 0.59
|
||||||
|
Other | | 0.01791 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11821 ave 11821 max 11821 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 770416 ave 770416 max 770416 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 770416
|
||||||
|
Ave neighs/atom = 198.97107
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_data template-mix.data
|
||||||
|
#write_restart template-mix.restart
|
||||||
|
write_restart template-mix.restart
|
||||||
|
System init for write_restart ...
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
read_restart template-mix.restart
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||||
|
restoring atom style template from restart
|
||||||
|
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
restoring pair style lj/cut from restart
|
||||||
|
restoring bond style harmonic from restart
|
||||||
|
restoring angle style harmonic from restart
|
||||||
|
restoring dihedral style harmonic from restart
|
||||||
|
3872 atoms
|
||||||
|
3072 template bonds
|
||||||
|
3072 template angles
|
||||||
|
3072 template dihedrals
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
|
run 2000
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||||
|
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
|
||||||
|
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
|
||||||
|
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
|
||||||
|
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
|
||||||
|
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
|
||||||
|
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
|
||||||
|
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
|
||||||
|
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
|
||||||
|
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
|
||||||
|
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
|
||||||
|
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
|
||||||
|
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
|
||||||
|
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
|
||||||
|
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
|
||||||
|
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
|
||||||
|
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
|
||||||
|
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
|
||||||
|
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
|
||||||
|
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
|
||||||
|
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
|
||||||
|
Loop time of 13.2399 on 1 procs for 2000 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 12.13 | 12.13 | 12.13 | 0.0 | 91.61
|
||||||
|
Bond | 0.42044 | 0.42044 | 0.42044 | 0.0 | 3.18
|
||||||
|
Neigh | 0.52469 | 0.52469 | 0.52469 | 0.0 | 3.96
|
||||||
|
Comm | 0.072857 | 0.072857 | 0.072857 | 0.0 | 0.55
|
||||||
|
Output | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.00
|
||||||
|
Modify | 0.076918 | 0.076918 | 0.076918 | 0.0 | 0.58
|
||||||
|
Other | | 0.0148 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 3872 ave 3872 max 3872 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11685 ave 11685 max 11685 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 770346 ave 770346 max 770346 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 770346
|
||||||
|
Ave neighs/atom = 198.953
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm template-mix.restart
|
||||||
|
Total wall time: 0:00:31
|
||||||
296
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
296
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
@ -0,0 +1,296 @@
|
|||||||
|
LAMMPS (27 Jun 2024)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 3: continuing from restart file
|
||||||
|
|
||||||
|
# run the first part and write out restart
|
||||||
|
include in.template-mix
|
||||||
|
# demo for atom style template simulating a cyclohexane methane mixture
|
||||||
|
# part 1: creating system with create_atoms
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
atom_style template cychex
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style harmonic
|
||||||
|
|
||||||
|
lattice sc 6.0
|
||||||
|
Lattice spacing in x,y,z = 6 6 6
|
||||||
|
variable boxlen index 4.0
|
||||||
|
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||||
|
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||||
|
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
|
||||||
|
create_atoms 0 box mol cychex 734594
|
||||||
|
Created 3072 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
create_atoms 2 random 800 495437 box
|
||||||
|
Created 800 atoms
|
||||||
|
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 14.027
|
||||||
|
mass 2 16.043
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.1180 3.905
|
||||||
|
pair_coeff 2 2 0.2940 3.730
|
||||||
|
|
||||||
|
bond_coeff 1 260.00 1.5260
|
||||||
|
angle_coeff 1 63.0 112.40
|
||||||
|
dihedral_coeff 1 2.0 1 3
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
minimize 0.001 0.001 500 1000
|
||||||
|
Generated 1 of 1 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 = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||||
|
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||||
|
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||||
|
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
|
||||||
|
Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms
|
||||||
|
|
||||||
|
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
|
||||||
|
Force two-norm initial, final = 8.7430661e+18 74.636836
|
||||||
|
Force max component initial, final = 4.1468626e+18 8.680078
|
||||||
|
Final line search alpha, max atom move = 0.0032186724 0.027938327
|
||||||
|
Iterations, force evaluations = 204 328
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.59281 | 0.6027 | 0.60956 | 0.8 | 83.77
|
||||||
|
Bond | 0.018776 | 0.020785 | 0.026388 | 2.2 | 2.89
|
||||||
|
Neigh | 0.054209 | 0.054242 | 0.054273 | 0.0 | 7.54
|
||||||
|
Comm | 0.018189 | 0.03064 | 0.042206 | 4.9 | 4.26
|
||||||
|
Output | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.01107 | | | 1.54
|
||||||
|
|
||||||
|
Nlocal: 968 ave 980 max 954 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 6630 ave 6644 max 6616 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 193550 ave 195957 max 191376 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 774200
|
||||||
|
Ave neighs/atom = 199.94835
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 14
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
velocity all create 100.0 6234235
|
||||||
|
fix 1 all nvt temp 100.0 300.0 1.0
|
||||||
|
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||||
|
run 2500
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
|
||||||
|
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
|
||||||
|
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
|
||||||
|
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
|
||||||
|
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
|
||||||
|
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
|
||||||
|
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
|
||||||
|
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
|
||||||
|
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
|
||||||
|
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
|
||||||
|
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
|
||||||
|
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
|
||||||
|
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
|
||||||
|
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
|
||||||
|
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
|
||||||
|
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
|
||||||
|
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
|
||||||
|
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
|
||||||
|
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
|
||||||
|
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
|
||||||
|
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
|
||||||
|
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
|
||||||
|
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
|
||||||
|
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
|
||||||
|
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
|
||||||
|
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||||
|
Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.7864 | 3.836 | 3.8948 | 2.2 | 88.64
|
||||||
|
Bond | 0.13058 | 0.13362 | 0.13735 | 0.8 | 3.09
|
||||||
|
Neigh | 0.13597 | 0.13601 | 0.13605 | 0.0 | 3.14
|
||||||
|
Comm | 0.12304 | 0.18542 | 0.23763 | 10.5 | 4.28
|
||||||
|
Output | 0.00033524 | 0.00036705 | 0.00045513 | 0.0 | 0.01
|
||||||
|
Modify | 0.027504 | 0.027917 | 0.028571 | 0.3 | 0.65
|
||||||
|
Other | | 0.008118 | | | 0.19
|
||||||
|
|
||||||
|
Nlocal: 968 ave 986 max 944 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||||
|
Nghost: 6379.75 ave 6407 max 6352 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 192584 ave 196718 max 188693 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 770338
|
||||||
|
Ave neighs/atom = 198.95093
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_data template-mix.data
|
||||||
|
#write_restart template-mix.restart
|
||||||
|
write_restart template-mix.restart
|
||||||
|
System init for write_restart ...
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
|
||||||
|
# now restart
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
molecule cychex cyclohexane.mol
|
||||||
|
Read molecule template cychex:
|
||||||
|
LAMMPS molecule file. Cyclohexane(UA)
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
6 atoms with max type 1
|
||||||
|
6 bonds with max type 1
|
||||||
|
6 angles with max type 1
|
||||||
|
6 dihedrals with max type 1
|
||||||
|
0 impropers with max type 0
|
||||||
|
read_restart template-mix.restart
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||||
|
restoring atom style template from restart
|
||||||
|
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
restoring pair style lj/cut from restart
|
||||||
|
restoring bond style harmonic from restart
|
||||||
|
restoring angle style harmonic from restart
|
||||||
|
restoring dihedral style harmonic from restart
|
||||||
|
3872 atoms
|
||||||
|
3072 template bonds
|
||||||
|
3072 template angles
|
||||||
|
3072 template dihedrals
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
fix 1 all nvt temp 300.0 300.0 1.0
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||||
|
run 2000
|
||||||
|
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, 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/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||||
|
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
|
||||||
|
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
|
||||||
|
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
|
||||||
|
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
|
||||||
|
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
|
||||||
|
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
|
||||||
|
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
|
||||||
|
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
|
||||||
|
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
|
||||||
|
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
|
||||||
|
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
|
||||||
|
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
|
||||||
|
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
|
||||||
|
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
|
||||||
|
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
|
||||||
|
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
|
||||||
|
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
|
||||||
|
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
|
||||||
|
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
|
||||||
|
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
|
||||||
|
Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms
|
||||||
|
|
||||||
|
Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-step/s
|
||||||
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.0514 | 3.1162 | 3.2058 | 3.3 | 87.05
|
||||||
|
Bond | 0.10377 | 0.10776 | 0.11194 | 1.0 | 3.01
|
||||||
|
Neigh | 0.14121 | 0.14125 | 0.1413 | 0.0 | 3.95
|
||||||
|
Comm | 0.092144 | 0.18542 | 0.25437 | 14.1 | 5.18
|
||||||
|
Output | 0.00025632 | 0.00028151 | 0.00035298 | 0.0 | 0.01
|
||||||
|
Modify | 0.02193 | 0.022227 | 0.022584 | 0.2 | 0.62
|
||||||
|
Other | | 0.006618 | | | 0.18
|
||||||
|
|
||||||
|
Nlocal: 968 ave 984 max 948 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Nghost: 6349.5 ave 6370 max 6330 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 192457 ave 196654 max 187154 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 769828
|
||||||
|
Ave neighs/atom = 198.81921
|
||||||
|
Ave special neighs/atom = 3.9669421
|
||||||
|
Neighbor list builds = 35
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# clean up
|
||||||
|
shell rm template-mix.restart
|
||||||
|
Total wall time: 0:00:08
|
||||||
@ -1,106 +0,0 @@
|
|||||||
LAMMPS (22 Oct 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
|
||||||
# part 3: continuing from restart file
|
|
||||||
|
|
||||||
molecule cychex cyclohexane.mol
|
|
||||||
Read molecule template cychex:
|
|
||||||
1 molecules
|
|
||||||
6 atoms with max type 1
|
|
||||||
6 bonds with max type 1
|
|
||||||
6 angles with max type 1
|
|
||||||
6 dihedrals with max type 1
|
|
||||||
0 impropers with max type 0
|
|
||||||
read_restart molecular-mix.restart
|
|
||||||
Reading restart file ...
|
|
||||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
|
||||||
restoring atom style molecular from restart
|
|
||||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
restoring pair style lj/cut from restart
|
|
||||||
restoring bond style harmonic from restart
|
|
||||||
restoring angle style harmonic from restart
|
|
||||||
restoring dihedral style harmonic from restart
|
|
||||||
3872 atoms
|
|
||||||
3072 bonds
|
|
||||||
3072 angles
|
|
||||||
3072 dihedrals
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.0 0.0 0.0
|
|
||||||
special bond factors coul: 0.0 0.0 0.0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
2 = max # of 1-3 neighbors
|
|
||||||
4 = max # of 1-4 neighbors
|
|
||||||
5 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.002 seconds
|
|
||||||
read_restart CPU = 0.008 seconds
|
|
||||||
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
|
||||||
run 2000
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7, 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/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 10.74 | 10.74 | 10.74 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
|
||||||
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
|
|
||||||
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
|
|
||||||
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
|
|
||||||
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
|
|
||||||
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
|
|
||||||
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
|
|
||||||
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
|
|
||||||
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
|
|
||||||
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
|
|
||||||
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
|
|
||||||
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
|
|
||||||
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
|
|
||||||
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
|
|
||||||
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
|
|
||||||
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
|
|
||||||
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
|
|
||||||
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
|
|
||||||
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
|
|
||||||
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
|
|
||||||
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
|
|
||||||
Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms
|
|
||||||
|
|
||||||
Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 timesteps/s
|
|
||||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 14.116 | 14.116 | 14.116 | 0.0 | 90.56
|
|
||||||
Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77
|
|
||||||
Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40
|
|
||||||
Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53
|
|
||||||
Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00
|
|
||||||
Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50
|
|
||||||
Other | | 0.03761 | | | 0.24
|
|
||||||
|
|
||||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11633.0 ave 11633 max 11633 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 770365.0 ave 770365 max 770365 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 770365
|
|
||||||
Ave neighs/atom = 198.95790
|
|
||||||
Ave special neighs/atom = 3.9669421
|
|
||||||
Neighbor list builds = 35
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:15
|
|
||||||
@ -1,107 +0,0 @@
|
|||||||
LAMMPS (22 Oct 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
|
||||||
# part 3: continuing from restart file
|
|
||||||
|
|
||||||
molecule cychex cyclohexane.mol
|
|
||||||
Read molecule template cychex:
|
|
||||||
1 molecules
|
|
||||||
6 atoms with max type 1
|
|
||||||
6 bonds with max type 1
|
|
||||||
6 angles with max type 1
|
|
||||||
6 dihedrals with max type 1
|
|
||||||
0 impropers with max type 0
|
|
||||||
read_restart molecular-mix.restart
|
|
||||||
Reading restart file ...
|
|
||||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
|
||||||
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697)
|
|
||||||
restoring atom style molecular from restart
|
|
||||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
restoring pair style lj/cut from restart
|
|
||||||
restoring bond style harmonic from restart
|
|
||||||
restoring angle style harmonic from restart
|
|
||||||
restoring dihedral style harmonic from restart
|
|
||||||
3872 atoms
|
|
||||||
3072 bonds
|
|
||||||
3072 angles
|
|
||||||
3072 dihedrals
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.0 0.0 0.0
|
|
||||||
special bond factors coul: 0.0 0.0 0.0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
2 = max # of 1-3 neighbors
|
|
||||||
4 = max # of 1-4 neighbors
|
|
||||||
5 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
read_restart CPU = 0.031 seconds
|
|
||||||
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
|
||||||
run 2000
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7, 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/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
|
||||||
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
|
|
||||||
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
|
|
||||||
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
|
|
||||||
400 302 -4951.4895 1664.5419 197.74463 10784.638
|
|
||||||
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
|
|
||||||
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
|
|
||||||
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
|
|
||||||
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
|
|
||||||
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
|
|
||||||
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
|
|
||||||
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
|
|
||||||
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
|
|
||||||
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
|
|
||||||
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
|
|
||||||
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
|
|
||||||
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
|
|
||||||
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
|
|
||||||
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
|
|
||||||
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
|
|
||||||
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
|
|
||||||
Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms
|
|
||||||
|
|
||||||
Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s
|
|
||||||
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43
|
|
||||||
Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92
|
|
||||||
Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49
|
|
||||||
Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71
|
|
||||||
Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02
|
|
||||||
Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64
|
|
||||||
Other | | 0.145 | | | 2.78
|
|
||||||
|
|
||||||
Nlocal: 968.000 ave 979 max 948 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
|
||||||
Nghost: 6321.25 ave 6336 max 6309 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
||||||
Neighs: 192540.0 ave 195406 max 187182 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 770161
|
|
||||||
Ave neighs/atom = 198.90522
|
|
||||||
Ave special neighs/atom = 3.9669421
|
|
||||||
Neighbor list builds = 35
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:05
|
|
||||||
@ -1,102 +0,0 @@
|
|||||||
LAMMPS (22 Oct 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
|
||||||
# part 3: continuing from restart file
|
|
||||||
|
|
||||||
molecule cychex cyclohexane.mol
|
|
||||||
Read molecule template cychex:
|
|
||||||
1 molecules
|
|
||||||
6 atoms with max type 1
|
|
||||||
6 bonds with max type 1
|
|
||||||
6 angles with max type 1
|
|
||||||
6 dihedrals with max type 1
|
|
||||||
0 impropers with max type 0
|
|
||||||
read_restart template-mix.restart
|
|
||||||
Reading restart file ...
|
|
||||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
|
||||||
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
|
|
||||||
restoring atom style template from restart
|
|
||||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
restoring pair style lj/cut from restart
|
|
||||||
restoring bond style harmonic from restart
|
|
||||||
restoring angle style harmonic from restart
|
|
||||||
restoring dihedral style harmonic from restart
|
|
||||||
3872 atoms
|
|
||||||
3072 template bonds
|
|
||||||
3072 template angles
|
|
||||||
3072 template dihedrals
|
|
||||||
read_restart CPU = 0.002 seconds
|
|
||||||
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
|
||||||
run 2000
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7, 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/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
|
||||||
2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
|
|
||||||
2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
|
|
||||||
2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
|
|
||||||
2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
|
|
||||||
3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
|
|
||||||
3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
|
|
||||||
3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
|
|
||||||
3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
|
|
||||||
3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
|
|
||||||
3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
|
|
||||||
3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
|
|
||||||
3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
|
|
||||||
3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
|
|
||||||
3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
|
|
||||||
4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
|
|
||||||
4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
|
|
||||||
4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
|
|
||||||
4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
|
|
||||||
4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
|
|
||||||
4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
|
|
||||||
Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
|
|
||||||
|
|
||||||
Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/s
|
|
||||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
|
|
||||||
Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
|
|
||||||
Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
|
|
||||||
Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
|
|
||||||
Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
|
|
||||||
Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
|
|
||||||
Other | | 0.03687 | | | 0.24
|
|
||||||
|
|
||||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11670.0 ave 11670 max 11670 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 770032.0 ave 770032 max 770032 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 770032
|
|
||||||
Ave neighs/atom = 198.87190
|
|
||||||
Ave special neighs/atom = 3.9669421
|
|
||||||
Neighbor list builds = 35
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:15
|
|
||||||
@ -1,101 +0,0 @@
|
|||||||
LAMMPS (22 Oct 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# demo for atom style template simulating a cyclohexane methane mixture
|
|
||||||
# part 3: continuing from restart file
|
|
||||||
|
|
||||||
molecule cychex cyclohexane.mol
|
|
||||||
Read molecule template cychex:
|
|
||||||
1 molecules
|
|
||||||
6 atoms with max type 1
|
|
||||||
6 bonds with max type 1
|
|
||||||
6 angles with max type 1
|
|
||||||
6 dihedrals with max type 1
|
|
||||||
0 impropers with max type 0
|
|
||||||
read_restart template-mix.restart
|
|
||||||
Reading restart file ...
|
|
||||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
|
||||||
restoring atom style template from restart
|
|
||||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
restoring pair style lj/cut from restart
|
|
||||||
restoring bond style harmonic from restart
|
|
||||||
restoring angle style harmonic from restart
|
|
||||||
restoring dihedral style harmonic from restart
|
|
||||||
3872 atoms
|
|
||||||
3072 template bonds
|
|
||||||
3072 template angles
|
|
||||||
3072 template dihedrals
|
|
||||||
read_restart CPU = 0.006 seconds
|
|
||||||
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
fix 1 all nvt temp 300.0 300.0 1.0
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
|
||||||
run 2000
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7, 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/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
|
||||||
2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
|
|
||||||
2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
|
|
||||||
2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
|
|
||||||
2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
|
|
||||||
3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
|
|
||||||
3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
|
|
||||||
3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
|
|
||||||
3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
|
|
||||||
3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
|
|
||||||
3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
|
|
||||||
3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
|
|
||||||
3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
|
|
||||||
3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
|
|
||||||
3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
|
|
||||||
4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
|
|
||||||
4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
|
|
||||||
4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
|
|
||||||
4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
|
|
||||||
4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
|
|
||||||
4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
|
|
||||||
Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
|
|
||||||
|
|
||||||
Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s
|
|
||||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
|
|
||||||
Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
|
|
||||||
Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
|
|
||||||
Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
|
|
||||||
Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
|
|
||||||
Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
|
|
||||||
Other | | 0.01937 | | | 0.44
|
|
||||||
|
|
||||||
Nlocal: 968.000 ave 977 max 956 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
||||||
Nghost: 6322.75 ave 6345 max 6308 min
|
|
||||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
|
||||||
Neighs: 192555.0 ave 195249 max 188636 min
|
|
||||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
|
||||||
|
|
||||||
Total # of neighbors = 770221
|
|
||||||
Ave neighs/atom = 198.92071
|
|
||||||
Ave special neighs/atom = 3.9669421
|
|
||||||
Neighbor list builds = 34
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:04
|
|
||||||
@ -196,6 +196,7 @@ MODULE LIBLAMMPS
|
|||||||
PROCEDURE, NOPASS :: config_has_jpeg_support => lmp_config_has_jpeg_support
|
PROCEDURE, NOPASS :: config_has_jpeg_support => lmp_config_has_jpeg_support
|
||||||
PROCEDURE, NOPASS :: config_has_ffmpeg_support &
|
PROCEDURE, NOPASS :: config_has_ffmpeg_support &
|
||||||
=> lmp_config_has_ffmpeg_support
|
=> lmp_config_has_ffmpeg_support
|
||||||
|
PROCEDURE, NOPASS :: config_has_curl_support => lmp_config_has_curl_support
|
||||||
PROCEDURE, NOPASS :: config_has_exceptions => lmp_config_has_exceptions
|
PROCEDURE, NOPASS :: config_has_exceptions => lmp_config_has_exceptions
|
||||||
PROCEDURE, NOPASS :: config_has_package => lmp_config_has_package
|
PROCEDURE, NOPASS :: config_has_package => lmp_config_has_package
|
||||||
PROCEDURE, NOPASS :: config_package_count => lammps_config_package_count
|
PROCEDURE, NOPASS :: config_package_count => lammps_config_package_count
|
||||||
@ -793,6 +794,12 @@ MODULE LIBLAMMPS
|
|||||||
INTEGER(c_int) :: lammps_config_has_ffmpeg_support
|
INTEGER(c_int) :: lammps_config_has_ffmpeg_support
|
||||||
END FUNCTION lammps_config_has_ffmpeg_support
|
END FUNCTION lammps_config_has_ffmpeg_support
|
||||||
|
|
||||||
|
FUNCTION lammps_config_has_curl_support() BIND(C)
|
||||||
|
IMPORT :: c_int
|
||||||
|
IMPLICIT NONE
|
||||||
|
INTEGER(c_int) :: lammps_config_has_curl_support
|
||||||
|
END FUNCTION lammps_config_has_curl_support
|
||||||
|
|
||||||
FUNCTION lammps_config_has_exceptions() BIND(C)
|
FUNCTION lammps_config_has_exceptions() BIND(C)
|
||||||
IMPORT :: c_int
|
IMPORT :: c_int
|
||||||
IMPLICIT NONE
|
IMPLICIT NONE
|
||||||
@ -2881,6 +2888,14 @@ CONTAINS
|
|||||||
lmp_config_has_ffmpeg_support = (has_ffmpeg_support /= 0_c_int)
|
lmp_config_has_ffmpeg_support = (has_ffmpeg_support /= 0_c_int)
|
||||||
END FUNCTION lmp_config_has_ffmpeg_support
|
END FUNCTION lmp_config_has_ffmpeg_support
|
||||||
|
|
||||||
|
! equivalent function to lammps_config_has_curl_support
|
||||||
|
LOGICAL FUNCTION lmp_config_has_curl_support()
|
||||||
|
INTEGER(c_int) :: has_curl_support
|
||||||
|
|
||||||
|
has_curl_support = lammps_config_has_curl_support()
|
||||||
|
lmp_config_has_curl_support = (has_curl_support /= 0_c_int)
|
||||||
|
END FUNCTION lmp_config_has_curl_support
|
||||||
|
|
||||||
! equivalent function to lammps_config_has_exceptions
|
! equivalent function to lammps_config_has_exceptions
|
||||||
LOGICAL FUNCTION lmp_config_has_exceptions()
|
LOGICAL FUNCTION lmp_config_has_exceptions()
|
||||||
INTEGER(c_int) :: has_exceptions
|
INTEGER(c_int) :: has_exceptions
|
||||||
|
|||||||
@ -25,6 +25,7 @@ COLVARS_INCFLAGS = -DCOLVARS_LAMMPS $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_I
|
|||||||
COLVARS_SRCS = \
|
COLVARS_SRCS = \
|
||||||
colvaratoms.cpp \
|
colvaratoms.cpp \
|
||||||
colvarbias_abf.cpp \
|
colvarbias_abf.cpp \
|
||||||
|
colvarbias_abmd.cpp \
|
||||||
colvarbias_alb.cpp \
|
colvarbias_alb.cpp \
|
||||||
colvarbias.cpp \
|
colvarbias.cpp \
|
||||||
colvarbias_histogram.cpp \
|
colvarbias_histogram.cpp \
|
||||||
@ -59,6 +60,7 @@ COLVARS_SRCS = \
|
|||||||
colvarscript_commands.cpp \
|
colvarscript_commands.cpp \
|
||||||
colvarscript_commands_bias.cpp \
|
colvarscript_commands_bias.cpp \
|
||||||
colvarscript_commands_colvar.cpp \
|
colvarscript_commands_colvar.cpp \
|
||||||
|
colvars_memstream.cpp \
|
||||||
colvartypes.cpp \
|
colvartypes.cpp \
|
||||||
colvarvalue.cpp \
|
colvarvalue.cpp \
|
||||||
colvar_neuralnetworkcompute.cpp
|
colvar_neuralnetworkcompute.cpp
|
||||||
|
|||||||
@ -1,201 +1,230 @@
|
|||||||
|
|
||||||
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvardeps.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
|
||||||
|
colvartypes.h ../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
colvarproxy_volmaps.h colvarparse.h colvarparams.h colvaratoms.h \
|
colvarproxy_volmaps.h colvaratoms.h colvar_rotation_derivative.h
|
||||||
colvardeps.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
|
||||||
colvars_version.h colvar.h colvarvalue.h colvartypes.h colvarparse.h \
|
colvars_version.h colvar.h colvarvalue.h colvartypes.h \
|
||||||
colvarparams.h colvardeps.h colvarbias_abf.h colvarproxy.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvarbias_abf.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvarbias.h colvargrid.h colvar_UIestimator.h
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvargrid.h \
|
||||||
|
colvar_UIestimator.h colvars_memstream.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarbias_abmd.o: colvarbias_abmd.cpp \
|
||||||
|
colvarbias_abmd.h colvarbias_restraint.h colvarbias.h colvar.h \
|
||||||
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
|
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
|
colvarproxy_volmaps.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvar.h \
|
||||||
|
colvarvalue.h colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvarbias.h colvar.h colvarparse.h colvarparams.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarvalue.h colvarbias.h \
|
||||||
colvardeps.h colvargrid.h
|
colvar.h colvarparse.h colvarparams.h colvardeps.h colvargrid.h \
|
||||||
|
colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
|
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarvalue.h \
|
||||||
colvarbias_histogram.h colvarbias.h colvargrid.h
|
colvarparse.h colvarparams.h colvardeps.h colvarbias_histogram.h \
|
||||||
|
colvarbias.h colvargrid.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_histogram_reweight_amd.o: \
|
$(COLVARS_OBJ_DIR)colvarbias_histogram_reweight_amd.o: \
|
||||||
colvarbias_histogram_reweight_amd.cpp \
|
colvarbias_histogram_reweight_amd.cpp \
|
||||||
colvarbias_histogram_reweight_amd.h colvarbias_histogram.h colvarbias.h \
|
colvarbias_histogram_reweight_amd.h colvarbias_histogram.h colvarbias.h \
|
||||||
colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvardeps.h colvargrid.h colvarproxy.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvargrid.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarvalue.h \
|
||||||
colvarbias_meta.h colvarbias.h colvargrid.h
|
colvarparse.h colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h \
|
||||||
|
colvargrid.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
|
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvarbias_restraint.h colvarbias.h colvar.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarvalue.h \
|
||||||
colvarparse.h colvarparams.h colvardeps.h
|
colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
|
||||||
|
colvarparams.h colvardeps.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \
|
$(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvar_geometricpath.h
|
colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
|
$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
|
||||||
colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
|
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
|
||||||
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
|
|
||||||
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
|
|
||||||
colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
|
|
||||||
colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \
|
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
|
||||||
colvarproxy_volmaps.h colvardeps.h colvar.h colvarcomp.h \
|
|
||||||
colvar_arithmeticpath.h colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
|
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
|
|
||||||
colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
|
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
|
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
|
||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
|
||||||
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
|
|
||||||
colvar_geometricpath.h
|
colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarvalue.h \
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
colvarmodule.h colvars_version.h colvartypes.h \
|
||||||
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \
|
|
||||||
colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \
|
|
||||||
colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
|
|
||||||
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvar_arithmeticpath.h colvar_geometricpath.h \
|
colvar_geometricpath.h colvar_arithmeticpath.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
|
||||||
|
colvarmodule.h colvars_version.h colvaratoms.h colvarproxy.h \
|
||||||
|
colvartypes.h ../../src/math_eigen_impl.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvarparse.h colvarvalue.h colvarparams.h colvardeps.h colvar.h \
|
||||||
|
colvarcomp.h colvar_geometricpath.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
|
||||||
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvar_geometricpath.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
|
||||||
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvar_geometricpath.h colvar_rotation_derivative.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
|
||||||
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvar_geometricpath.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \
|
||||||
|
colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \
|
||||||
|
colvarvalue.h colvartypes.h ../../src/math_eigen_impl.h colvar.h \
|
||||||
|
colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
|
||||||
|
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
|
colvarproxy_volmaps.h colvar_geometricpath.h \
|
||||||
colvar_neuralnetworkcompute.h
|
colvar_neuralnetworkcompute.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \
|
$(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \
|
||||||
colvarcomp.h colvarmodule.h colvars_version.h colvar.h colvarvalue.h \
|
colvarcomp.h colvarmodule.h colvars_version.h colvaratoms.h \
|
||||||
colvartypes.h colvarparse.h colvarparams.h colvardeps.h colvaratoms.h \
|
colvarproxy.h colvartypes.h ../../src/math_eigen_impl.h colvarproxy_io.h \
|
||||||
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
|
colvarparse.h colvarvalue.h colvarparams.h colvardeps.h colvar.h \
|
||||||
|
colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
|
$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvar_geometricpath.h
|
colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
|
$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
|
|
||||||
colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
|
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
|
||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
|
||||||
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
|
|
||||||
colvar_geometricpath.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
|
|
||||||
colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
|
|
||||||
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \
|
colvar_geometricpath.h colvar_rotation_derivative.h
|
||||||
colvarbias.h colvarscript_commands.h colvarscript_commands_colvar.h \
|
$(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
|
||||||
colvarscript_commands_bias.h
|
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
|
||||||
|
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvar_geometricpath.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
|
||||||
|
colvarvalue.h colvartypes.h ../../src/math_eigen_impl.h colvarparse.h \
|
||||||
|
colvarparams.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
|
||||||
|
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
|
colvardeps.h colvar.h colvar_geometricpath.h colvarbias.h \
|
||||||
|
colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
|
||||||
|
colvarvalue.h colvarparams.h
|
||||||
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \
|
||||||
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvardeps.h colvargrid.h colvargrid_def.h colvarproxy.h \
|
||||||
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \
|
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
colvargrid.h colvargrid_def.h
|
colvarproxy_volmaps.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
|
colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
|
||||||
colvarparams.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \
|
||||||
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvardeps.h \
|
|
||||||
colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
|
|
||||||
colvarbias_alb.h colvarbias_histogram.h \
|
|
||||||
colvarbias_histogram_reweight_amd.h colvarbias_meta.h \
|
|
||||||
colvarbias_restraint.h colvarscript.h colvarscript_commands.h \
|
|
||||||
colvarscript_commands_colvar.h colvarscript_commands_bias.h \
|
|
||||||
colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
|
|
||||||
colvar_geometricpath.h colvarmodule_refs.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
|
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
|
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
|
||||||
colvarparams.h
|
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
|
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
colvarproxy_volmaps.h colvarscript.h colvarbias.h colvar.h colvarparse.h \
|
colvarproxy_volmaps.h colvar.h colvardeps.h colvarbias.h \
|
||||||
colvarparams.h colvardeps.h colvarscript_commands.h \
|
colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_abmd.h \
|
||||||
colvarscript_commands_colvar.h colvarscript_commands_bias.h \
|
colvarbias_restraint.h colvarbias_alb.h colvarbias_histogram.h \
|
||||||
colvaratoms.h colvarmodule_utils.h
|
colvarbias_histogram_reweight_amd.h colvarbias_meta.h colvarscript.h \
|
||||||
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \
|
||||||
|
colvar_geometricpath.h colvars_memstream.h colvarmodule_refs.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
|
||||||
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarparams.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
|
||||||
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h \
|
||||||
|
colvars_memstream.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
|
||||||
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarvalue.h \
|
||||||
|
colvarparse.h colvarparams.h colvardeps.h colvarbias.h colvarscript.h \
|
||||||
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h colvarmodule_utils.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_io.o: colvarproxy_io.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarproxy_io.o: colvarproxy_io.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy_io.h
|
colvars_version.h colvarproxy_io.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
|
$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h
|
colvarproxy_tcl.h colvarproxy_volmaps.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_system.o: colvarproxy_system.cpp \
|
$(COLVARS_OBJ_DIR)colvarproxy_system.o: colvarproxy_system.cpp \
|
||||||
colvarmodule.h colvars_version.h colvartypes.h colvarproxy_system.h
|
colvarmodule.h colvars_version.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarproxy_system.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvaratoms.h colvarparse.h colvarparams.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvaratoms.h colvarparse.h \
|
||||||
colvardeps.h
|
colvarvalue.h colvarparams.h colvardeps.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \
|
$(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarproxy_volmaps.h \
|
colvarmodule.h colvars_version.h colvarproxy_volmaps.h \
|
||||||
colvarmodule_utils.h
|
colvarmodule_utils.h
|
||||||
$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \
|
$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \
|
||||||
colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \
|
colvarmodule.h colvars_version.h colvartypes.h \
|
||||||
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
|
||||||
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
|
colvarvalue.h colvarparams.h colvarscript.h colvarscript_commands.h \
|
||||||
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \
|
$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \
|
||||||
colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \
|
colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
|
colvarbias.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarscript.h \
|
||||||
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h
|
||||||
$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \
|
$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \
|
||||||
colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \
|
colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \
|
||||||
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \
|
colvars_version.h colvartypes.h ../../src/math_eigen_impl.h \
|
||||||
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \
|
colvarproxy_volmaps.h colvarbias.h colvar.h colvarvalue.h colvarparse.h \
|
||||||
colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \
|
colvarparams.h colvardeps.h colvarscript.h colvarscript_commands.h \
|
||||||
colvarscript_commands_bias.h
|
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \
|
$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \
|
||||||
colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \
|
colvarscript_commands_colvar.cpp colvar.h colvarmodule.h \
|
||||||
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \
|
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \
|
colvarproxy_volmaps.h colvarscript.h colvarscript_commands.h \
|
||||||
colvarscript_commands_bias.h
|
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvars_memstream.o: colvars_memstream.cpp \
|
||||||
|
colvarmodule.h colvars_version.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvarvalue.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
|
||||||
colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
|
colvars_version.h colvartypes.h ../../src/math_eigen_impl.h \
|
||||||
colvarparams.h ../../src/math_eigen_impl.h
|
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
|
||||||
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarparse.h colvarvalue.h \
|
||||||
|
colvarparams.h colvardeps.h colvar_rotation_derivative.h
|
||||||
$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarvalue.h colvartypes.h
|
colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
|
../../src/math_eigen_impl.h colvars_memstream.h
|
||||||
$(COLVARS_OBJ_DIR)colvar_neuralnetworkcompute.o: \
|
$(COLVARS_OBJ_DIR)colvar_neuralnetworkcompute.o: \
|
||||||
colvar_neuralnetworkcompute.cpp colvar_neuralnetworkcompute.h \
|
colvar_neuralnetworkcompute.cpp colvar_neuralnetworkcompute.h \
|
||||||
colvarparse.h colvarmodule.h colvars_version.h colvarvalue.h \
|
colvarparse.h colvarmodule.h colvars_version.h colvarvalue.h \
|
||||||
colvartypes.h colvarparams.h colvarproxy.h colvarproxy_io.h \
|
colvartypes.h ../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \
|
||||||
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h
|
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
|
||||||
|
colvarproxy_volmaps.h
|
||||||
|
|||||||
@ -16,13 +16,18 @@
|
|||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarvalue.h"
|
#include "colvarvalue.h"
|
||||||
#include "colvarparse.h"
|
#include "colvarparse.h"
|
||||||
#include "colvar.h"
|
|
||||||
#include "colvarcomp.h"
|
#include "colvarcomp.h"
|
||||||
#include "colvarscript.h"
|
#include "colvar.h"
|
||||||
|
#include "colvarbias.h"
|
||||||
|
#include "colvars_memstream.h"
|
||||||
|
|
||||||
|
|
||||||
|
std::map<std::string, std::function<colvar::cvc *()>> colvar::global_cvc_map =
|
||||||
|
std::map<std::string, std::function<colvar::cvc *()>>();
|
||||||
|
|
||||||
|
std::map<std::string, std::string> colvar::global_cvc_desc_map =
|
||||||
|
std::map<std::string, std::string>();
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> colvar::global_cvc_map = std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>();
|
|
||||||
#endif
|
|
||||||
|
|
||||||
colvar::colvar()
|
colvar::colvar()
|
||||||
{
|
{
|
||||||
@ -36,6 +41,8 @@ colvar::colvar()
|
|||||||
dev_null = 0.0;
|
dev_null = 0.0;
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
matching_state = false;
|
||||||
|
|
||||||
expand_boundaries = false;
|
expand_boundaries = false;
|
||||||
|
|
||||||
description = "uninitialized colvar";
|
description = "uninitialized colvar";
|
||||||
@ -131,7 +138,14 @@ int colvar::init(std::string const &conf)
|
|||||||
|
|
||||||
// Sort array of cvcs based on their names
|
// Sort array of cvcs based on their names
|
||||||
// Note: default CVC names are in input order for same type of CVC
|
// Note: default CVC names are in input order for same type of CVC
|
||||||
std::sort(cvcs.begin(), cvcs.end(), colvar::compare_cvc);
|
std::sort(cvcs.begin(), cvcs.end(),
|
||||||
|
[](std::shared_ptr<colvar::cvc> const &cvc1,
|
||||||
|
std::shared_ptr<colvar::cvc> const &cvc2) -> bool {
|
||||||
|
if (cvc1 && cvc2) {
|
||||||
|
return cvc1->name < cvc2->name;
|
||||||
|
}
|
||||||
|
return false;
|
||||||
|
});
|
||||||
|
|
||||||
if(cvcs.size() > 1) {
|
if(cvcs.size() > 1) {
|
||||||
cvm::log("Sorted list of components for this scripted colvar:\n");
|
cvm::log("Sorted list of components for this scripted colvar:\n");
|
||||||
@ -186,9 +200,9 @@ int colvar::init(std::string const &conf)
|
|||||||
|
|
||||||
if ((cvcs[i])->sup_np < 0) {
|
if ((cvcs[i])->sup_np < 0) {
|
||||||
cvm::log("Warning: you chose a negative exponent in the combination; "
|
cvm::log("Warning: you chose a negative exponent in the combination; "
|
||||||
"if you apply forces, the simulation may become unstable "
|
"if you apply forces, the simulation may become unstable "
|
||||||
"when the component \""+
|
"when the component \""+
|
||||||
(cvcs[i])->function_type+"\" approaches zero.\n");
|
(cvcs[i])->function_type()+"\" approaches zero.\n");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -295,7 +309,7 @@ int colvar::init(std::string const &conf)
|
|||||||
error_code |= init_grid_parameters(conf);
|
error_code |= init_grid_parameters(conf);
|
||||||
|
|
||||||
// Detect if we have a single component that is an alchemical lambda
|
// Detect if we have a single component that is an alchemical lambda
|
||||||
if (is_enabled(f_cv_single_cvc) && cvcs[0]->function_type == "alchLambda") {
|
if (is_enabled(f_cv_single_cvc) && cvcs[0]->function_type() == "alchLambda") {
|
||||||
enable(f_cv_external);
|
enable(f_cv_external);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -468,13 +482,6 @@ int colvar::init_custom_function(std::string const &conf)
|
|||||||
size_t pos = 0;
|
size_t pos = 0;
|
||||||
if (key_lookup(conf, "customFunction", &expr, &pos)) {
|
if (key_lookup(conf, "customFunction", &expr, &pos)) {
|
||||||
std::string msg("Error: customFunction requires the Lepton library.");
|
std::string msg("Error: customFunction requires the Lepton library.");
|
||||||
#if (__cplusplus < 201103L)
|
|
||||||
// NOTE: this is not ideal; testing for the Lepton library's version would
|
|
||||||
// be more accurate, but also less portable
|
|
||||||
msg +=
|
|
||||||
std::string(" Note also that recent versions of Lepton require C++11: "
|
|
||||||
"please see https://colvars.github.io/README-c++11.html.");
|
|
||||||
#endif
|
|
||||||
return cvm::error(msg, COLVARS_NOT_IMPLEMENTED);
|
return cvm::error(msg, COLVARS_NOT_IMPLEMENTED);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -697,9 +704,14 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
|
|||||||
}
|
}
|
||||||
if (ext_gamma != 0.0) {
|
if (ext_gamma != 0.0) {
|
||||||
enable(f_cv_Langevin);
|
enable(f_cv_Langevin);
|
||||||
|
cvm::main()->cite_feature("BAOA integrator");
|
||||||
ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs
|
ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs
|
||||||
// Adjust Langevin sigma for slow time step if time_step_factor != 1
|
// Adjust Langevin sigma for slow time step if time_step_factor != 1
|
||||||
ext_sigma = cvm::sqrt(2.0 * proxy->boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
|
// Eq. (6a) in https://doi.org/10.1021/acs.jctc.2c00585
|
||||||
|
ext_sigma = cvm::sqrt((1.0 - cvm::exp(-2.0 * ext_gamma * cvm::dt() * cvm::real(time_step_factor)))
|
||||||
|
* ext_mass * proxy->boltzmann() * temp);
|
||||||
|
} else {
|
||||||
|
ext_sigma = 0.0;
|
||||||
}
|
}
|
||||||
|
|
||||||
get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false);
|
get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false);
|
||||||
@ -744,75 +756,56 @@ int colvar::init_output_flags(std::string const &conf)
|
|||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
// C++11
|
template <typename def_class_name>
|
||||||
template<typename def_class_name> int colvar::init_components_type(std::string const &,
|
void colvar::add_component_type(char const *def_description, char const *def_config_key)
|
||||||
char const * /* def_desc */,
|
{
|
||||||
char const *def_config_key) {
|
if (global_cvc_map.count(def_config_key) == 0) {
|
||||||
// global_cvc_map is only supported in the C++11 case
|
global_cvc_map[def_config_key] = []() {
|
||||||
global_cvc_map[def_config_key] = [](const std::string& cvc_conf){return new def_class_name(cvc_conf);};
|
return new def_class_name();
|
||||||
// TODO: maybe it is better to do more check to avoid duplication in the map?
|
};
|
||||||
return COLVARS_OK;
|
global_cvc_desc_map[def_config_key] = std::string(def_description);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
int colvar::init_components_type_from_global_map(const std::string& conf,
|
|
||||||
const char* def_config_key) {
|
int colvar::init_components_type(const std::string& conf, const char* def_config_key) {
|
||||||
#else
|
|
||||||
template<typename def_class_name> int colvar::init_components_type(std::string const & conf,
|
|
||||||
char const * /* def_desc */,
|
|
||||||
char const *def_config_key) {
|
|
||||||
#endif
|
|
||||||
size_t def_count = 0;
|
size_t def_count = 0;
|
||||||
std::string def_conf = "";
|
std::string def_conf = "";
|
||||||
size_t pos = 0;
|
size_t pos = 0;
|
||||||
|
int error_code = COLVARS_OK;
|
||||||
while ( this->key_lookup(conf,
|
while ( this->key_lookup(conf,
|
||||||
def_config_key,
|
def_config_key,
|
||||||
&def_conf,
|
&def_conf,
|
||||||
&pos) ) {
|
&pos) ) {
|
||||||
if (!def_conf.size()) continue;
|
|
||||||
cvm::log("Initializing "
|
cvm::log("Initializing "
|
||||||
"a new \""+std::string(def_config_key)+"\" component"+
|
"a new \""+std::string(def_config_key)+"\" component"+
|
||||||
(cvm::debug() ? ", with configuration:\n"+def_conf
|
(cvm::debug() ? ", with configuration:\n"+def_conf
|
||||||
: ".\n"));
|
: ".\n"));
|
||||||
|
cvc *cvcp = global_cvc_map[def_config_key]();
|
||||||
|
if (!cvcp) {
|
||||||
|
return cvm::error("Error: in creating object of type \"" + std::string(def_config_key) +
|
||||||
|
"\".\n",
|
||||||
|
COLVARS_MEMORY_ERROR);
|
||||||
|
}
|
||||||
|
cvcs.push_back(std::shared_ptr<colvar::cvc>(cvcp));
|
||||||
|
|
||||||
cvm::increase_depth();
|
cvm::increase_depth();
|
||||||
// only the following line is different from init_components_type
|
int error_code_this = cvcp->init(def_conf);
|
||||||
// in the non-C++11 case
|
if (error_code_this == COLVARS_OK) {
|
||||||
#if (__cplusplus >= 201103L)
|
// Checking for invalid keywords only if the parsing was successful, otherwise any
|
||||||
cvc *cvcp = global_cvc_map.at(def_config_key)(def_conf);
|
// early-returns due to errors would raise false positives
|
||||||
#else
|
error_code_this |= cvcp->check_keywords(def_conf, def_config_key);
|
||||||
cvc *cvcp = new def_class_name(def_conf);
|
}
|
||||||
#endif
|
cvm::decrease_depth();
|
||||||
if (cvcp != NULL) {
|
if (error_code_this != COLVARS_OK) {
|
||||||
cvcs.push_back(cvcp);
|
error_code |=
|
||||||
cvcp->check_keywords(def_conf, def_config_key);
|
cvm::error("Error: in setting up component \"" + std::string(def_config_key) + "\".\n",
|
||||||
cvcp->set_function_type(def_config_key);
|
COLVARS_INPUT_ERROR);
|
||||||
if (cvm::get_error()) {
|
|
||||||
cvm::error("Error: in setting up component \""+
|
|
||||||
std::string(def_config_key)+"\".\n", COLVARS_INPUT_ERROR);
|
|
||||||
return COLVARS_INPUT_ERROR;
|
|
||||||
}
|
|
||||||
cvm::decrease_depth();
|
|
||||||
} else {
|
|
||||||
cvm::decrease_depth();
|
|
||||||
cvm::error("Error: in allocating component \""+
|
|
||||||
std::string(def_config_key)+"\".\n",
|
|
||||||
COLVARS_MEMORY_ERROR);
|
|
||||||
return COLVARS_MEMORY_ERROR;
|
|
||||||
}
|
|
||||||
|
|
||||||
if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) {
|
|
||||||
if (! cvcp->is_enabled(f_cvc_periodic)) {
|
|
||||||
cvm::error("Error: invalid use of period and/or "
|
|
||||||
"wrapAround in a \""+
|
|
||||||
std::string(def_config_key)+
|
|
||||||
"\" component.\n"+
|
|
||||||
"Period: "+cvm::to_str(cvcp->period) +
|
|
||||||
" wrapAround: "+cvm::to_str(cvcp->wrap_center),
|
|
||||||
COLVARS_INPUT_ERROR);
|
|
||||||
return COLVARS_INPUT_ERROR;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// Set default name if it doesn't have one
|
||||||
if ( ! cvcs.back()->name.size()) {
|
if ( ! cvcs.back()->name.size()) {
|
||||||
std::ostringstream s;
|
std::ostringstream s;
|
||||||
s << def_config_key << std::setfill('0') << std::setw(4) << ++def_count;
|
s << def_config_key << std::setfill('0') << std::setw(4) << ++def_count;
|
||||||
@ -822,135 +815,138 @@ template<typename def_class_name> int colvar::init_components_type(std::string c
|
|||||||
|
|
||||||
cvcs.back()->setup();
|
cvcs.back()->setup();
|
||||||
if (cvm::debug()) {
|
if (cvm::debug()) {
|
||||||
cvm::log("Done initializing a \""+
|
cvm::log("Done initializing a \"" + std::string(def_config_key) + "\" component" +
|
||||||
std::string(def_config_key)+
|
(cvm::debug() ? ", named \"" + cvcs.back()->name + "\"" : "") + ".\n");
|
||||||
"\" component"+
|
|
||||||
(cvm::debug() ?
|
|
||||||
", named \""+cvcs.back()->name+"\""
|
|
||||||
: "")+".\n");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
def_conf = "";
|
def_conf = "";
|
||||||
if (cvm::debug()) {
|
if (cvm::debug()) {
|
||||||
cvm::log("Parsed "+cvm::to_str(cvcs.size())+
|
cvm::log("Parsed " + cvm::to_str(cvcs.size()) + " components at this time.\n");
|
||||||
" components at this time.\n");
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
return COLVARS_OK;
|
return error_code;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvar::define_component_types()
|
||||||
|
{
|
||||||
|
colvarproxy *proxy = cvm::main()->proxy;
|
||||||
|
|
||||||
|
add_component_type<distance>("distance", "distance");
|
||||||
|
add_component_type<distance_vec>("distance vector", "distanceVec");
|
||||||
|
add_component_type<cartesian>("Cartesian coordinates", "cartesian");
|
||||||
|
add_component_type<distance_dir>("distance vector direction", "distanceDir");
|
||||||
|
add_component_type<distance_z>("distance projection on an axis", "distanceZ");
|
||||||
|
add_component_type<distance_xy>("distance projection on a plane", "distanceXY");
|
||||||
|
add_component_type<polar_theta>("spherical polar angle theta", "polarTheta");
|
||||||
|
add_component_type<polar_phi>("spherical azimuthal angle phi", "polarPhi");
|
||||||
|
add_component_type<distance_inv>("average distance weighted by inverse power", "distanceInv");
|
||||||
|
add_component_type<distance_pairs>("N1xN2-long vector of pairwise distances", "distancePairs");
|
||||||
|
add_component_type<dipole_magnitude>("dipole magnitude", "dipoleMagnitude");
|
||||||
|
add_component_type<coordnum>("coordination number", "coordNum");
|
||||||
|
add_component_type<selfcoordnum>("self-coordination number", "selfCoordNum");
|
||||||
|
add_component_type<groupcoordnum>("group-coordination number", "groupCoord");
|
||||||
|
add_component_type<angle>("angle", "angle");
|
||||||
|
add_component_type<dipole_angle>("dipole angle", "dipoleAngle");
|
||||||
|
add_component_type<dihedral>("dihedral", "dihedral");
|
||||||
|
add_component_type<h_bond>("hydrogen bond", "hBond");
|
||||||
|
|
||||||
|
if (proxy->check_atom_name_selections_available() == COLVARS_OK) {
|
||||||
|
add_component_type<alpha_angles>("alpha helix", "alpha");
|
||||||
|
add_component_type<dihedPC>("dihedral principal component", "dihedralPC");
|
||||||
|
}
|
||||||
|
|
||||||
|
add_component_type<orientation>("orientation", "orientation");
|
||||||
|
add_component_type<orientation_angle>("orientation angle", "orientationAngle");
|
||||||
|
add_component_type<orientation_proj>("orientation projection", "orientationProj");
|
||||||
|
add_component_type<tilt>("tilt", "tilt");
|
||||||
|
add_component_type<spin_angle>("spin angle", "spinAngle");
|
||||||
|
add_component_type<rmsd>("RMSD", "rmsd");
|
||||||
|
add_component_type<gyration>("radius of gyration", "gyration");
|
||||||
|
add_component_type<inertia>("moment of inertia", "inertia");
|
||||||
|
add_component_type<inertia_z>("moment of inertia around an axis", "inertiaZ");
|
||||||
|
add_component_type<eigenvector>("eigenvector", "eigenvector");
|
||||||
|
add_component_type<alch_lambda>("alchemical coupling parameter", "alchLambda");
|
||||||
|
add_component_type<alch_Flambda>("force on alchemical coupling parameter", "alchFLambda");
|
||||||
|
add_component_type<aspath>("arithmetic path collective variables (s)", "aspath");
|
||||||
|
add_component_type<azpath>("arithmetic path collective variables (z)", "azpath");
|
||||||
|
add_component_type<gspath>("geometrical path collective variables (s)", "gspath");
|
||||||
|
add_component_type<gzpath>("geometrical path collective variables (z)", "gzpath");
|
||||||
|
add_component_type<linearCombination>("linear combination of other collective variables", "linearCombination");
|
||||||
|
add_component_type<gspathCV>("geometrical path collective variables (s) for other CVs", "gspathCV");
|
||||||
|
add_component_type<gzpathCV>("geometrical path collective variables (z) for other CVs", "gzpathCV");
|
||||||
|
add_component_type<aspathCV>("arithmetic path collective variables (s) for other CVs", "aspathCV");
|
||||||
|
add_component_type<azpathCV>("arithmetic path collective variables (s) for other CVs", "azpathCV");
|
||||||
|
add_component_type<euler_phi>("euler phi angle of the optimal orientation", "eulerPhi");
|
||||||
|
add_component_type<euler_psi>("euler psi angle of the optimal orientation", "eulerPsi");
|
||||||
|
add_component_type<euler_theta>("euler theta angle of the optimal orientation", "eulerTheta");
|
||||||
|
|
||||||
|
#ifdef LEPTON
|
||||||
|
add_component_type<customColvar>("CV with support of the Lepton custom function", "customColvar");
|
||||||
|
#endif
|
||||||
|
|
||||||
|
add_component_type<neuralNetwork>("neural network CV for other CVs", "neuralNetwork");
|
||||||
|
|
||||||
|
if (proxy->check_volmaps_available() == COLVARS_OK) {
|
||||||
|
add_component_type<map_total>("total value of atomic map", "mapTotal");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvar::init_components(std::string const &conf)
|
int colvar::init_components(std::string const &conf)
|
||||||
{
|
{
|
||||||
int error_code = COLVARS_OK;
|
int error_code = COLVARS_OK;
|
||||||
size_t i = 0, j = 0;
|
size_t i = 0, j = 0;
|
||||||
|
|
||||||
// in the non-C++11 case, the components are initialized directly by init_components_type;
|
if (global_cvc_map.empty()) {
|
||||||
// in the C++11 case, the components are stored in the global_cvc_map at first
|
define_component_types();
|
||||||
// by init_components_type, and then the map is iterated to initialize all components.
|
}
|
||||||
error_code |= init_components_type<distance>(conf, "distance", "distance");
|
|
||||||
error_code |= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
|
|
||||||
error_code |= init_components_type<cartesian>(conf, "Cartesian coordinates", "cartesian");
|
|
||||||
error_code |= init_components_type<distance_dir>(conf, "distance vector "
|
|
||||||
"direction", "distanceDir");
|
|
||||||
error_code |= init_components_type<distance_z>(conf, "distance projection "
|
|
||||||
"on an axis", "distanceZ");
|
|
||||||
error_code |= init_components_type<distance_xy>(conf, "distance projection "
|
|
||||||
"on a plane", "distanceXY");
|
|
||||||
error_code |= init_components_type<polar_theta>(conf, "spherical polar angle theta",
|
|
||||||
"polarTheta");
|
|
||||||
error_code |= init_components_type<polar_phi>(conf, "spherical azimuthal angle phi",
|
|
||||||
"polarPhi");
|
|
||||||
error_code |= init_components_type<distance_inv>(conf, "average distance "
|
|
||||||
"weighted by inverse power", "distanceInv");
|
|
||||||
error_code |= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
|
|
||||||
"of pairwise distances", "distancePairs");
|
|
||||||
error_code |= init_components_type<dipole_magnitude>(conf, "dipole magnitude",
|
|
||||||
"dipoleMagnitude");
|
|
||||||
error_code |= init_components_type<coordnum>(conf, "coordination "
|
|
||||||
"number", "coordNum");
|
|
||||||
error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
|
|
||||||
"number", "selfCoordNum");
|
|
||||||
error_code |= init_components_type<groupcoordnum>(conf, "group-coordination "
|
|
||||||
"number", "groupCoord");
|
|
||||||
error_code |= init_components_type<angle>(conf, "angle", "angle");
|
|
||||||
error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
|
|
||||||
error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
|
|
||||||
error_code |= init_components_type<h_bond>(conf, "hydrogen bond", "hBond");
|
|
||||||
error_code |= init_components_type<alpha_angles>(conf, "alpha helix", "alpha");
|
|
||||||
error_code |= init_components_type<dihedPC>(conf, "dihedral "
|
|
||||||
"principal component", "dihedralPC");
|
|
||||||
error_code |= init_components_type<orientation>(conf, "orientation", "orientation");
|
|
||||||
error_code |= init_components_type<orientation_angle>(conf, "orientation "
|
|
||||||
"angle", "orientationAngle");
|
|
||||||
error_code |= init_components_type<orientation_proj>(conf, "orientation "
|
|
||||||
"projection", "orientationProj");
|
|
||||||
error_code |= init_components_type<tilt>(conf, "tilt", "tilt");
|
|
||||||
error_code |= init_components_type<spin_angle>(conf, "spin angle", "spinAngle");
|
|
||||||
error_code |= init_components_type<rmsd>(conf, "RMSD", "rmsd");
|
|
||||||
error_code |= init_components_type<gyration>(conf, "radius of "
|
|
||||||
"gyration", "gyration");
|
|
||||||
error_code |= init_components_type<inertia>(conf, "moment of "
|
|
||||||
"inertia", "inertia");
|
|
||||||
error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
|
|
||||||
error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
|
|
||||||
error_code |= init_components_type<alch_lambda>(conf, "alchemical coupling parameter", "alchLambda");
|
|
||||||
error_code |= init_components_type<alch_Flambda>(conf, "force on alchemical coupling parameter", "alchFLambda");
|
|
||||||
error_code |= init_components_type<gspath>(conf, "geometrical path collective variables (s)", "gspath");
|
|
||||||
error_code |= init_components_type<gzpath>(conf, "geometrical path collective variables (z)", "gzpath");
|
|
||||||
error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "linearCombination");
|
|
||||||
error_code |= init_components_type<gspathCV>(conf, "geometrical path collective variables (s) for other CVs", "gspathCV");
|
|
||||||
error_code |= init_components_type<gzpathCV>(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV");
|
|
||||||
error_code |= init_components_type<aspathCV>(conf, "arithmetic path collective variables (s) for other CVs", "aspathCV");
|
|
||||||
error_code |= init_components_type<azpathCV>(conf, "arithmetic path collective variables (s) for other CVs", "azpathCV");
|
|
||||||
error_code |= init_components_type<euler_phi>(conf, "euler phi angle of the optimal orientation", "eulerPhi");
|
|
||||||
error_code |= init_components_type<euler_psi>(conf, "euler psi angle of the optimal orientation", "eulerPsi");
|
|
||||||
error_code |= init_components_type<euler_theta>(conf, "euler theta angle of the optimal orientation", "eulerTheta");
|
|
||||||
#ifdef LEPTON
|
|
||||||
error_code |= init_components_type<customColvar>(conf, "CV with support of the lepton custom function", "customColvar");
|
|
||||||
#endif
|
|
||||||
error_code |= init_components_type<neuralNetwork>(conf, "neural network CV for other CVs", "NeuralNetwork");
|
|
||||||
|
|
||||||
error_code |= init_components_type<map_total>(conf, "total value of atomic map", "mapTotal");
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
// iterate over all available CVC in the map
|
// iterate over all available CVC in the map
|
||||||
for (auto it = global_cvc_map.begin(); it != global_cvc_map.end(); ++it) {
|
for (auto it = global_cvc_map.begin(); it != global_cvc_map.end(); ++it) {
|
||||||
error_code |= init_components_type_from_global_map(conf, it->first.c_str());
|
error_code |= init_components_type(conf, it->first.c_str());
|
||||||
// TODO: is it better to check the error code here?
|
// TODO: is it better to check the error code here?
|
||||||
if (error_code != COLVARS_OK) {
|
if (error_code != COLVARS_OK) {
|
||||||
cvm::log("Failed to initialize " + it->first + " with the following configuration:\n");
|
cvm::log("Failed to initialize " + it->first + " with the following configuration:\n");
|
||||||
cvm::log(conf);
|
cvm::log(conf);
|
||||||
// TODO: should it stop here?
|
// TODO: should it stop here?
|
||||||
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
#endif
|
|
||||||
if (!cvcs.size() || (error_code != COLVARS_OK)) {
|
if (!cvcs.size()) {
|
||||||
cvm::error("Error: no valid components were provided "
|
std::string msg("Error: no valid components were provided for this collective variable.\n");
|
||||||
"for this collective variable.\n",
|
msg += "Currently available component types are: \n";
|
||||||
COLVARS_INPUT_ERROR);
|
for (auto it = global_cvc_desc_map.begin(); it != global_cvc_desc_map.end(); ++it) {
|
||||||
return COLVARS_INPUT_ERROR;
|
msg += " " + it->first + " -- " + it->second + "\n";
|
||||||
|
}
|
||||||
|
msg += "\nPlease note that some of the above types may still be unavailable, irrespective of this error.\n";
|
||||||
|
error_code |= cvm::error(msg, COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
|
|
||||||
// Check for uniqueness of CVC names (esp. if user-provided)
|
// Check for uniqueness of CVC names (esp. if user-provided)
|
||||||
for (i = 0; i < cvcs.size(); i++) {
|
for (i = 0; i < cvcs.size(); i++) {
|
||||||
for (j = i+1; j < cvcs.size(); j++) {
|
for (j = i + 1; j < cvcs.size(); j++) {
|
||||||
if (cvcs[i]->name == cvcs[j]->name) {
|
if (cvcs[i]->name == cvcs[j]->name) {
|
||||||
cvm::error("Components " + cvm::to_str(i) + " and " + cvm::to_str(j) +\
|
error_code |= cvm::error("Components " + cvm::to_str(i) + " and " + cvm::to_str(j) +
|
||||||
" cannot have the same name \"" + cvcs[i]->name+ "\".\n", COLVARS_INPUT_ERROR);
|
" cannot have the same name \"" + cvcs[i]->name + "\".\n",
|
||||||
return COLVARS_INPUT_ERROR;
|
COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
n_active_cvcs = cvcs.size();
|
if (error_code == COLVARS_OK) {
|
||||||
|
// Store list of children cvcs for dependency checking purposes
|
||||||
// Store list of children cvcs for dependency checking purposes
|
for (i = 0; i < cvcs.size(); i++) {
|
||||||
for (i = 0; i < cvcs.size(); i++) {
|
add_child(cvcs[i].get());
|
||||||
add_child(cvcs[i]);
|
}
|
||||||
|
// By default all CVCs are active at the start
|
||||||
|
n_active_cvcs = cvcs.size();
|
||||||
|
cvm::log("All components initialized.\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
cvm::log("All components initialized.\n");
|
return error_code;
|
||||||
|
|
||||||
return COLVARS_OK;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -1220,7 +1216,7 @@ int colvar::init_dependencies() {
|
|||||||
|
|
||||||
// Initialize feature_states for each instance
|
// Initialize feature_states for each instance
|
||||||
feature_states.reserve(f_cv_ntot);
|
feature_states.reserve(f_cv_ntot);
|
||||||
for (i = 0; i < f_cv_ntot; i++) {
|
for (i = feature_states.size(); i < f_cv_ntot; i++) {
|
||||||
feature_states.push_back(feature_state(true, false));
|
feature_states.push_back(feature_state(true, false));
|
||||||
// Most features are available, so we set them so
|
// Most features are available, so we set them so
|
||||||
// and list exceptions below
|
// and list exceptions below
|
||||||
@ -1283,14 +1279,10 @@ colvar::~colvar()
|
|||||||
// for dependency purposes
|
// for dependency purposes
|
||||||
remove_all_children();
|
remove_all_children();
|
||||||
|
|
||||||
for (std::vector<cvc *>::reverse_iterator ci = cvcs.rbegin();
|
for (auto ci = cvcs.rbegin(); ci != cvcs.rend(); ++ci) {
|
||||||
ci != cvcs.rend();
|
// Clear all children of this cvc (i.e. its atom groups), because the cvc base class destructor
|
||||||
++ci) {
|
// can't do it early enough and we don't want to have each cvc derived class do it separately
|
||||||
// clear all children of this cvc (i.e. its atom groups)
|
|
||||||
// because the cvc base class destructor can't do it early enough
|
|
||||||
// and we don't want to have each cvc derived class do it separately
|
|
||||||
(*ci)->remove_all_children();
|
(*ci)->remove_all_children();
|
||||||
delete *ci;
|
|
||||||
}
|
}
|
||||||
cvcs.clear();
|
cvcs.clear();
|
||||||
|
|
||||||
@ -1512,6 +1504,7 @@ int colvar::collect_cvc_values()
|
|||||||
cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");
|
cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");
|
||||||
|
|
||||||
if (after_restart) {
|
if (after_restart) {
|
||||||
|
x_old = x_restart;
|
||||||
if (cvm::proxy->simulation_running()) {
|
if (cvm::proxy->simulation_running()) {
|
||||||
cvm::real const jump2 = dist2(x, x_restart) / (width*width);
|
cvm::real const jump2 = dist2(x, x_restart) / (width*width);
|
||||||
if (jump2 > 0.25) {
|
if (jump2 > 0.25) {
|
||||||
@ -1555,12 +1548,12 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
|
|||||||
(cvcs[i])->debug_gradients();
|
(cvcs[i])->debug_gradients();
|
||||||
}
|
}
|
||||||
|
|
||||||
cvm::decrease_depth();
|
|
||||||
|
|
||||||
if (cvm::debug())
|
if (cvm::debug())
|
||||||
cvm::log("Done calculating gradients of colvar \""+this->name+"\".\n");
|
cvm::log("Done calculating gradients of colvar \""+this->name+"\".\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
cvm::decrease_depth();
|
||||||
|
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1706,12 +1699,13 @@ int colvar::calc_colvar_properties()
|
|||||||
// Do the same if no simulation is running (eg. VMD postprocessing)
|
// Do the same if no simulation is running (eg. VMD postprocessing)
|
||||||
if ((cvm::step_relative() == 0 && !after_restart) || x_ext.type() == colvarvalue::type_notset || !cvm::proxy->simulation_running()) {
|
if ((cvm::step_relative() == 0 && !after_restart) || x_ext.type() == colvarvalue::type_notset || !cvm::proxy->simulation_running()) {
|
||||||
x_ext = x;
|
x_ext = x;
|
||||||
|
cvm::log("Initializing extended coordinate to colvar value.\n");
|
||||||
if (is_enabled(f_cv_reflecting_lower_boundary) && x_ext < lower_boundary) {
|
if (is_enabled(f_cv_reflecting_lower_boundary) && x_ext < lower_boundary) {
|
||||||
cvm::log("Warning: initializing extended coordinate to reflective lower boundary, as colvar value is below.");
|
cvm::log("Warning: initializing extended coordinate to reflective lower boundary, as colvar value is below.\n");
|
||||||
x_ext = lower_boundary;
|
x_ext = lower_boundary;
|
||||||
}
|
}
|
||||||
if (is_enabled(f_cv_reflecting_upper_boundary) && x_ext > upper_boundary) {
|
if (is_enabled(f_cv_reflecting_upper_boundary) && x_ext > upper_boundary) {
|
||||||
cvm::log("Warning: initializing extended coordinate to reflective upper boundary, as colvar value is above.");
|
cvm::log("Warning: initializing extended coordinate to reflective upper boundary, as colvar value is above.\n");
|
||||||
x_ext = upper_boundary;
|
x_ext = upper_boundary;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1721,8 +1715,18 @@ int colvar::calc_colvar_properties()
|
|||||||
// Special case of a repeated timestep (eg. multiple NAMD "run" statements)
|
// Special case of a repeated timestep (eg. multiple NAMD "run" statements)
|
||||||
// revert values of the extended coordinate and velocity prior to latest integration
|
// revert values of the extended coordinate and velocity prior to latest integration
|
||||||
if (cvm::proxy->simulation_running() && cvm::step_relative() == prev_timestep) {
|
if (cvm::proxy->simulation_running() && cvm::step_relative() == prev_timestep) {
|
||||||
x_ext = prev_x_ext;
|
// Detect jumps due to discrete changes in coordinates (eg. in replica exchange schemes)
|
||||||
v_ext = prev_v_ext;
|
cvm::real const jump2 = dist2(x, x_old) / (width*width);
|
||||||
|
if (jump2 > 0.25) {
|
||||||
|
cvm::log("Detected discrete jump in colvar value from "
|
||||||
|
+ cvm::to_str(x_old) + " to " + cvm::to_str(x) + ".\n");
|
||||||
|
cvm::log("Reinitializing extended coordinate to colvar value.\n");
|
||||||
|
x_ext = x;
|
||||||
|
} else {
|
||||||
|
cvm::log("Reinitializing extended coordinate to last value.\n");
|
||||||
|
x_ext = prev_x_ext;
|
||||||
|
v_ext = prev_v_ext;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
// report the restraint center as "value"
|
// report the restraint center as "value"
|
||||||
// These position and velocities come from integration at the _previous timestep_ in update_forces_energy()
|
// These position and velocities come from integration at the _previous timestep_ in update_forces_energy()
|
||||||
@ -1830,9 +1834,11 @@ void colvar::update_extended_Lagrangian()
|
|||||||
f += fb_actual;
|
f += fb_actual;
|
||||||
}
|
}
|
||||||
|
|
||||||
fr = f;
|
// fr: bias force on extended variable (without harmonic spring), for output in trajectory
|
||||||
// External force has been scaled for a 1-timestep impulse, scale it back because we will
|
fr = f;
|
||||||
// integrate it with the colvar's own timestep factor
|
|
||||||
|
// External force has been scaled for an inner-timestep impulse (for the back-end integrator)
|
||||||
|
// here we scale it back because this integrator uses only the outer (long) timestep
|
||||||
f_ext = f / cvm::real(time_step_factor);
|
f_ext = f / cvm::real(time_step_factor);
|
||||||
|
|
||||||
colvarvalue f_system(fr.type()); // force exterted by the system on the extended DOF
|
colvarvalue f_system(fr.type()); // force exterted by the system on the extended DOF
|
||||||
@ -1845,15 +1851,14 @@ void colvar::update_extended_Lagrangian()
|
|||||||
} else {
|
} else {
|
||||||
// the total force is applied to the fictitious mass, while the
|
// the total force is applied to the fictitious mass, while the
|
||||||
// atoms only feel the harmonic force + wall force
|
// atoms only feel the harmonic force + wall force
|
||||||
// fr: bias force on extended variable (without harmonic spring), for output in trajectory
|
|
||||||
// f_ext: total force on extended variable (including harmonic spring)
|
// f_ext: total force on extended variable (including harmonic spring)
|
||||||
// f: - initially, external biasing force
|
// f: - initially, external biasing force
|
||||||
// - after this code block, colvar force to be applied to atomic coordinates
|
// - after this code block, colvar force to be applied to atomic coordinates
|
||||||
// ie. spring force (fb_actual will be added just below)
|
// ie. spring force (fb_actual will be added just below)
|
||||||
f_system = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x);
|
f_system = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x);
|
||||||
f = -1.0 * f_system;
|
f = -1.0 * f_system;
|
||||||
// Coupling force is a slow force, to be applied to atomic coords impulse-style
|
// Coupling force will be applied to atomic coords impulse-style
|
||||||
// over a single MD timestep
|
// over an inner timestep of the back-end integrator
|
||||||
f *= cvm::real(time_step_factor);
|
f *= cvm::real(time_step_factor);
|
||||||
}
|
}
|
||||||
f_ext += f_system;
|
f_ext += f_system;
|
||||||
@ -1873,34 +1878,57 @@ void colvar::update_extended_Lagrangian()
|
|||||||
prev_x_ext = x_ext;
|
prev_x_ext = x_ext;
|
||||||
prev_v_ext = v_ext;
|
prev_v_ext = v_ext;
|
||||||
|
|
||||||
// leapfrog: starting from x_i, f_i, v_(i-1/2)
|
// BAOA (GSD) integrator as formulated in https://doi.org/10.1021/acs.jctc.2c00585
|
||||||
v_ext += (0.5 * dt) * f_ext / ext_mass;
|
// starting from x_t, f_t, v_(t-1/2)
|
||||||
// Because of leapfrog, kinetic energy at time i is approximate
|
// Variation: the velocity step is split in two to estimate the kinetic energy at time t
|
||||||
|
// so this is more of a "BBAOA" scheme: a rearranged BAOAB where the second B is deferred
|
||||||
|
// to the next time step for implementation reasons (waiting for the force calculation)
|
||||||
|
|
||||||
|
// [B] Eq. (10a) split into two half-steps
|
||||||
|
// would reduce to leapfrog when gamma = 0 if this was the reported velocity
|
||||||
|
v_ext += 0.5 * dt * f_ext / ext_mass;
|
||||||
|
|
||||||
|
// Kinetic energy at t
|
||||||
kinetic_energy = 0.5 * ext_mass * v_ext * v_ext;
|
kinetic_energy = 0.5 * ext_mass * v_ext * v_ext;
|
||||||
|
|
||||||
|
// Potential energy at t
|
||||||
potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x);
|
potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x);
|
||||||
// leap to v_(i+1/2)
|
|
||||||
|
// Total energy will lag behind position by one timestep
|
||||||
|
// (current kinetic energy is not accessible before the next force calculation)
|
||||||
|
|
||||||
|
v_ext += 0.5 * dt * f_ext / ext_mass;
|
||||||
|
// Final v_ext lags behind x_ext by half a timestep
|
||||||
|
|
||||||
|
// [A] Half step in position (10b)
|
||||||
|
x_ext += dt * v_ext / 2.0;
|
||||||
|
|
||||||
|
// [O] leap to v_(i+1/2) (10c)
|
||||||
if (is_enabled(f_cv_Langevin)) {
|
if (is_enabled(f_cv_Langevin)) {
|
||||||
v_ext -= dt * ext_gamma * v_ext;
|
|
||||||
colvarvalue rnd(x);
|
colvarvalue rnd(x);
|
||||||
rnd.set_random();
|
rnd.set_random();
|
||||||
v_ext += dt * ext_sigma * rnd / ext_mass;
|
// ext_sigma has been computed at init time according to (10c)
|
||||||
|
v_ext = cvm::exp(- 1.0 * dt * ext_gamma) * v_ext + ext_sigma * rnd / ext_mass;
|
||||||
}
|
}
|
||||||
v_ext += (0.5 * dt) * f_ext / ext_mass;
|
// [A] Second half step in position (10d)
|
||||||
x_ext += dt * v_ext;
|
x_ext += dt * v_ext / 2.0;
|
||||||
|
|
||||||
cvm::real delta = 0; // Length of overshoot past either reflecting boundary
|
cvm::real delta = 0; // Length of overshoot past either reflecting boundary
|
||||||
if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) ||
|
if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) ||
|
||||||
(is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) {
|
(is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) {
|
||||||
|
// Reflect arrival position
|
||||||
x_ext -= 2.0 * delta;
|
x_ext -= 2.0 * delta;
|
||||||
v_ext *= -1.0;
|
// Bounce happened on average at t+1/2 -> reflect velocity at t+1/2
|
||||||
if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) ||
|
v_ext = -0.5 * (prev_v_ext + v_ext);
|
||||||
(is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) {
|
if ((is_enabled(f_cv_reflecting_lower_boundary) && (x_ext - lower_boundary) < 0.0) ||
|
||||||
|
(is_enabled(f_cv_reflecting_upper_boundary) && (x_ext - upper_boundary) > 0.0)) {
|
||||||
cvm::error("Error: extended coordinate value " + cvm::to_str(x_ext) + " is still outside boundaries after reflection.\n");
|
cvm::error("Error: extended coordinate value " + cvm::to_str(x_ext) + " is still outside boundaries after reflection.\n");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
x_ext.apply_constraints();
|
x_ext.apply_constraints();
|
||||||
this->wrap(x_ext);
|
this->wrap(x_ext);
|
||||||
|
|
||||||
if (is_enabled(f_cv_external)) {
|
if (is_enabled(f_cv_external)) {
|
||||||
// Colvar value is constrained to the extended value
|
// Colvar value is constrained to the extended value
|
||||||
x = x_ext;
|
x = x_ext;
|
||||||
@ -1914,9 +1942,8 @@ int colvar::end_of_step()
|
|||||||
if (cvm::debug())
|
if (cvm::debug())
|
||||||
cvm::log("End of step for colvar \""+this->name+"\".\n");
|
cvm::log("End of step for colvar \""+this->name+"\".\n");
|
||||||
|
|
||||||
if (is_enabled(f_cv_fdiff_velocity)) {
|
// Used for fdiff_velocity and for detecting jumps for extended Lagrangian colvars
|
||||||
x_old = x;
|
x_old = x;
|
||||||
}
|
|
||||||
|
|
||||||
if (is_enabled(f_cv_subtract_applied_force)) {
|
if (is_enabled(f_cv_subtract_applied_force)) {
|
||||||
f_old = f;
|
f_old = f;
|
||||||
@ -2256,44 +2283,65 @@ void colvar::wrap(colvarvalue &x_unwrapped) const
|
|||||||
|
|
||||||
std::istream & colvar::read_state(std::istream &is)
|
std::istream & colvar::read_state(std::istream &is)
|
||||||
{
|
{
|
||||||
std::streampos const start_pos = is.tellg();
|
auto const start_pos = is.tellg();
|
||||||
|
|
||||||
std::string conf;
|
std::string conf;
|
||||||
if ( !(is >> colvarparse::read_block("colvar", &conf)) ) {
|
if ( !(is >> colvarparse::read_block("colvar", &conf)) ||
|
||||||
|
(check_matching_state(conf) != COLVARS_OK) ) {
|
||||||
// this is not a colvar block
|
// this is not a colvar block
|
||||||
is.clear();
|
is.clear();
|
||||||
is.seekg(start_pos, std::ios::beg);
|
is.seekg(start_pos);
|
||||||
is.setstate(std::ios::failbit);
|
is.setstate(std::ios::failbit);
|
||||||
return is;
|
return is;
|
||||||
}
|
}
|
||||||
|
|
||||||
{
|
if (!matching_state) {
|
||||||
std::string check_name = "";
|
// No errors reading, but this state is not for this colvar; rewind
|
||||||
get_keyval(conf, "name", check_name,
|
is.seekg(start_pos);
|
||||||
std::string(""), colvarparse::parse_silent);
|
return is;
|
||||||
if (check_name.size() == 0) {
|
|
||||||
cvm::error("Error: Collective variable in the "
|
|
||||||
"restart file without any identifier.\n", COLVARS_INPUT_ERROR);
|
|
||||||
is.clear();
|
|
||||||
is.seekg(start_pos, std::ios::beg);
|
|
||||||
is.setstate(std::ios::failbit);
|
|
||||||
return is;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (check_name != name) {
|
|
||||||
if (cvm::debug()) {
|
|
||||||
cvm::log("Ignoring state of colvar \""+check_name+
|
|
||||||
"\": this colvar is named \""+name+"\".\n");
|
|
||||||
}
|
|
||||||
is.seekg(start_pos, std::ios::beg);
|
|
||||||
return is;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (set_state_params(conf) != COLVARS_OK) {
|
||||||
|
is.clear();
|
||||||
|
is.seekg(start_pos);
|
||||||
|
is.setstate(std::ios::failbit);
|
||||||
|
}
|
||||||
|
|
||||||
|
return is;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvar::check_matching_state(std::string const &conf)
|
||||||
|
{
|
||||||
|
std::string check_name = "";
|
||||||
|
get_keyval(conf, "name", check_name, std::string(""), colvarparse::parse_silent);
|
||||||
|
|
||||||
|
if (check_name.size() == 0) {
|
||||||
|
return cvm::error("Error: Collective variable in the "
|
||||||
|
"state file without any identifier.\n", COLVARS_INPUT_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (check_name != name) {
|
||||||
|
if (cvm::debug()) {
|
||||||
|
cvm::log("Ignoring state of colvar \""+check_name+
|
||||||
|
"\": this colvar is named \""+name+"\".\n");
|
||||||
|
}
|
||||||
|
matching_state = false;
|
||||||
|
} else {
|
||||||
|
matching_state = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvar::set_state_params(std::string const &conf)
|
||||||
|
{
|
||||||
|
int error_code = COLVARS_OK;
|
||||||
if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) {
|
if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) {
|
||||||
cvm::log("Error: restart file does not contain "
|
error_code |= cvm::error("Error: restart file does not contain "
|
||||||
"the value of the colvar \""+
|
"the value of the colvar \""+
|
||||||
name+"\" .\n");
|
name+"\" .\n", COLVARS_INPUT_ERROR);
|
||||||
} else {
|
} else {
|
||||||
cvm::log("Restarting collective variable \""+name+"\" from value: "+
|
cvm::log("Restarting collective variable \""+name+"\" from value: "+
|
||||||
cvm::to_str(x)+"\n");
|
cvm::to_str(x)+"\n");
|
||||||
@ -2306,9 +2354,10 @@ std::istream & colvar::read_state(std::istream &is)
|
|||||||
colvarvalue(x.type()), colvarparse::parse_silent)) ||
|
colvarvalue(x.type()), colvarparse::parse_silent)) ||
|
||||||
!(get_keyval(conf, "extended_v", v_ext,
|
!(get_keyval(conf, "extended_v", v_ext,
|
||||||
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
|
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
|
||||||
cvm::log("Error: restart file does not contain "
|
error_code |= cvm::error("Error: restart file does not contain "
|
||||||
"\"extended_x\" or \"extended_v\" for the colvar \""+
|
"\"extended_x\" or \"extended_v\" for the colvar \""+
|
||||||
name+"\", but you requested \"extendedLagrangian\".\n");
|
name+"\", but you requested \"extendedLagrangian\".\n",
|
||||||
|
COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
x_reported = x_ext;
|
x_reported = x_ext;
|
||||||
} else {
|
} else {
|
||||||
@ -2319,9 +2368,10 @@ std::istream & colvar::read_state(std::istream &is)
|
|||||||
|
|
||||||
if ( !(get_keyval(conf, "v", v_fdiff,
|
if ( !(get_keyval(conf, "v", v_fdiff,
|
||||||
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
|
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
|
||||||
cvm::log("Error: restart file does not contain "
|
error_code |= cvm::error("Error: restart file does not contain "
|
||||||
"the velocity for the colvar \""+
|
"the velocity for the colvar \""+
|
||||||
name+"\", but you requested \"outputVelocity\".\n");
|
name+"\", but you requested \"outputVelocity\".\n",
|
||||||
|
COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (is_enabled(f_cv_extended_Lagrangian)) {
|
if (is_enabled(f_cv_extended_Lagrangian)) {
|
||||||
@ -2331,6 +2381,41 @@ std::istream & colvar::read_state(std::istream &is)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
cvm::memory_stream &colvar::read_state(cvm::memory_stream &is)
|
||||||
|
{
|
||||||
|
auto const start_pos = is.tellg();
|
||||||
|
std::string key, data;
|
||||||
|
if (is >> key) {
|
||||||
|
if (key == "colvar") {
|
||||||
|
// Read a formatted config string, then read the state parameters from it
|
||||||
|
if (is >> data) {
|
||||||
|
if (set_state_params(data) == COLVARS_OK) {
|
||||||
|
return is;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
auto const error_pos = is.tellg();
|
||||||
|
|
||||||
|
is.clear();
|
||||||
|
is.seekg(start_pos);
|
||||||
|
is.setstate(std::ios::failbit);
|
||||||
|
|
||||||
|
std::string error_msg("Error: in reading state data for colvar \"" + name + " at position " +
|
||||||
|
cvm::to_str(error_pos) + " in unformatted stream.\n");
|
||||||
|
if (key.size() && key != "colvar") {
|
||||||
|
error_msg += "; the keyword read was \"" + key + "\", but \"colvar\" was expected";
|
||||||
|
}
|
||||||
|
if (data.size()) {
|
||||||
|
error_msg += "; the configuration string read was not recognized";
|
||||||
|
}
|
||||||
|
error_msg += ".\n";
|
||||||
|
cvm::error(error_msg, COLVARS_INPUT_ERROR);
|
||||||
return is;
|
return is;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -2345,7 +2430,7 @@ std::istream & colvar::read_traj(std::istream &is)
|
|||||||
cvm::log("Error: in reading the value of colvar \""+
|
cvm::log("Error: in reading the value of colvar \""+
|
||||||
this->name+"\" from trajectory.\n");
|
this->name+"\" from trajectory.\n");
|
||||||
is.clear();
|
is.clear();
|
||||||
is.seekg(start_pos, std::ios::beg);
|
is.seekg(start_pos);
|
||||||
is.setstate(std::ios::failbit);
|
is.setstate(std::ios::failbit);
|
||||||
return is;
|
return is;
|
||||||
}
|
}
|
||||||
@ -2385,10 +2470,23 @@ std::istream & colvar::read_traj(std::istream &is)
|
|||||||
|
|
||||||
// ******************** OUTPUT FUNCTIONS ********************
|
// ******************** OUTPUT FUNCTIONS ********************
|
||||||
|
|
||||||
std::ostream & colvar::write_state(std::ostream &os) {
|
std::ostream & colvar::write_state(std::ostream &os) const
|
||||||
|
{
|
||||||
|
os << "colvar {\n" << get_state_params() << "}\n\n";
|
||||||
|
|
||||||
os << "colvar {\n"
|
if (runave_outfile.size() > 0) {
|
||||||
<< " name " << name << "\n"
|
cvm::main()->proxy->flush_output_stream(runave_outfile);
|
||||||
|
}
|
||||||
|
|
||||||
|
return os;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
std::string const colvar::get_state_params() const
|
||||||
|
{
|
||||||
|
std::ostringstream os;
|
||||||
|
|
||||||
|
os << " name " << name << "\n"
|
||||||
<< " x "
|
<< " x "
|
||||||
<< std::setprecision(cvm::cv_prec)
|
<< std::setprecision(cvm::cv_prec)
|
||||||
<< std::setw(cvm::cv_width)
|
<< std::setw(cvm::cv_width)
|
||||||
@ -2412,7 +2510,13 @@ std::ostream & colvar::write_state(std::ostream &os) {
|
|||||||
<< v_reported << "\n";
|
<< v_reported << "\n";
|
||||||
}
|
}
|
||||||
|
|
||||||
os << "}\n\n";
|
return os.str();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
cvm::memory_stream & colvar::write_state(cvm::memory_stream &os) const
|
||||||
|
{
|
||||||
|
os << std::string("colvar") << get_state_params();
|
||||||
|
|
||||||
if (runave_outfile.size() > 0) {
|
if (runave_outfile.size() > 0) {
|
||||||
cvm::main()->proxy->flush_output_stream(runave_outfile);
|
cvm::main()->proxy->flush_output_stream(runave_outfile);
|
||||||
@ -2875,14 +2979,11 @@ int colvar::calc_runave()
|
|||||||
runave_variance *= 1.0 / cvm::real(runave_length-1);
|
runave_variance *= 1.0 / cvm::real(runave_length-1);
|
||||||
|
|
||||||
if (runave_outfile.size() > 0) {
|
if (runave_outfile.size() > 0) {
|
||||||
std::ostream &runave_os = proxy->output_stream(runave_outfile);
|
std::ostream &runave_os =
|
||||||
runave_os << std::setw(cvm::it_width) << cvm::step_relative()
|
proxy->output_stream(runave_outfile, "running average output file");
|
||||||
<< " "
|
runave_os << std::setw(cvm::it_width) << cvm::step_relative() << " "
|
||||||
<< std::setprecision(cvm::cv_prec)
|
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << runave << " "
|
||||||
<< std::setw(cvm::cv_width)
|
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
|
||||||
<< runave << " "
|
|
||||||
<< std::setprecision(cvm::cv_prec)
|
|
||||||
<< std::setw(cvm::cv_width)
|
|
||||||
<< cvm::sqrt(runave_variance) << "\n";
|
<< cvm::sqrt(runave_variance) << "\n";
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -10,12 +10,11 @@
|
|||||||
#ifndef COLVAR_H
|
#ifndef COLVAR_H
|
||||||
#define COLVAR_H
|
#define COLVAR_H
|
||||||
|
|
||||||
#include <iostream>
|
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
#include <map>
|
|
||||||
#include <functional>
|
#include <functional>
|
||||||
#endif
|
#include <list>
|
||||||
|
#include <iosfwd>
|
||||||
|
#include <map>
|
||||||
|
#include <memory>
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarvalue.h"
|
#include "colvarvalue.h"
|
||||||
@ -91,7 +90,7 @@ public:
|
|||||||
/// calculations, \link colvarbias_abf \endlink, it is used to
|
/// calculations, \link colvarbias_abf \endlink, it is used to
|
||||||
/// calculate the grid spacing in the direction of this collective
|
/// calculate the grid spacing in the direction of this collective
|
||||||
/// variable.
|
/// variable.
|
||||||
cvm::real width;
|
cvm::real width = 1.0;
|
||||||
|
|
||||||
/// \brief Implementation of the feature list for colvar
|
/// \brief Implementation of the feature list for colvar
|
||||||
static std::vector<feature *> cv_features;
|
static std::vector<feature *> cv_features;
|
||||||
@ -184,13 +183,13 @@ protected:
|
|||||||
/// Previous velocity of the restraint center
|
/// Previous velocity of the restraint center
|
||||||
colvarvalue prev_v_ext;
|
colvarvalue prev_v_ext;
|
||||||
/// Mass of the restraint center
|
/// Mass of the restraint center
|
||||||
cvm::real ext_mass;
|
cvm::real ext_mass = 0.0;
|
||||||
/// Restraint force constant
|
/// Restraint force constant
|
||||||
cvm::real ext_force_k;
|
cvm::real ext_force_k = 0.0;
|
||||||
/// Friction coefficient for Langevin extended dynamics
|
/// Friction coefficient for Langevin extended dynamics
|
||||||
cvm::real ext_gamma;
|
cvm::real ext_gamma = 0.0;
|
||||||
/// Amplitude of Gaussian white noise for Langevin extended dynamics
|
/// Amplitude of Gaussian white noise for Langevin extended dynamics
|
||||||
cvm::real ext_sigma;
|
cvm::real ext_sigma = 0.0;
|
||||||
|
|
||||||
/// \brief Applied force on extended DOF, for output (unscaled if using MTS)
|
/// \brief Applied force on extended DOF, for output (unscaled if using MTS)
|
||||||
colvarvalue fr;
|
colvarvalue fr;
|
||||||
@ -224,14 +223,14 @@ public:
|
|||||||
colvarvalue ft;
|
colvarvalue ft;
|
||||||
|
|
||||||
/// Period, if this variable is periodic
|
/// Period, if this variable is periodic
|
||||||
cvm::real period;
|
cvm::real period = 0.0;
|
||||||
|
|
||||||
/// Center of wrapping, if this variable is periodic
|
/// Center of wrapping, if this variable is periodic
|
||||||
cvm::real wrap_center;
|
cvm::real wrap_center = 0.0;
|
||||||
|
|
||||||
/// \brief Expand the boundaries of multiples of width, to keep the
|
/// \brief Expand the boundaries of multiples of width, to keep the
|
||||||
/// value always within range
|
/// value always within range
|
||||||
bool expand_boundaries;
|
bool expand_boundaries = false;
|
||||||
|
|
||||||
/// \brief Location of the lower boundary
|
/// \brief Location of the lower boundary
|
||||||
colvarvalue lower_boundary;
|
colvarvalue lower_boundary;
|
||||||
@ -252,6 +251,9 @@ public:
|
|||||||
/// Main init function
|
/// Main init function
|
||||||
int init(std::string const &conf);
|
int init(std::string const &conf);
|
||||||
|
|
||||||
|
/// Populate the map of available CVC types
|
||||||
|
void define_component_types();
|
||||||
|
|
||||||
/// Parse the CVC configuration and allocate their data
|
/// Parse the CVC configuration and allocate their data
|
||||||
int init_components(std::string const &conf);
|
int init_components(std::string const &conf);
|
||||||
|
|
||||||
@ -271,17 +273,13 @@ public:
|
|||||||
virtual int init_dependencies();
|
virtual int init_dependencies();
|
||||||
|
|
||||||
private:
|
private:
|
||||||
/// Parse the CVC configuration for all components of a certain type
|
|
||||||
template<typename def_class_name> int init_components_type(std::string const & conf,
|
/// Declare an available CVC type and its description, register them in the global map
|
||||||
char const *def_desc,
|
template <typename def_class_name>
|
||||||
char const *def_config_key);
|
void add_component_type(char const *description, char const *config_key);
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
/// For the C++11 case, the names of all available components are
|
/// Initialize any CVC objects matching the given key
|
||||||
/// registered in the global map at first, and then the CVC configuration
|
int init_components_type(const std::string &conf, const char *config_key);
|
||||||
/// is parsed by this function
|
|
||||||
int init_components_type_from_global_map(const std::string& conf,
|
|
||||||
const char* def_config_key);
|
|
||||||
#endif
|
|
||||||
|
|
||||||
public:
|
public:
|
||||||
|
|
||||||
@ -387,10 +385,10 @@ public:
|
|||||||
protected:
|
protected:
|
||||||
|
|
||||||
/// \brief Number of CVC objects with an active flag
|
/// \brief Number of CVC objects with an active flag
|
||||||
size_t n_active_cvcs;
|
size_t n_active_cvcs = 0;
|
||||||
|
|
||||||
/// Sum of square coefficients for active cvcs
|
/// Sum of square coefficients for active cvcs
|
||||||
cvm::real active_cvc_square_norm;
|
cvm::real active_cvc_square_norm = 0.0;
|
||||||
|
|
||||||
/// Update the sum of square coefficients for active cvcs
|
/// Update the sum of square coefficients for active cvcs
|
||||||
void update_active_cvc_square_norm();
|
void update_active_cvc_square_norm();
|
||||||
@ -460,16 +458,35 @@ public:
|
|||||||
/// Write a label to the trajectory file (comment line)
|
/// Write a label to the trajectory file (comment line)
|
||||||
std::ostream & write_traj_label(std::ostream &os);
|
std::ostream & write_traj_label(std::ostream &os);
|
||||||
|
|
||||||
/// Read the collective variable from a restart file
|
/// Read the colvar's state from a formatted input stream
|
||||||
std::istream & read_state(std::istream &is);
|
std::istream & read_state(std::istream &is);
|
||||||
/// Write the collective variable to a restart file
|
|
||||||
std::ostream & write_state(std::ostream &os);
|
/// Read the colvar's state from an unformatted input stream
|
||||||
|
cvm::memory_stream & read_state(cvm::memory_stream &is);
|
||||||
|
|
||||||
|
/// Check the name of the bias vs. the given string, set the matching_state flag accordingly
|
||||||
|
int check_matching_state(std::string const &state_conf);
|
||||||
|
|
||||||
|
/// Read the values of colvar mutable data from a string (used by both versions of read_state())
|
||||||
|
int set_state_params(std::string const &state_conf);
|
||||||
|
|
||||||
|
/// Write the state information of this colvar in a block of text, suitable for later parsing
|
||||||
|
std::string const get_state_params() const;
|
||||||
|
|
||||||
|
/// Write the colvar's state to a formatted output stream
|
||||||
|
std::ostream & write_state(std::ostream &os) const;
|
||||||
|
|
||||||
|
/// Write the colvar's state to an unformatted output stream
|
||||||
|
cvm::memory_stream & write_state(cvm::memory_stream &os) const;
|
||||||
|
|
||||||
/// Write output files (if defined, e.g. in analysis mode)
|
/// Write output files (if defined, e.g. in analysis mode)
|
||||||
int write_output_files();
|
int write_output_files();
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
|
/// Flag used to tell if the state string being read is for this colvar
|
||||||
|
bool matching_state;
|
||||||
|
|
||||||
/// Previous value (to calculate velocities during analysis)
|
/// Previous value (to calculate velocities during analysis)
|
||||||
colvarvalue x_old;
|
colvarvalue x_old;
|
||||||
|
|
||||||
@ -554,15 +571,15 @@ protected:
|
|||||||
/// Current value of the running average
|
/// Current value of the running average
|
||||||
colvarvalue runave;
|
colvarvalue runave;
|
||||||
/// Current value of the square deviation from the running average
|
/// Current value of the square deviation from the running average
|
||||||
cvm::real runave_variance;
|
cvm::real runave_variance = 0.0;
|
||||||
|
|
||||||
/// Calculate the running average and its standard deviation
|
/// Calculate the running average and its standard deviation
|
||||||
int calc_runave();
|
int calc_runave();
|
||||||
|
|
||||||
/// If extended Lagrangian active: colvar kinetic energy
|
/// If extended Lagrangian active: colvar kinetic energy
|
||||||
cvm::real kinetic_energy;
|
cvm::real kinetic_energy = 0.0;
|
||||||
/// If extended Lagrangian active: colvar harmonic potential
|
/// If extended Lagrangian active: colvar harmonic potential
|
||||||
cvm::real potential_energy;
|
cvm::real potential_energy = 0.0;
|
||||||
|
|
||||||
public:
|
public:
|
||||||
|
|
||||||
@ -601,8 +618,9 @@ public:
|
|||||||
class dihedPC;
|
class dihedPC;
|
||||||
class alch_lambda;
|
class alch_lambda;
|
||||||
class alch_Flambda;
|
class alch_Flambda;
|
||||||
class componentDisabled;
|
|
||||||
class CartesianBasedPath;
|
class CartesianBasedPath;
|
||||||
|
class aspath;
|
||||||
|
class azpath;
|
||||||
class gspath;
|
class gspath;
|
||||||
class gzpath;
|
class gzpath;
|
||||||
class linearCombination;
|
class linearCombination;
|
||||||
@ -626,21 +644,19 @@ public:
|
|||||||
// components that do not handle any atoms directly
|
// components that do not handle any atoms directly
|
||||||
class map_total;
|
class map_total;
|
||||||
|
|
||||||
/// getter of the global cvc map
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
/// A global mapping of cvc names to the cvc constructors
|
/// A global mapping of cvc names to the cvc constructors
|
||||||
static const std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& get_global_cvc_map() {
|
static const std::map<std::string, std::function<colvar::cvc *()>> &get_global_cvc_map()
|
||||||
return global_cvc_map;
|
{
|
||||||
|
return global_cvc_map;
|
||||||
}
|
}
|
||||||
#endif
|
|
||||||
|
|
||||||
/// \brief function for sorting cvcs by their names
|
/// \brief function for sorting cvcs by their names
|
||||||
static bool compare_cvc(const colvar::cvc* const i, const colvar::cvc* const j);
|
static bool compare_cvc(const colvar::cvc* const i, const colvar::cvc* const j);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
/// \brief Array of \link colvar::cvc \endlink objects
|
/// Array of components objects
|
||||||
std::vector<cvc *> cvcs;
|
std::vector<std::shared_ptr<colvar::cvc>> cvcs;
|
||||||
|
|
||||||
/// \brief Flags to enable or disable cvcs at next colvar evaluation
|
/// \brief Flags to enable or disable cvcs at next colvar evaluation
|
||||||
std::vector<bool> cvc_flags;
|
std::vector<bool> cvc_flags;
|
||||||
@ -671,10 +687,11 @@ protected:
|
|||||||
double dev_null;
|
double dev_null;
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
/// A global mapping of cvc names to the cvc constructors
|
/// A global mapping of cvc names to the cvc constructors
|
||||||
static std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> global_cvc_map;
|
static std::map<std::string, std::function<colvar::cvc *()>> global_cvc_map;
|
||||||
#endif
|
|
||||||
|
/// A global mapping of cvc names to the corresponding descriptions
|
||||||
|
static std::map<std::string, std::string> global_cvc_desc_map;
|
||||||
|
|
||||||
/// Volmap numeric IDs, one for each CVC (-1 if not available)
|
/// Volmap numeric IDs, one for each CVC (-1 if not available)
|
||||||
std::vector<int> volmap_ids_;
|
std::vector<int> volmap_ids_;
|
||||||
@ -762,4 +779,3 @@ inline void colvar::reset_bias_force() {
|
|||||||
}
|
}
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
|||||||
@ -7,126 +7,84 @@
|
|||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <limits>
|
#include <limits>
|
||||||
#include <string>
|
#include <string>
|
||||||
|
#include <algorithm>
|
||||||
|
|
||||||
namespace ArithmeticPathCV {
|
namespace ArithmeticPathCV {
|
||||||
|
|
||||||
using std::vector;
|
using std::vector;
|
||||||
|
|
||||||
enum path_sz {S, Z};
|
template <typename scalar_type>
|
||||||
|
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
|
||||||
class ArithmeticPathBase {
|
class ArithmeticPathBase {
|
||||||
public:
|
public:
|
||||||
ArithmeticPathBase() {}
|
ArithmeticPathBase() {}
|
||||||
virtual ~ArithmeticPathBase() {}
|
~ArithmeticPathBase() {}
|
||||||
virtual void initialize(size_t p_num_elements, size_t p_total_frames, double p_lambda, const vector<element_type>& p_element, const vector<double>& p_weights);
|
void initialize(size_t p_num_elements, size_t p_total_frames, scalar_type p_lambda, const vector<scalar_type>& p_weights);
|
||||||
virtual void updateDistanceToReferenceFrames() = 0;
|
void reComputeLambda(const vector<scalar_type>& rmsd_between_refs);
|
||||||
virtual void computeValue();
|
template <typename element_type>
|
||||||
virtual void computeDerivatives();
|
void computeValue(const vector<vector<element_type>>& frame_element_distances, scalar_type *s = nullptr, scalar_type *z = nullptr);
|
||||||
virtual void compute();
|
// can only be called after computeValue() for element-wise derivatives and store derivatives of i-th frame to dsdx and dzdx
|
||||||
virtual void reComputeLambda(const vector<scalar_type>& rmsd_between_refs);
|
template <typename element_type>
|
||||||
|
void computeDerivatives(const vector<vector<element_type>>& frame_element_distances, vector<vector<element_type>> *dsdx = nullptr, vector<vector<element_type>> *dzdx = nullptr);
|
||||||
protected:
|
protected:
|
||||||
scalar_type lambda;
|
scalar_type lambda;
|
||||||
vector<scalar_type> weights;
|
vector<scalar_type> squared_weights;
|
||||||
size_t num_elements;
|
size_t num_elements;
|
||||||
size_t total_frames;
|
size_t total_frames;
|
||||||
vector< vector<element_type> > frame_element_distances;
|
vector<scalar_type> exponents;
|
||||||
scalar_type s;
|
scalar_type max_exponent;
|
||||||
scalar_type z;
|
scalar_type saved_exponent_sum;
|
||||||
vector<element_type> dsdx;
|
|
||||||
vector<element_type> dzdx;
|
|
||||||
private:
|
|
||||||
// intermediate variables
|
|
||||||
vector<scalar_type> s_numerator_frame;
|
|
||||||
vector<scalar_type> s_denominator_frame;
|
|
||||||
scalar_type numerator_s;
|
|
||||||
scalar_type denominator_s;
|
|
||||||
scalar_type normalization_factor;
|
scalar_type normalization_factor;
|
||||||
|
scalar_type saved_s;
|
||||||
};
|
};
|
||||||
|
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
template <typename scalar_type>
|
||||||
void ArithmeticPathBase<element_type, scalar_type, path_type>::initialize(size_t p_num_elements, size_t p_total_frames, double p_lambda, const vector<element_type>& p_element, const vector<double>& p_weights) {
|
void ArithmeticPathBase<scalar_type>::initialize(size_t p_num_elements, size_t p_total_frames, scalar_type p_lambda, const vector<scalar_type>& p_weights) {
|
||||||
lambda = p_lambda;
|
lambda = p_lambda;
|
||||||
weights = p_weights;
|
for (size_t i = 0; i < p_weights.size(); ++i) squared_weights.push_back(p_weights[i] * p_weights[i]);
|
||||||
num_elements = p_num_elements;
|
num_elements = p_num_elements;
|
||||||
total_frames = p_total_frames;
|
total_frames = p_total_frames;
|
||||||
frame_element_distances.resize(total_frames, p_element);
|
exponents.resize(total_frames);
|
||||||
for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
|
|
||||||
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
|
||||||
frame_element_distances[i_frame][j_elem].reset();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
s = scalar_type(0);
|
|
||||||
z = scalar_type(0);
|
|
||||||
dsdx = p_element;
|
|
||||||
dzdx = p_element;
|
|
||||||
s_numerator_frame.resize(total_frames, scalar_type(0));
|
|
||||||
s_denominator_frame.resize(total_frames, scalar_type(0));
|
|
||||||
numerator_s = scalar_type(0);
|
|
||||||
denominator_s = scalar_type(0);
|
|
||||||
normalization_factor = 1.0 / static_cast<scalar_type>(total_frames - 1);
|
normalization_factor = 1.0 / static_cast<scalar_type>(total_frames - 1);
|
||||||
|
saved_s = scalar_type();
|
||||||
|
saved_exponent_sum = scalar_type();
|
||||||
|
max_exponent = scalar_type();
|
||||||
}
|
}
|
||||||
|
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
template <typename scalar_type>
|
||||||
void ArithmeticPathBase<element_type, scalar_type, path_type>::computeValue() {
|
template <typename element_type>
|
||||||
updateDistanceToReferenceFrames();
|
void ArithmeticPathBase<scalar_type>::computeValue(
|
||||||
numerator_s = scalar_type(0);
|
const vector<vector<element_type>>& frame_element_distances,
|
||||||
denominator_s = scalar_type(0);
|
scalar_type *s, scalar_type *z)
|
||||||
for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
|
{
|
||||||
scalar_type exponent_tmp = scalar_type(0);
|
for (size_t i_frame = 0; i_frame < total_frames; ++i_frame) {
|
||||||
|
scalar_type exponent_tmp = scalar_type();
|
||||||
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
||||||
exponent_tmp += weights[j_elem] * frame_element_distances[i_frame][j_elem] * weights[j_elem] * frame_element_distances[i_frame][j_elem];
|
exponent_tmp += squared_weights[j_elem] * frame_element_distances[i_frame][j_elem] * frame_element_distances[i_frame][j_elem];
|
||||||
}
|
}
|
||||||
exponent_tmp = exponent_tmp * -1.0 * lambda;
|
exponents[i_frame] = exponent_tmp * -1.0 * lambda;
|
||||||
// prevent underflow if the argument of cvm::exp is less than -708.4
|
if (i_frame == 0 || exponents[i_frame] > max_exponent) max_exponent = exponents[i_frame];
|
||||||
if (exponent_tmp > -708.4) {
|
|
||||||
exponent_tmp = cvm::exp(exponent_tmp);
|
|
||||||
} else {
|
|
||||||
exponent_tmp = 0;
|
|
||||||
}
|
|
||||||
numerator_s += static_cast<scalar_type>(i_frame) * exponent_tmp;
|
|
||||||
denominator_s += exponent_tmp;
|
|
||||||
s_numerator_frame[i_frame] = static_cast<scalar_type>(i_frame) * exponent_tmp;
|
|
||||||
s_denominator_frame[i_frame] = exponent_tmp;
|
|
||||||
}
|
}
|
||||||
s = numerator_s / denominator_s * normalization_factor;
|
scalar_type log_sum_exp_0 = scalar_type();
|
||||||
z = -1.0 / lambda * cvm::logn(denominator_s);
|
scalar_type log_sum_exp_1 = scalar_type();
|
||||||
}
|
for (size_t i_frame = 0; i_frame < total_frames; ++i_frame) {
|
||||||
|
exponents[i_frame] = cvm::exp(exponents[i_frame] - max_exponent);
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
log_sum_exp_0 += exponents[i_frame];
|
||||||
void ArithmeticPathBase<element_type, scalar_type, path_type>::compute() {
|
log_sum_exp_1 += i_frame * exponents[i_frame];
|
||||||
computeValue();
|
}
|
||||||
computeDerivatives();
|
saved_exponent_sum = log_sum_exp_0;
|
||||||
}
|
log_sum_exp_0 = max_exponent + cvm::logn(log_sum_exp_0);
|
||||||
|
log_sum_exp_1 = max_exponent + cvm::logn(log_sum_exp_1);
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
saved_s = normalization_factor * cvm::exp(log_sum_exp_1 - log_sum_exp_0);
|
||||||
void ArithmeticPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
|
if (s != nullptr) {
|
||||||
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
*s = saved_s;
|
||||||
element_type dsdxj_numerator_part1(dsdx[j_elem]);
|
}
|
||||||
element_type dsdxj_numerator_part2(dsdx[j_elem]);
|
if (z != nullptr) {
|
||||||
element_type dzdxj_numerator(dsdx[j_elem]);
|
*z = -1.0 / lambda * log_sum_exp_0;
|
||||||
dsdxj_numerator_part1.reset();
|
|
||||||
dsdxj_numerator_part2.reset();
|
|
||||||
dzdxj_numerator.reset();
|
|
||||||
for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
|
|
||||||
element_type derivative_tmp = -2.0 * lambda * weights[j_elem] * weights[j_elem] * frame_element_distances[i_frame][j_elem];
|
|
||||||
dsdxj_numerator_part1 += s_numerator_frame[i_frame] * derivative_tmp;
|
|
||||||
dsdxj_numerator_part2 += s_denominator_frame[i_frame] * derivative_tmp;
|
|
||||||
dzdxj_numerator += s_denominator_frame[i_frame] * derivative_tmp;
|
|
||||||
}
|
|
||||||
dsdxj_numerator_part1 *= denominator_s;
|
|
||||||
dsdxj_numerator_part2 *= numerator_s;
|
|
||||||
if ((dsdxj_numerator_part1 - dsdxj_numerator_part2).norm() < std::numeric_limits<scalar_type>::min()) {
|
|
||||||
dsdx[j_elem] = 0;
|
|
||||||
} else {
|
|
||||||
dsdx[j_elem] = (dsdxj_numerator_part1 - dsdxj_numerator_part2) / (denominator_s * denominator_s) * normalization_factor;
|
|
||||||
}
|
|
||||||
dzdx[j_elem] = -1.0 / lambda * dzdxj_numerator / denominator_s;
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
template <typename element_type, typename scalar_type, path_sz path_type>
|
template <typename scalar_type>
|
||||||
void ArithmeticPathBase<element_type, scalar_type, path_type>::reComputeLambda(const vector<scalar_type>& rmsd_between_refs) {
|
void ArithmeticPathBase<scalar_type>::reComputeLambda(const vector<scalar_type>& rmsd_between_refs) {
|
||||||
scalar_type mean_square_displacements = 0.0;
|
scalar_type mean_square_displacements = 0.0;
|
||||||
for (size_t i_frame = 1; i_frame < total_frames; ++i_frame) {
|
for (size_t i_frame = 1; i_frame < total_frames; ++i_frame) {
|
||||||
cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n"));
|
cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n"));
|
||||||
@ -135,6 +93,45 @@ void ArithmeticPathBase<element_type, scalar_type, path_type>::reComputeLambda(c
|
|||||||
mean_square_displacements /= scalar_type(total_frames - 1);
|
mean_square_displacements /= scalar_type(total_frames - 1);
|
||||||
lambda = 1.0 / mean_square_displacements;
|
lambda = 1.0 / mean_square_displacements;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// frame-wise derivatives for frames using optimal rotation
|
||||||
|
template <typename scalar_type>
|
||||||
|
template <typename element_type>
|
||||||
|
void ArithmeticPathBase<scalar_type>::computeDerivatives(
|
||||||
|
const vector<vector<element_type>>& frame_element_distances,
|
||||||
|
vector<vector<element_type>> *dsdx,
|
||||||
|
vector<vector<element_type>> *dzdx)
|
||||||
|
{
|
||||||
|
vector<scalar_type> softmax_out, tmps;
|
||||||
|
softmax_out.reserve(total_frames);
|
||||||
|
tmps.reserve(total_frames);
|
||||||
|
for (size_t i_frame = 0; i_frame < total_frames; ++i_frame) {
|
||||||
|
softmax_out.push_back(exponents[i_frame] / saved_exponent_sum);
|
||||||
|
tmps.push_back(
|
||||||
|
(static_cast<scalar_type>(i_frame) -
|
||||||
|
static_cast<scalar_type>(total_frames - 1) * saved_s) *
|
||||||
|
normalization_factor);
|
||||||
|
}
|
||||||
|
if (dsdx != nullptr) {
|
||||||
|
for (size_t i_frame = 0; i_frame < total_frames; ++i_frame) {
|
||||||
|
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
||||||
|
(*dsdx)[i_frame][j_elem] =
|
||||||
|
-2.0 * squared_weights[j_elem] * lambda *
|
||||||
|
frame_element_distances[i_frame][j_elem] *
|
||||||
|
softmax_out[i_frame] * tmps[i_frame];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (dzdx != nullptr) {
|
||||||
|
for (size_t i_frame = 0; i_frame < total_frames; ++i_frame) {
|
||||||
|
for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
|
||||||
|
(*dzdx)[i_frame][j_elem] =
|
||||||
|
2.0 * squared_weights[j_elem] * softmax_out[i_frame] *
|
||||||
|
frame_element_distances[i_frame][j_elem];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
#endif // ARITHMETICPATHCV_H
|
#endif // ARITHMETICPATHCV_H
|
||||||
|
|||||||
@ -8,12 +8,13 @@
|
|||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
|
||||||
|
#include <algorithm>
|
||||||
|
#include <cmath>
|
||||||
|
#include <string>
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
|
|
||||||
#include <vector>
|
|
||||||
#include <cmath>
|
|
||||||
#include <algorithm>
|
|
||||||
#include <string>
|
|
||||||
|
|
||||||
namespace GeometricPathCV {
|
namespace GeometricPathCV {
|
||||||
|
|
||||||
@ -171,10 +172,14 @@ void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFr
|
|||||||
sign = -1;
|
sign = -1;
|
||||||
}
|
}
|
||||||
if (cvm::fabs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
|
if (cvm::fabs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
|
||||||
std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n";
|
std::string message(
|
||||||
std::cout << " Please check your configuration or increase restraint on z(σ)\n";
|
"Warning: Geometrical pathCV relies on the assumption that the second closest frame is "
|
||||||
|
"the neighbouring frame\n"
|
||||||
|
" Please check your configuration or increase restraint on z(σ)\n");
|
||||||
for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
|
for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
|
||||||
std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n";
|
message += "Frame index: " + cvm::to_str(frame_index[i_frame]) +
|
||||||
|
" ; optimal RMSD = " + cvm::to_str(frame_distances[frame_index[i_frame]]) +
|
||||||
|
"\n";
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
min_frame_index_1 = frame_index[0]; // s_m
|
min_frame_index_1 = frame_index[0]; // s_m
|
||||||
|
|||||||
@ -10,7 +10,6 @@
|
|||||||
#include <iostream>
|
#include <iostream>
|
||||||
#include <fstream>
|
#include <fstream>
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
#include "colvar_neuralnetworkcompute.h"
|
#include "colvar_neuralnetworkcompute.h"
|
||||||
#include "colvarparse.h"
|
#include "colvarparse.h"
|
||||||
#include "colvarproxy.h"
|
#include "colvarproxy.h"
|
||||||
@ -272,9 +271,12 @@ std::vector<std::vector<double>> neuralNetworkCompute::multiply_matrix(const std
|
|||||||
const size_t t = B[0].size();
|
const size_t t = B[0].size();
|
||||||
std::vector<std::vector<double>> C(m, std::vector<double>(t, 0.0));
|
std::vector<std::vector<double>> C(m, std::vector<double>(t, 0.0));
|
||||||
for (size_t i = 0; i < m; ++i) {
|
for (size_t i = 0; i < m; ++i) {
|
||||||
for (size_t j = 0; j < t; ++j) {
|
for (size_t k = 0; k < n; ++k) {
|
||||||
for (size_t k = 0; k < n; ++k) {
|
const auto tmp = A[i][k];
|
||||||
C[i][j] += A[i][k] * B[k][j];
|
auto& C_i = C[i];
|
||||||
|
auto& B_k = B[k];
|
||||||
|
for (size_t j = 0; j < t; ++j) {
|
||||||
|
C_i[j] += tmp * B_k[j];
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -306,5 +308,3 @@ void neuralNetworkCompute::compute() {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
#endif
|
|
||||||
|
|||||||
@ -7,7 +7,6 @@
|
|||||||
// If you wish to distribute your changes, please submit them to the
|
// If you wish to distribute your changes, please submit them to the
|
||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
#if (__cplusplus >= 201103L)
|
|
||||||
#ifndef NEURALNETWORKCOMPUTE_H
|
#ifndef NEURALNETWORKCOMPUTE_H
|
||||||
#define NEURALNETWORKCOMPUTE_H
|
#define NEURALNETWORKCOMPUTE_H
|
||||||
|
|
||||||
@ -145,4 +144,3 @@ public:
|
|||||||
|
|
||||||
}
|
}
|
||||||
#endif
|
#endif
|
||||||
#endif
|
|
||||||
|
|||||||
627
lib/colvars/colvar_rotation_derivative.h
Normal file
627
lib/colvars/colvar_rotation_derivative.h
Normal file
@ -0,0 +1,627 @@
|
|||||||
|
#ifndef COLVAR_ROTATION_DERIVATIVE
|
||||||
|
#define COLVAR_ROTATION_DERIVATIVE
|
||||||
|
|
||||||
|
#include "colvartypes.h"
|
||||||
|
#include <type_traits>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
/// \brief Helper function for loading the ia-th atom in the vector pos to x, y and z (C++11 SFINAE is used)
|
||||||
|
template <typename T, typename std::enable_if<std::is_same<T, cvm::atom_pos>::value, bool>::type = true>
|
||||||
|
inline void read_atom_coord(
|
||||||
|
size_t ia, const std::vector<T>& pos,
|
||||||
|
cvm::real* x, cvm::real* y, cvm::real* z) {
|
||||||
|
*x = pos[ia].x;
|
||||||
|
*y = pos[ia].y;
|
||||||
|
*z = pos[ia].z;
|
||||||
|
}
|
||||||
|
|
||||||
|
template <typename T, typename std::enable_if<std::is_same<T, cvm::atom>::value, bool>::type = true>
|
||||||
|
inline void read_atom_coord(
|
||||||
|
size_t ia, const std::vector<T>& pos,
|
||||||
|
cvm::real* x, cvm::real* y, cvm::real* z) {
|
||||||
|
*x = pos[ia].pos.x;
|
||||||
|
*y = pos[ia].pos.y;
|
||||||
|
*z = pos[ia].pos.z;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// \brief Helper enum class for specifying options in rotation_derivative::prepare_derivative
|
||||||
|
enum class rotation_derivative_dldq {
|
||||||
|
/// Require the derivative of the leading eigenvalue with respect to the atom coordinats
|
||||||
|
use_dl = 1 << 0,
|
||||||
|
/// Require the derivative of the leading eigenvector with respect to the atom coordinats
|
||||||
|
use_dq = 1 << 1
|
||||||
|
};
|
||||||
|
|
||||||
|
inline constexpr rotation_derivative_dldq operator|(rotation_derivative_dldq Lhs, rotation_derivative_dldq Rhs) {
|
||||||
|
return static_cast<rotation_derivative_dldq>(
|
||||||
|
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Lhs) |
|
||||||
|
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Rhs));
|
||||||
|
}
|
||||||
|
|
||||||
|
inline constexpr bool operator&(rotation_derivative_dldq Lhs, rotation_derivative_dldq Rhs)
|
||||||
|
{
|
||||||
|
return (static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Lhs) &
|
||||||
|
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Rhs));
|
||||||
|
}
|
||||||
|
|
||||||
|
/// \brief Helper class for calculating the derivative of rotation
|
||||||
|
template <typename T1, typename T2>
|
||||||
|
struct rotation_derivative {
|
||||||
|
static_assert(std::is_same<T1, cvm::atom_pos>::value || std::is_same<T1, cvm::atom>::value,
|
||||||
|
"class template rotation_derivative only supports cvm::atom_pos or cvm::atom types.");
|
||||||
|
static_assert(std::is_same<T2, cvm::atom_pos>::value || std::is_same<T2, cvm::atom>::value,
|
||||||
|
"class template rotation_derivative only supports cvm::atom_pos or cvm::atom types.");
|
||||||
|
/// \brief Reference to the rotation
|
||||||
|
const cvm::rotation &m_rot;
|
||||||
|
/// \brief Reference to the atom positions of group 1
|
||||||
|
const std::vector<T1> &m_pos1;
|
||||||
|
/// \brief Reference to the atom positions of group 2
|
||||||
|
const std::vector<T2> &m_pos2;
|
||||||
|
/// \brief Temporary variable that will be updated if prepare_derivative called
|
||||||
|
cvm::real tmp_Q0Q0[4][4];
|
||||||
|
cvm::real tmp_Q0Q0_L[4][4][4];
|
||||||
|
/*! @brief Constructor of the cvm::rotation::derivative class
|
||||||
|
* @param[in] rot The cvm::rotation object (must have called
|
||||||
|
* `calc_optimal_rotation` before calling
|
||||||
|
* `calc_derivative_wrt_group1` and
|
||||||
|
* `calc_derivative_wrt_group2`)
|
||||||
|
* @param[in] pos1 The atom positions of group 1
|
||||||
|
* @param[in] pos2 The atom positions of group 2
|
||||||
|
*/
|
||||||
|
rotation_derivative(
|
||||||
|
const cvm::rotation &rot,
|
||||||
|
const std::vector<T1> &pos1,
|
||||||
|
const std::vector<T2> &pos2):
|
||||||
|
m_rot(rot), m_pos1(pos1), m_pos2(pos2) {};
|
||||||
|
/*! @brief This function must be called before `calc_derivative_wrt_group1`
|
||||||
|
* and `calc_derivative_wrt_group2` in order to prepare the tmp_Q0Q0
|
||||||
|
* and tmp_Q0Q0_L.
|
||||||
|
* @param[in] require_dl_dq Require the calculation of the derivatives of L or/and Q
|
||||||
|
* with respect to atoms.
|
||||||
|
*/
|
||||||
|
void prepare_derivative(rotation_derivative_dldq require_dl_dq) {
|
||||||
|
if (require_dl_dq & rotation_derivative_dldq::use_dl) {
|
||||||
|
const auto &Q0 = m_rot.S_eigvec[0];
|
||||||
|
tmp_Q0Q0[0][0] = Q0[0] * Q0[0];
|
||||||
|
tmp_Q0Q0[0][1] = Q0[0] * Q0[1];
|
||||||
|
tmp_Q0Q0[0][2] = Q0[0] * Q0[2];
|
||||||
|
tmp_Q0Q0[0][3] = Q0[0] * Q0[3];
|
||||||
|
tmp_Q0Q0[1][0] = Q0[1] * Q0[0];
|
||||||
|
tmp_Q0Q0[1][1] = Q0[1] * Q0[1];
|
||||||
|
tmp_Q0Q0[1][2] = Q0[1] * Q0[2];
|
||||||
|
tmp_Q0Q0[1][3] = Q0[1] * Q0[3];
|
||||||
|
tmp_Q0Q0[2][0] = Q0[2] * Q0[0];
|
||||||
|
tmp_Q0Q0[2][1] = Q0[2] * Q0[1];
|
||||||
|
tmp_Q0Q0[2][2] = Q0[2] * Q0[2];
|
||||||
|
tmp_Q0Q0[2][3] = Q0[2] * Q0[3];
|
||||||
|
tmp_Q0Q0[3][0] = Q0[3] * Q0[0];
|
||||||
|
tmp_Q0Q0[3][1] = Q0[3] * Q0[1];
|
||||||
|
tmp_Q0Q0[3][2] = Q0[3] * Q0[2];
|
||||||
|
tmp_Q0Q0[3][3] = Q0[3] * Q0[3];
|
||||||
|
}
|
||||||
|
if (require_dl_dq & rotation_derivative_dldq::use_dq) {
|
||||||
|
const auto &Q0 = m_rot.S_eigvec[0];
|
||||||
|
const auto &Q1 = m_rot.S_eigvec[1];
|
||||||
|
const auto &Q2 = m_rot.S_eigvec[2];
|
||||||
|
const auto &Q3 = m_rot.S_eigvec[3];
|
||||||
|
cvm::real const L0 = m_rot.S_eigval[0];
|
||||||
|
cvm::real const L1 = m_rot.S_eigval[1];
|
||||||
|
cvm::real const L2 = m_rot.S_eigval[2];
|
||||||
|
cvm::real const L3 = m_rot.S_eigval[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[0] * Q0[0]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[0] * Q0[0]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[0] * Q0[0]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[0] * Q0[0]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[0] * Q0[0]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[0] * Q0[0]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[0] * Q0[0]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[0] * Q0[0]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[0] * Q0[1]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[0] * Q0[1]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[0] * Q0[1]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[0] * Q0[1]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[0] * Q0[1]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[0] * Q0[1]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[0] * Q0[1]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[0] * Q0[1]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[0] * Q0[2]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[0] * Q0[2]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[0] * Q0[2]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[0] * Q0[2]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[0] * Q0[2]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[0] * Q0[2]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[0] * Q0[2]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[0] * Q0[2]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[0] * Q0[3]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[0] * Q0[3]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[0] * Q0[3]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[0] * Q0[3]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[0] * Q0[3]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[0] * Q0[3]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[0] * Q0[3]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[0] * Q0[3]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[1] * Q0[0]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[1] * Q0[0]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[1] * Q0[0]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[1] * Q0[0]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[1] * Q0[0]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[1] * Q0[0]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[1] * Q0[0]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[1] * Q0[0]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[1] * Q0[1]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[1] * Q0[1]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[1] * Q0[1]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[1] * Q0[1]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[1] * Q0[1]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[1] * Q0[1]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[1] * Q0[1]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[1] * Q0[1]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[1] * Q0[2]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[1] * Q0[2]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[1] * Q0[2]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[1] * Q0[2]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[1] * Q0[2]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[1] * Q0[2]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[1] * Q0[2]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[1] * Q0[2]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[1] * Q0[3]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[1] * Q0[3]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[1] * Q0[3]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[1] * Q0[3]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[1] * Q0[3]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[1] * Q0[3]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[1] * Q0[3]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[1] * Q0[3]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[2] * Q0[0]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[2] * Q0[0]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[2] * Q0[0]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[2] * Q0[0]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[2] * Q0[0]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[2] * Q0[0]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[2] * Q0[0]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[2] * Q0[0]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[2] * Q0[1]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[2] * Q0[1]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[2] * Q0[1]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[2] * Q0[1]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[2] * Q0[1]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[2] * Q0[1]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[2] * Q0[1]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[2] * Q0[1]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[2] * Q0[2]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[2] * Q0[2]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[2] * Q0[2]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[2] * Q0[2]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[2] * Q0[2]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[2] * Q0[2]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[2] * Q0[2]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[2] * Q0[2]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[2] * Q0[3]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[2] * Q0[3]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[2] * Q0[3]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[2] * Q0[3]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[2] * Q0[3]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[2] * Q0[3]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[2] * Q0[3]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[2] * Q0[3]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[3] * Q0[0]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[3] * Q0[0]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[3] * Q0[0]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[3] * Q0[0]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[3] * Q0[0]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[3] * Q0[0]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[3] * Q0[0]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[3] * Q0[0]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[3] * Q0[1]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[3] * Q0[1]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[3] * Q0[1]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[3] * Q0[1]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[3] * Q0[1]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[3] * Q0[1]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[3] * Q0[1]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[3] * Q0[1]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[3] * Q0[2]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[3] * Q0[2]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[3] * Q0[2]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[3] * Q0[2]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[3] * Q0[2]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[3] * Q0[2]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[3] * Q0[2]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[3] * Q0[2]) / (L0-L3) * Q3[3];
|
||||||
|
|
||||||
|
tmp_Q0Q0_L[0][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[0] +
|
||||||
|
(Q2[3] * Q0[3]) / (L0-L2) * Q2[0] +
|
||||||
|
(Q3[3] * Q0[3]) / (L0-L3) * Q3[0];
|
||||||
|
tmp_Q0Q0_L[1][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[1] +
|
||||||
|
(Q2[3] * Q0[3]) / (L0-L2) * Q2[1] +
|
||||||
|
(Q3[3] * Q0[3]) / (L0-L3) * Q3[1];
|
||||||
|
tmp_Q0Q0_L[2][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[2] +
|
||||||
|
(Q2[3] * Q0[3]) / (L0-L2) * Q2[2] +
|
||||||
|
(Q3[3] * Q0[3]) / (L0-L3) * Q3[2];
|
||||||
|
tmp_Q0Q0_L[3][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[3] +
|
||||||
|
(Q2[3] * Q0[3]) / (L0-L2) * Q2[3] +
|
||||||
|
(Q3[3] * Q0[3]) / (L0-L3) * Q3[3];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
/*! @brief Actual implementation of the derivative calculation
|
||||||
|
* @param[in] ds The derivative of matrix S with respect to an atom of
|
||||||
|
* either group 1 or group 2
|
||||||
|
* @param[out] dl0_out The output of derivative of L
|
||||||
|
* @param[out] dq0_out The output of derivative of Q
|
||||||
|
* @param[out] ds_out The output of derivative of overlap matrix S
|
||||||
|
*/
|
||||||
|
void calc_derivative_impl(
|
||||||
|
const cvm::rvector (&ds)[4][4],
|
||||||
|
cvm::rvector* const dl0_out,
|
||||||
|
cvm::vector1d<cvm::rvector>* const dq0_out,
|
||||||
|
cvm::matrix2d<cvm::rvector>* const ds_out) const {
|
||||||
|
if (ds_out != nullptr) {
|
||||||
|
// this code path is for debug_gradients, so not necessary to unroll the loop
|
||||||
|
*ds_out = cvm::matrix2d<cvm::rvector>(4, 4);
|
||||||
|
for (int i = 0; i < 4; ++i) {
|
||||||
|
for (int j = 0; j < 4; ++j) {
|
||||||
|
(*ds_out)[i][j] = ds[i][j];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (dl0_out != nullptr) {
|
||||||
|
/* manually loop unrolling of the following loop:
|
||||||
|
dl0_1.reset();
|
||||||
|
for (size_t i = 0; i < 4; i++) {
|
||||||
|
for (size_t j = 0; j < 4; j++) {
|
||||||
|
dl0_1 += Q0[i] * ds_1[i][j] * Q0[j];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
*dl0_out = tmp_Q0Q0[0][0] * ds[0][0] +
|
||||||
|
tmp_Q0Q0[0][1] * ds[0][1] +
|
||||||
|
tmp_Q0Q0[0][2] * ds[0][2] +
|
||||||
|
tmp_Q0Q0[0][3] * ds[0][3] +
|
||||||
|
tmp_Q0Q0[1][0] * ds[1][0] +
|
||||||
|
tmp_Q0Q0[1][1] * ds[1][1] +
|
||||||
|
tmp_Q0Q0[1][2] * ds[1][2] +
|
||||||
|
tmp_Q0Q0[1][3] * ds[1][3] +
|
||||||
|
tmp_Q0Q0[2][0] * ds[2][0] +
|
||||||
|
tmp_Q0Q0[2][1] * ds[2][1] +
|
||||||
|
tmp_Q0Q0[2][2] * ds[2][2] +
|
||||||
|
tmp_Q0Q0[2][3] * ds[2][3] +
|
||||||
|
tmp_Q0Q0[3][0] * ds[3][0] +
|
||||||
|
tmp_Q0Q0[3][1] * ds[3][1] +
|
||||||
|
tmp_Q0Q0[3][2] * ds[3][2] +
|
||||||
|
tmp_Q0Q0[3][3] * ds[3][3];
|
||||||
|
}
|
||||||
|
if (dq0_out != nullptr) {
|
||||||
|
// we can skip this check if a fixed-size array is used
|
||||||
|
if (dq0_out->size() != 4) dq0_out->resize(4);
|
||||||
|
/* manually loop unrolling of the following loop:
|
||||||
|
dq0_1.reset();
|
||||||
|
for (size_t p = 0; p < 4; p++) {
|
||||||
|
for (size_t i = 0; i < 4; i++) {
|
||||||
|
for (size_t j = 0; j < 4; j++) {
|
||||||
|
dq0_1[p] +=
|
||||||
|
(Q1[i] * ds_1[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
|
||||||
|
(Q2[i] * ds_1[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
|
||||||
|
(Q3[i] * ds_1[i][j] * Q0[j]) / (L0-L3) * Q3[p];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
(*dq0_out)[0] = tmp_Q0Q0_L[0][0][0] * ds[0][0] +
|
||||||
|
tmp_Q0Q0_L[0][0][1] * ds[0][1] +
|
||||||
|
tmp_Q0Q0_L[0][0][2] * ds[0][2] +
|
||||||
|
tmp_Q0Q0_L[0][0][3] * ds[0][3] +
|
||||||
|
tmp_Q0Q0_L[0][1][0] * ds[1][0] +
|
||||||
|
tmp_Q0Q0_L[0][1][1] * ds[1][1] +
|
||||||
|
tmp_Q0Q0_L[0][1][2] * ds[1][2] +
|
||||||
|
tmp_Q0Q0_L[0][1][3] * ds[1][3] +
|
||||||
|
tmp_Q0Q0_L[0][2][0] * ds[2][0] +
|
||||||
|
tmp_Q0Q0_L[0][2][1] * ds[2][1] +
|
||||||
|
tmp_Q0Q0_L[0][2][2] * ds[2][2] +
|
||||||
|
tmp_Q0Q0_L[0][2][3] * ds[2][3] +
|
||||||
|
tmp_Q0Q0_L[0][3][0] * ds[3][0] +
|
||||||
|
tmp_Q0Q0_L[0][3][1] * ds[3][1] +
|
||||||
|
tmp_Q0Q0_L[0][3][2] * ds[3][2] +
|
||||||
|
tmp_Q0Q0_L[0][3][3] * ds[3][3];
|
||||||
|
|
||||||
|
(*dq0_out)[1] = tmp_Q0Q0_L[1][0][0] * ds[0][0] +
|
||||||
|
tmp_Q0Q0_L[1][0][1] * ds[0][1] +
|
||||||
|
tmp_Q0Q0_L[1][0][2] * ds[0][2] +
|
||||||
|
tmp_Q0Q0_L[1][0][3] * ds[0][3] +
|
||||||
|
tmp_Q0Q0_L[1][1][0] * ds[1][0] +
|
||||||
|
tmp_Q0Q0_L[1][1][1] * ds[1][1] +
|
||||||
|
tmp_Q0Q0_L[1][1][2] * ds[1][2] +
|
||||||
|
tmp_Q0Q0_L[1][1][3] * ds[1][3] +
|
||||||
|
tmp_Q0Q0_L[1][2][0] * ds[2][0] +
|
||||||
|
tmp_Q0Q0_L[1][2][1] * ds[2][1] +
|
||||||
|
tmp_Q0Q0_L[1][2][2] * ds[2][2] +
|
||||||
|
tmp_Q0Q0_L[1][2][3] * ds[2][3] +
|
||||||
|
tmp_Q0Q0_L[1][3][0] * ds[3][0] +
|
||||||
|
tmp_Q0Q0_L[1][3][1] * ds[3][1] +
|
||||||
|
tmp_Q0Q0_L[1][3][2] * ds[3][2] +
|
||||||
|
tmp_Q0Q0_L[1][3][3] * ds[3][3];
|
||||||
|
|
||||||
|
(*dq0_out)[2] = tmp_Q0Q0_L[2][0][0] * ds[0][0] +
|
||||||
|
tmp_Q0Q0_L[2][0][1] * ds[0][1] +
|
||||||
|
tmp_Q0Q0_L[2][0][2] * ds[0][2] +
|
||||||
|
tmp_Q0Q0_L[2][0][3] * ds[0][3] +
|
||||||
|
tmp_Q0Q0_L[2][1][0] * ds[1][0] +
|
||||||
|
tmp_Q0Q0_L[2][1][1] * ds[1][1] +
|
||||||
|
tmp_Q0Q0_L[2][1][2] * ds[1][2] +
|
||||||
|
tmp_Q0Q0_L[2][1][3] * ds[1][3] +
|
||||||
|
tmp_Q0Q0_L[2][2][0] * ds[2][0] +
|
||||||
|
tmp_Q0Q0_L[2][2][1] * ds[2][1] +
|
||||||
|
tmp_Q0Q0_L[2][2][2] * ds[2][2] +
|
||||||
|
tmp_Q0Q0_L[2][2][3] * ds[2][3] +
|
||||||
|
tmp_Q0Q0_L[2][3][0] * ds[3][0] +
|
||||||
|
tmp_Q0Q0_L[2][3][1] * ds[3][1] +
|
||||||
|
tmp_Q0Q0_L[2][3][2] * ds[3][2] +
|
||||||
|
tmp_Q0Q0_L[2][3][3] * ds[3][3];
|
||||||
|
|
||||||
|
(*dq0_out)[3] = tmp_Q0Q0_L[3][0][0] * ds[0][0] +
|
||||||
|
tmp_Q0Q0_L[3][0][1] * ds[0][1] +
|
||||||
|
tmp_Q0Q0_L[3][0][2] * ds[0][2] +
|
||||||
|
tmp_Q0Q0_L[3][0][3] * ds[0][3] +
|
||||||
|
tmp_Q0Q0_L[3][1][0] * ds[1][0] +
|
||||||
|
tmp_Q0Q0_L[3][1][1] * ds[1][1] +
|
||||||
|
tmp_Q0Q0_L[3][1][2] * ds[1][2] +
|
||||||
|
tmp_Q0Q0_L[3][1][3] * ds[1][3] +
|
||||||
|
tmp_Q0Q0_L[3][2][0] * ds[2][0] +
|
||||||
|
tmp_Q0Q0_L[3][2][1] * ds[2][1] +
|
||||||
|
tmp_Q0Q0_L[3][2][2] * ds[2][2] +
|
||||||
|
tmp_Q0Q0_L[3][2][3] * ds[2][3] +
|
||||||
|
tmp_Q0Q0_L[3][3][0] * ds[3][0] +
|
||||||
|
tmp_Q0Q0_L[3][3][1] * ds[3][1] +
|
||||||
|
tmp_Q0Q0_L[3][3][2] * ds[3][2] +
|
||||||
|
tmp_Q0Q0_L[3][3][3] * ds[3][3];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
/*! @brief Calculate the derivatives of S, the leading eigenvalue L and
|
||||||
|
* the leading eigenvector Q with respect to `m_pos1`
|
||||||
|
* @param[in] ia The index the of atom
|
||||||
|
* @param[out] dl0_1_out The output of derivative of L with respect to
|
||||||
|
* ia-th atom of group 1
|
||||||
|
* @param[out] dq0_1_out The output of derivative of Q with respect to
|
||||||
|
* ia-th atom of group 1
|
||||||
|
* @param[out] ds_1_out The output of derivative of overlap matrix S with
|
||||||
|
* respect to ia-th atom of group 1
|
||||||
|
*/
|
||||||
|
void calc_derivative_wrt_group1(
|
||||||
|
size_t ia, cvm::rvector* const dl0_1_out = nullptr,
|
||||||
|
cvm::vector1d<cvm::rvector>* const dq0_1_out = nullptr,
|
||||||
|
cvm::matrix2d<cvm::rvector>* const ds_1_out = nullptr) const {
|
||||||
|
if (dl0_1_out == nullptr && dq0_1_out == nullptr) return;
|
||||||
|
cvm::real a2x, a2y, a2z;
|
||||||
|
// we can get rid of the helper function read_atom_coord if C++17 (constexpr) is available
|
||||||
|
read_atom_coord(ia, m_pos2, &a2x, &a2y, &a2z);
|
||||||
|
cvm::rvector ds_1[4][4];
|
||||||
|
ds_1[0][0].set( a2x, a2y, a2z);
|
||||||
|
ds_1[1][0].set( 0.0, a2z, -a2y);
|
||||||
|
ds_1[0][1] = ds_1[1][0];
|
||||||
|
ds_1[2][0].set(-a2z, 0.0, a2x);
|
||||||
|
ds_1[0][2] = ds_1[2][0];
|
||||||
|
ds_1[3][0].set( a2y, -a2x, 0.0);
|
||||||
|
ds_1[0][3] = ds_1[3][0];
|
||||||
|
ds_1[1][1].set( a2x, -a2y, -a2z);
|
||||||
|
ds_1[2][1].set( a2y, a2x, 0.0);
|
||||||
|
ds_1[1][2] = ds_1[2][1];
|
||||||
|
ds_1[3][1].set( a2z, 0.0, a2x);
|
||||||
|
ds_1[1][3] = ds_1[3][1];
|
||||||
|
ds_1[2][2].set(-a2x, a2y, -a2z);
|
||||||
|
ds_1[3][2].set( 0.0, a2z, a2y);
|
||||||
|
ds_1[2][3] = ds_1[3][2];
|
||||||
|
ds_1[3][3].set(-a2x, -a2y, a2z);
|
||||||
|
calc_derivative_impl(ds_1, dl0_1_out, dq0_1_out, ds_1_out);
|
||||||
|
}
|
||||||
|
/*! @brief Calculate the derivatives of S, the leading eigenvalue L and
|
||||||
|
* the leading eigenvector Q with respect to `m_pos2`
|
||||||
|
* @param[in] ia The index the of atom
|
||||||
|
* @param[out] dl0_2_out The output of derivative of L with respect to
|
||||||
|
* ia-th atom of group 2
|
||||||
|
* @param[out] dq0_2_out The output of derivative of Q with respect to
|
||||||
|
* ia-th atom of group 2
|
||||||
|
* @param[out] ds_2_out The output of derivative of overlap matrix S with
|
||||||
|
* respect to ia-th atom of group 2
|
||||||
|
*/
|
||||||
|
void calc_derivative_wrt_group2(
|
||||||
|
size_t ia, cvm::rvector* const dl0_2_out = nullptr,
|
||||||
|
cvm::vector1d<cvm::rvector>* const dq0_2_out = nullptr,
|
||||||
|
cvm::matrix2d<cvm::rvector>* const ds_2_out = nullptr) const {
|
||||||
|
if (dl0_2_out == nullptr && dq0_2_out == nullptr) return;
|
||||||
|
cvm::real a1x, a1y, a1z;
|
||||||
|
// we can get rid of the helper function read_atom_coord if C++17 (constexpr) is available
|
||||||
|
read_atom_coord(ia, m_pos1, &a1x, &a1y, &a1z);
|
||||||
|
cvm::rvector ds_2[4][4];
|
||||||
|
ds_2[0][0].set( a1x, a1y, a1z);
|
||||||
|
ds_2[1][0].set( 0.0, -a1z, a1y);
|
||||||
|
ds_2[0][1] = ds_2[1][0];
|
||||||
|
ds_2[2][0].set( a1z, 0.0, -a1x);
|
||||||
|
ds_2[0][2] = ds_2[2][0];
|
||||||
|
ds_2[3][0].set(-a1y, a1x, 0.0);
|
||||||
|
ds_2[0][3] = ds_2[3][0];
|
||||||
|
ds_2[1][1].set( a1x, -a1y, -a1z);
|
||||||
|
ds_2[2][1].set( a1y, a1x, 0.0);
|
||||||
|
ds_2[1][2] = ds_2[2][1];
|
||||||
|
ds_2[3][1].set( a1z, 0.0, a1x);
|
||||||
|
ds_2[1][3] = ds_2[3][1];
|
||||||
|
ds_2[2][2].set(-a1x, a1y, -a1z);
|
||||||
|
ds_2[3][2].set( 0.0, a1z, a1y);
|
||||||
|
ds_2[2][3] = ds_2[3][2];
|
||||||
|
ds_2[3][3].set(-a1x, -a1y, a1z);
|
||||||
|
calc_derivative_impl(ds_2, dl0_2_out, dq0_2_out, ds_2_out);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
/*! @brief Function for debugging gradients (allow using either
|
||||||
|
* std::vector<cvm::atom_pos> or std::vector<cvm::atom> for
|
||||||
|
* pos1 and pos2)
|
||||||
|
* @param[in] pos1 Atom positions of group 1
|
||||||
|
* @param[in] pos2 Atom positions of group 2
|
||||||
|
*/
|
||||||
|
template<typename T1, typename T2>
|
||||||
|
void debug_gradients(
|
||||||
|
cvm::rotation &rot,
|
||||||
|
const std::vector<T1> &pos1,
|
||||||
|
const std::vector<T2> &pos2) {
|
||||||
|
static_assert(std::is_same<T1, cvm::atom_pos>::value || std::is_same<T1, cvm::atom>::value, "");
|
||||||
|
static_assert(std::is_same<T2, cvm::atom_pos>::value || std::is_same<T2, cvm::atom>::value, "");
|
||||||
|
// eigenvalues and eigenvectors
|
||||||
|
cvm::real const L0 = rot.S_eigval[0];
|
||||||
|
cvm::real const L1 = rot.S_eigval[1];
|
||||||
|
cvm::real const L2 = rot.S_eigval[2];
|
||||||
|
cvm::real const L3 = rot.S_eigval[3];
|
||||||
|
cvm::quaternion const Q0(rot.S_eigvec[0]);
|
||||||
|
cvm::quaternion const Q1(rot.S_eigvec[1]);
|
||||||
|
cvm::quaternion const Q2(rot.S_eigvec[2]);
|
||||||
|
cvm::quaternion const Q3(rot.S_eigvec[3]);
|
||||||
|
|
||||||
|
cvm::log("L0 = "+cvm::to_str(L0, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q0 = "+cvm::to_str(Q0, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q0*Q0 = "+cvm::to_str(Q0.inner(Q0), cvm::cv_width, cvm::cv_prec)+
|
||||||
|
"\n");
|
||||||
|
cvm::log("L1 = "+cvm::to_str(L1, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q1 = "+cvm::to_str(Q1, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q0*Q1 = "+cvm::to_str(Q0.inner(Q1), cvm::cv_width, cvm::cv_prec)+
|
||||||
|
"\n");
|
||||||
|
cvm::log("L2 = "+cvm::to_str(L2, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q2 = "+cvm::to_str(Q2, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q0*Q2 = "+cvm::to_str(Q0.inner(Q2), cvm::cv_width, cvm::cv_prec)+
|
||||||
|
"\n");
|
||||||
|
cvm::log("L3 = "+cvm::to_str(L3, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q3 = "+cvm::to_str(Q3, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", Q0*Q3 = "+cvm::to_str(Q0.inner(Q3), cvm::cv_width, cvm::cv_prec)+
|
||||||
|
"\n");
|
||||||
|
|
||||||
|
rotation_derivative<T1, T2> deriv(rot, pos1, pos2);
|
||||||
|
cvm::rvector dl0_2;
|
||||||
|
cvm::vector1d<cvm::rvector> dq0_2(4);
|
||||||
|
cvm::matrix2d<cvm::rvector> ds_2;
|
||||||
|
#ifdef COLVARS_LAMMPS
|
||||||
|
MathEigen::Jacobi<cvm::real,
|
||||||
|
cvm::real[4],
|
||||||
|
cvm::real[4][4]> *ecalc =
|
||||||
|
reinterpret_cast<MathEigen::Jacobi<cvm::real,
|
||||||
|
cvm::real[4],
|
||||||
|
cvm::real[4][4]> *>(rot.jacobi);
|
||||||
|
#endif
|
||||||
|
deriv.prepare_derivative(rotation_derivative_dldq::use_dl | rotation_derivative_dldq::use_dq);
|
||||||
|
cvm::real S_new[4][4];
|
||||||
|
cvm::real S_new_eigval[4];
|
||||||
|
cvm::real S_new_eigvec[4][4];
|
||||||
|
for (size_t ia = 0; ia < pos2.size(); ++ia) {
|
||||||
|
// cvm::real const &a1x = pos1[ia].x;
|
||||||
|
// cvm::real const &a1y = pos1[ia].y;
|
||||||
|
// cvm::real const &a1z = pos1[ia].z;
|
||||||
|
deriv.calc_derivative_wrt_group2(ia, &dl0_2, &dq0_2, &ds_2);
|
||||||
|
// make an infitesimal move along each cartesian coordinate of
|
||||||
|
// this atom, and solve again the eigenvector problem
|
||||||
|
for (size_t comp = 0; comp < 3; comp++) {
|
||||||
|
std::memcpy(S_new, rot.S_backup, sizeof(cvm::real) * 4 * 4);
|
||||||
|
std::memset(S_new_eigval, 0, sizeof(cvm::real) * 4);
|
||||||
|
std::memset(S_new_eigvec, 0, sizeof(cvm::real) * 4 * 4);
|
||||||
|
for (size_t i = 0; i < 4; i++) {
|
||||||
|
for (size_t j = 0; j < 4; j++) {
|
||||||
|
S_new[i][j] +=
|
||||||
|
colvarmodule::debug_gradients_step_size * ds_2[i][j][comp];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
#ifdef COLVARS_LAMMPS
|
||||||
|
ecalc->Diagonalize(S_new, S_new_eigval, S_new_eigvec);
|
||||||
|
#else
|
||||||
|
NR::diagonalize_matrix(S_new, S_new_eigval, S_new_eigvec);
|
||||||
|
#endif
|
||||||
|
cvm::real const &L0_new = S_new_eigval[0];
|
||||||
|
cvm::quaternion const Q0_new(S_new_eigvec[0]);
|
||||||
|
|
||||||
|
cvm::real const DL0 = (dl0_2[comp]) * colvarmodule::debug_gradients_step_size;
|
||||||
|
cvm::quaternion const DQ0(dq0_2[0][comp] * colvarmodule::debug_gradients_step_size,
|
||||||
|
dq0_2[1][comp] * colvarmodule::debug_gradients_step_size,
|
||||||
|
dq0_2[2][comp] * colvarmodule::debug_gradients_step_size,
|
||||||
|
dq0_2[3][comp] * colvarmodule::debug_gradients_step_size);
|
||||||
|
|
||||||
|
cvm::log( "|(l_0+dl_0) - l_0^new|/l_0 = "+
|
||||||
|
cvm::to_str(cvm::fabs(L0+DL0 - L0_new)/L0, cvm::cv_width, cvm::cv_prec)+
|
||||||
|
", |(q_0+dq_0) - q_0^new| = "+
|
||||||
|
cvm::to_str((Q0+DQ0 - Q0_new).norm(), cvm::cv_width, cvm::cv_prec)+
|
||||||
|
"\n");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif // COLVAR_ROTATION_DERIVATIVE
|
||||||
@ -13,10 +13,12 @@
|
|||||||
#include <sstream>
|
#include <sstream>
|
||||||
#include <iomanip>
|
#include <iomanip>
|
||||||
|
|
||||||
|
#include "colvardeps.h"
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarproxy.h"
|
#include "colvarproxy.h"
|
||||||
#include "colvarparse.h"
|
#include "colvarparse.h"
|
||||||
#include "colvaratoms.h"
|
#include "colvaratoms.h"
|
||||||
|
#include "colvar_rotation_derivative.h"
|
||||||
|
|
||||||
|
|
||||||
cvm::atom::atom()
|
cvm::atom::atom()
|
||||||
@ -118,6 +120,11 @@ cvm::atom_group::~atom_group()
|
|||||||
fitting_group = NULL;
|
fitting_group = NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (rot_deriv != nullptr) {
|
||||||
|
delete rot_deriv;
|
||||||
|
rot_deriv = nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
cvm::main()->unregister_named_atom_group(this);
|
cvm::main()->unregister_named_atom_group(this);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -226,6 +233,7 @@ int cvm::atom_group::init()
|
|||||||
b_dummy = false;
|
b_dummy = false;
|
||||||
b_user_defined_fit = false;
|
b_user_defined_fit = false;
|
||||||
fitting_group = NULL;
|
fitting_group = NULL;
|
||||||
|
rot_deriv = nullptr;
|
||||||
|
|
||||||
noforce = false;
|
noforce = false;
|
||||||
|
|
||||||
@ -278,7 +286,7 @@ int cvm::atom_group::init_dependencies() {
|
|||||||
// Initialize feature_states for each instance
|
// Initialize feature_states for each instance
|
||||||
// default as unavailable, not enabled
|
// default as unavailable, not enabled
|
||||||
feature_states.reserve(f_ag_ntot);
|
feature_states.reserve(f_ag_ntot);
|
||||||
for (i = 0; i < colvardeps::f_ag_ntot; i++) {
|
for (i = feature_states.size(); i < colvardeps::f_ag_ntot; i++) {
|
||||||
feature_states.push_back(feature_state(false, false));
|
feature_states.push_back(feature_state(false, false));
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -317,6 +325,13 @@ int cvm::atom_group::setup()
|
|||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
void cvm::atom_group::setup_rotation_derivative() {
|
||||||
|
if (rot_deriv != nullptr) delete rot_deriv;
|
||||||
|
rot_deriv = new rotation_derivative<cvm::atom, cvm::atom_pos>(
|
||||||
|
rot, fitting_group ? fitting_group->atoms : this->atoms, ref_pos
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
void cvm::atom_group::update_total_mass()
|
void cvm::atom_group::update_total_mass()
|
||||||
{
|
{
|
||||||
@ -383,7 +398,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
// }
|
// }
|
||||||
// colvarparse::Parse_Mode mode = parse_normal;
|
// colvarparse::Parse_Mode mode = parse_normal;
|
||||||
|
|
||||||
int parse_error = COLVARS_OK;
|
int error_code = COLVARS_OK;
|
||||||
|
|
||||||
// Optional group name will let other groups reuse atom definition
|
// Optional group name will let other groups reuse atom definition
|
||||||
if (get_keyval(group_conf, "name", name)) {
|
if (get_keyval(group_conf, "name", name)) {
|
||||||
@ -433,7 +448,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
cvm::error("Error: cannot find atom group with name " + atoms_of + ".\n");
|
cvm::error("Error: cannot find atom group with name " + atoms_of + ".\n");
|
||||||
return COLVARS_ERROR;
|
return COLVARS_ERROR;
|
||||||
}
|
}
|
||||||
parse_error |= add_atoms_of_group(ag);
|
error_code |= add_atoms_of_group(ag);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -447,7 +462,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
std::string numbers_conf = "";
|
std::string numbers_conf = "";
|
||||||
size_t pos = 0;
|
size_t pos = 0;
|
||||||
while (key_lookup(group_conf, "atomNumbers", &numbers_conf, &pos)) {
|
while (key_lookup(group_conf, "atomNumbers", &numbers_conf, &pos)) {
|
||||||
parse_error |= add_atom_numbers(numbers_conf);
|
error_code |= add_atom_numbers(numbers_conf);
|
||||||
numbers_conf = "";
|
numbers_conf = "";
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -456,7 +471,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
std::string index_group_name;
|
std::string index_group_name;
|
||||||
if (get_keyval(group_conf, "indexGroup", index_group_name)) {
|
if (get_keyval(group_conf, "indexGroup", index_group_name)) {
|
||||||
// use an index group from the index file read globally
|
// use an index group from the index file read globally
|
||||||
parse_error |= add_index_group(index_group_name);
|
error_code |= add_index_group(index_group_name);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -465,7 +480,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
size_t pos = 0;
|
size_t pos = 0;
|
||||||
while (key_lookup(group_conf, "atomNumbersRange",
|
while (key_lookup(group_conf, "atomNumbersRange",
|
||||||
&range_conf, &pos)) {
|
&range_conf, &pos)) {
|
||||||
parse_error |= add_atom_numbers_range(range_conf);
|
error_code |= add_atom_numbers_range(range_conf);
|
||||||
range_conf = "";
|
range_conf = "";
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -492,7 +507,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
cvm::error("Error: more instances of \"atomNameResidueRange\" than "
|
cvm::error("Error: more instances of \"atomNameResidueRange\" than "
|
||||||
"values of \"psfSegID\".\n", COLVARS_INPUT_ERROR);
|
"values of \"psfSegID\".\n", COLVARS_INPUT_ERROR);
|
||||||
} else {
|
} else {
|
||||||
parse_error |= add_atom_name_residue_range(psf_segids.size() ?
|
error_code |= add_atom_name_residue_range(psf_segids.size() ?
|
||||||
*psii : std::string(""), range_conf);
|
*psii : std::string(""), range_conf);
|
||||||
if (psf_segids.size()) psii++;
|
if (psf_segids.size()) psii++;
|
||||||
}
|
}
|
||||||
@ -517,26 +532,26 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", COLVARS_INPUT_ERROR);
|
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
|
|
||||||
// NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function
|
error_code |= cvm::main()->proxy->load_atoms_pdb(atoms_file_name.c_str(), *this, atoms_col,
|
||||||
parse_error |= cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
|
atoms_col_value);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// Catch any errors from all the initialization steps above
|
// Catch any errors from all the initialization steps above
|
||||||
if (parse_error || cvm::get_error()) return (parse_error || cvm::get_error());
|
if (error_code || cvm::get_error()) return (error_code || cvm::get_error());
|
||||||
|
|
||||||
// checks of doubly-counted atoms have been handled by add_atom() already
|
// checks of doubly-counted atoms have been handled by add_atom() already
|
||||||
|
|
||||||
if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
|
if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
|
||||||
|
|
||||||
parse_error |= set_dummy();
|
error_code |= set_dummy();
|
||||||
parse_error |= set_dummy_pos(dummy_atom_pos);
|
error_code |= set_dummy_pos(dummy_atom_pos);
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
|
|
||||||
if (!(atoms_ids.size())) {
|
if (!(atoms_ids.size())) {
|
||||||
parse_error |= cvm::error("Error: no atoms defined for atom group \""+
|
error_code |= cvm::error("Error: no atoms defined for atom group \"" + key + "\".\n",
|
||||||
key+"\".\n", COLVARS_INPUT_ERROR);
|
COLVARS_INPUT_ERROR);
|
||||||
}
|
}
|
||||||
|
|
||||||
// whether these atoms will ever receive forces or not
|
// whether these atoms will ever receive forces or not
|
||||||
@ -546,7 +561,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
}
|
}
|
||||||
|
|
||||||
// Now that atoms are defined we can parse the detailed fitting options
|
// Now that atoms are defined we can parse the detailed fitting options
|
||||||
parse_error |= parse_fitting_options(group_conf);
|
error_code |= parse_fitting_options(group_conf);
|
||||||
|
|
||||||
if (is_enabled(f_ag_scalable) && !b_dummy) {
|
if (is_enabled(f_ag_scalable) && !b_dummy) {
|
||||||
cvm::log("Enabling scalable calculation for group \""+this->key+"\".\n");
|
cvm::log("Enabling scalable calculation for group \""+this->key+"\".\n");
|
||||||
@ -583,7 +598,9 @@ int cvm::atom_group::parse(std::string const &group_conf)
|
|||||||
cvm::log(print_atom_ids());
|
cvm::log(print_atom_ids());
|
||||||
}
|
}
|
||||||
|
|
||||||
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
if (is_enabled(f_ag_rotate)) setup_rotation_derivative();
|
||||||
|
|
||||||
|
return error_code;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -883,8 +900,6 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
|
|||||||
"to its radius of gyration), the optimal rotation and its gradients may become discontinuous. "
|
"to its radius of gyration), the optimal rotation and its gradients may become discontinuous. "
|
||||||
"If that happens, use fittingGroup (or a different definition for it if already defined) "
|
"If that happens, use fittingGroup (or a different definition for it if already defined) "
|
||||||
"to align the coordinates.\n");
|
"to align the coordinates.\n");
|
||||||
// initialize rot member data
|
|
||||||
rot.request_group1_gradients(group_for_fit->size());
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -912,7 +927,6 @@ void cvm::atom_group::do_feature_side_effects(int id)
|
|||||||
if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) {
|
if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) {
|
||||||
atom_group *group_for_fit = fitting_group ? fitting_group : this;
|
atom_group *group_for_fit = fitting_group ? fitting_group : this;
|
||||||
group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0));
|
group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0));
|
||||||
rot.request_group1_gradients(group_for_fit->size());
|
|
||||||
}
|
}
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
@ -1045,17 +1059,18 @@ void cvm::atom_group::calc_apply_roto_translation()
|
|||||||
// rotate the group (around the center of geometry if f_ag_center is
|
// rotate the group (around the center of geometry if f_ag_center is
|
||||||
// enabled, around the origin otherwise)
|
// enabled, around the origin otherwise)
|
||||||
rot.calc_optimal_rotation(fitting_group ?
|
rot.calc_optimal_rotation(fitting_group ?
|
||||||
fitting_group->positions() :
|
fitting_group->atoms:
|
||||||
this->positions(),
|
this->atoms,
|
||||||
ref_pos);
|
ref_pos);
|
||||||
|
const auto rot_mat = rot.matrix();
|
||||||
|
|
||||||
cvm::atom_iter ai;
|
cvm::atom_iter ai;
|
||||||
for (ai = this->begin(); ai != this->end(); ai++) {
|
for (ai = this->begin(); ai != this->end(); ai++) {
|
||||||
ai->pos = rot.rotate(ai->pos);
|
ai->pos = rot_mat * ai->pos;
|
||||||
}
|
}
|
||||||
if (fitting_group) {
|
if (fitting_group) {
|
||||||
for (ai = fitting_group->begin(); ai != fitting_group->end(); ai++) {
|
for (ai = fitting_group->begin(); ai != fitting_group->end(); ai++) {
|
||||||
ai->pos = rot.rotate(ai->pos);
|
ai->pos = rot_mat * ai->pos;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -1095,9 +1110,10 @@ void cvm::atom_group::read_velocities()
|
|||||||
|
|
||||||
if (is_enabled(f_ag_rotate)) {
|
if (is_enabled(f_ag_rotate)) {
|
||||||
|
|
||||||
|
const auto rot_mat = rot.matrix();
|
||||||
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
||||||
ai->read_velocity();
|
ai->read_velocity();
|
||||||
ai->vel = rot.rotate(ai->vel);
|
ai->vel = rot_mat * ai->vel;
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
@ -1116,9 +1132,10 @@ void cvm::atom_group::read_total_forces()
|
|||||||
|
|
||||||
if (is_enabled(f_ag_rotate)) {
|
if (is_enabled(f_ag_rotate)) {
|
||||||
|
|
||||||
|
const auto rot_mat = rot.matrix();
|
||||||
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
||||||
ai->read_total_force();
|
ai->read_total_force();
|
||||||
ai->total_force = rot.rotate(ai->total_force);
|
ai->total_force = rot_mat * ai->total_force;
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
@ -1200,52 +1217,71 @@ void cvm::atom_group::calc_fit_gradients()
|
|||||||
if (cvm::debug())
|
if (cvm::debug())
|
||||||
cvm::log("Calculating fit gradients.\n");
|
cvm::log("Calculating fit gradients.\n");
|
||||||
|
|
||||||
cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this;
|
if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate))
|
||||||
|
calc_fit_gradients_impl<true, true>();
|
||||||
if (is_enabled(f_ag_center)) {
|
if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate))
|
||||||
// add the center of geometry contribution to the gradients
|
calc_fit_gradients_impl<true, false>();
|
||||||
cvm::rvector atom_grad;
|
if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate))
|
||||||
|
calc_fit_gradients_impl<false, true>();
|
||||||
for (size_t i = 0; i < this->size(); i++) {
|
if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate))
|
||||||
atom_grad += atoms[i].grad;
|
calc_fit_gradients_impl<false, false>();
|
||||||
}
|
|
||||||
if (is_enabled(f_ag_rotate)) atom_grad = (rot.inverse()).rotate(atom_grad);
|
|
||||||
atom_grad *= (-1.0)/(cvm::real(group_for_fit->size()));
|
|
||||||
|
|
||||||
for (size_t j = 0; j < group_for_fit->size(); j++) {
|
|
||||||
group_for_fit->fit_gradients[j] = atom_grad;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (is_enabled(f_ag_rotate)) {
|
|
||||||
|
|
||||||
// add the rotation matrix contribution to the gradients
|
|
||||||
cvm::rotation const rot_inv = rot.inverse();
|
|
||||||
|
|
||||||
for (size_t i = 0; i < this->size(); i++) {
|
|
||||||
|
|
||||||
// compute centered, unrotated position
|
|
||||||
cvm::atom_pos const pos_orig =
|
|
||||||
rot_inv.rotate((is_enabled(f_ag_center) ? (atoms[i].pos - ref_pos_cog) : (atoms[i].pos)));
|
|
||||||
|
|
||||||
// calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i
|
|
||||||
cvm::quaternion const dxdq =
|
|
||||||
rot.q.position_derivative_inner(pos_orig, atoms[i].grad);
|
|
||||||
|
|
||||||
for (size_t j = 0; j < group_for_fit->size(); j++) {
|
|
||||||
// multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients
|
|
||||||
for (size_t iq = 0; iq < 4; iq++) {
|
|
||||||
group_for_fit->fit_gradients[j] += dxdq[iq] * rot.dQ0_1[j][iq];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (cvm::debug())
|
if (cvm::debug())
|
||||||
cvm::log("Done calculating fit gradients.\n");
|
cvm::log("Done calculating fit gradients.\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
template <bool B_ag_center, bool B_ag_rotate>
|
||||||
|
void cvm::atom_group::calc_fit_gradients_impl() {
|
||||||
|
cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this;
|
||||||
|
// the center of geometry contribution to the gradients
|
||||||
|
cvm::rvector atom_grad;
|
||||||
|
// the rotation matrix contribution to the gradients
|
||||||
|
const auto rot_inv = rot.inverse().matrix();
|
||||||
|
// temporary variables for computing and summing derivatives
|
||||||
|
cvm::real sum_dxdq[4] = {0, 0, 0, 0};
|
||||||
|
cvm::vector1d<cvm::rvector> dq0_1(4);
|
||||||
|
// loop 1: iterate over the current atom group
|
||||||
|
for (size_t i = 0; i < size(); i++) {
|
||||||
|
cvm::atom_pos pos_orig;
|
||||||
|
if (B_ag_center) {
|
||||||
|
atom_grad += atoms[i].grad;
|
||||||
|
if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog);
|
||||||
|
} else {
|
||||||
|
if (B_ag_rotate) pos_orig = atoms[i].pos;
|
||||||
|
}
|
||||||
|
if (B_ag_rotate) {
|
||||||
|
// calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i
|
||||||
|
cvm::quaternion const dxdq =
|
||||||
|
rot.q.position_derivative_inner(pos_orig, atoms[i].grad);
|
||||||
|
sum_dxdq[0] += dxdq[0];
|
||||||
|
sum_dxdq[1] += dxdq[1];
|
||||||
|
sum_dxdq[2] += dxdq[2];
|
||||||
|
sum_dxdq[3] += dxdq[3];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (B_ag_center) {
|
||||||
|
if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad;
|
||||||
|
atom_grad *= (-1.0)/(cvm::real(group_for_fit->size()));
|
||||||
|
}
|
||||||
|
// loop 2: iterate over the fitting group
|
||||||
|
if (B_ag_rotate) rot_deriv->prepare_derivative(rotation_derivative_dldq::use_dq);
|
||||||
|
for (size_t j = 0; j < group_for_fit->size(); j++) {
|
||||||
|
if (B_ag_center) {
|
||||||
|
group_for_fit->fit_gradients[j] = atom_grad;
|
||||||
|
}
|
||||||
|
if (B_ag_rotate) {
|
||||||
|
rot_deriv->calc_derivative_wrt_group1(j, nullptr, &dq0_1);
|
||||||
|
// multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients
|
||||||
|
group_for_fit->fit_gradients[j] += sum_dxdq[0] * dq0_1[0] +
|
||||||
|
sum_dxdq[1] * dq0_1[1] +
|
||||||
|
sum_dxdq[2] * dq0_1[2] +
|
||||||
|
sum_dxdq[3] * dq0_1[3];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
std::vector<cvm::atom_pos> cvm::atom_group::positions() const
|
std::vector<cvm::atom_pos> cvm::atom_group::positions() const
|
||||||
{
|
{
|
||||||
if (b_dummy) {
|
if (b_dummy) {
|
||||||
@ -1373,9 +1409,9 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
|
|||||||
if (is_enabled(f_ag_rotate)) {
|
if (is_enabled(f_ag_rotate)) {
|
||||||
|
|
||||||
// rotate forces back to the original frame
|
// rotate forces back to the original frame
|
||||||
cvm::rotation const rot_inv = rot.inverse();
|
const auto rot_inv = rot.inverse().matrix();
|
||||||
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
||||||
ai->apply_force(rot_inv.rotate(force * ai->grad));
|
ai->apply_force(rot_inv * (force * ai->grad));
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
@ -1418,9 +1454,9 @@ void cvm::atom_group::apply_force(cvm::rvector const &force)
|
|||||||
|
|
||||||
if (is_enabled(f_ag_rotate)) {
|
if (is_enabled(f_ag_rotate)) {
|
||||||
|
|
||||||
cvm::rotation const rot_inv = rot.inverse();
|
const auto rot_inv = rot.inverse().matrix();
|
||||||
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
|
||||||
ai->apply_force(rot_inv.rotate((ai->mass/total_mass) * force));
|
ai->apply_force(rot_inv * ((ai->mass/total_mass) * force));
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user