forked from lijiext/lammps
Merge pull request #1241 from akohlmey/collected-small-fixes
Collected small changes and updates for stable release
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
0165f18d59
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@ -126,3 +126,6 @@ python/* @rbberger
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doc/utils/*/* @rbberger
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doc/utils/*/* @rbberger
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doc/Makefile @rbberger
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doc/Makefile @rbberger
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doc/README @rbberger
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doc/README @rbberger
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# for releases
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src/version.h @sjplimp
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@ -1,7 +1,7 @@
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# Makefile for LAMMPS documentation
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# Makefile for LAMMPS documentation
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SHELL = /bin/bash
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SHELL = /bin/bash
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SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py)
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SHA1 = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
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BUILDDIR = /tmp/lammps-docs-$(SHA1)
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BUILDDIR = /tmp/lammps-docs-$(SHA1)
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RSTDIR = $(BUILDDIR)/rst
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RSTDIR = $(BUILDDIR)/rst
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VENV = $(BUILDDIR)/docenv
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VENV = $(BUILDDIR)/docenv
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@ -735,66 +735,69 @@ from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
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:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
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:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
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PLUMED can be linked into MD codes in three different modes: static,
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PLUMED can be linked into MD codes in three different modes: static,
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shared, and runtime. With the "static" mode, all the code that PLUMED requires
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shared, and runtime. With the "static" mode, all the code that PLUMED
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is linked statically into LAMMPS. LAMMPS is then fully
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requires is linked statically into LAMMPS. LAMMPS is then fully
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independent from the PLUMED installation, but you have to
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independent from the PLUMED installation, but you have to rebuild/relink
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rebuild/relink it in order to update the PLUMED code inside it. With
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it in order to update the PLUMED code inside it. With the "shared"
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the "shared" linkage mode, LAMMPS is linked to a shared library
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linkage mode, LAMMPS is linked to a shared library that contains the
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that contains the PLUMED code. This library should preferably be installed in a
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PLUMED code. This library should preferably be installed in a globally
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globally accessible location. When PLUMED is linked in this way the same library
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accessible location. When PLUMED is linked in this way the same library
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can be used by multiple MD packages. Furthermore, the PLUMED library LAMMPS uses can be updated
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can be used by multiple MD packages. Furthermore, the PLUMED library
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without the need for a recompile of LAMMPS for as
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LAMMPS uses can be updated without the need for a recompile of LAMMPS
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long as the shared PLUMED library is ABI-compatible.
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for as long as the shared PLUMED library is ABI-compatible.
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The third linkage
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The third linkage mode is "runtime" which allows the user to specify
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mode is "runtime" which allows the user to specify which PLUMED kernel should be used at runtime
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which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
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by using the PLUMED_KERNEL environment
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environment variable. This variable should point to the location of the
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variable. This variable should point to the location of the libplumedKernel.so
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libplumedKernel.so dynamical shared object, which is then loaded at
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dynamical shared object, which is then loaded at runtime. This mode of linking is
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runtime. This mode of linking is particularly convenient for doing
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particularly convenient for doing PLUMED development and comparing
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PLUMED development and comparing multiple PLUMED versions as these sorts
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multiple PLUMED versions as these sorts of comparisons can be done without recompiling the hosting MD
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of comparisons can be done without recompiling the hosting MD code. All
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code. All three linkage modes are supported by LAMMPS on selected
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three linkage modes are supported by LAMMPS on selected operating
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operating systems (e.g. Linux) and using either CMake or traditional
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systems (e.g. Linux) and using either CMake or traditional make
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make build. The "static" mode should be the most portable, while the "runtime"
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build. The "static" mode should be the most portable, while the
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mode support in LAMMPS makes the most assumptions about operating
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"runtime" mode support in LAMMPS makes the most assumptions about
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system and compiler environment. If one mode does not work, try a
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operating system and compiler environment. If one mode does not work,
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different one, switch to a different build system, consider
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try a different one, switch to a different build system, consider a
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a global PLUMED installation or consider downloading PLUMED during the LAMMPS build.
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global PLUMED installation or consider downloading PLUMED during the
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LAMMPS build.
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[CMake build]:
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[CMake build]:
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When the "-D PKG_USER-PLUMED" flag is included in the cmake command you must ensure that
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When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
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GSL is installed in locations that are specified in your environment. There
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must ensure that GSL is installed in locations that are specified in
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are then two additional commands that control the manner in which PLUMED is obtained and linked
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your environment. There are then two additional commands that control
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into LAMMPS.
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the manner in which PLUMED is obtained and linked into LAMMPS.
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-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
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-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
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-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
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-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
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If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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downloaded (the version of PLUMED that will be downloaded is hard-coded to a vetted version of
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downloaded (the version of PLUMED that will be downloaded is hard-coded
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PLUMED, usually a recent stable release version) and built inside the
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to a vetted version of PLUMED, usually a recent stable release version)
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CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default),
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and built inside the CMake build directory. If DOWNLOAD_PLUMED is set
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CMake will try to detect and link to an installed version of PLUMED.
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to "no" (the default), CMake will try to detect and link to an installed
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For this to work, the PLUMED library has to be installed into a
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version of PLUMED. For this to work, the PLUMED library has to be
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location where the pkg-config tool can find it or the PKG_CONFIG_PATH
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installed into a location where the pkg-config tool can find it or the
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environment variable has to be set up accordingly. PLUMED should be installed
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PKG_CONFIG_PATH environment variable has to be set up accordingly.
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in such a location if you compile it using the default make; make install commands.
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PLUMED should be installed in such a location if you compile it using
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the default make; make install commands.
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The PLUMED_MODE setting determines the linkage mode for the PLUMED
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The PLUMED_MODE setting determines the linkage mode for the PLUMED
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library. The allowed values for this flag are "static" (default), "shared", or "runtime".
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library. The allowed values for this flag are "static" (default),
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For a discussion of PLUMED linkage modes, please see above. When
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"shared", or "runtime". For a discussion of PLUMED linkage modes,
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DOWNLOAD_PLUMED is enabled the static linkage mode is recommended.
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please see above. When DOWNLOAD_PLUMED is enabled the static linkage
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mode is recommended.
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[Traditional make]:
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[Traditional make]:
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PLUMED needs to be installed before the USER-PLUMED package is installed
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PLUMED needs to be installed before the USER-PLUMED package is installed
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so that LAMMPS can find the right settings when compiling and linking the LAMMPS executable.
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so that LAMMPS can find the right settings when compiling and linking
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You can either download and build PLUMED inside the LAMMPS plumed library folder or use
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the LAMMPS executable. You can either download and build PLUMED inside
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a previously installed PLUMED library and point LAMMPS to its
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the LAMMPS plumed library folder or use a previously installed PLUMED
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location. You also have to choose the linkage mode: "static" (default),
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library and point LAMMPS to its location. You also have to choose the
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"shared" or "runtime". For a discussion of PLUMED linkage modes, please
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linkage mode: "static" (default), "shared" or "runtime". For a
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||||||
see above.
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discussion of PLUMED linkage modes, please see above.
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Download/compilation/configuration of the plumed library can be done
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Download/compilation/configuration of the plumed library can be done
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from the src folder through the following make args:
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from the src folder through the following make args:
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||||||
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@ -808,10 +811,10 @@ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installati
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Note that 2 symbolic (soft) links, "includelink" and "liblink" are
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Note that 2 symbolic (soft) links, "includelink" and "liblink" are
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||||||
created in lib/plumed that point to the location of the PLUMED build to
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created in lib/plumed that point to the location of the PLUMED build to
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use. A new file lib/plumed/Makefile.lammps is also created with
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use. A new file lib/plumed/Makefile.lammps is also created with settings
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settings suitable for LAMMPS to compile and link PLUMED using the desired
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suitable for LAMMPS to compile and link PLUMED using the desired linkage
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||||||
linkage mode. After this step is completed, you can install the
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mode. After this step is completed, you can install the USER-PLUMED
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USER-PLUMED package and compile LAMMPS in the usual manner:
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package and compile LAMMPS in the usual manner:
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make yes-user-plumed
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make yes-user-plumed
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make machine :pre
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make machine :pre
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@ -461,10 +461,10 @@ last snapshot. This can be accomplished with something the following
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commands:
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commands:
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variable Dhop equal 0.6
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variable Dhop equal 0.6
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variable check atom "c_dsp[4] > v_Dhop"
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variable check atom "c_dsp\[4\] > v_Dhop"
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compute dsp all displace/atom refresh check
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compute dsp all displace/atom refresh check
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dump 1 all custom 20 tmp.dump id type x y z
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dump 1 all custom 20 tmp.dump id type x y z
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dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
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dump_modify 1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre
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The "compute displace/atom"_compute_displace_atom.html command
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The "compute displace/atom"_compute_displace_atom.html command
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calculates the displacement of each atom from its reference position.
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calculates the displacement of each atom from its reference position.
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@ -32,11 +32,10 @@ enhance the sampling of phase space.
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The documentation included here only describes the fix plumed command
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The documentation included here only describes the fix plumed command
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itself. This command is LAMMPS specific, whereas most of the
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itself. This command is LAMMPS specific, whereas most of the
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functionality implemented in PLUMED will work with a range of
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functionality implemented in PLUMED will work with a range of MD codes,
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MD codes, and when PLUMED is used as a stand alone code for analysis.
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and when PLUMED is used as a stand alone code for analysis. The full
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The full "documentation for PLUMED"_plumeddocs is available online and
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"documentation for PLUMED"_plumeddocs is available online and included
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included in the PLUMED source code. The PLUMED library development is
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in the PLUMED source code. The PLUMED library development is hosted at
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hosted at
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"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
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"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
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A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
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A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
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||||||
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@ -54,11 +53,12 @@ have been set.
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The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
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The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
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to PLUMED and there can only be one instance of the plumed fix at a
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to PLUMED and there can only be one instance of the plumed fix at a
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time. The way the plumed fix is implemented ensures that the minimum amount of information
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time. The way the plumed fix is implemented ensures that the minimum
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required is communicated. Furthermore, PLUMED supports multiple, completely independent
|
amount of information required is communicated. Furthermore, PLUMED
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collective variables, multiple independent biases and multiple
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supports multiple, completely independent collective variables, multiple
|
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independent forms of analysis. There is thus really no restriction in
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independent biases and multiple independent forms of analysis. There is
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functionality by only allowing only one plumed fix in the LAMMPS input.
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thus really no restriction in functionality by only allowing only one
|
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plumed fix in the LAMMPS input.
|
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|
||||||
The {plumedfile} keyword allows the user to specify the name of the
|
The {plumedfile} keyword allows the user to specify the name of the
|
||||||
PLUMED input file. Instructions as to what should be included in a
|
PLUMED input file. Instructions as to what should be included in a
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||||||
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||||||
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@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
|
||||||
accuracy = desired relative error in forces
|
accuracy = desired relative error in forces
|
||||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||||
{scafacos} values = method accuracy
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{scafacos} values = method accuracy
|
||||||
method = fmm or p2nfft or ewald or direct
|
method = fmm or p2nfft or p3m or ewald or direct
|
||||||
accuracy = desired relative error in forces :pre
|
accuracy = desired relative error in forces :pre
|
||||||
:ule
|
:ule
|
||||||
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|
||||||
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@ -392,6 +392,8 @@ the same bond/angle/dihedral are weighted by the
|
||||||
"special_bonds"_special_bonds.html command. Likewise it does not
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"special_bonds"_special_bonds.html command. Likewise it does not
|
||||||
support the "TIP4P water style" where a fictitious charge site is
|
support the "TIP4P water style" where a fictitious charge site is
|
||||||
introduced in each water molecule.
|
introduced in each water molecule.
|
||||||
|
Finally, the methods {p3m} and {ewald} do not support computing the
|
||||||
|
virial, so this contribution is not included.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
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|
||||||
|
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|
||||||
|
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@ -1,5 +1,4 @@
|
||||||
variable sname index h_atom
|
variable sname index h_atom
|
||||||
log ${sname}.spe.log
|
|
||||||
|
|
||||||
units real
|
units real
|
||||||
newton on
|
newton on
|
||||||
|
|
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
thermo 1
|
thermo 1
|
||||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
run 0
|
run 10
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
variable sname index h_molecule
|
variable sname index h_molecule
|
||||||
log ${sname}.spe.log
|
|
||||||
|
|
||||||
units real
|
units real
|
||||||
newton on
|
newton on
|
||||||
|
|
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
thermo 1
|
thermo 1
|
||||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
run 0
|
run 10
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,100 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_atom
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
processors 1 * *
|
||||||
|
|
||||||
|
|
||||||
|
atom_style wavepacket
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_atom
|
||||||
|
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2 atoms
|
||||||
|
|
||||||
|
#neighbor 2.0 nsq
|
||||||
|
|
||||||
|
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
fix 1 all nve/awpmd
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute energies all pair awpmd/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]
|
||||||
|
|
||||||
|
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)
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.52918
|
||||||
|
ghost atom cutoff = 2.52918
|
||||||
|
binsize = 1.26459, bins = 1 1 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair awpmd/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
|
||||||
|
1 -266.3192 -266.3192 0 266.32746 0 -532.64666 0 0 159.30733 -0
|
||||||
|
2 -266.3192 -266.3192 1.7273458e-17 266.32797 0 -532.64718 0 5.7948873e-15 169.14686 6.6606909e-13
|
||||||
|
3 -266.3192 -266.3192 4.6899813e-15 266.32927 0 -532.64847 0 1.5733915e-12 194.06892 1.8084691e-10
|
||||||
|
4 -266.3192 -266.3192 1.4824973e-13 266.33199 0 -532.6512 0 4.9734712e-11 246.65762 5.7165485e-09
|
||||||
|
5 -266.3192 -266.3192 1.9298888e-12 266.33712 0 -532.65632 0 6.4743771e-10 345.53056 7.441702e-08
|
||||||
|
6 -266.3192 -266.3192 1.5343223e-11 266.34601 0 -532.66521 0 5.1473332e-09 516.91949 5.9163869e-07
|
||||||
|
7 -266.3192 -266.3192 8.8661674e-11 266.36051 0 -532.6797 0 2.9744154e-08 796.4357 3.4188175e-06
|
||||||
|
8 -266.31919 -266.31919 4.0865149e-10 266.38304 0 -532.70223 0 1.3709411e-07 1231.0302 1.5757709e-05
|
||||||
|
9 -266.31918 -266.31918 1.5889509e-09 266.41674 0 -532.73592 0 5.3306012e-07 1881.1652 6.1270366e-05
|
||||||
|
10 -266.31916 -266.31916 5.4070747e-09 266.46554 0 -532.7847 0 1.8139615e-06 2823.2238 0.00020849822
|
||||||
|
Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms
|
||||||
|
|
||||||
|
Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 timesteps/s
|
||||||
|
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00030851 | 0.00030851 | 0.00030851 | 0.0 | 42.55
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0001204 | 0.0001204 | 0.0001204 | 0.0 | 16.61
|
||||||
|
Output | 0.00028038 | 0.00028038 | 0.00028038 | 0.0 | 38.67
|
||||||
|
Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.85
|
||||||
|
Other | | 9.537e-06 | | | 1.32
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 248 ave 248 max 248 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 225 ave 225 max 225 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 225
|
||||||
|
Ave neighs/atom = 112.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,100 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_atom
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
processors 1 * *
|
||||||
|
|
||||||
|
|
||||||
|
atom_style wavepacket
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_atom
|
||||||
|
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2 atoms
|
||||||
|
|
||||||
|
#neighbor 2.0 nsq
|
||||||
|
|
||||||
|
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
fix 1 all nve/awpmd
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute energies all pair awpmd/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]
|
||||||
|
|
||||||
|
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)
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.52918
|
||||||
|
ghost atom cutoff = 2.52918
|
||||||
|
binsize = 1.26459, bins = 1 1 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair awpmd/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
|
||||||
|
1 -266.3192 -266.3192 0 266.32789 0 -532.64709 0 0 167.49891 -0
|
||||||
|
2 -266.3192 -266.3192 1.219316e-15 266.3314 0 -532.6506 0 4.0905525e-13 235.2267 4.7017146e-11
|
||||||
|
3 -266.3192 -266.3192 8.3179871e-14 266.34548 0 -532.66468 0 2.7905123e-11 506.68594 3.2074377e-09
|
||||||
|
4 -266.3192 -266.3192 4.4091748e-12 266.39036 0 -532.70955 0 1.4791868e-09 1372.0565 1.7001894e-07
|
||||||
|
5 -266.31916 -266.31916 9.8904198e-11 266.51357 0 -532.83273 0 3.3180309e-08 3748.6725 3.8137718e-06
|
||||||
|
6 -266.31893 -266.31893 1.3132578e-09 266.81733 0 -533.13626 0 4.4057077e-07 9611.8807 5.0639565e-05
|
||||||
|
7 -266.31762 -266.31762 1.2317167e-08 267.50719 0 -533.82481 0 4.1321544e-06 22950.26 0.00047495321
|
||||||
|
8 -266.31123 -266.31123 9.0048883e-08 268.97689 0 -535.28812 0 3.0209534e-05 51470.197 0.0034723086
|
||||||
|
9 -266.28324 -266.28324 5.4612621e-07 271.95757 0 -538.24082 0 0.00018321403 109735.25 0.02105877
|
||||||
|
10 -266.17113 -266.17114 2.8729529e-06 277.79384 0 -543.96498 0 0.00096381615 225424.02 0.11078182
|
||||||
|
Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms
|
||||||
|
|
||||||
|
Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s
|
||||||
|
87.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 6.3419e-05 | 0.00012642 | 0.00030923 | 0.0 | 7.16
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00073171 | 0.00086534 | 0.001025 | 0.0 | 49.01
|
||||||
|
Output | 0.00063562 | 0.00075388 | 0.00094962 | 0.0 | 42.70
|
||||||
|
Modify | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.25
|
||||||
|
Other | | 1.55e-05 | | | 0.88
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 2 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 249.5 ave 250 max 248 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 56.25 ave 225 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 225
|
||||||
|
Ave neighs/atom = 112.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,100 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_molecule
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
processors 1 * *
|
||||||
|
|
||||||
|
|
||||||
|
atom_style wavepacket
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_molecule
|
||||||
|
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
|
||||||
|
#neighbor 2.0 nsq
|
||||||
|
|
||||||
|
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
fix 1 all nve/awpmd
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute energies all pair awpmd/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]
|
||||||
|
|
||||||
|
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)
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.52918
|
||||||
|
ghost atom cutoff = 2.52918
|
||||||
|
binsize = 1.26459, bins = 1 1 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair awpmd/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
|
||||||
|
1 30360.49 30360.489 0.0009272222 39540.081 2.0463631e-12 -9179.5926 0 0.10368794 1.3476061e+09 35.753932
|
||||||
|
2 67447.779 67447.776 0.00370884 80547.07 -1.1368684e-12 -13099.294 0 0.41474633 2.8529839e+09 143.01385
|
||||||
|
3 3713046.5 3713046.5 0.0041850026 3803060.3 -1.29603e-10 -90013.788 0 0.46799388 1.4486958e+11 161.3748
|
||||||
|
4 2445632.1 2445620 12.171486 2452194.4 -9.777068e-11 -6574.4062 0 1361.0937 -6.5572589e+08 469335.68
|
||||||
|
5 2434860.1 2434845.9 14.215419 2433638.8 -1.0663825e-10 1207.1541 0 1589.6595 -359380.29 548150.31
|
||||||
|
6 2444984.1 2444969.8 14.215428 2451100 5.1841198e-11 -6130.1373 0 1589.6605 -5.6327282e+08 548150.63
|
||||||
|
7 2436128.7 2436110.9 17.793789 2434903.7 2.0190782e-10 1207.154 0 1989.8158 -221406.77 686133.18
|
||||||
|
8 2444786.5 2444768.7 17.793798 2450583.8 -1.1027623e-10 -5815.0651 0 1989.8169 -5.0227031e+08 686133.54
|
||||||
|
9 2437198.9 2437175.9 22.942086 2435968.8 2.2600943e-10 1207.1538 0 2565.5315 -22903.736 884652.88
|
||||||
|
10 2444787.1 2444764.2 22.942097 2450333.1 -3.1832315e-11 -5568.9214 0 2565.5327 -4.5741803e+08 884653.3
|
||||||
|
Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms
|
||||||
|
|
||||||
|
Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s
|
||||||
|
85.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00088882 | 0.00088882 | 0.00088882 | 0.0 | 56.09
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00031352 | 0.00031352 | 0.00031352 | 0.0 | 19.79
|
||||||
|
Output | 0.00036216 | 0.00036216 | 0.00036216 | 0.0 | 22.86
|
||||||
|
Modify | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.38
|
||||||
|
Other | | 1.407e-05 | | | 0.89
|
||||||
|
|
||||||
|
Nlocal: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 596 ave 596 max 596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 966 ave 966 max 966 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 966
|
||||||
|
Ave neighs/atom = 241.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,100 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_molecule
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
processors 1 * *
|
||||||
|
|
||||||
|
|
||||||
|
atom_style wavepacket
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_molecule
|
||||||
|
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
|
||||||
|
#neighbor 2.0 nsq
|
||||||
|
|
||||||
|
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
fix 1 all nve/awpmd
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute energies all pair awpmd/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]
|
||||||
|
|
||||||
|
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)
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.52918
|
||||||
|
ghost atom cutoff = 2.52918
|
||||||
|
binsize = 1.26459, bins = 1 1 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair awpmd/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
|
||||||
|
1 30360.982 30360.981 0.0009272222 39540.638 -1.1368684e-12 -9179.6571 0 0.10368794 1.3476263e+09 35.753932
|
||||||
|
2 67459.392 67459.388 0.0037086548 80559.71 6.5938366e-12 -13100.322 0 0.41472561 2.8534514e+09 143.0067
|
||||||
|
3 3732209.2 3732209.2 0.0041861902 3822452.2 -3.1604941e-11 -90242.984 0 0.46812669 1.4561246e+11 161.42059
|
||||||
|
4 2482974.7 2482961.9 12.860712 2489531.2 -2.2896529e-10 -6569.2968 0 1438.1675 -6.5458119e+08 495912.44
|
||||||
|
5 2472238.2 2472223.2 14.933049 2471015.7 -1.6120794e-10 1207.5188 0 1669.9095 -324992.65 575822.3
|
||||||
|
6 2482233.1 2482218.1 14.933057 2488321.7 -2.0691004e-11 -6103.5677 0 1669.9104 -5.5786438e+08 575822.62
|
||||||
|
7 2473498.5 2473479.8 18.61401 2472272.3 1.459739e-10 1207.5167 0 2081.5382 -183348.11 717761.12
|
||||||
|
8 2481621.3 2481602.6 18.614019 2487299.1 7.0258466e-11 -5696.4589 0 2081.5393 -4.7962801e+08 717761.48
|
||||||
|
9 2474506.2 2474482.2 24.021181 2473274.7 2.1395863e-10 1207.508 0 2686.2029 24318.554 926263.07
|
||||||
|
10 2480376.3 2480352.2 24.021192 2485505 -8.5719876e-11 -5152.7478 0 2686.2041 -3.8355089e+08 926263.48
|
||||||
|
Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms
|
||||||
|
|
||||||
|
Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s
|
||||||
|
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00011826 | 0.00027376 | 0.00073862 | 0.0 | 10.23
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00080514 | 0.0011864 | 0.001574 | 0.9 | 44.31
|
||||||
|
Output | 0.00094914 | 0.0011944 | 0.0017326 | 0.9 | 44.61
|
||||||
|
Modify | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.17
|
||||||
|
Other | | 1.824e-05 | | | 0.68
|
||||||
|
|
||||||
|
Nlocal: 1 ave 4 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 599 ave 600 max 596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 241.5 ave 966 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 966
|
||||||
|
Ave neighs/atom = 241.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Apr 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
dimension 3
|
dimension 3
|
||||||
|
|
@ -21,7 +20,7 @@ pair_style table spline 15000
|
||||||
|
|
||||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||||
|
|
||||||
neigh_modify delay 0 every 1 check yes one 10000
|
neigh_modify delay 0 every 1 check yes one 10000
|
||||||
neighbor 12.0 bin
|
neighbor 12.0 bin
|
||||||
|
|
@ -90,54 +89,54 @@ Neighbor list info ...
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
|
||||||
Step Temp PotEng TotEng Press Volume
|
Step Temp PotEng TotEng Press Volume
|
||||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
|
||||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
|
||||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
|
||||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
|
||||||
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
|
2500 305.51905 1051.59 1932.2314 -34.076658 66487.327
|
||||||
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
|
3000 291.76224 1053.524 1894.5121 45.522865 65879.535
|
||||||
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
|
3500 297.65795 1017.1028 1875.085 -79.41965 67185.19
|
||||||
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
|
4000 285.98779 1042.3622 1866.7058 88.549172 66357.051
|
||||||
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
|
4500 295.35 1071.4505 1922.7801 -16.75965 65378.949
|
||||||
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
|
5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38
|
||||||
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
|
5500 292.40422 1085.3901 1928.2287 161.88502 65677.644
|
||||||
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
|
6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05
|
||||||
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
|
6500 308.03807 1046.1413 1934.0436 249.70237 66052.045
|
||||||
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
|
7000 289.33716 1037.9657 1871.9636 47.662734 66782.578
|
||||||
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
|
7500 297.3092 1032.356 1889.3329 -24.049617 66129.95
|
||||||
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
|
8000 298.27827 1044.118 1903.8882 -26.61809 66720.381
|
||||||
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
|
8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559
|
||||||
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
|
9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4
|
||||||
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
|
9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848
|
||||||
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
|
10000 309.9256 1043.5321 1936.875 -103.81403 66222.21
|
||||||
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
|
Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
|
||||||
|
|
||||||
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
|
Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
|
Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39
|
||||||
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
|
Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44
|
||||||
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
|
Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68
|
||||||
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
|
Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00
|
||||||
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
|
Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25
|
||||||
Other | | 0.1252 | | | 0.36
|
Other | | 0.1042 | | | 0.25
|
||||||
|
|
||||||
Nlocal: 968 ave 968 max 968 min
|
Nlocal: 968 ave 968 max 968 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 9112 ave 9112 max 9112 min
|
Nghost: 9215 ave 9215 max 9215 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 404392 ave 404392 max 404392 min
|
Neighs: 411837 ave 411837 max 411837 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 404392
|
Total # of neighbors = 411837
|
||||||
Ave neighs/atom = 417.76
|
Ave neighs/atom = 425.451
|
||||||
Neighbor list builds = 13
|
Neighbor list builds = 13
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
Total wall time: 0:00:34
|
Total wall time: 0:00:42
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Apr 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
dimension 3
|
dimension 3
|
||||||
|
|
@ -21,7 +20,7 @@ pair_style table spline 15000
|
||||||
|
|
||||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||||
|
|
||||||
neigh_modify delay 0 every 1 check yes one 10000
|
neigh_modify delay 0 every 1 check yes one 10000
|
||||||
neighbor 12.0 bin
|
neighbor 12.0 bin
|
||||||
|
|
@ -90,54 +89,54 @@ Neighbor list info ...
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
|
||||||
Step Temp PotEng TotEng Press Volume
|
Step Temp PotEng TotEng Press Volume
|
||||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
|
||||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
|
||||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
|
||||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
|
||||||
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
|
2500 305.51905 1051.59 1932.2314 -34.076657 66487.327
|
||||||
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
|
3000 291.76224 1053.524 1894.5121 45.522919 65879.535
|
||||||
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
|
3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183
|
||||||
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
|
4000 285.99141 1042.379 1866.733 88.735986 66356.756
|
||||||
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
|
4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597
|
||||||
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
|
5000 292.47 1012.3769 1855.405 -255.07433 67527.215
|
||||||
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
|
5500 294.04431 1080.4547 1928.0208 192.6588 65811.742
|
||||||
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
|
6000 300.45893 986.16669 1852.2225 -167.3405 67858.175
|
||||||
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
|
6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704
|
||||||
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
|
7000 312.11968 1032.7392 1932.4065 152.17956 66016.299
|
||||||
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
|
7500 306.80585 1032.1157 1916.4662 51.07705 66875.727
|
||||||
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
|
8000 292.30957 1048.9003 1891.4661 61.280503 65894.103
|
||||||
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
|
8500 297.79592 1013.4061 1871.786 -133.01136 66842.574
|
||||||
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
|
9000 290.36753 1043.7732 1880.7412 65.208248 66010.86
|
||||||
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
|
9500 288.92211 1077.8835 1910.6851 46.291982 65674.639
|
||||||
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
|
10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692
|
||||||
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
|
Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
|
||||||
|
|
||||||
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
|
Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
|
||||||
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
|
Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35
|
||||||
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
|
Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33
|
||||||
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
|
Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42
|
||||||
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
|
Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02
|
||||||
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
|
Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28
|
||||||
Other | | 0.3112 | | | 1.08
|
Other | | 0.08323 | | | 0.60
|
||||||
|
|
||||||
Nlocal: 242 ave 244 max 239 min
|
Nlocal: 242 ave 248 max 232 min
|
||||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
Nghost: 5718.5 ave 5736 max 5702 min
|
Nghost: 5845.75 ave 5877 max 5808 min
|
||||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||||
Neighs: 100703 ave 108064 max 93454 min
|
Neighs: 104313 ave 113860 max 95507 min
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
Total # of neighbors = 402813
|
Total # of neighbors = 417252
|
||||||
Ave neighs/atom = 416.129
|
Ave neighs/atom = 431.045
|
||||||
Neighbor list builds = 14
|
Neighbor list builds = 13
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
Total wall time: 0:00:28
|
Total wall time: 0:00:14
|
||||||
|
|
@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||||
#dump_modify out sort id
|
#dump_modify out sort id
|
||||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
run 1000000
|
run 10000
|
||||||
|
|
||||||
#write_restart config.${number}.*
|
#write_restart config.${number}.*
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,172 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 1
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex1
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10 velocities
|
||||||
|
10 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
8 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
10 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7525
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||||
|
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
fix 1 all nve/dot
|
||||||
|
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1.92828
|
||||||
|
ghost atom cutoff = 1.92828
|
||||||
|
binsize = 0.964142, bins = 42 42 42
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||||
|
(1) pair oxdna/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||||
|
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||||
|
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||||
|
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||||
|
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||||
|
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||||
|
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||||
|
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||||
|
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||||
|
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||||
|
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||||
|
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
|
||||||
|
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
|
||||||
|
|
||||||
|
Performance: 60875.649 tau/day, 70457.927 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 | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
|
||||||
|
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
|
||||||
|
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
|
||||||
|
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
|
||||||
|
Other | | 0.002982 | | | 2.10
|
||||||
|
|
||||||
|
Nlocal: 10 ave 10 max 10 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: 43 ave 43 max 43 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 43
|
||||||
|
Ave neighs/atom = 4.3
|
||||||
|
Ave special neighs/atom = 3.6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,172 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 1
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex1
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10 velocities
|
||||||
|
10 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
8 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
10 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7525
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||||
|
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
fix 1 all nve/dot
|
||||||
|
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1.92828
|
||||||
|
ghost atom cutoff = 1.92828
|
||||||
|
binsize = 0.964142, bins = 42 42 42
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||||
|
(1) pair oxdna/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||||
|
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||||
|
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||||
|
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||||
|
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||||
|
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||||
|
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||||
|
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||||
|
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||||
|
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||||
|
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||||
|
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
|
||||||
|
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
|
||||||
|
|
||||||
|
Performance: 64220.659 tau/day, 74329.466 timesteps/s
|
||||||
|
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
|
||||||
|
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
|
||||||
|
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
|
||||||
|
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
|
||||||
|
Other | | 0.05989 | | | 44.52
|
||||||
|
|
||||||
|
Nlocal: 2.5 ave 5 max 0 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 7.5 ave 10 max 5 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Neighs: 17.5 ave 33 max 0 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 70
|
||||||
|
Ave neighs/atom = 7
|
||||||
|
Ave special neighs/atom = 3.6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||||
#dump_modify out sort id
|
#dump_modify out sort id
|
||||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
run 1000000
|
run 10000
|
||||||
|
|
||||||
#write_restart config.${number}.*
|
#write_restart config.${number}.*
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,172 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 2
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex2
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
16 atoms
|
||||||
|
reading velocities ...
|
||||||
|
16 velocities
|
||||||
|
16 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
13 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
16 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7525
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||||
|
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
#fix 1 all nve/dot
|
||||||
|
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1.92828
|
||||||
|
ghost atom cutoff = 1.92828
|
||||||
|
binsize = 0.964142, bins = 42 42 42
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||||
|
(1) pair oxdna/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||||
|
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
|
||||||
|
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
|
||||||
|
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
|
||||||
|
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
|
||||||
|
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
|
||||||
|
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
|
||||||
|
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
|
||||||
|
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
|
||||||
|
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
|
||||||
|
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
|
||||||
|
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
|
||||||
|
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
|
||||||
|
|
||||||
|
Performance: 29234.801 tau/day, 33836.575 timesteps/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 | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
|
||||||
|
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
|
||||||
|
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||||
|
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
|
||||||
|
Other | | 0.003813 | | | 1.29
|
||||||
|
|
||||||
|
Nlocal: 16 ave 16 max 16 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: 88 ave 88 max 88 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 88
|
||||||
|
Ave neighs/atom = 5.5
|
||||||
|
Ave special neighs/atom = 3.75
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,172 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 2
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex2
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
16 atoms
|
||||||
|
reading velocities ...
|
||||||
|
16 velocities
|
||||||
|
16 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
13 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
16 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7525
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||||
|
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
#fix 1 all nve/dot
|
||||||
|
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1.92828
|
||||||
|
ghost atom cutoff = 1.92828
|
||||||
|
binsize = 0.964142, bins = 42 42 42
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||||
|
(1) pair oxdna/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||||
|
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
|
||||||
|
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
|
||||||
|
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
|
||||||
|
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
|
||||||
|
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
|
||||||
|
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
|
||||||
|
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
|
||||||
|
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
|
||||||
|
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
|
||||||
|
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
|
||||||
|
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
|
||||||
|
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
|
||||||
|
|
||||||
|
Performance: 34303.820 tau/day, 39703.495 timesteps/s
|
||||||
|
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
|
||||||
|
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
|
||||||
|
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
|
||||||
|
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
|
||||||
|
Other | | 0.1208 | | | 47.96
|
||||||
|
|
||||||
|
Nlocal: 4 ave 8 max 0 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 9 ave 10 max 8 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Neighs: 34.5 ave 67 max 0 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 138
|
||||||
|
Ave neighs/atom = 8.625
|
||||||
|
Ave special neighs/atom = 3.75
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||||
#dump_modify out sort id
|
#dump_modify out sort id
|
||||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
run 1000000
|
run 10000
|
||||||
|
|
||||||
#write_restart config.${number}.*
|
#write_restart config.${number}.*
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,178 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 1
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex1
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10 velocities
|
||||||
|
10 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
8 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
10 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna2/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7564
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||||
|
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||||
|
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
fix 1 all nve/dot
|
||||||
|
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.6274
|
||||||
|
ghost atom cutoff = 2.6274
|
||||||
|
binsize = 1.3137, bins = 31 31 31
|
||||||
|
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||||
|
(1) pair oxdna2/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||||
|
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||||
|
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||||
|
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||||
|
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||||
|
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||||
|
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
|
||||||
|
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
|
||||||
|
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
|
||||||
|
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
|
||||||
|
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
|
||||||
|
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||||
|
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
|
||||||
|
|
||||||
|
Performance: 57828.835 tau/day, 66931.522 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 | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
|
||||||
|
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
|
||||||
|
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||||
|
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
|
||||||
|
Other | | 0.004268 | | | 2.86
|
||||||
|
|
||||||
|
Nlocal: 10 ave 10 max 10 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: 45 ave 45 max 45 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 45
|
||||||
|
Ave neighs/atom = 4.5
|
||||||
|
Ave special neighs/atom = 3.6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,178 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 1
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex1
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10 velocities
|
||||||
|
10 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
8 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
10 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna2/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7564
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||||
|
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||||
|
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
fix 1 all nve/dot
|
||||||
|
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.6274
|
||||||
|
ghost atom cutoff = 2.6274
|
||||||
|
binsize = 1.3137, bins = 31 31 31
|
||||||
|
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||||
|
(1) pair oxdna2/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||||
|
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||||
|
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||||
|
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||||
|
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||||
|
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||||
|
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
|
||||||
|
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
|
||||||
|
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
|
||||||
|
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
|
||||||
|
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
|
||||||
|
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||||
|
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
|
||||||
|
|
||||||
|
Performance: 59247.054 tau/day, 68572.979 timesteps/s
|
||||||
|
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
|
||||||
|
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
|
||||||
|
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
|
||||||
|
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
|
||||||
|
Other | | 0.06674 | | | 45.76
|
||||||
|
|
||||||
|
Nlocal: 2.5 ave 5 max 0 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 7.5 ave 10 max 5 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Neighs: 18.5 ave 35 max 0 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 74
|
||||||
|
Ave neighs/atom = 7.4
|
||||||
|
Ave special neighs/atom = 3.6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||||
#dump_modify out sort id
|
#dump_modify out sort id
|
||||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
run 1000000
|
run 10000
|
||||||
|
|
||||||
#write_restart config.${number}.*
|
#write_restart config.${number}.*
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,178 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 2
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex2
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
16 atoms
|
||||||
|
reading velocities ...
|
||||||
|
16 velocities
|
||||||
|
16 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
13 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
16 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna2/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7564
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||||
|
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||||
|
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
#fix 1 all nve/dot
|
||||||
|
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.6274
|
||||||
|
ghost atom cutoff = 2.6274
|
||||||
|
binsize = 1.3137, bins = 31 31 31
|
||||||
|
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||||
|
(1) pair oxdna2/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||||
|
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||||
|
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
|
||||||
|
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
|
||||||
|
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
|
||||||
|
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
|
||||||
|
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
|
||||||
|
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
|
||||||
|
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
|
||||||
|
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
|
||||||
|
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
|
||||||
|
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
|
||||||
|
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
|
||||||
|
|
||||||
|
Performance: 26356.746 tau/day, 30505.493 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 | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
|
||||||
|
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
|
||||||
|
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
|
||||||
|
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
|
||||||
|
Other | | 0.003398 | | | 1.04
|
||||||
|
|
||||||
|
Nlocal: 16 ave 16 max 16 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: 116 ave 116 max 116 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 116
|
||||||
|
Ave neighs/atom = 7.25
|
||||||
|
Ave special neighs/atom = 3.75
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,178 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable number equal 2
|
||||||
|
variable ofreq equal 1000
|
||||||
|
variable efreq equal 1000
|
||||||
|
|
||||||
|
units lj
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
newton off
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style hybrid bond ellipsoid
|
||||||
|
atom_modify sort 0 1.0
|
||||||
|
|
||||||
|
# Pair interactions require lists of neighbours to be calculated
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
read_data data.duplex2
|
||||||
|
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
16 atoms
|
||||||
|
reading velocities ...
|
||||||
|
16 velocities
|
||||||
|
16 ellipsoids
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
reading bonds ...
|
||||||
|
13 bonds
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
|
||||||
|
set atom * mass 3.1575
|
||||||
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
|
16 atoms in group all
|
||||||
|
|
||||||
|
# oxDNA bond interactions - FENE backbone
|
||||||
|
bond_style oxdna2/fene
|
||||||
|
bond_coeff * 2.0 0.25 0.7564
|
||||||
|
|
||||||
|
# oxDNA pair interactions
|
||||||
|
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||||
|
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||||
|
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||||
|
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||||
|
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||||
|
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||||
|
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||||
|
|
||||||
|
# NVE ensemble
|
||||||
|
#fix 1 all nve/dot
|
||||||
|
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
#fix 1 all nve/asphere
|
||||||
|
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||||
|
|
||||||
|
timestep 1e-5
|
||||||
|
|
||||||
|
#comm_style tiled
|
||||||
|
#fix 3 all balance 10000 1.1 rcb
|
||||||
|
|
||||||
|
#compute mol all chunk/atom molecule
|
||||||
|
#compute mychunk all vcm/chunk mol
|
||||||
|
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||||
|
|
||||||
|
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||||
|
|
||||||
|
#compute quat all property/atom quatw quati quatj quatk
|
||||||
|
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||||
|
#dump_modify quat sort id
|
||||||
|
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
compute erot all erotate/asphere
|
||||||
|
compute ekin all ke
|
||||||
|
compute epot all pe
|
||||||
|
variable erot equal c_erot
|
||||||
|
variable ekin equal c_ekin
|
||||||
|
variable epot equal c_epot
|
||||||
|
variable etot equal c_erot+c_ekin+c_epot
|
||||||
|
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
|
|
||||||
|
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||||
|
#dump_modify out sort id
|
||||||
|
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.6274
|
||||||
|
ghost atom cutoff = 2.6274
|
||||||
|
binsize = 1.3137, bins = 31 31 31
|
||||||
|
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||||
|
(1) pair oxdna2/excv, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||||
|
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||||
|
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
|
||||||
|
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
|
||||||
|
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
|
||||||
|
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
|
||||||
|
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
|
||||||
|
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
|
||||||
|
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
|
||||||
|
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
|
||||||
|
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
|
||||||
|
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
|
||||||
|
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
|
||||||
|
|
||||||
|
Performance: 29625.313 tau/day, 34288.557 timesteps/s
|
||||||
|
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
|
||||||
|
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
|
||||||
|
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
|
||||||
|
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
|
||||||
|
Other | | 0.139 | | | 47.65
|
||||||
|
|
||||||
|
Nlocal: 4 ave 8 max 0 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 11 ave 14 max 8 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 46 ave 89 max 0 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 184
|
||||||
|
Ave neighs/atom = 11.5
|
||||||
|
Ave special neighs/atom = 3.75
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
#write_restart config.${number}.*
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
read_data data.pegc12e8.gz
|
read_data data.pegc12e8.gz
|
||||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||||
2 by 1 by 1 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
40140 atoms
|
40140 atoms
|
||||||
reading velocities ...
|
reading velocities ...
|
||||||
|
|
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
|
||||||
thermo_style multi
|
thermo_style multi
|
||||||
thermo 200
|
thermo 200
|
||||||
run 1000
|
run 1000
|
||||||
Memory usage per processor = 12.4188 Mbytes
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 15 15 45
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk, 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) = 47.18 | 47.18 | 47.18 Mbytes
|
||||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||||
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
|
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
|
||||||
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
|
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
|
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
|
||||||
---------------- Step 200 ----- CPU = 8.7547 (sec) ----------------
|
---------------- Step 200 ----- CPU = 11.2079 (sec) ----------------
|
||||||
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
|
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
|
||||||
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
|
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
|
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
|
||||||
---------------- Step 400 ----- CPU = 17.7479 (sec) ----------------
|
---------------- Step 400 ----- CPU = 22.6137 (sec) ----------------
|
||||||
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
|
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
|
||||||
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
|
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
|
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
|
||||||
---------------- Step 600 ----- CPU = 26.7299 (sec) ----------------
|
---------------- Step 600 ----- CPU = 33.9441 (sec) ----------------
|
||||||
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
|
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
|
||||||
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
|
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
|
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
|
||||||
---------------- Step 800 ----- CPU = 35.8941 (sec) ----------------
|
---------------- Step 800 ----- CPU = 45.4291 (sec) ----------------
|
||||||
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
|
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
|
||||||
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
|
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
|
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
|
||||||
---------------- Step 1000 ----- CPU = 45.1542 (sec) ----------------
|
---------------- Step 1000 ----- CPU = 56.9328 (sec) ----------------
|
||||||
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
|
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
|
||||||
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
|
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
|
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
|
||||||
|
Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms
|
||||||
|
|
||||||
Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
|
Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s
|
||||||
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27
|
Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11
|
||||||
Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14
|
Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65
|
||||||
Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34
|
Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94
|
||||||
Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49
|
Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26
|
||||||
Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00
|
Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00
|
||||||
Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19
|
Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83
|
||||||
Other | | 0.2571 | | | 0.57
|
Other | | 0.1154 | | | 0.20
|
||||||
|
|
||||||
Nlocal: 20070 ave 20100 max 20040 min
|
Nlocal: 40140 ave 40140 max 40140 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 20230.5 ave 20241 max 20220 min
|
Nghost: 25966 ave 25966 max 25966 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
|
Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 5686756
|
Total # of neighbors = 5686756
|
||||||
Ave neighs/atom = 141.673
|
Ave neighs/atom = 141.673
|
||||||
|
|
@ -113,3 +124,4 @@ Neighbor list builds = 38
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
#write_restart pegc12e8-1.restart
|
#write_restart pegc12e8-1.restart
|
||||||
|
|
||||||
|
Total wall time: 0:00:57
|
||||||
|
|
@ -0,0 +1,127 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
atom_style angle
|
||||||
|
|
||||||
|
# enforce that in z-direction there is only one
|
||||||
|
# processor (could be two) for optimal performance
|
||||||
|
processors * * 1
|
||||||
|
|
||||||
|
# read topology and force field
|
||||||
|
pair_style lj/sdk 15.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style sdk
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
|
read_data data.pegc12e8.gz
|
||||||
|
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
40140 atoms
|
||||||
|
reading velocities ...
|
||||||
|
40140 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
13284 bonds
|
||||||
|
reading angles ...
|
||||||
|
12177 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 3.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 5.0
|
||||||
|
#dump 1 all xtc 200 pegc12e8-1.xtc
|
||||||
|
#dump_modify 1 unwrap yes
|
||||||
|
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
|
||||||
|
#dump_modify 2 unwrap yes
|
||||||
|
|
||||||
|
velocity all create 303.0 46659 mom yes rot yes dist gaussian
|
||||||
|
|
||||||
|
fix 1 all nvt temp 303.0 303.0 100.0
|
||||||
|
|
||||||
|
thermo_style multi
|
||||||
|
thermo 200
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 15 15 45
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk, 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) = 15.87 | 15.87 | 15.87 Mbytes
|
||||||
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||||
|
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
|
||||||
|
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
|
||||||
|
---------------- Step 200 ----- CPU = 3.0597 (sec) ----------------
|
||||||
|
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
|
||||||
|
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
|
||||||
|
---------------- Step 400 ----- CPU = 6.2514 (sec) ----------------
|
||||||
|
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
|
||||||
|
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
|
||||||
|
---------------- Step 600 ----- CPU = 9.4073 (sec) ----------------
|
||||||
|
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
|
||||||
|
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
|
||||||
|
---------------- Step 800 ----- CPU = 12.6096 (sec) ----------------
|
||||||
|
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
|
||||||
|
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
|
||||||
|
---------------- Step 1000 ----- CPU = 15.9134 (sec) ----------------
|
||||||
|
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
|
||||||
|
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
|
||||||
|
Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms
|
||||||
|
|
||||||
|
Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 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 | 13.325 | 13.6 | 13.755 | 4.7 | 85.46
|
||||||
|
Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57
|
||||||
|
Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79
|
||||||
|
Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61
|
||||||
|
Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00
|
||||||
|
Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09
|
||||||
|
Other | | 0.0768 | | | 0.48
|
||||||
|
|
||||||
|
Nlocal: 10035 ave 10084 max 9971 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Nghost: 14548.8 ave 14610 max 14509 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5686756
|
||||||
|
Ave neighs/atom = 141.673
|
||||||
|
Ave special neighs/atom = 1.26861
|
||||||
|
Neighbor list builds = 38
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_restart pegc12e8-1.restart
|
||||||
|
|
||||||
|
Total wall time: 0:00:16
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
read_data data.pegc12e8.gz
|
read_data data.pegc12e8.gz
|
||||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||||
2 by 1 by 1 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
40140 atoms
|
40140 atoms
|
||||||
reading velocities ...
|
reading velocities ...
|
||||||
|
|
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
|
||||||
thermo_style multi
|
thermo_style multi
|
||||||
thermo 200
|
thermo 200
|
||||||
run 1000
|
run 1000
|
||||||
Memory usage per processor = 12.4188 Mbytes
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 15 15 45
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk, 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) = 47.18 | 47.18 | 47.18 Mbytes
|
||||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||||
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
|
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
|
||||||
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
|
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
|
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
|
||||||
---------------- Step 200 ----- CPU = 8.6552 (sec) ----------------
|
---------------- Step 200 ----- CPU = 11.2074 (sec) ----------------
|
||||||
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
|
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
|
||||||
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
|
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
|
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
|
||||||
---------------- Step 400 ----- CPU = 17.5807 (sec) ----------------
|
---------------- Step 400 ----- CPU = 22.6113 (sec) ----------------
|
||||||
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
|
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
|
||||||
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
|
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
|
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
|
||||||
---------------- Step 600 ----- CPU = 28.1043 (sec) ----------------
|
---------------- Step 600 ----- CPU = 34.0551 (sec) ----------------
|
||||||
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
|
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
|
||||||
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
|
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
|
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
|
||||||
---------------- Step 800 ----- CPU = 40.5132 (sec) ----------------
|
---------------- Step 800 ----- CPU = 45.5316 (sec) ----------------
|
||||||
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
|
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
|
||||||
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
|
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
|
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
|
||||||
---------------- Step 1000 ----- CPU = 52.8166 (sec) ----------------
|
---------------- Step 1000 ----- CPU = 56.9111 (sec) ----------------
|
||||||
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
|
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
|
||||||
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
|
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
|
||||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
|
||||||
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
|
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
|
||||||
|
Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms
|
||||||
|
|
||||||
Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
|
Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s
|
||||||
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79
|
Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22
|
||||||
Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88
|
Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55
|
||||||
Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42
|
Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94
|
||||||
Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27
|
Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26
|
||||||
Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00
|
Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00
|
||||||
Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12
|
Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83
|
||||||
Other | | 0.2731 | | | 0.52
|
Other | | 0.1127 | | | 0.20
|
||||||
|
|
||||||
Nlocal: 20070 ave 20109 max 20031 min
|
Nlocal: 40140 ave 40140 max 40140 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 20234 ave 20281 max 20187 min
|
Nghost: 25968 ave 25968 max 25968 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
|
Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 5691680
|
Total # of neighbors = 5691680
|
||||||
Ave neighs/atom = 141.796
|
Ave neighs/atom = 141.796
|
||||||
|
|
@ -113,3 +124,4 @@ Neighbor list builds = 38
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
#write_restart pegc12e8-1.restart
|
#write_restart pegc12e8-1.restart
|
||||||
|
|
||||||
|
Total wall time: 0:00:57
|
||||||
|
|
@ -0,0 +1,127 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
atom_style angle
|
||||||
|
|
||||||
|
# enforce that in z-direction there is only one
|
||||||
|
# processor (could be two) for optimal performance
|
||||||
|
processors * * 1
|
||||||
|
|
||||||
|
# read topology and force field
|
||||||
|
pair_style lj/sdk 15.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
|
read_data data.pegc12e8.gz
|
||||||
|
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
40140 atoms
|
||||||
|
reading velocities ...
|
||||||
|
40140 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
13284 bonds
|
||||||
|
reading angles ...
|
||||||
|
12177 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 3.0 bin
|
||||||
|
neigh_modify delay 5
|
||||||
|
|
||||||
|
timestep 5.0
|
||||||
|
#dump 1 all xtc 200 pegc12e8-1.xtc
|
||||||
|
#dump_modify 1 unwrap yes
|
||||||
|
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
|
||||||
|
#dump_modify 2 unwrap yes
|
||||||
|
|
||||||
|
velocity all create 303.0 46659 mom yes rot yes dist gaussian
|
||||||
|
|
||||||
|
fix 1 all nvt temp 303.0 303.0 100.0
|
||||||
|
|
||||||
|
thermo_style multi
|
||||||
|
thermo 200
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 15 15 45
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk, 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) = 15.87 | 15.87 | 15.87 Mbytes
|
||||||
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||||
|
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
|
||||||
|
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
|
||||||
|
---------------- Step 200 ----- CPU = 3.0107 (sec) ----------------
|
||||||
|
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
|
||||||
|
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
|
||||||
|
---------------- Step 400 ----- CPU = 6.1324 (sec) ----------------
|
||||||
|
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
|
||||||
|
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
|
||||||
|
---------------- Step 600 ----- CPU = 9.3443 (sec) ----------------
|
||||||
|
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
|
||||||
|
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
|
||||||
|
---------------- Step 800 ----- CPU = 12.5388 (sec) ----------------
|
||||||
|
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
|
||||||
|
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
|
||||||
|
---------------- Step 1000 ----- CPU = 15.7416 (sec) ----------------
|
||||||
|
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
|
||||||
|
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
|
||||||
|
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
|
||||||
|
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
|
||||||
|
Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms
|
||||||
|
|
||||||
|
Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 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 | 13.591 | 13.612 | 13.626 | 0.4 | 86.47
|
||||||
|
Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47
|
||||||
|
Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79
|
||||||
|
Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65
|
||||||
|
Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00
|
||||||
|
Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13
|
||||||
|
Other | | 0.07576 | | | 0.48
|
||||||
|
|
||||||
|
Nlocal: 10035 ave 10098 max 10004 min
|
||||||
|
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||||
|
Nghost: 14546.5 ave 14564 max 14503 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5691680
|
||||||
|
Ave neighs/atom = 141.796
|
||||||
|
Ave special neighs/atom = 1.26861
|
||||||
|
Neighbor list builds = 38
|
||||||
|
Dangerous builds = 0
|
||||||
|
#write_restart pegc12e8-1.restart
|
||||||
|
|
||||||
|
Total wall time: 0:00:15
|
||||||
|
|
@ -0,0 +1,145 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# coarse grained SDS surfactant monolayer
|
||||||
|
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
atom_style full
|
||||||
|
processors * * 1
|
||||||
|
|
||||||
|
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style sdk
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
|
read_data data.sds.gz
|
||||||
|
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
31280 atoms
|
||||||
|
reading velocities ...
|
||||||
|
31280 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
4096 bonds
|
||||||
|
reading angles ...
|
||||||
|
3072 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_coeff 1 4 coul/long # SO4 SOD
|
||||||
|
pair_coeff 4 4 coul/long # SOD SOD
|
||||||
|
pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
|
||||||
|
pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
|
||||||
|
pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
|
||||||
|
pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
|
||||||
|
pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
|
||||||
|
pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
|
||||||
|
pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
|
||||||
|
pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
|
||||||
|
pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
|
||||||
|
pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
|
||||||
|
pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
|
||||||
|
pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
|
||||||
|
pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
|
||||||
|
pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
|
||||||
|
pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W
|
||||||
|
|
||||||
|
|
||||||
|
group charged type 1 4
|
||||||
|
2048 atoms in group charged
|
||||||
|
atom_modify first charged
|
||||||
|
|
||||||
|
kspace_style pppm/cg 0.00001
|
||||||
|
kspace_modify order 3
|
||||||
|
|
||||||
|
comm_modify mode multi
|
||||||
|
neighbor 2.0 multi
|
||||||
|
neigh_modify delay 4 every 2 check yes
|
||||||
|
|
||||||
|
timestep 10.0
|
||||||
|
|
||||||
|
fix 1 all nvt temp 310.0 310.0 100.0
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 100
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
|
G vector (1/distance) = 0.0416781
|
||||||
|
grid = 8 4 12
|
||||||
|
stencil order = 3
|
||||||
|
estimated absolute RMS force accuracy = 0.00248777
|
||||||
|
estimated relative force accuracy = 7.49185e-06
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 1155 384
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 4 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 28.5
|
||||||
|
ghost atom cutoff = 28.5
|
||||||
|
binsize = 8.5, bins = 27 14 48
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair lj/sdk, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/newton
|
||||||
|
stencil: half/multi/3d/newton
|
||||||
|
bin: standard
|
||||||
|
(2) pair coul/long, perpetual, skip from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
PPPM/cg optimization cutoff: 1e-05
|
||||||
|
Total charged atoms: 6.5%
|
||||||
|
Min/max charged atoms/proc: 6.5% 6.5%
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 35.49 | 35.49 | 35.49 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
|
||||||
|
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
|
||||||
|
20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751
|
||||||
|
30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129
|
||||||
|
40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838
|
||||||
|
50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457
|
||||||
|
60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545
|
||||||
|
70 310.13623 -249262.32 2595.874 -217750.35 -26.276067
|
||||||
|
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
|
||||||
|
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
|
||||||
|
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
|
||||||
|
Loop time of 9.61984 on 1 procs for 100 steps with 31280 atoms
|
||||||
|
|
||||||
|
Performance: 8.981 ns/day, 2.672 hours/ns, 10.395 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 | 7.2928 | 7.2928 | 7.2928 | 0.0 | 75.81
|
||||||
|
Bond | 0.036198 | 0.036198 | 0.036198 | 0.0 | 0.38
|
||||||
|
Kspace | 0.053125 | 0.053125 | 0.053125 | 0.0 | 0.55
|
||||||
|
Neigh | 2.117 | 2.117 | 2.117 | 0.0 | 22.01
|
||||||
|
Comm | 0.029731 | 0.029731 | 0.029731 | 0.0 | 0.31
|
||||||
|
Output | 0.0014369 | 0.0014369 | 0.0014369 | 0.0 | 0.01
|
||||||
|
Modify | 0.079014 | 0.079014 | 0.079014 | 0.0 | 0.82
|
||||||
|
Other | | 0.01051 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 31280 ave 31280 max 31280 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 16629 ave 16629 max 16629 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3.40168e+06 ave 3.40168e+06 max 3.40168e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3401676
|
||||||
|
Ave neighs/atom = 108.749
|
||||||
|
Ave special neighs/atom = 0.458312
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:10
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# coarse grained SDS surfactant monolayer
|
# coarse grained SDS surfactant monolayer
|
||||||
|
|
||||||
|
|
@ -58,7 +57,7 @@ atom_modify first charged
|
||||||
kspace_style pppm/cg 0.00001
|
kspace_style pppm/cg 0.00001
|
||||||
kspace_modify order 3
|
kspace_modify order 3
|
||||||
|
|
||||||
communicate multi
|
comm_modify mode multi
|
||||||
neighbor 2.0 multi
|
neighbor 2.0 multi
|
||||||
neigh_modify delay 4 every 2 check yes
|
neigh_modify delay 4 every 2 check yes
|
||||||
|
|
||||||
|
|
@ -70,6 +69,7 @@ thermo 10
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.0416781
|
G vector (1/distance) = 0.0416781
|
||||||
grid = 8 4 12
|
grid = 8 4 12
|
||||||
stencil order = 3
|
stencil order = 3
|
||||||
|
|
@ -77,10 +77,27 @@ PPPM initialization ...
|
||||||
estimated relative force accuracy = 7.49185e-06
|
estimated relative force accuracy = 7.49185e-06
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 525 96
|
3d grid and FFT values/proc = 525 96
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 4 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 28.5
|
||||||
|
ghost atom cutoff = 28.5
|
||||||
|
binsize = 8.5, bins = 27 14 48
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair lj/sdk, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/newton
|
||||||
|
stencil: half/multi/3d/newton
|
||||||
|
bin: standard
|
||||||
|
(2) pair coul/long, perpetual, skip from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
PPPM/cg optimization cutoff: 1e-05
|
PPPM/cg optimization cutoff: 1e-05
|
||||||
Total charged atoms: 6.5%
|
Total charged atoms: 6.5%
|
||||||
Min/max charged atoms/proc: 6.4% 6.7%
|
Min/max charged atoms/proc: 6.4% 6.7%
|
||||||
Memory usage per processor = 7.66668 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
|
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
|
||||||
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
|
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
|
||||||
|
|
@ -93,22 +110,22 @@ Step Temp E_pair E_mol TotEng Press
|
||||||
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
|
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
|
||||||
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
|
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
|
||||||
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
|
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
|
||||||
|
Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms
|
||||||
|
|
||||||
Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms
|
Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s
|
||||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95
|
Pair | 1.8639 | 1.8913 | 1.9283 | 1.8 | 74.33
|
||||||
Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53
|
Bond | 0.0092797 | 0.0094567 | 0.0095828 | 0.1 | 0.37
|
||||||
Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45
|
Kspace | 0.018389 | 0.056616 | 0.084424 | 10.7 | 2.23
|
||||||
Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57
|
Neigh | 0.53553 | 0.53569 | 0.53605 | 0.0 | 21.05
|
||||||
Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22
|
Comm | 0.023819 | 0.02433 | 0.02506 | 0.3 | 0.96
|
||||||
Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02
|
Output | 0.00058866 | 0.00084978 | 0.0016243 | 0.0 | 0.03
|
||||||
Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86
|
Modify | 0.021841 | 0.022059 | 0.022308 | 0.1 | 0.87
|
||||||
Other | | 0.01665 | | | 0.41
|
Other | | 0.004233 | | | 0.17
|
||||||
|
|
||||||
Nlocal: 7820 ave 7866 max 7774 min
|
Nlocal: 7820 ave 7866 max 7774 min
|
||||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
|
@ -125,3 +142,4 @@ Dangerous builds = 0
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:02
|
||||||
|
|
@ -0,0 +1,129 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# coarse grained SDS surfactant monolayer
|
||||||
|
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
atom_style full
|
||||||
|
processors * * 1
|
||||||
|
|
||||||
|
pair_style lj/sdk/coul/long 15.0
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style sdk
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
|
||||||
|
read_data data.sds.gz
|
||||||
|
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
31280 atoms
|
||||||
|
reading velocities ...
|
||||||
|
31280 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
4096 bonds
|
||||||
|
reading angles ...
|
||||||
|
3072 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4
|
||||||
|
pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
|
||||||
|
pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
|
||||||
|
pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
|
||||||
|
pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
|
||||||
|
pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
|
||||||
|
pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
|
||||||
|
pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
|
||||||
|
pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
|
||||||
|
pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
|
||||||
|
pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
|
||||||
|
pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
|
||||||
|
pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
|
||||||
|
pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
|
||||||
|
pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W
|
||||||
|
|
||||||
|
kspace_style pppm/cg 0.00001
|
||||||
|
kspace_modify order 3
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify delay 4 every 2 check yes
|
||||||
|
|
||||||
|
timestep 10.0
|
||||||
|
|
||||||
|
fix 1 all nvt temp 310.0 310.0 100.0
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 100
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
|
G vector (1/distance) = 0.0789325
|
||||||
|
grid = 15 8 25
|
||||||
|
stencil order = 3
|
||||||
|
estimated absolute RMS force accuracy = 0.00275556
|
||||||
|
estimated relative force accuracy = 8.29828e-06
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 5544 3000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 4 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 17
|
||||||
|
ghost atom cutoff = 17
|
||||||
|
binsize = 8.5, bins = 27 14 48
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
PPPM/cg optimization cutoff: 1e-05
|
||||||
|
Total charged atoms: 6.5%
|
||||||
|
Min/max charged atoms/proc: 6.5% 6.5%
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
|
||||||
|
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
|
||||||
|
20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631
|
||||||
|
30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902
|
||||||
|
40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066
|
||||||
|
50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007
|
||||||
|
60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965
|
||||||
|
70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691
|
||||||
|
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
|
||||||
|
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
|
||||||
|
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
|
||||||
|
Loop time of 9.23618 on 1 procs for 100 steps with 31280 atoms
|
||||||
|
|
||||||
|
Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 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 | 7.7363 | 7.7363 | 7.7363 | 0.0 | 83.76
|
||||||
|
Bond | 0.032901 | 0.032901 | 0.032901 | 0.0 | 0.36
|
||||||
|
Kspace | 0.078907 | 0.078907 | 0.078907 | 0.0 | 0.85
|
||||||
|
Neigh | 1.2706 | 1.2706 | 1.2706 | 0.0 | 13.76
|
||||||
|
Comm | 0.026005 | 0.026005 | 0.026005 | 0.0 | 0.28
|
||||||
|
Output | 0.0014131 | 0.0014131 | 0.0014131 | 0.0 | 0.02
|
||||||
|
Modify | 0.079446 | 0.079446 | 0.079446 | 0.0 | 0.86
|
||||||
|
Other | | 0.01055 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 31280 ave 31280 max 31280 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 15812 ave 15812 max 15812 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3352103
|
||||||
|
Ave neighs/atom = 107.164
|
||||||
|
Ave special neighs/atom = 0.458312
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:09
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# coarse grained SDS surfactant monolayer
|
# coarse grained SDS surfactant monolayer
|
||||||
|
|
||||||
|
|
@ -62,6 +61,7 @@ thermo 10
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.0789325
|
G vector (1/distance) = 0.0789325
|
||||||
grid = 15 8 25
|
grid = 15 8 25
|
||||||
stencil order = 3
|
stencil order = 3
|
||||||
|
|
@ -69,10 +69,22 @@ PPPM initialization ...
|
||||||
estimated relative force accuracy = 8.29828e-06
|
estimated relative force accuracy = 8.29828e-06
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 2156 840
|
3d grid and FFT values/proc = 2156 840
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 4 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 17
|
||||||
|
ghost atom cutoff = 17
|
||||||
|
binsize = 8.5, bins = 27 14 48
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/sdk/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
PPPM/cg optimization cutoff: 1e-05
|
PPPM/cg optimization cutoff: 1e-05
|
||||||
Total charged atoms: 6.5%
|
Total charged atoms: 6.5%
|
||||||
Min/max charged atoms/proc: 6.4% 6.7%
|
Min/max charged atoms/proc: 6.4% 6.7%
|
||||||
Memory usage per processor = 8.05923 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 17.32 | 17.32 | 17.32 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
|
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
|
||||||
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
|
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
|
||||||
|
|
@ -85,22 +97,22 @@ Step Temp E_pair E_mol TotEng Press
|
||||||
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
|
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
|
||||||
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
|
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
|
||||||
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
|
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
|
||||||
|
Loop time of 2.45408 on 4 procs for 100 steps with 31280 atoms
|
||||||
|
|
||||||
Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms
|
Performance: 35.207 ns/day, 0.682 hours/ns, 40.748 timesteps/s
|
||||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 25.046 ns/day 0.958 hours/ns 28.988 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 2.7883 | 2.817 | 2.8415 | 1.1 | 81.66
|
Pair | 2.0065 | 2.0143 | 2.0326 | 0.8 | 82.08
|
||||||
Bond | 0.017868 | 0.018973 | 0.020636 | 0.7 | 0.55
|
Bond | 0.0084255 | 0.0086145 | 0.0088007 | 0.1 | 0.35
|
||||||
Kspace | 0.063881 | 0.088012 | 0.11571 | 6.2 | 2.55
|
Kspace | 0.033373 | 0.052041 | 0.060933 | 4.8 | 2.12
|
||||||
Neigh | 0.42765 | 0.42828 | 0.42882 | 0.1 | 12.41
|
Neigh | 0.32741 | 0.32748 | 0.32754 | 0.0 | 13.34
|
||||||
Comm | 0.043887 | 0.044575 | 0.045079 | 0.2 | 1.29
|
Comm | 0.022403 | 0.023025 | 0.023735 | 0.4 | 0.94
|
||||||
Output | 0.00072694 | 0.00096422 | 0.0016718 | 1.3 | 0.03
|
Output | 0.00060058 | 0.00086623 | 0.0016549 | 0.0 | 0.04
|
||||||
Modify | 0.035513 | 0.035955 | 0.036887 | 0.3 | 1.04
|
Modify | 0.022533 | 0.022723 | 0.022876 | 0.1 | 0.93
|
||||||
Other | | 0.01597 | | | 0.46
|
Other | | 0.005038 | | | 0.21
|
||||||
|
|
||||||
Nlocal: 7820 ave 7866 max 7775 min
|
Nlocal: 7820 ave 7866 max 7775 min
|
||||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||||
|
|
@ -114,3 +126,4 @@ Ave neighs/atom = 107.164
|
||||||
Ave special neighs/atom = 0.458312
|
Ave special neighs/atom = 0.458312
|
||||||
Neighbor list builds = 10
|
Neighbor list builds = 10
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -15,7 +14,7 @@ kspace_style pppm 0.0001
|
||||||
|
|
||||||
read_data data.peptide
|
read_data data.peptide
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||||
1 by 1 by 2 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
2004 atoms
|
2004 atoms
|
||||||
reading velocities ...
|
reading velocities ...
|
||||||
|
|
@ -78,134 +77,179 @@ thermo 10
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
estimated absolute RMS force accuracy = 0.0228209
|
||||||
estimated relative force accuracy = 6.87243e-05
|
estimated relative force accuracy = 6.87243e-05
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 6776 1800
|
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: Creating proxy instance
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||||
colvars: # indexFile = "" [default]
|
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||||
colvars: # analysis = off [default]
|
colvars: http://dx.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: # colvarsTrajFrequency = 1
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
colvars: # colvarsRestartFrequency = 1000
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
colvars: # scriptedColvarForces = off [default]
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
colvars: # scriptingAfterBiases = off [default]
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new collective variable.
|
colvars: Initializing a new collective variable.
|
||||||
colvars: # name = one
|
colvars: # name = "one"
|
||||||
colvars: Initializing a new "distance" component.
|
colvars: Initializing a new "distance" component.
|
||||||
|
colvars: # name = "" [default]
|
||||||
colvars: # componentCoeff = 1 [default]
|
colvars: # componentCoeff = 1 [default]
|
||||||
colvars: # componentExp = 1 [default]
|
colvars: # componentExp = 1 [default]
|
||||||
colvars: # period = 0 [default]
|
colvars: # period = 0 [default]
|
||||||
colvars: # wrapAround = 0 [default]
|
colvars: # wrapAround = 0 [default]
|
||||||
colvars: # forceNoPBC = off [default]
|
colvars: # forceNoPBC = off [default]
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
colvars: # scalable = on [default]
|
||||||
colvars: Initializing atom group "group1".
|
colvars: Initializing atom group "group1".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
colvars: # printAtomIDs = off [default]
|
||||||
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||||
colvars: Initializing atom group "group2".
|
colvars: Initializing atom group "group2".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
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: All components initialized.
|
||||||
|
colvars: # timeStepFactor = 1 [default]
|
||||||
colvars: # width = 1 [default]
|
colvars: # width = 1 [default]
|
||||||
colvars: # lowerBoundary = 0 [default]
|
colvars: # lowerBoundary = 0 [default]
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
colvars: # upperBoundary = 0 [default]
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
colvars: # expandBoundaries = off [default]
|
||||||
colvars: # extendedLagrangian = off [default]
|
colvars: # extendedLagrangian = off [default]
|
||||||
colvars: # outputValue = on [default]
|
colvars: # outputValue = on [default]
|
||||||
colvars: # outputVelocity = off [default]
|
colvars: # outputVelocity = off [default]
|
||||||
colvars: # outputSystemForce = off [default]
|
colvars: # outputTotalForce = off [default]
|
||||||
colvars: # outputAppliedForce = off [default]
|
colvars: # outputAppliedForce = off [default]
|
||||||
|
colvars: # subtractAppliedForce = off [default]
|
||||||
|
colvars: # runAve = off [default]
|
||||||
|
colvars: # corrFunc = off [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new collective variable.
|
colvars: Initializing a new collective variable.
|
||||||
colvars: # name = two
|
colvars: # name = "two"
|
||||||
colvars: Initializing a new "distance" component.
|
colvars: Initializing a new "distance" component.
|
||||||
|
colvars: # name = "" [default]
|
||||||
colvars: # componentCoeff = 1 [default]
|
colvars: # componentCoeff = 1 [default]
|
||||||
colvars: # componentExp = 1 [default]
|
colvars: # componentExp = 1 [default]
|
||||||
colvars: # period = 0 [default]
|
colvars: # period = 0 [default]
|
||||||
colvars: # wrapAround = 0 [default]
|
colvars: # wrapAround = 0 [default]
|
||||||
colvars: # forceNoPBC = off [default]
|
colvars: # forceNoPBC = off [default]
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
colvars: # scalable = on [default]
|
||||||
colvars: Initializing atom group "group1".
|
colvars: Initializing atom group "group1".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
colvars: # printAtomIDs = off [default]
|
||||||
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||||
colvars: Initializing atom group "group2".
|
colvars: Initializing atom group "group2".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
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: All components initialized.
|
||||||
|
colvars: # timeStepFactor = 1 [default]
|
||||||
colvars: # width = 1 [default]
|
colvars: # width = 1 [default]
|
||||||
colvars: # lowerBoundary = 0 [default]
|
colvars: # lowerBoundary = 0 [default]
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
colvars: # upperBoundary = 0 [default]
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
colvars: # expandBoundaries = off [default]
|
||||||
colvars: # extendedLagrangian = off [default]
|
colvars: # extendedLagrangian = off [default]
|
||||||
colvars: # outputValue = on [default]
|
colvars: # outputValue = on [default]
|
||||||
colvars: # outputVelocity = off [default]
|
colvars: # outputVelocity = off [default]
|
||||||
colvars: # outputSystemForce = off [default]
|
colvars: # outputTotalForce = off [default]
|
||||||
colvars: # outputAppliedForce = off [default]
|
colvars: # outputAppliedForce = off [default]
|
||||||
|
colvars: # subtractAppliedForce = off [default]
|
||||||
|
colvars: # runAve = off [default]
|
||||||
|
colvars: # corrFunc = off [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables initialized, 2 in total.
|
colvars: Collective variables initialized, 2 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new "harmonic" instance.
|
colvars: Initializing a new "harmonic" instance.
|
||||||
colvars: # name = h_pot
|
colvars: # name = "h_pot"
|
||||||
colvars: # colvars = { one, two }
|
colvars: # colvars = { one, two }
|
||||||
colvars: # outputEnergy = off [default]
|
colvars: # outputEnergy = off [default]
|
||||||
colvars: # forceConstant = 100
|
colvars: # timeStepFactor = 1 [default]
|
||||||
|
colvars: # writeTISamples = off [default]
|
||||||
|
colvars: # writeTIPMF = off [default]
|
||||||
colvars: # centers = { 10, 10 }
|
colvars: # centers = { 10, 10 }
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
colvars: # targetCenters = { 10, 10 } [default]
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
colvars: # outputCenters = off [default]
|
||||||
colvars: # outputAccumulatedWork = off [default]
|
colvars: # forceConstant = 100
|
||||||
|
colvars: # targetForceConstant = -1 [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
colvars: Collective variables biases initialized, 1 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables module initialized.
|
colvars: Collective variables module (re)initialized.
|
||||||
colvars: ----------------------------------------------------------------------
|
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:0/0. 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 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:0/0. 4 atoms: total mass = 15.035.
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
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
|
SHAKE stats (type/ave/delta) on step 0
|
||||||
4 1.111 1.44264e-05
|
4 1.111 1.44264e-05
|
||||||
6 0.996998 7.26967e-06
|
6 0.996998 7.26967e-06
|
||||||
|
|
@ -215,51 +259,52 @@ SHAKE stats (type/ave/delta) on step 0
|
||||||
14 0.96 0
|
14 0.96 0
|
||||||
18 0.957206 4.37979e-05
|
18 0.957206 4.37979e-05
|
||||||
31 104.519 0.00396029
|
31 104.519 0.00396029
|
||||||
Memory usage per processor = 10.4104 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
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
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||||
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
|
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||||
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
|
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||||
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
|
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||||
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
|
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||||
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.818 55.459511 0.20679816
|
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||||
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
|
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||||
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.62715 11.433633
|
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||||
80 267.51476 -5206.4041 -6282.6428 1076.2386 -6456.6352 31.611841 6.3553235
|
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||||
90 278.15512 -5245.383 -6364.4288 1119.0458 -6499.8036 28.849902 0.36938817
|
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
SHAKE stats (type/ave/delta) on step 100
|
||||||
4 1.11098 8.97185e-05
|
4 1.11098 8.97155e-05
|
||||||
6 0.996996 1.00569e-05
|
6 0.996996 1.00568e-05
|
||||||
8 1.08 6.02346e-06
|
8 1.08 6.02345e-06
|
||||||
10 1.111 1.84257e-05
|
10 1.111 1.84253e-05
|
||||||
12 1.08 7.27136e-06
|
12 1.08 7.2713e-06
|
||||||
14 0.959996 0
|
14 0.959996 0
|
||||||
18 0.957198 3.36078e-05
|
18 0.957198 3.36079e-05
|
||||||
31 104.52 0.00306008
|
31 104.52 0.0030599
|
||||||
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
|
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
|
||||||
|
|
||||||
Loop time of 1.04673 on 2 procs for 100 steps with 2004 atoms
|
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
||||||
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 16.509 ns/day 1.454 hours/ns 95.536 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.76537 | 0.76832 | 0.77127 | 0.3 | 73.40
|
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
||||||
Bond | 0.0024452 | 0.0025067 | 0.0025682 | 0.1 | 0.24
|
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
||||||
Kspace | 0.088877 | 0.092861 | 0.096845 | 1.3 | 8.87
|
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
||||||
Neigh | 0.13657 | 0.13657 | 0.13658 | 0.0 | 13.05
|
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
||||||
Comm | 0.0172 | 0.018169 | 0.019137 | 0.7 | 1.74
|
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
||||||
Output | 0.0002296 | 0.00031686 | 0.00040412 | 0.5 | 0.03
|
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
||||||
Modify | 0.025518 | 0.025554 | 0.025591 | 0.0 | 2.44
|
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
||||||
Other | | 0.002431 | | | 0.23
|
Other | | 0.001615 | | | 0.07
|
||||||
|
|
||||||
Nlocal: 1002 ave 1013 max 991 min
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 8629.5 ave 8641 max 8618 min
|
Nghost: 11124 ave 11124 max 11124 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 354118 ave 356534 max 351703 min
|
Neighs: 708237 ave 708237 max 708237 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 708237
|
Total # of neighbors = 708237
|
||||||
Ave neighs/atom = 353.412
|
Ave neighs/atom = 353.412
|
||||||
|
|
@ -269,279 +314,316 @@ Dangerous builds = 2
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
estimated absolute RMS force accuracy = 0.0228209
|
||||||
estimated relative force accuracy = 6.87243e-05
|
estimated relative force accuracy = 6.87243e-05
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 6776 1800
|
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:0/0. 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 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:0/0. 4 atoms: total mass = 15.035.
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
SHAKE stats (type/ave/delta) on step 100
|
||||||
4 1.11098 8.97185e-05
|
4 1.11098 8.97155e-05
|
||||||
6 0.996996 1.00569e-05
|
6 0.996996 1.00568e-05
|
||||||
8 1.08 6.02346e-06
|
8 1.08 6.02345e-06
|
||||||
10 1.111 1.84257e-05
|
10 1.111 1.84253e-05
|
||||||
12 1.08 7.27136e-06
|
12 1.08 7.2713e-06
|
||||||
14 0.959996 0
|
14 0.959996 0
|
||||||
18 0.957198 3.36078e-05
|
18 0.957198 3.36079e-05
|
||||||
31 104.52 0.00306008
|
31 104.52 0.0030599
|
||||||
Memory usage per processor = 10.4104 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
|
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||||
110 266.26279 -5341.2085 -6412.4103 1071.2018 -6552.7566 33.572973 1.9229795
|
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||||
120 262.66439 -5386.2495 -6442.9746 1056.7251 -6587.5499 29.859549 2.712489
|
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||||
130 252.83437 -5422.5446 -6439.7226 1017.1779 -6580.4751 25.979056 1.2031649
|
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||||
140 253.85101 -5452.1904 -6473.4584 1021.268 -6609.4883 26.071526 0.30586448
|
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
||||||
150 261.31821 -5490.4808 -6541.7901 1051.3093 -6646.615 16.258546 6.904992
|
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
||||||
160 255.73714 -5521.6048 -6550.4609 1028.8561 -6658.1531 19.717543 12.339834
|
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
||||||
170 253.42881 -5540.0985 -6559.668 1019.5695 -6656.6862 23.293616 10.289885
|
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||||
180 248.51049 -5550.3254 -6550.1079 999.78252 -6661.4178 26.200082 3.4339077
|
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
||||||
190 250.80375 -5555.2616 -6564.2702 1009.0086 -6666.1496 25.536628 3.3495235
|
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
SHAKE stats (type/ave/delta) on step 200
|
||||||
4 1.111 1.81287e-06
|
4 1.111 1.81266e-06
|
||||||
6 0.997 7.79626e-07
|
6 0.997 7.79424e-07
|
||||||
8 1.08 1.08933e-06
|
8 1.08 1.08903e-06
|
||||||
10 1.111 2.96498e-07
|
10 1.111 2.96503e-07
|
||||||
12 1.08 4.69169e-07
|
12 1.08 4.69038e-07
|
||||||
14 0.960001 0
|
14 0.960001 0
|
||||||
18 0.957201 3.76617e-06
|
18 0.957201 3.76471e-06
|
||||||
31 104.52 0.000411076
|
31 104.52 0.000411055
|
||||||
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
|
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
|
||||||
|
|
||||||
Loop time of 1.00434 on 2 procs for 100 steps with 2004 atoms
|
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
||||||
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 17.205 ns/day 1.395 hours/ns 99.568 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.78001 | 0.78091 | 0.78181 | 0.1 | 77.75
|
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
||||||
Bond | 0.0025158 | 0.0025688 | 0.0026219 | 0.1 | 0.26
|
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
||||||
Kspace | 0.093375 | 0.094821 | 0.096266 | 0.5 | 9.44
|
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
||||||
Neigh | 0.080238 | 0.08025 | 0.080261 | 0.0 | 7.99
|
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
||||||
Comm | 0.01671 | 0.017204 | 0.017699 | 0.4 | 1.71
|
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
||||||
Output | 0.0002296 | 0.00031531 | 0.00040102 | 0.5 | 0.03
|
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
||||||
Modify | 0.025788 | 0.025804 | 0.02582 | 0.0 | 2.57
|
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
||||||
Other | | 0.002469 | | | 0.25
|
Other | | 0.001596 | | | 0.08
|
||||||
|
|
||||||
Nlocal: 1002 ave 1014 max 990 min
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 8654 ave 8667 max 8641 min
|
Nghost: 11159 ave 11159 max 11159 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 354044 ave 355332 max 352756 min
|
Neighs: 708083 ave 708083 max 708083 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 708088
|
Total # of neighbors = 708083
|
||||||
Ave neighs/atom = 353.337
|
Ave neighs/atom = 353.335
|
||||||
Ave special neighs/atom = 2.34032
|
Ave special neighs/atom = 2.34032
|
||||||
Neighbor list builds = 7
|
Neighbor list builds = 7
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
colvars: Resetting the Collective Variables module.
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
estimated absolute RMS force accuracy = 0.0228209
|
||||||
estimated relative force accuracy = 6.87243e-05
|
estimated relative force accuracy = 6.87243e-05
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 6776 1800
|
3d grid and FFT values/proc = 10648 3375
|
||||||
colvars: Creating proxy instance
|
colvars: Creating proxy instance
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||||
colvars: # indexFile = "" [default]
|
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||||
colvars: # analysis = off [default]
|
colvars: http://dx.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: # colvarsTrajFrequency = 1
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
colvars: # colvarsRestartFrequency = 1000
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
colvars: # scriptedColvarForces = off [default]
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
colvars: # scriptingAfterBiases = off [default]
|
||||||
colvars: The final output state file will be "out2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new collective variable.
|
colvars: Initializing a new collective variable.
|
||||||
colvars: # name = one
|
colvars: # name = "one"
|
||||||
colvars: Initializing a new "distance" component.
|
colvars: Initializing a new "distance" component.
|
||||||
|
colvars: # name = "" [default]
|
||||||
colvars: # componentCoeff = 1 [default]
|
colvars: # componentCoeff = 1 [default]
|
||||||
colvars: # componentExp = 1 [default]
|
colvars: # componentExp = 1 [default]
|
||||||
colvars: # period = 0 [default]
|
colvars: # period = 0 [default]
|
||||||
colvars: # wrapAround = 0 [default]
|
colvars: # wrapAround = 0 [default]
|
||||||
colvars: # forceNoPBC = off [default]
|
colvars: # forceNoPBC = off [default]
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
colvars: # scalable = on [default]
|
||||||
colvars: Initializing atom group "group1".
|
colvars: Initializing atom group "group1".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
colvars: # printAtomIDs = off [default]
|
||||||
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||||
colvars: Initializing atom group "group2".
|
colvars: Initializing atom group "group2".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
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: All components initialized.
|
||||||
|
colvars: # timeStepFactor = 1 [default]
|
||||||
colvars: # width = 1 [default]
|
colvars: # width = 1 [default]
|
||||||
colvars: # lowerBoundary = 0 [default]
|
colvars: # lowerBoundary = 0 [default]
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
colvars: # upperBoundary = 0 [default]
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
colvars: # expandBoundaries = off [default]
|
||||||
colvars: # extendedLagrangian = off [default]
|
colvars: # extendedLagrangian = off [default]
|
||||||
colvars: # outputValue = on [default]
|
colvars: # outputValue = on [default]
|
||||||
colvars: # outputVelocity = off [default]
|
colvars: # outputVelocity = off [default]
|
||||||
colvars: # outputSystemForce = off [default]
|
colvars: # outputTotalForce = off [default]
|
||||||
colvars: # outputAppliedForce = off [default]
|
colvars: # outputAppliedForce = off [default]
|
||||||
|
colvars: # subtractAppliedForce = off [default]
|
||||||
|
colvars: # runAve = off [default]
|
||||||
|
colvars: # corrFunc = off [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new collective variable.
|
colvars: Initializing a new collective variable.
|
||||||
colvars: # name = two
|
colvars: # name = "two"
|
||||||
colvars: Initializing a new "distance" component.
|
colvars: Initializing a new "distance" component.
|
||||||
|
colvars: # name = "" [default]
|
||||||
colvars: # componentCoeff = 1 [default]
|
colvars: # componentCoeff = 1 [default]
|
||||||
colvars: # componentExp = 1 [default]
|
colvars: # componentExp = 1 [default]
|
||||||
colvars: # period = 0 [default]
|
colvars: # period = 0 [default]
|
||||||
colvars: # wrapAround = 0 [default]
|
colvars: # wrapAround = 0 [default]
|
||||||
colvars: # forceNoPBC = off [default]
|
colvars: # forceNoPBC = off [default]
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
colvars: # scalable = on [default]
|
||||||
colvars: Initializing atom group "group1".
|
colvars: Initializing atom group "group1".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
colvars: # printAtomIDs = off [default]
|
||||||
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||||
colvars: Initializing atom group "group2".
|
colvars: Initializing atom group "group2".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
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: All components initialized.
|
||||||
|
colvars: # timeStepFactor = 1 [default]
|
||||||
colvars: # width = 1 [default]
|
colvars: # width = 1 [default]
|
||||||
colvars: # lowerBoundary = 0 [default]
|
colvars: # lowerBoundary = 0 [default]
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
colvars: # upperBoundary = 0 [default]
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
colvars: # expandBoundaries = off [default]
|
||||||
colvars: # extendedLagrangian = off [default]
|
colvars: # extendedLagrangian = off [default]
|
||||||
colvars: # outputValue = on [default]
|
colvars: # outputValue = on [default]
|
||||||
colvars: # outputVelocity = off [default]
|
colvars: # outputVelocity = off [default]
|
||||||
colvars: # outputSystemForce = off [default]
|
colvars: # outputTotalForce = off [default]
|
||||||
colvars: # outputAppliedForce = off [default]
|
colvars: # outputAppliedForce = off [default]
|
||||||
|
colvars: # subtractAppliedForce = off [default]
|
||||||
|
colvars: # runAve = off [default]
|
||||||
|
colvars: # corrFunc = off [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables initialized, 2 in total.
|
colvars: Collective variables initialized, 2 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new "harmonic" instance.
|
colvars: Initializing a new "harmonic" instance.
|
||||||
colvars: # name = h_pot
|
colvars: # name = "h_pot"
|
||||||
colvars: # colvars = { one, two }
|
colvars: # colvars = { one, two }
|
||||||
colvars: # outputEnergy = off [default]
|
colvars: # outputEnergy = off [default]
|
||||||
colvars: # forceConstant = 100
|
colvars: # timeStepFactor = 1 [default]
|
||||||
|
colvars: # writeTISamples = off [default]
|
||||||
|
colvars: # writeTIPMF = off [default]
|
||||||
colvars: # centers = { 10, 10 }
|
colvars: # centers = { 10, 10 }
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
colvars: # targetCenters = { 10, 10 } [default]
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
colvars: # outputCenters = off [default]
|
||||||
colvars: # outputAccumulatedWork = off [default]
|
colvars: # forceConstant = 100
|
||||||
|
colvars: # targetForceConstant = -1 [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
colvars: Collective variables biases initialized, 1 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
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 from file "out.colvars.state".
|
||||||
colvars: Restarting collective variable "one" from value: 10.0128
|
colvars: Restarting collective variable "one" from value: 10.0128
|
||||||
colvars: Restarting collective variable "two" from value: 9.62236
|
colvars: Restarting collective variable "two" from value: 9.62236
|
||||||
colvars: Restarting harmonic bias "h_pot".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables module initialized.
|
colvars: The restart output state file will be "rest.colvars.state".
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: The final output state file will be "out2.colvars.state".
|
||||||
colvars: Initializing step number as firstTimestep.
|
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:0/0. 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 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:0/0. 4 atoms: total mass = 15.035.
|
||||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
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
|
SHAKE stats (type/ave/delta) on step 200
|
||||||
4 1.111 1.81287e-06
|
4 1.111 1.81266e-06
|
||||||
6 0.997 7.79626e-07
|
6 0.997 7.79424e-07
|
||||||
8 1.08 1.08933e-06
|
8 1.08 1.08903e-06
|
||||||
10 1.111 2.96498e-07
|
10 1.111 2.96503e-07
|
||||||
12 1.08 4.69169e-07
|
12 1.08 4.69038e-07
|
||||||
14 0.960001 0
|
14 0.960001 0
|
||||||
18 0.957201 3.76617e-06
|
18 0.957201 3.76471e-06
|
||||||
31 104.52 0.000411076
|
31 104.52 0.000411055
|
||||||
Memory usage per processor = 10.4104 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
|
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||||
210 253.15173 -5538.5647 -6557.0194 1018.4547 -6672.044 37.671405 0.61299805
|
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
||||||
220 245.19832 -5522.5253 -6508.9826 986.45735 -6628.2043 36.656213 0.04862311
|
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
||||||
230 258.65093 -5495.7204 -6536.2989 1040.5785 -6658.0891 34.855426 0.22044707
|
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
||||||
240 260.80348 -5469.8527 -6519.0912 1049.2385 -6624.1806 31.576284 3.7570152
|
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
||||||
250 269.06517 -5438.3941 -6520.8701 1082.4761 -6616.3835 25.443998 8.6642401
|
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
||||||
260 266.10873 -5397.3229 -6467.905 1070.582 -6580.6583 26.873845 8.3331291
|
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
||||||
270 272.81399 -5350.8435 -6448.4015 1097.5579 -6563.7941 23.11303 10.972811
|
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
||||||
280 279.52614 -5307.9857 -6432.5473 1124.5616 -6557.7474 33.640052 8.5474491
|
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
||||||
290 286.8015 -5260.87 -6414.7011 1153.8311 -6515.4961 28.571844 5.9093384
|
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
||||||
SHAKE stats (type/ave/delta) on step 300
|
SHAKE stats (type/ave/delta) on step 300
|
||||||
4 1.111 1.79747e-05
|
4 1.111 1.79792e-05
|
||||||
6 0.997005 1.02624e-05
|
6 0.997005 1.02512e-05
|
||||||
8 1.08 1.84986e-05
|
8 1.08 1.85102e-05
|
||||||
10 1.111 9.9852e-06
|
10 1.111 9.98839e-06
|
||||||
12 1.08 8.8315e-06
|
12 1.08 8.84111e-06
|
||||||
14 0.960008 0
|
14 0.960008 0
|
||||||
18 0.957203 1.84856e-05
|
18 0.957203 1.8445e-05
|
||||||
31 104.52 0.00169095
|
31 104.52 0.00168383
|
||||||
300 291.51723 -5216.3366 -6389.1396 1172.803 -6503.1168 27.877108 2.2481775
|
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
|
||||||
|
|
||||||
Loop time of 1.0092 on 2 procs for 100 steps with 2004 atoms
|
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
||||||
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 17.123 ns/day 1.402 hours/ns 99.089 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.77015 | 0.77511 | 0.78007 | 0.6 | 76.80
|
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
||||||
Bond | 0.0022984 | 0.0024998 | 0.0027013 | 0.4 | 0.25
|
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
||||||
Kspace | 0.088884 | 0.093076 | 0.097267 | 1.4 | 9.22
|
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
||||||
Neigh | 0.092871 | 0.092888 | 0.092905 | 0.0 | 9.20
|
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
||||||
Comm | 0.016476 | 0.017 | 0.017524 | 0.4 | 1.68
|
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
||||||
Output | 0.00022602 | 0.00031459 | 0.00040317 | 0.5 | 0.03
|
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||||
Modify | 0.025814 | 0.025818 | 0.025823 | 0.0 | 2.56
|
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
||||||
Other | | 0.002488 | | | 0.25
|
Other | | 0.001731 | | | 0.08
|
||||||
|
|
||||||
Nlocal: 1002 ave 1024 max 980 min
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 8717.5 ave 8755 max 8680 min
|
Nghost: 11296 ave 11296 max 11296 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 354073 ave 358151 max 349995 min
|
Neighs: 708152 ave 708152 max 708152 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 708146
|
Total # of neighbors = 708152
|
||||||
Ave neighs/atom = 353.366
|
Ave neighs/atom = 353.369
|
||||||
Ave special neighs/atom = 2.34032
|
Ave special neighs/atom = 2.34032
|
||||||
Neighbor list builds = 8
|
Neighbor list builds = 8
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
colvars: Saving collective variables state to "out2.colvars.state".
|
colvars: Resetting the Collective Variables module.
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:06
|
||||||
|
|
@ -0,0 +1,629 @@
|
||||||
|
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: http://dx.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: http://dx.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
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
LAMMPS (27 Nov 2018)
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -15,7 +14,7 @@ kspace_style pppm 0.0001
|
||||||
|
|
||||||
read_data data.peptide
|
read_data data.peptide
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||||
1 by 1 by 2 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
2004 atoms
|
2004 atoms
|
||||||
reading velocities ...
|
reading velocities ...
|
||||||
|
|
@ -77,88 +76,122 @@ thermo 10
|
||||||
|
|
||||||
run 100
|
run 100
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
estimated absolute RMS force accuracy = 0.0228209
|
estimated absolute RMS force accuracy = 0.0228209
|
||||||
estimated relative force accuracy = 6.87243e-05
|
estimated relative force accuracy = 6.87243e-05
|
||||||
using double precision FFTs
|
using double precision FFTs
|
||||||
3d grid and FFT values/proc = 6776 1800
|
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: Creating proxy instance
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||||
colvars: # indexFile = "" [default]
|
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||||
colvars: # analysis = off [default]
|
colvars: http://dx.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: # colvarsTrajFrequency = 1
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
colvars: # colvarsRestartFrequency = 1000
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
colvars: # scriptedColvarForces = off [default]
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
colvars: # scriptingAfterBiases = off [default]
|
||||||
colvars: The final output state file will be "peptide2.colvars.state".
|
|
||||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new collective variable.
|
colvars: Initializing a new collective variable.
|
||||||
colvars: # name = one
|
colvars: # name = "one"
|
||||||
colvars: Initializing a new "distance" component.
|
colvars: Initializing a new "distance" component.
|
||||||
|
colvars: # name = "" [default]
|
||||||
colvars: # componentCoeff = 1 [default]
|
colvars: # componentCoeff = 1 [default]
|
||||||
colvars: # componentExp = 1 [default]
|
colvars: # componentExp = 1 [default]
|
||||||
colvars: # period = 0 [default]
|
colvars: # period = 0 [default]
|
||||||
colvars: # wrapAround = 0 [default]
|
colvars: # wrapAround = 0 [default]
|
||||||
colvars: # forceNoPBC = off [default]
|
colvars: # forceNoPBC = off [default]
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
colvars: # scalable = on [default]
|
||||||
colvars: Initializing atom group "group1".
|
colvars: Initializing atom group "group1".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
colvars: # printAtomIDs = off [default]
|
||||||
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||||
colvars: Initializing atom group "group2".
|
colvars: Initializing atom group "group2".
|
||||||
|
colvars: # name = "" [default]
|
||||||
|
colvars: # centerReference = off [default]
|
||||||
|
colvars: # rotateReference = off [default]
|
||||||
|
colvars: # atomsOfGroup = "" [default]
|
||||||
colvars: # indexGroup = "" [default]
|
colvars: # indexGroup = "" [default]
|
||||||
colvars: # psfSegID = [default]
|
colvars: # psfSegID = [default]
|
||||||
colvars: # atomsFile = "" [default]
|
colvars: # atomsFile = "" [default]
|
||||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||||
colvars: # enableForces = on [default]
|
colvars: # enableForces = on [default]
|
||||||
colvars: # disableForces = off [default]
|
|
||||||
colvars: # centerReference = off [default]
|
|
||||||
colvars: # rotateReference = off [default]
|
|
||||||
colvars: # enableFitGradients = on [default]
|
colvars: # enableFitGradients = on [default]
|
||||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 0.
|
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: All components initialized.
|
||||||
|
colvars: # timeStepFactor = 1 [default]
|
||||||
colvars: # width = 1 [default]
|
colvars: # width = 1 [default]
|
||||||
colvars: # lowerBoundary = 0 [default]
|
colvars: # lowerBoundary = 0 [default]
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
colvars: # upperBoundary = 0 [default]
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
colvars: # expandBoundaries = off [default]
|
||||||
colvars: # extendedLagrangian = off [default]
|
colvars: # extendedLagrangian = off [default]
|
||||||
colvars: # outputValue = on [default]
|
colvars: # outputValue = on [default]
|
||||||
colvars: # outputVelocity = off [default]
|
colvars: # outputVelocity = off [default]
|
||||||
colvars: # outputSystemForce = off [default]
|
colvars: # outputTotalForce = off [default]
|
||||||
colvars: # outputAppliedForce = off [default]
|
colvars: # outputAppliedForce = off [default]
|
||||||
|
colvars: # subtractAppliedForce = off [default]
|
||||||
|
colvars: # runAve = off [default]
|
||||||
|
colvars: # corrFunc = off [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables initialized, 1 in total.
|
colvars: Collective variables initialized, 1 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Initializing a new "harmonic" instance.
|
colvars: Initializing a new "harmonic" instance.
|
||||||
colvars: # name = h_pot
|
colvars: # name = "h_pot"
|
||||||
colvars: # colvars = { one }
|
colvars: # colvars = { one }
|
||||||
colvars: # outputEnergy = off [default]
|
colvars: # outputEnergy = off [default]
|
||||||
colvars: # forceConstant = 100
|
colvars: # timeStepFactor = 1 [default]
|
||||||
|
colvars: # writeTISamples = off [default]
|
||||||
|
colvars: # writeTIPMF = off [default]
|
||||||
colvars: # centers = { 10 }
|
colvars: # centers = { 10 }
|
||||||
colvars: # targetCenters = { 10 } [default]
|
colvars: # targetCenters = { 10 } [default]
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: # outputCenters = off [default]
|
colvars: # outputCenters = off [default]
|
||||||
colvars: # outputAccumulatedWork = off [default]
|
colvars: # forceConstant = 100
|
||||||
|
colvars: # targetForceConstant = -1 [default]
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
colvars: Collective variables biases initialized, 1 in total.
|
||||||
colvars: ----------------------------------------------------------------------
|
colvars: ----------------------------------------------------------------------
|
||||||
colvars: Collective variables module initialized.
|
colvars: Collective variables module (re)initialized.
|
||||||
colvars: ----------------------------------------------------------------------
|
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:0/0. 4 atoms: total mass = 15.035.
|
||||||
colvars: Re-initialized atom group one:0/1. 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
|
SHAKE stats (type/ave/delta) on step 0
|
||||||
4 1.111 1.44264e-05
|
4 1.111 1.44264e-05
|
||||||
6 0.996998 7.26967e-06
|
6 0.996998 7.26967e-06
|
||||||
|
|
@ -168,58 +201,60 @@ SHAKE stats (type/ave/delta) on step 0
|
||||||
14 0.96 0
|
14 0.96 0
|
||||||
18 0.957206 4.37979e-05
|
18 0.957206 4.37979e-05
|
||||||
31 104.519 0.00396029
|
31 104.519 0.00396029
|
||||||
Memory usage per processor = 10.4103 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
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
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
|
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||||
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
|
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||||
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
|
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||||
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8833 26.28765 20.573958
|
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||||
70 277.26045 -5224.8416 -6340.2881 1115.4465 -6447.8495 27.742889 0.69414895
|
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||||
80 268.01458 -5281.8501 -6360.0996 1078.2495 -6496.6062 20.300729 5.260642
|
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||||
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
|
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
SHAKE stats (type/ave/delta) on step 100
|
||||||
4 1.11096 0.000191466
|
4 1.11096 0.000191462
|
||||||
6 0.996989 3.5552e-05
|
6 0.996989 3.55508e-05
|
||||||
8 1.08 9.10001e-06
|
8 1.08 9.0997e-06
|
||||||
10 1.111 1.58547e-05
|
10 1.111 1.58544e-05
|
||||||
12 1.08 5.80613e-06
|
12 1.08 5.80604e-06
|
||||||
14 0.959997 0
|
14 0.959997 0
|
||||||
18 0.957198 2.92454e-05
|
18 0.957198 2.92445e-05
|
||||||
31 104.52 0.00239929
|
31 104.52 0.00239923
|
||||||
100 260.35617 -5387.2298 -6434.6687 1047.4389 -6534.1957 20.246734 0.075048991
|
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
|
||||||
|
|
||||||
Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms
|
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
|
||||||
98.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
Performance: 16.084 ns/day 1.492 hours/ns 93.076 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.77154 | 0.77308 | 0.77462 | 0.2 | 71.96
|
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
||||||
Bond | 0.0023637 | 0.0025266 | 0.0026896 | 0.3 | 0.24
|
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
||||||
Kspace | 0.095779 | 0.097411 | 0.099043 | 0.5 | 9.07
|
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
||||||
Neigh | 0.15521 | 0.15521 | 0.15522 | 0.0 | 14.45
|
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
||||||
Comm | 0.018134 | 0.018364 | 0.018594 | 0.2 | 1.71
|
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
||||||
Output | 0.00024295 | 0.00032854 | 0.00041413 | 0.5 | 0.03
|
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
||||||
Modify | 0.024936 | 0.024973 | 0.02501 | 0.0 | 2.32
|
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
||||||
Other | | 0.002498 | | | 0.23
|
Other | | 0.001465 | | | 0.06
|
||||||
|
|
||||||
Nlocal: 1002 ave 1010 max 994 min
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 8645 ave 8652 max 8638 min
|
Nghost: 11143 ave 11143 max 11143 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 354116 ave 356373 max 351860 min
|
Neighs: 708234 ave 708234 max 708234 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 708233
|
Total # of neighbors = 708234
|
||||||
Ave neighs/atom = 353.41
|
Ave neighs/atom = 353.41
|
||||||
Ave special neighs/atom = 2.34032
|
Ave special neighs/atom = 2.34032
|
||||||
Neighbor list builds = 13
|
Neighbor list builds = 13
|
||||||
Dangerous builds = 1
|
Dangerous builds = 1
|
||||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
colvars: Resetting the Collective Variables module.
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:02
|
||||||
|
|
@ -0,0 +1,260 @@
|
||||||
|
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: http://dx.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
|
||||||
|
|
@ -0,0 +1,163 @@
|
||||||
|
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
|
||||||
|
|
@ -0,0 +1,163 @@
|
||||||
|
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
|
||||||
|
|
@ -0,0 +1,158 @@
|
||||||
|
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
|
||||||
|
|
@ -0,0 +1,158 @@
|
||||||
|
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
|
||||||
|
|
@ -1,516 +0,0 @@
|
||||||
LAMMPS (21 May 2012-ICMS)
|
|
||||||
# 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
|
|
||||||
3 = max bonds/atom
|
|
||||||
6 = max angles/atom
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
1 = max impropers/atom
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
2004 atoms
|
|
||||||
2004 velocities
|
|
||||||
1365 bonds
|
|
||||||
786 angles
|
|
||||||
207 dihedrals
|
|
||||||
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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 10648 3375 5808
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
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
|
|
||||||
Memory usage per processor = 22.5866 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
|
|
||||||
10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
|
|
||||||
20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706
|
|
||||||
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344163 10.563914
|
|
||||||
40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392
|
|
||||||
50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801
|
|
||||||
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508
|
|
||||||
70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632
|
|
||||||
80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235
|
|
||||||
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97184e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84257e-05
|
|
||||||
12 1.08 7.27136e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36077e-05
|
|
||||||
31 104.52 0.00306008
|
|
||||||
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 1.86583 (78.0347)
|
|
||||||
Bond time (%) = 0.00628591 (0.262896)
|
|
||||||
Kspace time (%) = 0.165128 (6.90614)
|
|
||||||
Neigh time (%) = 0.314792 (13.1656)
|
|
||||||
Comm time (%) = 0.0111108 (0.464687)
|
|
||||||
Output time (%) = 0.000252724 (0.0105697)
|
|
||||||
Modify time (%) = 0.0253747 (1.06125)
|
|
||||||
Other time (%) = 0.0022521 (0.0941899)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.0274372 (16.6158)
|
|
||||||
FFT Gflps 3d (1d only) = 1.99867 2.86506
|
|
||||||
|
|
||||||
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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 10648 3375 5808
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Restarting from file "out.colvars.state".
|
|
||||||
colvars: Restarting collective variable "one" from value: 10.0137
|
|
||||||
colvars: Restarting collective variable "two" from value: 10.0649
|
|
||||||
colvars: Restarting harmonic bias "h_pot".
|
|
||||||
colvars: Reading current stage from the restart.
|
|
||||||
colvars: # stage = 3900175693153042431
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing step number as firstTimestep.
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97184e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84257e-05
|
|
||||||
12 1.08 7.27136e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36077e-05
|
|
||||||
31 104.52 0.00306008
|
|
||||||
Memory usage per processor = 22.5866 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
|
|
||||||
110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782
|
|
||||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877
|
|
||||||
130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628
|
|
||||||
140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247
|
|
||||||
150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974
|
|
||||||
160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821
|
|
||||||
170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878
|
|
||||||
180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065
|
|
||||||
190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.8129e-06
|
|
||||||
6 0.997 7.7964e-07
|
|
||||||
8 1.08 1.08934e-06
|
|
||||||
10 1.111 2.96501e-07
|
|
||||||
12 1.08 4.69174e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76571e-06
|
|
||||||
31 104.52 0.000411068
|
|
||||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 1.84544 (82.572)
|
|
||||||
Bond time (%) = 0.00609159 (0.27256)
|
|
||||||
Kspace time (%) = 0.163201 (7.30223)
|
|
||||||
Neigh time (%) = 0.183405 (8.20622)
|
|
||||||
Comm time (%) = 0.00959301 (0.429227)
|
|
||||||
Output time (%) = 0.000245094 (0.0109664)
|
|
||||||
Modify time (%) = 0.0247326 (1.10663)
|
|
||||||
Other time (%) = 0.00223875 (0.10017)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.0272989 (16.7271)
|
|
||||||
FFT Gflps 3d (1d only) = 2.0088 2.93901
|
|
||||||
|
|
||||||
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: 708088 ave 708088 max 708088 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708088
|
|
||||||
Ave neighs/atom = 353.337
|
|
||||||
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
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 10648 3375 5808
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out2.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
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: Restarting harmonic bias "h_pot".
|
|
||||||
colvars: Reading current stage from the restart.
|
|
||||||
colvars: # stage = 3900175693153042431
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing step number as firstTimestep.
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.8129e-06
|
|
||||||
6 0.997 7.7964e-07
|
|
||||||
8 1.08 1.08934e-06
|
|
||||||
10 1.111 2.96501e-07
|
|
||||||
12 1.08 4.69174e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76571e-06
|
|
||||||
31 104.52 0.000411068
|
|
||||||
Memory usage per processor = 22.5866 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
|
||||||
210 253.15043 -5538.5668 -6557.0163 1018.4495 -6672.041 37.67158 0.61296982
|
|
||||||
220 245.19746 -5522.5242 -6508.9781 986.4539 -6628.1999 36.656356 0.048624555
|
|
||||||
230 258.65299 -5495.7177 -6536.3046 1040.5868 -6658.0952 34.855726 0.22046598
|
|
||||||
240 260.80143 -5469.8517 -6519.0819 1049.2302 -6624.1723 31.576409 3.7570726
|
|
||||||
250 269.06507 -5438.3971 -6520.8727 1082.4757 -6616.3871 25.444125 8.6640978
|
|
||||||
260 266.10282 -5397.3162 -6467.8744 1070.5583 -6580.628 26.873936 8.3330854
|
|
||||||
270 272.81993 -5350.8393 -6448.4211 1097.5819 -6563.8139 23.113421 10.972906
|
|
||||||
280 279.52079 -5307.9855 -6432.5256 1124.5401 -6557.7274 33.641095 8.5474821
|
|
||||||
290 286.81184 -5260.8728 -6414.7455 1153.8727 -6515.5418 28.572468 5.9092648
|
|
||||||
SHAKE stats (type/ave/delta) on step 300
|
|
||||||
4 1.111 1.79733e-05
|
|
||||||
6 0.997005 1.02622e-05
|
|
||||||
8 1.08 1.84996e-05
|
|
||||||
10 1.111 9.98595e-06
|
|
||||||
12 1.08 8.83195e-06
|
|
||||||
14 0.960008 0
|
|
||||||
18 0.957203 1.84801e-05
|
|
||||||
31 104.52 0.00169221
|
|
||||||
300 291.51842 -5216.3285 -6389.1362 1172.8077 -6503.1141 27.877464 2.2482411
|
|
||||||
colvars: Saving collective variables state to "out2.colvars.state".
|
|
||||||
Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 1.83745 (81.6533)
|
|
||||||
Bond time (%) = 0.00609803 (0.270987)
|
|
||||||
Kspace time (%) = 0.162178 (7.20694)
|
|
||||||
Neigh time (%) = 0.207886 (9.23812)
|
|
||||||
Comm time (%) = 0.00977254 (0.434276)
|
|
||||||
Output time (%) = 0.000240803 (0.0107009)
|
|
||||||
Modify time (%) = 0.024461 (1.08701)
|
|
||||||
Other time (%) = 0.00221944 (0.0986283)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.0273609 (16.8709)
|
|
||||||
FFT Gflps 3d (1d only) = 2.00425 2.94806
|
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 11292 ave 11292 max 11292 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 708145 ave 708145 max 708145 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708145
|
|
||||||
Ave neighs/atom = 353.366
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
|
|
@ -1,516 +0,0 @@
|
||||||
LAMMPS (21 May 2012-ICMS)
|
|
||||||
# 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
|
|
||||||
3 = max bonds/atom
|
|
||||||
6 = max angles/atom
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
1 = max impropers/atom
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
2004 atoms
|
|
||||||
2004 velocities
|
|
||||||
1365 bonds
|
|
||||||
786 angles
|
|
||||||
207 dihedrals
|
|
||||||
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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 4312 960 3696
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
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
|
|
||||||
Memory usage per processor = 10.1924 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
|
|
||||||
10 305.06198 -5058.8898 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
|
|
||||||
20 311.00592 -4999.0545 -6250.2624 1251.2079 -6417.0984 47.695274 36.699706
|
|
||||||
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344162 10.563914
|
|
||||||
40 297.87524 -5020.8339 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392
|
|
||||||
50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.206798
|
|
||||||
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356507
|
|
||||||
70 277.835 -5163.9751 -6281.7331 1117.758 -6447.7014 39.627147 11.433632
|
|
||||||
80 267.51474 -5206.4042 -6282.6428 1076.2385 -6456.6352 31.611843 6.3553237
|
|
||||||
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8036 28.849898 0.36938879
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97184e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84257e-05
|
|
||||||
12 1.08 7.27136e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36077e-05
|
|
||||||
31 104.52 0.00306008
|
|
||||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 0.47104 (68.5966)
|
|
||||||
Bond time (%) = 0.00184608 (0.26884)
|
|
||||||
Kspace time (%) = 0.0808357 (11.7719)
|
|
||||||
Neigh time (%) = 0.0772016 (11.2427)
|
|
||||||
Comm time (%) = 0.0293136 (4.26888)
|
|
||||||
Output time (%) = 0.000323951 (0.0471764)
|
|
||||||
Modify time (%) = 0.0247293 (3.60128)
|
|
||||||
Other time (%) = 0.00139064 (0.202516)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.0117171 (14.4949)
|
|
||||||
FFT Gflps 3d (1d only) = 4.68018 10.009
|
|
||||||
|
|
||||||
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 181741 max 172943 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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 4312 960 3696
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Restarting from file "out.colvars.state".
|
|
||||||
colvars: Restarting collective variable "one" from value: 10.0137
|
|
||||||
colvars: Restarting collective variable "two" from value: 10.0649
|
|
||||||
colvars: Restarting harmonic bias "h_pot".
|
|
||||||
colvars: Reading current stage from the restart.
|
|
||||||
colvars: # stage = 8103505641670189088
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing step number as firstTimestep.
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97184e-05
|
|
||||||
6 0.996996 1.00568e-05
|
|
||||||
8 1.08 6.02345e-06
|
|
||||||
10 1.111 1.84257e-05
|
|
||||||
12 1.08 7.27136e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36077e-05
|
|
||||||
31 104.52 0.00306008
|
|
||||||
Memory usage per processor = 10.1967 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
|
||||||
110 266.26278 -5341.2101 -6412.4119 1071.2018 -6552.7582 33.572969 1.9229778
|
|
||||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859555 2.7124877
|
|
||||||
130 252.83442 -5422.5444 -6439.7226 1017.1781 -6580.4752 25.979048 1.2031628
|
|
||||||
140 253.85116 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071518 0.30586252
|
|
||||||
150 261.31828 -5490.48 -6541.7895 1051.3096 -6646.6145 16.25855 6.9049978
|
|
||||||
160 255.73681 -5521.6048 -6550.4596 1028.8548 -6658.1518 19.717536 12.339819
|
|
||||||
170 253.42879 -5540.1004 -6559.6697 1019.5694 -6656.688 23.293657 10.289879
|
|
||||||
180 248.51083 -5550.3244 -6550.1084 999.78393 -6661.4181 26.200057 3.433906
|
|
||||||
190 250.80387 -5555.2613 -6564.2703 1009.009 -6666.1497 25.536596 3.3495164
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.8129e-06
|
|
||||||
6 0.997 7.79639e-07
|
|
||||||
8 1.08 1.08934e-06
|
|
||||||
10 1.111 2.96501e-07
|
|
||||||
12 1.08 4.69175e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76571e-06
|
|
||||||
31 104.52 0.000411069
|
|
||||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
|
||||||
colvars: Saving collective variables state to "out.colvars.state".
|
|
||||||
Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 0.47279 (72.3723)
|
|
||||||
Bond time (%) = 0.00182116 (0.278774)
|
|
||||||
Kspace time (%) = 0.079544 (12.1762)
|
|
||||||
Neigh time (%) = 0.0451868 (6.91696)
|
|
||||||
Comm time (%) = 0.027427 (4.19838)
|
|
||||||
Output time (%) = 0.000316501 (0.0484483)
|
|
||||||
Modify time (%) = 0.0247022 (3.78129)
|
|
||||||
Other time (%) = 0.00148731 (0.227671)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.0109947 (13.8221)
|
|
||||||
FFT Gflps 3d (1d only) = 4.98769 10.1728
|
|
||||||
|
|
||||||
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: 177022 ave 182261 max 172093 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708086
|
|
||||||
Ave neighs/atom = 353.336
|
|
||||||
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
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 4312 960 3696
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "out2.colvars.state".
|
|
||||||
colvars: The trajectory file will be "out2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = off [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = two
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10, 10 }
|
|
||||||
colvars: # targetCenters = { 10, 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
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: Restarting harmonic bias "h_pot".
|
|
||||||
colvars: Reading current stage from the restart.
|
|
||||||
colvars: # stage = 8103505641670189088
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing step number as firstTimestep.
|
|
||||||
SHAKE stats (type/ave/delta) on step 200
|
|
||||||
4 1.111 1.8129e-06
|
|
||||||
6 0.997 7.79639e-07
|
|
||||||
8 1.08 1.08934e-06
|
|
||||||
10 1.111 2.96501e-07
|
|
||||||
12 1.08 4.69175e-07
|
|
||||||
14 0.960001 0
|
|
||||||
18 0.957201 3.76571e-06
|
|
||||||
31 104.52 0.000411069
|
|
||||||
Memory usage per processor = 10.201 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
|
||||||
210 253.15047 -5538.5669 -6557.0165 1018.4497 -6672.0412 37.671574 0.61297094
|
|
||||||
220 245.19752 -5522.5242 -6508.9784 986.45412 -6628.2001 36.656348 0.048624447
|
|
||||||
230 258.65297 -5495.7177 -6536.3044 1040.5868 -6658.0951 34.855726 0.22046446
|
|
||||||
240 260.8016 -5469.8518 -6519.0827 1049.2309 -6624.173 31.576408 3.757081
|
|
||||||
250 269.06524 -5438.3971 -6520.8735 1082.4764 -6616.3878 25.444134 8.6641098
|
|
||||||
260 266.10241 -5397.317 -6467.8736 1070.5566 -6580.6272 26.87393 8.333095
|
|
||||||
270 272.82004 -5350.8402 -6448.4225 1097.5823 -6563.8152 23.113398 10.972914
|
|
||||||
280 279.52006 -5307.9867 -6432.5238 1124.5371 -6557.7256 33.641067 8.5474809
|
|
||||||
290 286.81221 -5260.8707 -6414.7449 1153.8742 -6515.5413 28.572449 5.9092582
|
|
||||||
SHAKE stats (type/ave/delta) on step 300
|
|
||||||
4 1.111 1.79733e-05
|
|
||||||
6 0.997005 1.02621e-05
|
|
||||||
8 1.08 1.84996e-05
|
|
||||||
10 1.111 9.98591e-06
|
|
||||||
12 1.08 8.83192e-06
|
|
||||||
14 0.960008 0
|
|
||||||
18 0.957203 1.84805e-05
|
|
||||||
31 104.52 0.00169223
|
|
||||||
300 291.51901 -5216.3298 -6389.1399 1172.8101 -6503.1178 27.877408 2.2482392
|
|
||||||
colvars: Saving collective variables state to "out2.colvars.state".
|
|
||||||
Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 0.47307 (71.452)
|
|
||||||
Bond time (%) = 0.00178617 (0.269781)
|
|
||||||
Kspace time (%) = 0.0802494 (12.1208)
|
|
||||||
Neigh time (%) = 0.0528576 (7.98355)
|
|
||||||
Comm time (%) = 0.0277618 (4.19311)
|
|
||||||
Output time (%) = 0.000293612 (0.0443469)
|
|
||||||
Modify time (%) = 0.0245907 (3.71416)
|
|
||||||
Other time (%) = 0.00147164 (0.222275)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.011487 (14.3141)
|
|
||||||
FFT Gflps 3d (1d only) = 4.77392 9.91625
|
|
||||||
|
|
||||||
Nlocal: 501 ave 514 max 471 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
|
||||||
Nghost: 6609.75 ave 6681 max 6555 min
|
|
||||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
|
||||||
Neighs: 177036 ave 180240 max 169752 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
|
||||||
|
|
||||||
Total # of neighbors = 708146
|
|
||||||
Ave neighs/atom = 353.366
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
|
|
@ -1,182 +0,0 @@
|
||||||
LAMMPS (21 May 2012-ICMS)
|
|
||||||
# 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
|
|
||||||
3 = max bonds/atom
|
|
||||||
6 = max angles/atom
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
1 = max impropers/atom
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
2004 atoms
|
|
||||||
2004 velocities
|
|
||||||
1365 bonds
|
|
||||||
786 angles
|
|
||||||
207 dihedrals
|
|
||||||
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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 10648 3375 5808
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "peptide2.colvars.state".
|
|
||||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10 }
|
|
||||||
colvars: # targetCenters = { 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
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
|
|
||||||
Memory usage per processor = 22.5865 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
|
||||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.4169 21.367753 12.393269
|
|
||||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
|
||||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
|
||||||
40 297.5581 -5088.2156 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
|
||||||
50 296.80003 -5117.2926 -6311.3488 1194.0562 -6451.8274 30.631279 5.3320296
|
|
||||||
60 281.72797 -5188.4941 -6321.9139 1133.4198 -6427.8834 26.287652 20.573958
|
|
||||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742888 0.69414894
|
|
||||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606438
|
|
||||||
90 270.43386 -5334.0846 -6422.067 1087.9824 -6563.2486 39.845993 1.1832496
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191466
|
|
||||||
6 0.996989 3.5552e-05
|
|
||||||
8 1.08 9.1e-06
|
|
||||||
10 1.111 1.58547e-05
|
|
||||||
12 1.08 5.80613e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92453e-05
|
|
||||||
31 104.52 0.00239929
|
|
||||||
100 260.3562 -5387.2263 -6434.6653 1047.439 -6534.1923 20.24674 0.075048834
|
|
||||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
|
||||||
Loop time of 2.37975 on 1 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 1.83713 (77.1984)
|
|
||||||
Bond time (%) = 0.00636029 (0.267267)
|
|
||||||
Kspace time (%) = 0.162295 (6.81981)
|
|
||||||
Neigh time (%) = 0.336338 (14.1333)
|
|
||||||
Comm time (%) = 0.0106671 (0.448243)
|
|
||||||
Output time (%) = 0.000264168 (0.0111006)
|
|
||||||
Modify time (%) = 0.024472 (1.02834)
|
|
||||||
Other time (%) = 0.00222516 (0.0935038)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.028162 (17.3524)
|
|
||||||
FFT Gflps 3d (1d only) = 1.94723 2.85015
|
|
||||||
|
|
||||||
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: 708233 ave 708233 max 708233 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 708233
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
|
|
@ -1,182 +0,0 @@
|
||||||
LAMMPS (21 May 2012-ICMS)
|
|
||||||
# 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
|
|
||||||
3 = max bonds/atom
|
|
||||||
6 = max angles/atom
|
|
||||||
14 = max dihedrals/atom
|
|
||||||
1 = max impropers/atom
|
|
||||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
2004 atoms
|
|
||||||
2004 velocities
|
|
||||||
1365 bonds
|
|
||||||
786 angles
|
|
||||||
207 dihedrals
|
|
||||||
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 ...
|
|
||||||
G vector (1/distance) = 0.268721
|
|
||||||
grid = 15 15 15
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.01614
|
|
||||||
estimated relative force accuracy = 4.86052e-05
|
|
||||||
using single precision FFTs
|
|
||||||
brick FFT buffer size/proc = 4312 960 3696
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
|
||||||
colvars: # analysis = off [default]
|
|
||||||
colvars: # colvarsTrajFrequency = 1
|
|
||||||
colvars: # colvarsRestartFrequency = 1000
|
|
||||||
colvars: # colvarsTrajAppend = off [default]
|
|
||||||
colvars: The restart output state file will be "rest.colvars.state".
|
|
||||||
colvars: The final output state file will be "peptide2.colvars.state".
|
|
||||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Initializing a new collective variable.
|
|
||||||
colvars: # name = one
|
|
||||||
colvars: Initializing a new "distance" component.
|
|
||||||
colvars: # componentCoeff = 1 [default]
|
|
||||||
colvars: # componentExp = 1 [default]
|
|
||||||
colvars: # period = 0 [default]
|
|
||||||
colvars: # wrapAround = 0 [default]
|
|
||||||
colvars: # forceNoPBC = off [default]
|
|
||||||
colvars: # oneSiteSystemForce = off [default]
|
|
||||||
colvars: Initializing atom group "group1".
|
|
||||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: Initializing atom group "group2".
|
|
||||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
|
||||||
colvars: All components initialized.
|
|
||||||
colvars: # width = 1 [default]
|
|
||||||
colvars: # lowerBoundary = 0 [default]
|
|
||||||
colvars: # lowerWallConstant = 0 [default]
|
|
||||||
colvars: # upperBoundary = 0 [default]
|
|
||||||
colvars: # upperWallConstant = 0 [default]
|
|
||||||
colvars: # expandBoundaries = off [default]
|
|
||||||
colvars: # extendedLagrangian = off [default]
|
|
||||||
colvars: # outputValue = on [default]
|
|
||||||
colvars: # outputVelocity = off [default]
|
|
||||||
colvars: # outputSystemForce = off [default]
|
|
||||||
colvars: # outputAppliedForce = 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: # forceConstant = 100
|
|
||||||
colvars: # centers = { 10 }
|
|
||||||
colvars: # targetCenters = { 10 } [default]
|
|
||||||
colvars: # targetForceConstant = 0 [default]
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables biases initialized, 1 in total.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
colvars: Collective variables module initialized.
|
|
||||||
colvars: ----------------------------------------------------------------------
|
|
||||||
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
|
|
||||||
Memory usage per processor = 10.1924 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
|
||||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
|
||||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
|
||||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
|
||||||
30 316.97689 -5025.5598 -6300.7896 1275.2297 -6422.5336 27.323113 6.7588863
|
|
||||||
40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
|
||||||
50 296.80003 -5117.2927 -6311.3488 1194.0562 -6451.8275 30.631279 5.3320297
|
|
||||||
60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959
|
|
||||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414888
|
|
||||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606437
|
|
||||||
90 270.43386 -5334.0846 -6422.067 1087.9825 -6563.2486 39.845992 1.1832495
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191466
|
|
||||||
6 0.996989 3.5552e-05
|
|
||||||
8 1.08 9.10001e-06
|
|
||||||
10 1.111 1.58547e-05
|
|
||||||
12 1.08 5.80613e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92453e-05
|
|
||||||
31 104.52 0.00239929
|
|
||||||
100 260.35619 -5387.2298 -6434.6688 1047.439 -6534.1958 20.24674 0.07504876
|
|
||||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
|
||||||
Loop time of 0.650999 on 4 procs for 100 steps with 2004 atoms
|
|
||||||
|
|
||||||
Pair time (%) = 0.466917 (71.7232)
|
|
||||||
Bond time (%) = 0.00176847 (0.271655)
|
|
||||||
Kspace time (%) = 0.0588512 (9.04015)
|
|
||||||
Neigh time (%) = 0.0832494 (12.788)
|
|
||||||
Comm time (%) = 0.0190871 (2.93197)
|
|
||||||
Output time (%) = 0.000295341 (0.0453674)
|
|
||||||
Modify time (%) = 0.0194815 (2.99255)
|
|
||||||
Other time (%) = 0.00134867 (0.20717)
|
|
||||||
|
|
||||||
FFT time (% of Kspce) = 0.010457 (17.7686)
|
|
||||||
FFT Gflps 3d (1d only) = 5.24412 9.93123
|
|
||||||
|
|
||||||
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 181777 max 174301 min
|
|
||||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708233
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
|
|
@ -1,150 +0,0 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
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 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 ...
|
|
||||||
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 = 6776 1800
|
|
||||||
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
|
|
||||||
Memory usage per processor = 11.5952 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond sp
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
|
||||||
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
|
|
||||||
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
|
|
||||||
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
|
|
||||||
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
|
|
||||||
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816
|
|
||||||
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
|
|
||||||
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633
|
|
||||||
80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235
|
|
||||||
90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11098 8.97185e-05
|
|
||||||
6 0.996996 1.00569e-05
|
|
||||||
8 1.08 6.02346e-06
|
|
||||||
10 1.111 1.84257e-05
|
|
||||||
12 1.08 7.27136e-06
|
|
||||||
14 0.959996 0
|
|
||||||
18 0.957198 3.36078e-05
|
|
||||||
31 104.52 0.00306008
|
|
||||||
100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866
|
|
||||||
|
|
||||||
Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms
|
|
||||||
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45
|
|
||||||
Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24
|
|
||||||
Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70
|
|
||||||
Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62
|
|
||||||
Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77
|
|
||||||
Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62
|
|
||||||
Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36
|
|
||||||
Other | | 0.002651 | | | 0.25
|
|
||||||
|
|
||||||
Nlocal: 1002 ave 1013 max 991 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 8629.5 ave 8641 max 8618 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 354118 ave 356534 max 351703 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 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
|
|
||||||
|
|
@ -1,145 +0,0 @@
|
||||||
LAMMPS (20 Mar 2014-ICMS)
|
|
||||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
|
||||||
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 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 ...
|
|
||||||
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 = 6776 1800
|
|
||||||
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
|
|
||||||
Memory usage per processor = 11.5952 Mbytes
|
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond 3
|
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
|
||||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
|
||||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
|
|
||||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
|
||||||
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
|
|
||||||
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
|
|
||||||
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
|
|
||||||
70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
|
|
||||||
80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
|
|
||||||
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
|
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
|
||||||
4 1.11096 0.000191466
|
|
||||||
6 0.996989 3.5552e-05
|
|
||||||
8 1.08 9.10001e-06
|
|
||||||
10 1.111 1.58547e-05
|
|
||||||
12 1.08 5.80613e-06
|
|
||||||
14 0.959997 0
|
|
||||||
18 0.957198 2.92454e-05
|
|
||||||
31 104.52 0.00239929
|
|
||||||
100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
|
|
||||||
|
|
||||||
Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms
|
|
||||||
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s
|
|
||||||
|
|
||||||
MPI task timings breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99
|
|
||||||
Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24
|
|
||||||
Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04
|
|
||||||
Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77
|
|
||||||
Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81
|
|
||||||
Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63
|
|
||||||
Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29
|
|
||||||
Other | | 0.002705 | | | 0.25
|
|
||||||
|
|
||||||
Nlocal: 1002 ave 1010 max 994 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 8645 ave 8652 max 8638 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 354116 ave 356373 max 351860 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 708233
|
|
||||||
Ave neighs/atom = 353.41
|
|
||||||
Ave special neighs/atom = 2.34032
|
|
||||||
Neighbor list builds = 13
|
|
||||||
Dangerous builds = 1
|
|
||||||
|
|
@ -1,22 +1,23 @@
|
||||||
configuration {
|
configuration {
|
||||||
step 200
|
step 200
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
|
version 2018-11-16
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 1.00127641579482e+01
|
x 1.00127732034965e+01
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name two
|
name two
|
||||||
x 9.62235621950587e+00
|
x 9.62235997490241e+00
|
||||||
}
|
}
|
||||||
|
|
||||||
harmonic {
|
restraint {
|
||||||
configuration {
|
configuration {
|
||||||
|
step 200
|
||||||
name h_pot
|
name h_pot
|
||||||
stage 8103505641670189088
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,23 @@
|
||||||
|
configuration {
|
||||||
|
step 100
|
||||||
|
dt 2.000000e+00
|
||||||
|
version 2018-11-16
|
||||||
|
}
|
||||||
|
|
||||||
|
colvar {
|
||||||
|
name one
|
||||||
|
x 1.00136989326255e+01
|
||||||
|
}
|
||||||
|
|
||||||
|
colvar {
|
||||||
|
name two
|
||||||
|
x 1.00648830006091e+01
|
||||||
|
}
|
||||||
|
|
||||||
|
restraint {
|
||||||
|
configuration {
|
||||||
|
step 100
|
||||||
|
name h_pot
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
@ -1,102 +1,203 @@
|
||||||
# step one two
|
# step one two
|
||||||
100 1.00136999784453e+01 1.00648820764882e+01
|
0 9.93490813652661e+00 7.58366314453810e+00
|
||||||
101 1.00137686830422e+01 1.00611307186442e+01
|
1 9.95511870046091e+00 7.60655947684375e+00
|
||||||
102 1.00135851804620e+01 1.00551774768670e+01
|
2 9.97738607194270e+00 7.65732201855527e+00
|
||||||
103 1.00127019172615e+01 1.00448609599088e+01
|
3 1.00007618482085e+01 7.73339023313853e+00
|
||||||
104 1.00107148677220e+01 1.00279880647254e+01
|
4 1.00245083583281e+01 7.83083600267188e+00
|
||||||
105 1.00073753998706e+01 1.00031566249892e+01
|
5 1.00481503915519e+01 7.94485550041547e+00
|
||||||
106 1.00026887490897e+01 9.97035299845099e+00
|
6 1.00714236148569e+01 8.07022633606012e+00
|
||||||
107 9.99696380204809e+00 9.93114513453873e+00
|
7 1.00941640085929e+01 8.20149351409018e+00
|
||||||
108 9.99079173947846e+00 9.88834426761621e+00
|
8 1.01161917254501e+01 8.33270968029044e+00
|
||||||
109 9.98495634348822e+00 9.84525182069547e+00
|
9 1.01372195147989e+01 8.45743087998851e+00
|
||||||
110 9.98029608653331e+00 9.80488128973958e+00
|
10 1.01568094484822e+01 8.57063657043322e+00
|
||||||
111 9.97755063903513e+00 9.76956423088248e+00
|
11 1.01744058364969e+01 8.66916428851601e+00
|
||||||
112 9.97722827031026e+00 9.74089978578719e+00
|
12 1.01894584969823e+01 8.75011341291751e+00
|
||||||
113 9.97952719395978e+00 9.71964890219001e+00
|
13 1.02015949657517e+01 8.81261373358815e+00
|
||||||
114 9.98433213818614e+00 9.70572160189541e+00
|
14 1.02107634786499e+01 8.86010572643564e+00
|
||||||
115 9.99128820986690e+00 9.69882648932897e+00
|
15 1.02172802335367e+01 8.89996164389908e+00
|
||||||
116 9.99993078708906e+00 9.69906675982844e+00
|
16 1.02217586687617e+01 8.94046117354318e+00
|
||||||
117 1.00098268026590e+01 9.70676032193502e+00
|
17 1.02249400729821e+01 8.98764357480963e+00
|
||||||
118 1.00206800068605e+01 9.72193925284532e+00
|
18 1.02274821194763e+01 9.04385418276306e+00
|
||||||
119 1.00323638324515e+01 9.74392975114862e+00
|
19 1.02297694921722e+01 9.10767828090644e+00
|
||||||
120 1.00448758513666e+01 9.77144823009299e+00
|
20 1.02317948794015e+01 9.17521818721732e+00
|
||||||
121 1.00582368252610e+01 9.80293582393448e+00
|
21 1.02331324174422e+01 9.24256921345538e+00
|
||||||
122 1.00723784561855e+01 9.83653845611926e+00
|
22 1.02330115052436e+01 9.30670040650459e+00
|
||||||
123 1.00870571871815e+01 9.86996653086528e+00
|
23 1.02304888847637e+01 9.36477739916766e+00
|
||||||
124 1.01018149909563e+01 9.90067054070927e+00
|
24 1.02246905091409e+01 9.41471338314027e+00
|
||||||
125 1.01159957146856e+01 9.92637090832991e+00
|
25 1.02150557312054e+01 9.45578119421866e+00
|
||||||
126 1.01288197202732e+01 9.94568593115900e+00
|
26 1.02015018849614e+01 9.48855148434622e+00
|
||||||
127 1.01395051017779e+01 9.95858909349258e+00
|
27 1.01844563445019e+01 9.51414398880334e+00
|
||||||
128 1.01474031546764e+01 9.96651060978132e+00
|
28 1.01647618536435e+01 9.53348342780342e+00
|
||||||
129 1.01521102583250e+01 9.97197886676780e+00
|
29 1.01435075836914e+01 9.54736918677922e+00
|
||||||
130 1.01535305336566e+01 9.97782726175993e+00
|
30 1.01218448127414e+01 9.55679294480281e+00
|
||||||
131 1.01518703644018e+01 9.98617108245763e+00
|
31 1.01008234685872e+01 9.56289707955055e+00
|
||||||
132 1.01475651582407e+01 9.99754271679455e+00
|
32 1.00812605992407e+01 9.56689852729787e+00
|
||||||
133 1.01411660808109e+01 1.00106700599276e+01
|
33 1.00636482078211e+01 9.57008522470066e+00
|
||||||
134 1.01332313643590e+01 1.00230219318765e+01
|
34 1.00481219532447e+01 9.57404682801174e+00
|
||||||
135 1.01242577071328e+01 1.00317168123542e+01
|
35 1.00345149123742e+01 9.58097344406653e+00
|
||||||
136 1.01146539200964e+01 1.00343611311947e+01
|
36 1.00224896192326e+01 9.59352147402459e+00
|
||||||
137 1.01047327535065e+01 1.00296410219261e+01
|
37 1.00117065902086e+01 9.61412496221624e+00
|
||||||
138 1.00947009258946e+01 1.00175740354601e+01
|
38 1.00019625883763e+01 9.64369256665448e+00
|
||||||
139 1.00846525340704e+01 9.99930113951843e+00
|
39 9.99324045988116e+00 9.68100279483232e+00
|
||||||
140 1.00745850435896e+01 9.97645596333061e+00
|
40 9.98566198277188e+00 9.72340741886406e+00
|
||||||
141 1.00644392647413e+01 9.95041162930873e+00
|
41 9.97939087537504e+00 9.76737558060000e+00
|
||||||
142 1.00541491709691e+01 9.92180111647481e+00
|
42 9.97455220189940e+00 9.80830263552738e+00
|
||||||
143 1.00436823424749e+01 9.89050169056719e+00
|
43 9.97120052013341e+00 9.84185625268822e+00
|
||||||
144 1.00330636529660e+01 9.85603208426972e+00
|
44 9.96933202180119e+00 9.86623764187619e+00
|
||||||
145 1.00223839228086e+01 9.81818334237853e+00
|
45 9.96891976615505e+00 9.88235950966856e+00
|
||||||
146 1.00118047065649e+01 9.77758921505729e+00
|
46 9.96994868341340e+00 9.89287033859050e+00
|
||||||
147 1.00015612314349e+01 9.73590349870836e+00
|
47 9.97242707411381e+00 9.90111363064262e+00
|
||||||
148 9.99195527218088e+00 9.69551788236989e+00
|
48 9.97636549450466e+00 9.91016536955268e+00
|
||||||
149 9.98332631801527e+00 9.65911749675800e+00
|
49 9.98173560597232e+00 9.92197275407224e+00
|
||||||
150 9.97599491711484e+00 9.62915810268995e+00
|
50 9.98843048433684e+00 9.93674029911159e+00
|
||||||
151 9.97018870425343e+00 9.60717358806770e+00
|
51 9.99624064138588e+00 9.95286099036568e+00
|
||||||
152 9.96597676149386e+00 9.59319263515552e+00
|
52 1.00048525916104e+01 9.96759873289121e+00
|
||||||
153 9.96323912038658e+00 9.58560496094010e+00
|
53 1.00138780764319e+01 9.97821328789638e+00
|
||||||
154 9.96168472712778e+00 9.58154384221214e+00
|
54 1.00229204333232e+01 9.98289434996108e+00
|
||||||
155 9.96091708239459e+00 9.57764409185937e+00
|
55 1.00316676518615e+01 9.98113328544968e+00
|
||||||
156 9.96053284836430e+00 9.57094226701891e+00
|
56 1.00399758142293e+01 9.97358294450079e+00
|
||||||
157 9.96022340231744e+00 9.55966218699141e+00
|
57 1.00479031641095e+01 9.96154574170506e+00
|
||||||
158 9.95984104841431e+00 9.54367921177888e+00
|
58 1.00556838347250e+01 9.94624156425743e+00
|
||||||
159 9.95941115970323e+00 9.52452532866834e+00
|
59 1.00636555959318e+01 9.92816580065099e+00
|
||||||
160 9.95909775592352e+00 9.50490062318069e+00
|
60 1.00721640105110e+01 9.90692505955277e+00
|
||||||
161 9.95913472197875e+00 9.48781177595095e+00
|
61 1.00814536313753e+01 9.88155118527262e+00
|
||||||
162 9.95973716567135e+00 9.47562216260840e+00
|
62 1.00915547252798e+01 9.85098082230735e+00
|
||||||
163 9.96102283681378e+00 9.46939618474568e+00
|
63 1.01021918256653e+01 9.81456141006142e+00
|
||||||
164 9.96297512061468e+00 9.46883909503368e+00
|
64 1.01127650365675e+01 9.77251908261309e+00
|
||||||
165 9.96545450087319e+00 9.47284744786104e+00
|
65 1.01224426616504e+01 9.72626626484817e+00
|
||||||
166 9.96824446676367e+00 9.48032505757766e+00
|
66 1.01303500341168e+01 9.67844790721581e+00
|
||||||
167 9.97111490093449e+00 9.49080999053287e+00
|
67 1.01357827497794e+01 9.63264342158540e+00
|
||||||
168 9.97388723087919e+00 9.50468382474366e+00
|
68 1.01383594707679e+01 9.59267551611127e+00
|
||||||
169 9.97648454853684e+00 9.52297944488190e+00
|
69 1.01380701059532e+01 9.56168371312923e+00
|
||||||
170 9.97895120221314e+00 9.54683939172159e+00
|
70 1.01352290156399e+01 9.54132235576289e+00
|
||||||
171 9.98143439573287e+00 9.57673744631037e+00
|
71 1.01303782422632e+01 9.53145207033862e+00
|
||||||
172 9.98412851702981e+00 9.61177677879831e+00
|
72 1.01241807468998e+01 9.53052072472080e+00
|
||||||
173 9.98719912546727e+00 9.64941646139346e+00
|
73 1.01173118912092e+01 9.53632715678295e+00
|
||||||
174 9.99071466036109e+00 9.68581516318204e+00
|
74 1.01103471939659e+01 9.54668992740772e+00
|
||||||
175 9.99461255041478e+00 9.71674194992540e+00
|
75 1.01036629090248e+01 9.55984803752009e+00
|
||||||
176 9.99871362276481e+00 9.73875618365856e+00
|
76 1.00973931139318e+01 9.57467381743772e+00
|
||||||
177 1.00027752607551e+01 9.75023319932384e+00
|
77 1.00914805900150e+01 9.59078681449290e+00
|
||||||
178 1.00065593228689e+01 9.75187374895997e+00
|
78 1.00857806923796e+01 9.60849062320413e+00
|
||||||
179 1.00098932819698e+01 9.74651102922357e+00
|
79 1.00801732463746e+01 9.62847591791803e+00
|
||||||
180 1.00127089751067e+01 9.73824323715410e+00
|
80 1.00746211947647e+01 9.65137407697197e+00
|
||||||
181 1.00150539578018e+01 9.73118937807432e+00
|
81 1.00691682828698e+01 9.67731006831009e+00
|
||||||
182 1.00170703552922e+01 9.72834303011533e+00
|
82 1.00638992393184e+01 9.70564969348618e+00
|
||||||
183 1.00189424568686e+01 9.73087964994846e+00
|
83 1.00589006124327e+01 9.73510953407921e+00
|
||||||
184 1.00208211796404e+01 9.73798531353725e+00
|
84 1.00542402131510e+01 9.76420390471647e+00
|
||||||
185 1.00227525196798e+01 9.74722518450810e+00
|
85 1.00499602946160e+01 9.79180385249033e+00
|
||||||
186 1.00246411639883e+01 9.75544038568881e+00
|
86 1.00460706235439e+01 9.81755460563928e+00
|
||||||
187 1.00262714680409e+01 9.75985920611179e+00
|
87 1.00425414168408e+01 9.84200765912343e+00
|
||||||
188 1.00273770464779e+01 9.75895332491778e+00
|
88 1.00393046004480e+01 9.86642899323320e+00
|
||||||
189 1.00277296204562e+01 9.75275348211835e+00
|
89 1.00362677210398e+01 9.89232615597538e+00
|
||||||
190 1.00272109105395e+01 9.74260945002776e+00
|
90 1.00333326702222e+01 9.92077091295346e+00
|
||||||
191 1.00258469602549e+01 9.73056029017316e+00
|
91 1.00304190984417e+01 9.95163431119817e+00
|
||||||
192 1.00238019119674e+01 9.71852969006276e+00
|
92 1.00274924302484e+01 9.98320614724761e+00
|
||||||
193 1.00213411099718e+01 9.70760780505631e+00
|
93 1.00245832030580e+01 1.00126809229005e+01
|
||||||
194 1.00187745961566e+01 9.69771723529251e+00
|
94 1.00217818712298e+01 1.00372157022896e+01
|
||||||
195 1.00163957858114e+01 9.68783387106584e+00
|
95 1.00192174478224e+01 1.00549229065348e+01
|
||||||
196 1.00144342355802e+01 9.67665900893200e+00
|
96 1.00170334876474e+01 1.00654011519876e+01
|
||||||
197 1.00130379562453e+01 9.66342567131686e+00
|
97 1.00153609154724e+01 1.00697015600771e+01
|
||||||
198 1.00122840592666e+01 9.64853643967174e+00
|
98 1.00142801210350e+01 1.00698014812365e+01
|
||||||
199 1.00121986038636e+01 9.63383126934824e+00
|
99 1.00137749686339e+01 1.00677656407202e+01
|
||||||
200 1.00127641579482e+01 9.62235621950587e+00
|
100 1.00136989326255e+01 1.00648830006091e+01
|
||||||
|
100 1.00136989326255e+01 1.00648830006091e+01
|
||||||
|
101 1.00137674082083e+01 1.00611318434583e+01
|
||||||
|
102 1.00135836692120e+01 1.00551787890126e+01
|
||||||
|
103 1.00127001705469e+01 1.00448624179689e+01
|
||||||
|
104 1.00107128955990e+01 1.00279896008852e+01
|
||||||
|
105 1.00073732210918e+01 1.00031581615939e+01
|
||||||
|
106 1.00026863896858e+01 9.97035446256176e+00
|
||||||
|
107 9.99696129324890e+00 9.93114647843641e+00
|
||||||
|
108 9.99078911556410e+00 9.88834547941894e+00
|
||||||
|
109 9.98495363939735e+00 9.84525289783234e+00
|
||||||
|
110 9.98029333636388e+00 9.80488218664815e+00
|
||||||
|
111 9.97754787492958e+00 9.76956483721087e+00
|
||||||
|
112 9.97722552172005e+00 9.74089998776836e+00
|
||||||
|
113 9.97952448720610e+00 9.71964869280979e+00
|
||||||
|
114 9.98432949668635e+00 9.70572109422863e+00
|
||||||
|
115 9.99128565538624e+00 9.69882579496975e+00
|
||||||
|
116 9.99992834152120e+00 9.69906594532193e+00
|
||||||
|
117 1.00098244901113e+01 9.70675942684906e+00
|
||||||
|
118 1.00206778548564e+01 9.72193838510829e+00
|
||||||
|
119 1.00323618718055e+01 9.74392916146852e+00
|
||||||
|
120 1.00448741144078e+01 9.77144817149792e+00
|
||||||
|
121 1.00582353428180e+01 9.80293643028548e+00
|
||||||
|
122 1.00723772537607e+01 9.83653980628752e+00
|
||||||
|
123 1.00870562810006e+01 9.86996874359296e+00
|
||||||
|
124 1.01018143847617e+01 9.90067377124461e+00
|
||||||
|
125 1.01159953973120e+01 9.92637526075002e+00
|
||||||
|
126 1.01288196652442e+01 9.94569135970445e+00
|
||||||
|
127 1.01395052692626e+01 9.95859533688896e+00
|
||||||
|
128 1.01474034953817e+01 9.96651718147533e+00
|
||||||
|
129 1.01521107193303e+01 9.97198512417321e+00
|
||||||
|
130 1.01535310646235e+01 9.97783256102044e+00
|
||||||
|
131 1.01518709230597e+01 9.98617497185904e+00
|
||||||
|
132 1.01475657142497e+01 9.99754506682891e+00
|
||||||
|
133 1.01411666167305e+01 1.00106710657684e+01
|
||||||
|
134 1.01332318751871e+01 1.00230220357698e+01
|
||||||
|
135 1.01242581986854e+01 1.00317166064461e+01
|
||||||
|
136 1.01146544066986e+01 1.00343612487317e+01
|
||||||
|
137 1.01047332554016e+01 1.00296420246780e+01
|
||||||
|
138 1.00947014667735e+01 1.00175763327172e+01
|
||||||
|
139 1.00846531387645e+01 9.99930494674974e+00
|
||||||
|
140 1.00745857366623e+01 9.97646128131491e+00
|
||||||
|
141 1.00644400706802e+01 9.95041823440337e+00
|
||||||
|
142 1.00541501159131e+01 9.92180857541951e+00
|
||||||
|
143 1.00436834569978e+01 9.89050941872713e+00
|
||||||
|
144 1.00330649757401e+01 9.85603943350860e+00
|
||||||
|
145 1.00223855042347e+01 9.81818968302844e+00
|
||||||
|
146 1.00118066120717e+01 9.77759398920638e+00
|
||||||
|
147 1.00015635423691e+01 9.73590632972306e+00
|
||||||
|
148 9.99195808427061e+00 9.69551862637489e+00
|
||||||
|
149 9.98332973799261e+00 9.65911623085002e+00
|
||||||
|
150 9.97599905761175e+00 9.62915505877515e+00
|
||||||
|
151 9.97019367767784e+00 9.60716909686955e+00
|
||||||
|
152 9.96598267281873e+00 9.59318709200410e+00
|
||||||
|
153 9.96324605944343e+00 9.58559881047527e+00
|
||||||
|
154 9.96169276126796e+00 9.58153758556819e+00
|
||||||
|
155 9.96092625032814e+00 9.57763829311044e+00
|
||||||
|
156 9.96054315607791e+00 9.57093750799266e+00
|
||||||
|
157 9.96023482227745e+00 9.55965895377840e+00
|
||||||
|
158 9.95985352165466e+00 9.54367776307569e+00
|
||||||
|
159 9.95942460039566e+00 9.52452561463833e+00
|
||||||
|
160 9.95911205589222e+00 9.50490226824346e+00
|
||||||
|
161 9.95914975443396e+00 9.48781410600212e+00
|
||||||
|
162 9.95975278911406e+00 9.47562429341561e+00
|
||||||
|
163 9.96103890040379e+00 9.46939719079233e+00
|
||||||
|
164 9.96299147170478e+00 9.46883821286236e+00
|
||||||
|
165 9.96547099380307e+00 9.47284423942468e+00
|
||||||
|
166 9.96826097146115e+00 9.48031949605208e+00
|
||||||
|
167 9.97113131026389e+00 9.49080246783928e+00
|
||||||
|
168 9.97390346515378e+00 9.50467508257787e+00
|
||||||
|
169 9.97650055807565e+00 9.52297045210046e+00
|
||||||
|
170 9.97896696852481e+00 9.54683120799382e+00
|
||||||
|
171 9.98144993167344e+00 9.57673108800475e+00
|
||||||
|
172 9.98414386605973e+00 9.61177309775590e+00
|
||||||
|
173 9.98721435874383e+00 9.64941604907962e+00
|
||||||
|
174 9.99072987081047e+00 9.68581828149366e+00
|
||||||
|
175 9.99462784290560e+00 9.71674849920838e+00
|
||||||
|
176 9.99872910050856e+00 9.73876571566039e+00
|
||||||
|
177 1.00027910094647e+01 9.75024496509227e+00
|
||||||
|
178 1.00065753933095e+01 9.75188677631197e+00
|
||||||
|
179 1.00099096736715e+01 9.74652424002240e+00
|
||||||
|
180 1.00127256239536e+01 9.73825559652692e+00
|
||||||
|
181 1.00150707323506e+01 9.73120003142692e+00
|
||||||
|
182 1.00170870650914e+01 9.72835138795971e+00
|
||||||
|
183 1.00189588719574e+01 9.73088542644806e+00
|
||||||
|
184 1.00208370553711e+01 9.73798855694274e+00
|
||||||
|
185 1.00227676206971e+01 9.74722630488312e+00
|
||||||
|
186 1.00246552838286e+01 9.75544013816019e+00
|
||||||
|
187 1.00262844434324e+01 9.75985859738447e+00
|
||||||
|
188 1.00273887691195e+01 9.75895345517658e+00
|
||||||
|
189 1.00277400472209e+01 9.75275536148299e+00
|
||||||
|
190 1.00272200725279e+01 9.74261382746486e+00
|
||||||
|
191 1.00258549688160e+01 9.73056754269459e+00
|
||||||
|
192 1.00238089567536e+01 9.71853980670345e+00
|
||||||
|
193 1.00213474465750e+01 9.70762043885231e+00
|
||||||
|
194 1.00187805230869e+01 9.69773175124558e+00
|
||||||
|
195 1.00164016154513e+01 9.68784935173366e+00
|
||||||
|
196 1.00144402674219e+01 9.67667427007303e+00
|
||||||
|
197 1.00130444574495e+01 9.66343938720852e+00
|
||||||
|
198 1.00122912607270e+01 9.64854739476250e+00
|
||||||
|
199 1.00122066750836e+01 9.63383866331536e+00
|
||||||
|
200 1.00127732034965e+01 9.62235997490241e+00
|
||||||
|
|
|
||||||
|
|
@ -1,22 +1,23 @@
|
||||||
configuration {
|
configuration {
|
||||||
step 300
|
step 300
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
|
version 2018-11-16
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 9.95354148699614e+00
|
x 9.95315918568411e+00
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name two
|
name two
|
||||||
x 9.79310294857288e+00
|
x 9.79318883680258e+00
|
||||||
}
|
}
|
||||||
|
|
||||||
harmonic {
|
restraint {
|
||||||
configuration {
|
configuration {
|
||||||
|
step 300
|
||||||
name h_pot
|
name h_pot
|
||||||
stage 8103505641670189088
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,102 +1,102 @@
|
||||||
# step one two
|
# step one two
|
||||||
200 1.00127641579482e+01 9.62235621950587e+00
|
200 1.00127732034965e+01 9.62235997490241e+00
|
||||||
201 1.00139098397954e+01 9.61766067322651e+00
|
201 1.00139198864982e+01 9.61766167925624e+00
|
||||||
202 1.00154895322849e+01 9.62284260846102e+00
|
202 1.00155004339120e+01 9.62284272858813e+00
|
||||||
203 1.00172625720562e+01 9.63964717046032e+00
|
203 1.00172741972246e+01 9.63964899323068e+00
|
||||||
204 1.00188930177704e+01 9.66786064733448e+00
|
204 1.00189052021826e+01 9.66786718571673e+00
|
||||||
205 1.00199761813056e+01 9.70519780219794e+00
|
205 1.00199887119842e+01 9.70521202056400e+00
|
||||||
206 1.00200944106384e+01 9.74779969655747e+00
|
206 1.00201070660155e+01 9.74782380666112e+00
|
||||||
207 1.00188963572281e+01 9.79111374012340e+00
|
207 1.00189089093749e+01 9.79114913038349e+00
|
||||||
208 1.00161883604793e+01 9.83086787098858e+00
|
208 1.00162005540278e+01 9.83091553260188e+00
|
||||||
209 1.00120201470551e+01 9.86403984083060e+00
|
209 1.00120316562035e+01 9.86409994884863e+00
|
||||||
210 1.00067290723642e+01 9.88948240692241e+00
|
210 1.00067394529596e+01 9.88955328455197e+00
|
||||||
211 1.00009114042457e+01 9.90790280320401e+00
|
211 1.00009200584653e+01 9.90798080826055e+00
|
||||||
212 9.99530858712775e+00 9.92119319076851e+00
|
212 9.99531475905311e+00 9.92127385542524e+00
|
||||||
213 9.99063126799011e+00 9.93149262690681e+00
|
213 9.99063400342297e+00 9.93157198661852e+00
|
||||||
214 9.98737350983788e+00 9.94043951053174e+00
|
214 9.98737188807678e+00 9.94051482696048e+00
|
||||||
215 9.98567811211086e+00 9.94878566374960e+00
|
215 9.98567127567181e+00 9.94885527957784e+00
|
||||||
216 9.98529977833156e+00 9.95640488686023e+00
|
216 9.98528704043382e+00 9.95646746111755e+00
|
||||||
217 9.98567740511041e+00 9.96270367197379e+00
|
217 9.98565832937415e+00 9.96275739929720e+00
|
||||||
218 9.98609281741416e+00 9.96726160094494e+00
|
218 9.98606724184677e+00 9.96730423246689e+00
|
||||||
219 9.98586784093273e+00 9.97033437532426e+00
|
219 9.98583582550472e+00 9.97036378703713e+00
|
||||||
220 9.98454831898211e+00 9.97291246609646e+00
|
220 9.98451001643477e+00 9.97292736129215e+00
|
||||||
221 9.98202887687821e+00 9.97627400695988e+00
|
221 9.98198434901656e+00 9.97627439806637e+00
|
||||||
222 9.97858776161328e+00 9.98128372296812e+00
|
222 9.97853678731273e+00 9.98127100659218e+00
|
||||||
223 9.97481791063232e+00 9.98787692577356e+00
|
223 9.97475984191141e+00 9.98785371236258e+00
|
||||||
224 9.97146915301902e+00 9.99495319867179e+00
|
224 9.97140286510626e+00 9.99492286335624e+00
|
||||||
225 9.96924741695340e+00 1.00005781312739e+01
|
225 9.96917137580259e+00 1.00005443231922e+01
|
||||||
226 9.96863280571612e+00 1.00023562928510e+01
|
226 9.96854523900174e+00 1.00023222923235e+01
|
||||||
227 9.96977462939505e+00 9.99793468396390e+00
|
227 9.96967375964547e+00 9.99790273206806e+00
|
||||||
228 9.97249206995624e+00 9.98558877312050e+00
|
228 9.97237636771905e+00 9.98555960216881e+00
|
||||||
229 9.97637419760570e+00 9.96476526430303e+00
|
229 9.97624253505807e+00 9.96473792067690e+00
|
||||||
230 9.98093600414111e+00 9.93639297716863e+00
|
230 9.98078777310055e+00 9.93636511602182e+00
|
||||||
231 9.98577334632368e+00 9.90279138444459e+00
|
231 9.98560846780419e+00 9.90275990393703e+00
|
||||||
232 9.99066901099700e+00 9.86714667869485e+00
|
232 9.99048787217569e+00 9.86710855077386e+00
|
||||||
233 9.99562704815141e+00 9.83274230148512e+00
|
233 9.99543040822038e+00 9.83269539984149e+00
|
||||||
234 1.00008356809073e+01 9.80226834521352e+00
|
234 1.00006246021103e+01 9.80221208335553e+00
|
||||||
235 1.00065772362800e+01 9.77744581513232e+00
|
235 1.00063530848982e+01 9.77738136586701e+00
|
||||||
236 1.00131097048912e+01 9.75894408214992e+00
|
236 1.00128741709083e+01 9.75887400813685e+00
|
||||||
237 1.00205553485494e+01 9.74639403983496e+00
|
237 1.00203106975850e+01 9.74632163179798e+00
|
||||||
238 1.00288314258010e+01 9.73851464709533e+00
|
238 1.00285805371730e+01 9.73844350416337e+00
|
||||||
239 1.00376482262668e+01 9.73355843502651e+00
|
239 1.00373945897865e+01 9.73349215182819e+00
|
||||||
240 1.00465718867162e+01 9.72986544373201e+00
|
240 1.00463194539327e+01 9.72980720779576e+00
|
||||||
241 1.00551241447104e+01 9.72616365347388e+00
|
241 1.00548770491533e+01 9.72611599020063e+00
|
||||||
242 1.00628799016098e+01 9.72156081057173e+00
|
242 1.00626421174965e+01 9.72152572108181e+00
|
||||||
243 1.00695359569141e+01 9.71533506969961e+00
|
243 1.00693109823863e+01 9.71531423107737e+00
|
||||||
244 1.00749394351078e+01 9.70669135454371e+00
|
244 1.00747300690509e+01 9.70668632474813e+00
|
||||||
245 1.00790729024702e+01 9.69470862769774e+00
|
245 1.00788811512303e+01 9.69472082245661e+00
|
||||||
246 1.00820010382698e+01 9.67869454326621e+00
|
246 1.00818281591535e+01 9.67872530149764e+00
|
||||||
247 1.00837917095021e+01 9.65894101136318e+00
|
247 1.00836382918008e+01 9.65899116363609e+00
|
||||||
248 1.00844414119874e+01 9.63696223650643e+00
|
248 1.00843077585461e+01 9.63702967428387e+00
|
||||||
249 1.00838441989246e+01 9.61423476365400e+00
|
249 1.00837304601058e+01 9.61431312359133e+00
|
||||||
250 1.00818306797879e+01 9.59185059543549e+00
|
250 1.00817369874724e+01 9.59193249256670e+00
|
||||||
251 1.00782686429397e+01 9.57154356576350e+00
|
251 1.00781951382998e+01 9.57162234547176e+00
|
||||||
252 1.00731806695096e+01 9.55550278600070e+00
|
252 1.00731274409141e+01 9.55557274350384e+00
|
||||||
253 1.00668200834919e+01 9.54554307033366e+00
|
253 1.00667870632608e+01 9.54560001126946e+00
|
||||||
254 1.00596730176507e+01 9.54248962932697e+00
|
254 1.00596598859158e+01 9.54253147668434e+00
|
||||||
255 1.00523895763009e+01 9.54590976255577e+00
|
255 1.00523956909045e+01 9.54593692832520e+00
|
||||||
256 1.00456784264533e+01 9.55421544253452e+00
|
256 1.00457028282132e+01 9.55423082330650e+00
|
||||||
257 1.00402005024002e+01 9.56513899116782e+00
|
257 1.00402418669526e+01 9.56514761944992e+00
|
||||||
258 1.00364831006552e+01 9.57640458000444e+00
|
258 1.00365397691695e+01 9.57641296971103e+00
|
||||||
259 1.00348576492106e+01 9.58619146455749e+00
|
259 1.00349276270394e+01 9.58620624196598e+00
|
||||||
260 1.00354210621162e+01 9.59329709957898e+00
|
260 1.00355019919770e+01 9.59332346959128e+00
|
||||||
261 1.00380245202744e+01 9.59728096353517e+00
|
261 1.00381137097146e+01 9.59732188686984e+00
|
||||||
262 1.00422960600822e+01 9.59832037848005e+00
|
262 1.00423905760179e+01 9.59837618250971e+00
|
||||||
263 1.00476990763950e+01 9.59672497993560e+00
|
263 1.00477959188736e+01 9.59679324477687e+00
|
||||||
264 1.00536104533027e+01 9.59261911381189e+00
|
264 1.00537068007149e+01 9.59269523141530e+00
|
||||||
265 1.00594002482137e+01 9.58602304006163e+00
|
265 1.00594937260641e+01 9.58610120816249e+00
|
||||||
266 1.00644981793165e+01 9.57714719542419e+00
|
266 1.00645870781682e+01 9.57722117048002e+00
|
||||||
267 1.00684482704210e+01 9.56662135439055e+00
|
267 1.00685316571224e+01 9.56668493985151e+00
|
||||||
268 1.00709580655557e+01 9.55551489305294e+00
|
268 1.00710357823615e+01 9.55556251047062e+00
|
||||||
269 1.00719418900228e+01 9.54518226195314e+00
|
269 1.00720144042107e+01 9.54520978473172e+00
|
||||||
270 1.00715463773733e+01 9.53703197862875e+00
|
270 1.00716144493745e+01 9.53703781183182e+00
|
||||||
271 1.00701345227997e+01 9.53228911010047e+00
|
271 1.00701992199135e+01 9.53227489206590e+00
|
||||||
272 1.00682184887617e+01 9.53176321322706e+00
|
272 1.00682808706064e+01 9.53173333554826e+00
|
||||||
273 1.00663378629920e+01 9.53558933249131e+00
|
273 1.00663988075209e+01 9.53554943194497e+00
|
||||||
274 1.00649132448630e+01 9.54304329234477e+00
|
274 1.00649733063520e+01 9.54299862049767e+00
|
||||||
275 1.00641243212406e+01 9.55266696753925e+00
|
275 1.00641836485840e+01 9.55262143610080e+00
|
||||||
276 1.00638595454980e+01 9.56275901409309e+00
|
276 1.00639178664285e+01 9.56271517955029e+00
|
||||||
277 1.00637587244679e+01 9.57196213233751e+00
|
277 1.00638153921535e+01 9.57192148747872e+00
|
||||||
278 1.00633313189549e+01 9.57961568108488e+00
|
278 1.00633853985923e+01 9.57957875475062e+00
|
||||||
279 1.00621123193119e+01 9.58575692732997e+00
|
279 1.00621626720543e+01 9.58572327394556e+00
|
||||||
280 1.00598117112007e+01 9.59088855190189e+00
|
280 1.00598570838615e+01 9.59085686511578e+00
|
||||||
281 1.00564177173993e+01 9.59570566223894e+00
|
281 1.00564566071967e+01 9.59567423393283e+00
|
||||||
282 1.00522270044392e+01 9.60088836897012e+00
|
282 1.00522576614697e+01 9.60085550637412e+00
|
||||||
283 1.00477888199161e+01 9.60693590561625e+00
|
283 1.00478091897332e+01 9.60690040068280e+00
|
||||||
284 1.00437690523107e+01 9.61400570555926e+00
|
284 1.00437767664032e+01 9.61396708331890e+00
|
||||||
285 1.00407622307256e+01 9.62182265962647e+00
|
285 1.00407546813490e+01 9.62178118810825e+00
|
||||||
286 1.00391028258991e+01 9.62979902243492e+00
|
286 1.00390773261870e+01 9.62975547860500e+00
|
||||||
287 1.00387366035163e+01 9.63738040674711e+00
|
287 1.00386906040191e+01 9.63733595704590e+00
|
||||||
288 1.00391979793082e+01 9.64439605217689e+00
|
288 1.00391292740982e+01 9.64435229335154e+00
|
||||||
289 1.00397008587343e+01 9.65118231683256e+00
|
289 1.00396077171765e+01 9.65114124926381e+00
|
||||||
290 1.00393154139857e+01 9.65847479887268e+00
|
290 1.00391967746350e+01 9.65843904962787e+00
|
||||||
291 1.00371856971467e+01 9.66716430247627e+00
|
291 1.00370409303829e+01 9.66713735495098e+00
|
||||||
292 1.00327325013742e+01 9.67799413246555e+00
|
292 1.00325613495850e+01 9.67798035621834e+00
|
||||||
293 1.00257889436952e+01 9.69130066948859e+00
|
293 1.00255913568518e+01 9.69130440474672e+00
|
||||||
294 1.00166284740574e+01 9.70687426338097e+00
|
294 1.00164044158125e+01 9.70689841022156e+00
|
||||||
295 1.00058767991341e+01 9.72395332252100e+00
|
295 1.00056261321876e+01 9.72399810930261e+00
|
||||||
296 9.99433972822595e+00 9.74134088397850e+00
|
296 9.99406221883501e+00 9.74140402524052e+00
|
||||||
297 9.98281255441855e+00 9.75768650006539e+00
|
297 9.98250803362175e+00 9.75776438941627e+00
|
||||||
298 9.97193339524040e+00 9.77194269576588e+00
|
298 9.97160202027972e+00 9.77203069297329e+00
|
||||||
299 9.96211387496966e+00 9.78370254738211e+00
|
299 9.96175637151037e+00 9.78379375044905e+00
|
||||||
300 9.95354148699614e+00 9.79310294857288e+00
|
300 9.95315918568411e+00 9.79318883680258e+00
|
||||||
|
|
|
||||||
|
|
@ -1,17 +1,18 @@
|
||||||
configuration {
|
configuration {
|
||||||
step 100
|
step 100
|
||||||
dt 2.000000e+00
|
dt 2.000000e+00
|
||||||
|
version 2018-11-16
|
||||||
}
|
}
|
||||||
|
|
||||||
colvar {
|
colvar {
|
||||||
name one
|
name one
|
||||||
x 1.00387424212228e+01
|
x 1.00387423506482e+01
|
||||||
}
|
}
|
||||||
|
|
||||||
harmonic {
|
restraint {
|
||||||
configuration {
|
configuration {
|
||||||
|
step 100
|
||||||
name h_pot
|
name h_pot
|
||||||
stage 4044288781530052640
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,102 +1,102 @@
|
||||||
# step one
|
# step one
|
||||||
0 1.23398428397332e+01
|
0 1.23398428397332e+01
|
||||||
1 1.23379000531837e+01
|
1 1.23379000532662e+01
|
||||||
2 1.22833752132682e+01
|
2 1.22833752135957e+01
|
||||||
3 1.21783464524822e+01
|
3 1.21783464514507e+01
|
||||||
4 1.20268109152646e+01
|
4 1.20268109095184e+01
|
||||||
5 1.18342676552027e+01
|
5 1.18342676394048e+01
|
||||||
6 1.16071240696111e+01
|
6 1.16071240372003e+01
|
||||||
7 1.13522568477758e+01
|
7 1.13522567926249e+01
|
||||||
8 1.10769760454451e+01
|
8 1.10769759646337e+01
|
||||||
9 1.07892333501017e+01
|
9 1.07892332454600e+01
|
||||||
10 1.04978607983300e+01
|
10 1.04978606745989e+01
|
||||||
11 1.02148368912480e+01
|
11 1.02148367517604e+01
|
||||||
12 9.95820967758655e+00
|
12 9.95820954052204e+00
|
||||||
13 9.74528082635713e+00
|
13 9.74528077043305e+00
|
||||||
14 9.59065550809125e+00
|
14 9.59065564952749e+00
|
||||||
15 9.49025917553263e+00
|
15 9.49025959957862e+00
|
||||||
16 9.43254360388750e+00
|
16 9.43254431868731e+00
|
||||||
17 9.41011962734900e+00
|
17 9.41012058917623e+00
|
||||||
18 9.41602364253240e+00
|
18 9.41602481112176e+00
|
||||||
19 9.44413444723206e+00
|
19 9.44413580740584e+00
|
||||||
20 9.49001191595699e+00
|
20 9.49001346044027e+00
|
||||||
21 9.55036186844267e+00
|
21 9.55036359015270e+00
|
||||||
22 9.62258413071055e+00
|
22 9.62258602486444e+00
|
||||||
23 9.70460340526413e+00
|
23 9.70460545744668e+00
|
||||||
24 9.79475248209609e+00
|
24 9.79475465622561e+00
|
||||||
25 9.89135077720185e+00
|
25 9.89135302429916e+00
|
||||||
26 9.99213105078110e+00
|
26 9.99213332770717e+00
|
||||||
27 1.00938499722663e+01
|
27 1.00938522423366e+01
|
||||||
28 1.01925349210626e+01
|
28 1.01925371414626e+01
|
||||||
29 1.02845107805173e+01
|
29 1.02845129002944e+01
|
||||||
30 1.03676652352347e+01
|
30 1.03676671987640e+01
|
||||||
31 1.04416367894860e+01
|
31 1.04416385355998e+01
|
||||||
32 1.05071334937552e+01
|
32 1.05071349561950e+01
|
||||||
33 1.05650452299048e+01
|
33 1.05650463398331e+01
|
||||||
34 1.06158824214188e+01
|
34 1.06158831174766e+01
|
||||||
35 1.06595186275218e+01
|
35 1.06595188661313e+01
|
||||||
36 1.06948928511102e+01
|
36 1.06948926085038e+01
|
||||||
37 1.07202580715959e+01
|
37 1.07202573517647e+01
|
||||||
38 1.07337399401028e+01
|
38 1.07337387802787e+01
|
||||||
39 1.07331885445159e+01
|
39 1.07331870068021e+01
|
||||||
40 1.07158932314825e+01
|
40 1.07158913924701e+01
|
||||||
41 1.06789136129953e+01
|
41 1.06789115566470e+01
|
||||||
42 1.06198862520319e+01
|
42 1.06198840652253e+01
|
||||||
43 1.05380120055201e+01
|
43 1.05380097743725e+01
|
||||||
44 1.04346603936480e+01
|
44 1.04346581978275e+01
|
||||||
45 1.03132931131809e+01
|
45 1.03132910149185e+01
|
||||||
46 1.01792839195940e+01
|
46 1.01792819503691e+01
|
||||||
47 1.00398967921774e+01
|
47 1.00398949454818e+01
|
||||||
48 9.90373826474332e+00
|
48 9.90373650268307e+00
|
||||||
49 9.77934819842326e+00
|
49 9.77934647164350e+00
|
||||||
50 9.67344128626180e+00
|
50 9.67343955381284e+00
|
||||||
51 9.58957431460176e+00
|
51 9.58957255517495e+00
|
||||||
52 9.52771755964755e+00
|
52 9.52771577288560e+00
|
||||||
53 9.48463676001684e+00
|
53 9.48463495848957e+00
|
||||||
54 9.45495927636316e+00
|
54 9.45495747488851e+00
|
||||||
55 9.43277262066999e+00
|
55 9.43277083061229e+00
|
||||||
56 9.41329687195946e+00
|
56 9.41329510571902e+00
|
||||||
57 9.39418023785890e+00
|
57 9.39417852043035e+00
|
||||||
58 9.37608079167942e+00
|
58 9.37607916767444e+00
|
||||||
59 9.36244026161597e+00
|
59 9.36243879601093e+00
|
||||||
60 9.35853356967195e+00
|
60 9.35853234890725e+00
|
||||||
61 9.36993825765332e+00
|
61 9.36993739187210e+00
|
||||||
62 9.40084295384763e+00
|
62 9.40084256925489e+00
|
||||||
63 9.45286334548428e+00
|
63 9.45286356660258e+00
|
||||||
64 9.52464492798022e+00
|
64 9.52464585631223e+00
|
||||||
65 9.61230778865749e+00
|
65 9.61230948096192e+00
|
||||||
66 9.71074173620872e+00
|
66 9.71074418990813e+00
|
||||||
67 9.81506921139973e+00
|
67 9.81507236552599e+00
|
||||||
68 9.92117599348263e+00
|
68 9.92117974657176e+00
|
||||||
69 1.00244217575122e+01
|
69 1.00244259961919e+01
|
||||||
70 1.01178260477346e+01
|
70 1.01178306268727e+01
|
||||||
71 1.01986938379172e+01
|
71 1.01986985644537e+01
|
||||||
72 1.02670956368544e+01
|
72 1.02671003889995e+01
|
||||||
73 1.03213051063305e+01
|
73 1.03213098011429e+01
|
||||||
74 1.03597191337854e+01
|
74 1.03597236984298e+01
|
||||||
75 1.03817745676591e+01
|
75 1.03817789163109e+01
|
||||||
76 1.03880610583944e+01
|
76 1.03880650963390e+01
|
||||||
77 1.03809103738027e+01
|
77 1.03809140245635e+01
|
||||||
78 1.03645558156884e+01
|
78 1.03645590344102e+01
|
||||||
79 1.03441497701913e+01
|
79 1.03441525373194e+01
|
||||||
80 1.03243653409000e+01
|
80 1.03243676495902e+01
|
||||||
81 1.03082112818858e+01
|
81 1.03082131278348e+01
|
||||||
82 1.02961296917318e+01
|
82 1.02961310659179e+01
|
||||||
83 1.02862106580352e+01
|
83 1.02862115513553e+01
|
||||||
84 1.02756069146933e+01
|
84 1.02756073299153e+01
|
||||||
85 1.02618115908758e+01
|
85 1.02618115461408e+01
|
||||||
86 1.02435132305408e+01
|
86 1.02435127550163e+01
|
||||||
87 1.02212121470422e+01
|
87 1.02212112849545e+01
|
||||||
88 1.01972799936680e+01
|
88 1.01972788307491e+01
|
||||||
89 1.01743931780361e+01
|
89 1.01743918261207e+01
|
||||||
90 1.01538342930689e+01
|
90 1.01538328424605e+01
|
||||||
91 1.01363020288600e+01
|
91 1.01363005552771e+01
|
||||||
92 1.01223080393853e+01
|
92 1.01223066231827e+01
|
||||||
93 1.01118050646187e+01
|
93 1.01118037967830e+01
|
||||||
94 1.01038513159042e+01
|
94 1.01038502876980e+01
|
||||||
95 1.00967020139234e+01
|
95 1.00967012947728e+01
|
||||||
96 1.00885782989097e+01
|
96 1.00885779123137e+01
|
||||||
97 1.00784257293241e+01
|
97 1.00784256309007e+01
|
||||||
98 1.00661428832570e+01
|
98 1.00661429612272e+01
|
||||||
99 1.00524912515310e+01
|
99 1.00524913461711e+01
|
||||||
100 1.00387424212228e+01
|
100 1.00387423506482e+01
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
variable A string bulkNi
|
variable A string bulkNi
|
||||||
log $A.log
|
|
||||||
|
|
||||||
boundary p p p
|
boundary p p p
|
||||||
|
|
||||||
|
|
@ -26,7 +25,7 @@ fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
|
||||||
|
|
||||||
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||||
|
|
||||||
dump 1 all custom 1 $A.dump id x y z
|
#dump 1 all custom 1 $A.dump id x y z
|
||||||
run 0
|
run 0
|
||||||
|
|
||||||
unfix 1
|
unfix 1
|
||||||
|
|
@ -0,0 +1,72 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable A string bulkNi
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
units metal
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
lattice fcc 3.52
|
||||||
|
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||||
|
region box block 0 20 0 20 0 20
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 32000 atoms
|
||||||
|
Time spent = 0.0037179 secs
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
mass * 58.71
|
||||||
|
atom_modify sort 0 0
|
||||||
|
|
||||||
|
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
|
||||||
|
|
||||||
|
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual
|
||||||
|
|
||||||
|
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd
|
||||||
|
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd
|
||||||
|
|
||||||
|
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||||
|
fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed
|
||||||
|
|
||||||
|
#dump 1 all custom 1 $A.dump id x y z
|
||||||
|
run 0
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 21.91 | 21.91 | 21.91 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 0 0 0 0
|
||||||
|
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32000 atoms
|
||||||
|
|
||||||
|
314.6% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 9.537e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 32000 ave 32000 max 32000 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2461 ave 2461 max 2461 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
unfix 2
|
||||||
|
uncompute XRD
|
||||||
|
uncompute SAED
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:03:30
|
||||||
|
|
@ -0,0 +1,72 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable A string bulkNi
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
units metal
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
lattice fcc 3.52
|
||||||
|
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||||
|
region box block 0 20 0 20 0 20
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 32000 atoms
|
||||||
|
Time spent = 0.0010488 secs
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
mass * 58.71
|
||||||
|
atom_modify sort 0 0
|
||||||
|
|
||||||
|
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
|
||||||
|
|
||||||
|
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual
|
||||||
|
|
||||||
|
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd
|
||||||
|
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd
|
||||||
|
|
||||||
|
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||||
|
fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed
|
||||||
|
|
||||||
|
#dump 1 all custom 1 $A.dump id x y z
|
||||||
|
run 0
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 0 0 0 0
|
||||||
|
Loop time of 1.84774e-06 on 4 procs for 0 steps with 32000 atoms
|
||||||
|
|
||||||
|
162.4% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.848e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 8000 ave 8000 max 8000 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1041 ave 1041 max 1041 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
unfix 2
|
||||||
|
uncompute XRD
|
||||||
|
uncompute SAED
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:54
|
||||||
|
|
@ -1,5 +1,7 @@
|
||||||
LAMMPS (17 Jan 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
clear
|
clear
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style full
|
atom_style full
|
||||||
|
|
@ -119,7 +121,7 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
|
||||||
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update every 1 steps, delay 10 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
|
@ -132,13 +134,13 @@ Neighbor list info ...
|
||||||
pair build: half/bin/newton/tri
|
pair build: half/bin/newton/tri
|
||||||
stencil: half/bin/3d/newton/tri
|
stencil: half/bin/3d/newton/tri
|
||||||
bin: standard
|
bin: standard
|
||||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
WARNING: Inconsistent image flags (src/domain.cpp:782)
|
||||||
Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.23 | 21.23 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.23 | 21.23 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -11833.81 343.7619 -11490.048 -5.8508834
|
0 0 -11833.81 343.7619 -11490.048 -5.8508834
|
||||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms
|
Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms
|
||||||
|
|
||||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
314.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
|
@ -1,5 +1,7 @@
|
||||||
LAMMPS (17 Jan 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
clear
|
clear
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style full
|
atom_style full
|
||||||
|
|
@ -119,7 +121,7 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
|
||||||
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update every 1 steps, delay 10 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
|
@ -132,13 +134,13 @@ Neighbor list info ...
|
||||||
pair build: half/bin/newton/tri
|
pair build: half/bin/newton/tri
|
||||||
stencil: half/bin/3d/newton/tri
|
stencil: half/bin/3d/newton/tri
|
||||||
bin: standard
|
bin: standard
|
||||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
WARNING: Inconsistent image flags (src/domain.cpp:782)
|
||||||
Per MPI rank memory allocation (min/avg/max) = 20.68 | 20.68 | 20.68 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 20.68 | 20.68 | 20.68 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -11833.81 343.7619 -11490.048 -5.8508834
|
0 0 -11833.81 343.7619 -11490.048 -5.8508834
|
||||||
Loop time of 2.20537e-06 on 4 procs for 0 steps with 624 atoms
|
Loop time of 2.01464e-05 on 4 procs for 0 steps with 624 atoms
|
||||||
|
|
||||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
86.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
|
@ -149,7 +151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 2.205e-06 | | |100.00
|
Other | | 2.015e-05 | | |100.00
|
||||||
|
|
||||||
Nlocal: 156 ave 156 max 156 min
|
Nlocal: 156 ave 156 max 156 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
@ -1,5 +1,7 @@
|
||||||
LAMMPS (17 Jan 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
clear
|
clear
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style full
|
atom_style full
|
||||||
|
|
@ -120,9 +122,9 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
|
||||||
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
||||||
Ewald initialization ...
|
Ewald initialization ...
|
||||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.267593
|
G vector (1/distance) = 0.267593
|
||||||
estimated absolute RMS force accuracy = 0.000333665
|
estimated absolute RMS force accuracy = 0.000333665
|
||||||
estimated relative force accuracy = 1.00482e-06
|
estimated relative force accuracy = 1.00482e-06
|
||||||
|
|
@ -140,13 +142,13 @@ Neighbor list info ...
|
||||||
pair build: half/bin/newton/tri
|
pair build: half/bin/newton/tri
|
||||||
stencil: half/bin/3d/newton/tri
|
stencil: half/bin/3d/newton/tri
|
||||||
bin: standard
|
bin: standard
|
||||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
WARNING: Inconsistent image flags (src/domain.cpp:782)
|
||||||
Per MPI rank memory allocation (min/avg/max) = 34.64 | 34.64 | 34.64 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 34.64 | 34.64 | 34.64 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -16541.109 343.7619 -16197.347 -629.64956
|
0 0 -16541.109 343.7619 -16197.347 -629.64956
|
||||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms
|
Loop time of 1.19209e-06 on 1 procs for 0 steps with 624 atoms
|
||||||
|
|
||||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
167.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
|
@ -158,7 +160,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 9.537e-07 | | |100.00
|
Other | | 1.192e-06 | | |100.00
|
||||||
|
|
||||||
Nlocal: 624 ave 624 max 624 min
|
Nlocal: 624 ave 624 max 624 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
@ -1,5 +1,7 @@
|
||||||
LAMMPS (17 Jan 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
clear
|
clear
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units real
|
units real
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style full
|
atom_style full
|
||||||
|
|
@ -120,9 +122,9 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
|
||||||
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
# ------------------------ MOF-FF FORCE FIELD END --------------------------
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
||||||
Ewald initialization ...
|
Ewald initialization ...
|
||||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.267593
|
G vector (1/distance) = 0.267593
|
||||||
estimated absolute RMS force accuracy = 0.000333665
|
estimated absolute RMS force accuracy = 0.000333665
|
||||||
estimated relative force accuracy = 1.00482e-06
|
estimated relative force accuracy = 1.00482e-06
|
||||||
|
|
@ -140,13 +142,13 @@ Neighbor list info ...
|
||||||
pair build: half/bin/newton/tri
|
pair build: half/bin/newton/tri
|
||||||
stencil: half/bin/3d/newton/tri
|
stencil: half/bin/3d/newton/tri
|
||||||
bin: standard
|
bin: standard
|
||||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
WARNING: Inconsistent image flags (src/domain.cpp:782)
|
||||||
Per MPI rank memory allocation (min/avg/max) = 34.1 | 34.1 | 34.1 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 34.1 | 34.1 | 34.1 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -16541.109 343.7619 -16197.347 -629.64956
|
0 0 -16541.109 343.7619 -16197.347 -629.64956
|
||||||
Loop time of 6.13928e-06 on 4 procs for 0 steps with 624 atoms
|
Loop time of 2.71797e-05 on 4 procs for 0 steps with 624 atoms
|
||||||
|
|
||||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
84.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
|
@ -158,7 +160,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 6.139e-06 | | |100.00
|
Other | | 2.718e-05 | | |100.00
|
||||||
|
|
||||||
Nlocal: 156 ave 156 max 156 min
|
Nlocal: 156 ave 156 max 156 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (24 Oct 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -78,7 +77,7 @@ variable pe equal pe
|
||||||
|
|
||||||
run 101
|
run 101
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
|
|
@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0
|
||||||
14 0.96 0
|
14 0.96 0
|
||||||
18 0.957206 4.37979e-05
|
18 0.957206 4.37979e-05
|
||||||
31 104.519 0.00396029
|
31 104.519 0.00396029
|
||||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
|
||||||
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
|
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
|
||||||
|
|
@ -130,22 +129,22 @@ SHAKE stats (type/ave/delta) on step 100
|
||||||
31 104.52 0.000760401
|
31 104.52 0.000760401
|
||||||
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
|
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
|
||||||
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
|
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
|
||||||
Loop time of 2.12948 on 1 procs for 101 steps with 2004 atoms
|
Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms
|
||||||
|
|
||||||
Performance: 8.196 ns/day, 2.928 hours/ns, 47.429 timesteps/s
|
Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 1.757 | 1.757 | 1.757 | 0.0 | 82.51
|
Pair | 2.2617 | 2.2617 | 2.2617 | 0.0 | 82.71
|
||||||
Bond | 0.0052233 | 0.0052233 | 0.0052233 | 0.0 | 0.25
|
Bond | 0.0044148 | 0.0044148 | 0.0044148 | 0.0 | 0.16
|
||||||
Kspace | 0.14772 | 0.14772 | 0.14772 | 0.0 | 6.94
|
Kspace | 0.17883 | 0.17883 | 0.17883 | 0.0 | 6.54
|
||||||
Neigh | 0.16455 | 0.16455 | 0.16455 | 0.0 | 7.73
|
Neigh | 0.23945 | 0.23945 | 0.23945 | 0.0 | 8.76
|
||||||
Comm | 0.0083704 | 0.0083704 | 0.0083704 | 0.0 | 0.39
|
Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.43
|
||||||
Output | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.01
|
Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.01
|
||||||
Modify | 0.044411 | 0.044411 | 0.044411 | 0.0 | 2.09
|
Modify | 0.0365 | 0.0365 | 0.0365 | 0.0 | 1.33
|
||||||
Other | | 0.001851 | | | 0.09
|
Other | | 0.001611 | | | 0.06
|
||||||
|
|
||||||
Nlocal: 2004 ave 2004 max 2004 min
|
Nlocal: 2004 ave 2004 max 2004 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
LAMMPS (24 Oct 2018)
|
LAMMPS (27 Nov 2018)
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Solvated 5-mer peptide
|
# Solvated 5-mer peptide
|
||||||
|
|
||||||
|
|
@ -78,7 +77,7 @@ variable pe equal pe
|
||||||
|
|
||||||
run 101
|
run 101
|
||||||
PPPM initialization ...
|
PPPM initialization ...
|
||||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||||
G vector (1/distance) = 0.268725
|
G vector (1/distance) = 0.268725
|
||||||
grid = 15 15 15
|
grid = 15 15 15
|
||||||
stencil order = 5
|
stencil order = 5
|
||||||
|
|
@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0
|
||||||
14 0.96 0
|
14 0.96 0
|
||||||
18 0.957206 4.37979e-05
|
18 0.957206 4.37979e-05
|
||||||
31 104.519 0.00396029
|
31 104.519 0.00396029
|
||||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes
|
||||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
|
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
|
||||||
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
|
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
|
||||||
|
|
@ -118,7 +117,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||||
60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
|
60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
|
||||||
70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
|
70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
|
||||||
80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
|
80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
|
||||||
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014
|
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
|
||||||
SHAKE stats (type/ave/delta) on step 100
|
SHAKE stats (type/ave/delta) on step 100
|
||||||
4 1.111 2.06868e-06
|
4 1.111 2.06868e-06
|
||||||
6 0.996999 2.09521e-06
|
6 0.996999 2.09521e-06
|
||||||
|
|
@ -128,24 +127,24 @@ SHAKE stats (type/ave/delta) on step 100
|
||||||
14 0.959999 0
|
14 0.959999 0
|
||||||
18 0.9572 9.14098e-06
|
18 0.9572 9.14098e-06
|
||||||
31 104.52 0.000760401
|
31 104.52 0.000760401
|
||||||
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437
|
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
|
||||||
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
|
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
|
||||||
Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms
|
Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms
|
||||||
|
|
||||||
Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
|
Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s
|
||||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21
|
Pair | 0.57957 | 0.59988 | 0.62504 | 2.6 | 73.80
|
||||||
Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23
|
Bond | 0.00080013 | 0.0017412 | 0.0028315 | 2.1 | 0.21
|
||||||
Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95
|
Kspace | 0.075724 | 0.10008 | 0.12023 | 6.4 | 12.31
|
||||||
Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72
|
Neigh | 0.067733 | 0.067947 | 0.068168 | 0.1 | 8.36
|
||||||
Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85
|
Comm | 0.01375 | 0.014175 | 0.014681 | 0.3 | 1.74
|
||||||
Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07
|
Output | 0.00025511 | 0.00051183 | 0.001277 | 0.0 | 0.06
|
||||||
Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48
|
Modify | 0.026406 | 0.026436 | 0.026462 | 0.0 | 3.25
|
||||||
Other | | 0.005751 | | | 0.49
|
Other | | 0.002027 | | | 0.25
|
||||||
|
|
||||||
Nlocal: 501 ave 512 max 492 min
|
Nlocal: 501 ave 512 max 492 min
|
||||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
|
@ -159,4 +158,4 @@ Ave neighs/atom = 353.274
|
||||||
Ave special neighs/atom = 2.34032
|
Ave special neighs/atom = 2.34032
|
||||||
Neighbor list builds = 8
|
Neighbor list builds = 8
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:01
|
Total wall time: 0:00:00
|
||||||
|
|
@ -1,92 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
kspace_style scafacos ewald 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver ewald ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49647271 0 0.49647271 0 0
|
|
||||||
10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861
|
|
||||||
20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314
|
|
||||||
30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679
|
|
||||||
40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911
|
|
||||||
50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037
|
|
||||||
60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302
|
|
||||||
70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118
|
|
||||||
80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288
|
|
||||||
90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364
|
|
||||||
100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922
|
|
||||||
Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 102047.913 tau/day, 236.222 timesteps/s
|
|
||||||
99.2% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01
|
|
||||||
Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04
|
|
||||||
Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13
|
|
||||||
Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54
|
|
||||||
Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07
|
|
||||||
Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03
|
|
||||||
Other | | 0.000758 | | | 0.18
|
|
||||||
|
|
||||||
Nlocal: 18.75 ave 39 max 6 min
|
|
||||||
Histogram: 6 1 1 0 1 2 2 1 1 1
|
|
||||||
Nghost: 122.812 ave 195 max 63 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 1 3 4
|
|
||||||
Neighs: 160.625 ave 598 max 13 min
|
|
||||||
Histogram: 8 2 1 1 1 0 0 2 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 2570
|
|
||||||
Ave neighs/atom = 8.56667
|
|
||||||
Neighbor list builds = 23
|
|
||||||
Dangerous builds = 16
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,92 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
kspace_style scafacos ewald 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver ewald ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49647271 0 0.49647271 0 0
|
|
||||||
10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087
|
|
||||||
20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565
|
|
||||||
30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608
|
|
||||||
40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582
|
|
||||||
50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403
|
|
||||||
60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376
|
|
||||||
70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802
|
|
||||||
80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814
|
|
||||||
90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175
|
|
||||||
100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344
|
|
||||||
Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 74052.598 tau/day, 171.418 timesteps/s
|
|
||||||
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01
|
|
||||||
Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17
|
|
||||||
Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16
|
|
||||||
Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48
|
|
||||||
Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04
|
|
||||||
Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03
|
|
||||||
Other | | 0.00065 | | | 0.11
|
|
||||||
|
|
||||||
Nlocal: 37.5 ave 46 max 31 min
|
|
||||||
Histogram: 2 0 0 2 1 0 2 0 0 1
|
|
||||||
Nghost: 203.875 ave 212 max 192 min
|
|
||||||
Histogram: 1 0 1 0 0 2 1 0 0 3
|
|
||||||
Neighs: 321.625 ave 599 max 112 min
|
|
||||||
Histogram: 1 2 0 1 1 0 1 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 2573
|
|
||||||
Ave neighs/atom = 8.57667
|
|
||||||
Neighbor list builds = 23
|
|
||||||
Dangerous builds = 16
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,99 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 1.0e-3
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
|
|
||||||
10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
|
|
||||||
20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
|
|
||||||
30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
|
|
||||||
40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
|
|
||||||
50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
|
|
||||||
60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
|
|
||||||
70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
|
|
||||||
80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
|
|
||||||
90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
|
|
||||||
100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
|
|
||||||
Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 183509.107 tau/day, 424.790 timesteps/s
|
|
||||||
97.9% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31
|
|
||||||
Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15
|
|
||||||
Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97
|
|
||||||
Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16
|
|
||||||
Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06
|
|
||||||
Other | | 0.0007878 | | | 0.33
|
|
||||||
|
|
||||||
Nlocal: 18.75 ave 36 max 6 min
|
|
||||||
Histogram: 4 3 1 0 0 1 2 1 2 2
|
|
||||||
Nghost: 127 ave 196 max 71 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 1 6 1
|
|
||||||
Neighs: 153.688 ave 491 max 10 min
|
|
||||||
Histogram: 8 1 1 1 1 1 0 0 0 3
|
|
||||||
|
|
||||||
Total # of neighbors = 2459
|
|
||||||
Ave neighs/atom = 8.19667
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,99 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 1.0e-3
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
|
|
||||||
10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
|
|
||||||
20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
|
|
||||||
30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
|
|
||||||
40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
|
|
||||||
50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
|
|
||||||
60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
|
|
||||||
70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
|
|
||||||
80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
|
|
||||||
90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
|
|
||||||
100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
|
|
||||||
Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 110479.760 tau/day, 255.740 timesteps/s
|
|
||||||
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67
|
|
||||||
Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50
|
|
||||||
Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51
|
|
||||||
Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04
|
|
||||||
Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13
|
|
||||||
Other | | 0.0004461 | | | 0.11
|
|
||||||
|
|
||||||
Nlocal: 150 ave 159 max 141 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 392 ave 395 max 389 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 1229.5 ave 1773 max 686 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 2459
|
|
||||||
Ave neighs/atom = 8.19667
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,99 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 1.0e-3
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
|
|
||||||
10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
|
|
||||||
20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
|
|
||||||
30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
|
|
||||||
40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
|
|
||||||
50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
|
|
||||||
60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
|
|
||||||
70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
|
|
||||||
80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
|
|
||||||
90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
|
|
||||||
100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
|
|
||||||
Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 148735.741 tau/day, 344.296 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 | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41
|
|
||||||
Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37
|
|
||||||
Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84
|
|
||||||
Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09
|
|
||||||
Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11
|
|
||||||
Other | | 0.0004706 | | | 0.16
|
|
||||||
|
|
||||||
Nlocal: 75 ave 81 max 70 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
||||||
Nghost: 282.5 ave 290 max 274 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
|
||||||
Neighs: 614.75 ave 981 max 285 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 2459
|
|
||||||
Ave neighs/atom = 8.19667
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,99 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 1.0e-3
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
|
|
||||||
10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
|
|
||||||
20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
|
|
||||||
30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
|
|
||||||
40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
|
|
||||||
50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
|
|
||||||
60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
|
|
||||||
70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
|
|
||||||
80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
|
|
||||||
90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
|
|
||||||
100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
|
|
||||||
Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 147513.337 tau/day, 341.466 timesteps/s
|
|
||||||
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25
|
|
||||||
Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21
|
|
||||||
Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09
|
|
||||||
Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11
|
|
||||||
Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08
|
|
||||||
Other | | 0.0007486 | | | 0.26
|
|
||||||
|
|
||||||
Nlocal: 37.5 ave 45 max 31 min
|
|
||||||
Histogram: 1 1 1 1 1 0 1 0 1 1
|
|
||||||
Nghost: 200 ave 209 max 189 min
|
|
||||||
Histogram: 1 0 0 0 1 4 0 0 0 2
|
|
||||||
Neighs: 307.375 ave 514 max 115 min
|
|
||||||
Histogram: 2 1 0 1 1 0 0 0 1 2
|
|
||||||
|
|
||||||
Total # of neighbors = 2459
|
|
||||||
Ave neighs/atom = 8.19667
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,92 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
|
|
||||||
10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
|
|
||||||
20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
|
|
||||||
30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
|
|
||||||
40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
|
|
||||||
50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
|
|
||||||
60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
|
|
||||||
70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
|
|
||||||
80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
|
|
||||||
90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
|
|
||||||
100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
|
|
||||||
Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 272716.448 tau/day, 631.288 timesteps/s
|
|
||||||
99.4% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74
|
|
||||||
Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22
|
|
||||||
Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26
|
|
||||||
Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21
|
|
||||||
Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08
|
|
||||||
Other | | 0.0007506 | | | 0.47
|
|
||||||
|
|
||||||
Nlocal: 18.75 ave 33 max 6 min
|
|
||||||
Histogram: 2 6 0 0 0 0 2 1 2 3
|
|
||||||
Nghost: 128.875 ave 198 max 71 min
|
|
||||||
Histogram: 7 1 0 0 0 0 0 1 5 2
|
|
||||||
Neighs: 153.812 ave 490 max 14 min
|
|
||||||
Histogram: 8 0 3 0 1 1 0 0 1 2
|
|
||||||
|
|
||||||
Total # of neighbors = 2461
|
|
||||||
Ave neighs/atom = 8.20333
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,92 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
|
|
||||||
10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
|
|
||||||
20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
|
|
||||||
30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
|
|
||||||
40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
|
|
||||||
50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
|
|
||||||
60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
|
|
||||||
70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
|
|
||||||
80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
|
|
||||||
90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
|
|
||||||
100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
|
|
||||||
Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 97092.373 tau/day, 224.751 timesteps/s
|
|
||||||
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84
|
|
||||||
Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44
|
|
||||||
Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45
|
|
||||||
Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04
|
|
||||||
Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11
|
|
||||||
Other | | 0.0004425 | | | 0.10
|
|
||||||
|
|
||||||
Nlocal: 150 ave 157 max 143 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 399 ave 402 max 396 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 1230.5 ave 1756 max 705 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 2461
|
|
||||||
Ave neighs/atom = 8.20333
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,92 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.cloud_wall
|
|
||||||
orthogonal box = (0 0 0) to (10 10 10)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
300 atoms
|
|
||||||
|
|
||||||
velocity all set 0.0 0.0 0.0 mom no
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
|
|
||||||
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
|
||||||
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
#dump simple all custom 1000 id x y z vx vy vz
|
|
||||||
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
|
||||||
#dump_modify dmpvtk pad 7
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
|
|
||||||
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
|
||||||
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
|
|
||||||
10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
|
|
||||||
20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
|
|
||||||
30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
|
|
||||||
40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
|
|
||||||
50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
|
|
||||||
60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
|
|
||||||
70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
|
|
||||||
80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
|
|
||||||
90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
|
|
||||||
100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
|
|
||||||
Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms
|
|
||||||
|
|
||||||
Performance: 216363.074 tau/day, 500.840 timesteps/s
|
|
||||||
99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02
|
|
||||||
Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08
|
|
||||||
Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31
|
|
||||||
Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12
|
|
||||||
Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12
|
|
||||||
Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09
|
|
||||||
Other | | 0.0005245 | | | 0.26
|
|
||||||
|
|
||||||
Nlocal: 37.5 ave 42 max 33 min
|
|
||||||
Histogram: 2 1 0 1 0 0 1 0 1 2
|
|
||||||
Nghost: 202.25 ave 212 max 194 min
|
|
||||||
Histogram: 1 0 2 1 0 2 0 1 0 1
|
|
||||||
Neighs: 307.625 ave 505 max 129 min
|
|
||||||
Histogram: 3 0 0 1 1 0 0 0 1 2
|
|
||||||
|
|
||||||
Total # of neighbors = 2461
|
|
||||||
Ave neighs/atom = 8.20333
|
|
||||||
Neighbor list builds = 15
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000462294 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos ewald 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver ewald ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475938 0 0.50185691 -nan
|
|
||||||
10 1.500011 -1.747529 0 0.50193816 -nan
|
|
||||||
20 1.5000023 -1.7475152 0 0.50193898 -nan
|
|
||||||
30 1.4999308 -1.747404 0 0.50194285 -nan
|
|
||||||
40 1.4997722 -1.7471622 0 0.50194686 -nan
|
|
||||||
50 1.4995835 -1.746878 0 0.50194808 -nan
|
|
||||||
60 1.4996054 -1.7469114 0 0.50194749 -nan
|
|
||||||
70 1.5004341 -1.7481558 0 0.50194592 -nan
|
|
||||||
80 1.5033218 -1.7524875 0 0.50194458 -nan
|
|
||||||
90 1.5108306 -1.7637462 0 0.50194636 -nan
|
|
||||||
100 1.5292479 -1.7913449 0 0.50196695 -nan
|
|
||||||
Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 538.132 tau/day, 1.246 timesteps/s
|
|
||||||
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00
|
|
||||||
Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01
|
|
||||||
Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00
|
|
||||||
Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00
|
|
||||||
Other | | 0.001511 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 256 ave 256 max 256 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2816 ave 2816 max 2816 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 32768 ave 32768 max 32768 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:01:22
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000344753 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos ewald 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver ewald ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475938 0 0.50185691 11.99707
|
|
||||||
10 1.500011 -1.747529 0 0.50193816 11.997158
|
|
||||||
20 1.5000023 -1.7475152 0 0.50193898 11.997089
|
|
||||||
30 1.4999308 -1.747404 0 0.50194285 11.996517
|
|
||||||
40 1.4997722 -1.7471622 0 0.50194686 11.995248
|
|
||||||
50 1.4995835 -1.746878 0 0.50194808 11.993739
|
|
||||||
60 1.4996054 -1.7469114 0 0.50194749 11.993914
|
|
||||||
70 1.5004341 -1.7481558 0 0.50194592 12.000543
|
|
||||||
80 1.5033218 -1.7524875 0 0.50194458 12.023638
|
|
||||||
90 1.5108306 -1.7637462 0 0.50194636 12.083694
|
|
||||||
100 1.5292479 -1.7913449 0 0.50196695 12.230996
|
|
||||||
Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 76.218 tau/day, 0.176 timesteps/s
|
|
||||||
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00
|
|
||||||
Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00
|
|
||||||
Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00
|
|
||||||
Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00
|
|
||||||
Other | | 0.002497 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 2048 ave 2048 max 2048 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 7168 ave 7168 max 7168 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 262144 ave 262144 max 262144 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:09:38
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000232935 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos ewald 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver ewald ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475938 0 0.50185691 -nan
|
|
||||||
10 1.500011 -1.747529 0 0.50193816 -nan
|
|
||||||
20 1.5000023 -1.7475152 0 0.50193898 -nan
|
|
||||||
30 1.4999308 -1.747404 0 0.50194285 -nan
|
|
||||||
40 1.4997722 -1.7471622 0 0.50194686 -nan
|
|
||||||
50 1.4995835 -1.746878 0 0.50194808 -nan
|
|
||||||
60 1.4996054 -1.7469114 0 0.50194749 -nan
|
|
||||||
70 1.5004341 -1.7481558 0 0.50194592 -nan
|
|
||||||
80 1.5033218 -1.7524875 0 0.50194458 -nan
|
|
||||||
90 1.5108306 -1.7637462 0 0.50194636 -nan
|
|
||||||
100 1.5292479 -1.7913449 0 0.50196695 -nan
|
|
||||||
Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 279.720 tau/day, 0.647 timesteps/s
|
|
||||||
99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00
|
|
||||||
Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01
|
|
||||||
Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00
|
|
||||||
Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00
|
|
||||||
Other | | 0.001309 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 3584 ave 3584 max 3584 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 65536 ave 65536 max 65536 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:02:38
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000400543 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 0.001
|
|
||||||
kspace_modify scafacos tolerance energy
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475646 0 0.50188608 10.44368
|
|
||||||
10 1.5000016 -1.7475671 0 0.50188602 10.44369
|
|
||||||
20 1.4999827 -1.7475388 0 0.50188592 10.443564
|
|
||||||
30 1.4999016 -1.7474173 0 0.5018858 10.443023
|
|
||||||
40 1.4997356 -1.7471685 0 0.50188572 10.441917
|
|
||||||
50 1.4995414 -1.7468771 0 0.5018858 10.440623
|
|
||||||
60 1.4995587 -1.7469027 0 0.50188622 10.440739
|
|
||||||
70 1.5003837 -1.7481389 0 0.50188727 10.446238
|
|
||||||
80 1.5032684 -1.7524625 0 0.50188958 10.465466
|
|
||||||
90 1.5107749 -1.763714 0 0.50189507 10.515502
|
|
||||||
100 1.52919 -1.791306 0 0.50191895 10.638261
|
|
||||||
Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 10194.102 tau/day, 23.597 timesteps/s
|
|
||||||
99.6% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01
|
|
||||||
Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29
|
|
||||||
Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01
|
|
||||||
Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02
|
|
||||||
Other | | 0.002255 | | | 0.05
|
|
||||||
|
|
||||||
Nlocal: 256 ave 256 max 256 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2816 ave 2816 max 2816 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 32768 ave 32768 max 32768 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:06
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.0003407 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 0.001
|
|
||||||
kspace_modify scafacos tolerance energy
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475646 0 0.50188608 10.44368
|
|
||||||
10 1.5000016 -1.7475671 0 0.50188602 10.44369
|
|
||||||
20 1.4999827 -1.7475388 0 0.50188592 10.443564
|
|
||||||
30 1.4999016 -1.7474173 0 0.5018858 10.443023
|
|
||||||
40 1.4997356 -1.7471685 0 0.50188572 10.441917
|
|
||||||
50 1.4995414 -1.7468771 0 0.5018858 10.440623
|
|
||||||
60 1.4995587 -1.7469027 0 0.50188622 10.440739
|
|
||||||
70 1.5003837 -1.7481389 0 0.50188727 10.446238
|
|
||||||
80 1.5032684 -1.7524625 0 0.50188958 10.465466
|
|
||||||
90 1.5107749 -1.763714 0 0.50189507 10.515502
|
|
||||||
100 1.52919 -1.791306 0 0.50191895 10.638261
|
|
||||||
Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 2408.014 tau/day, 5.574 timesteps/s
|
|
||||||
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01
|
|
||||||
Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10
|
|
||||||
Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00
|
|
||||||
Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03
|
|
||||||
Other | | 0.002716 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 2048 ave 2048 max 2048 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 7168 ave 7168 max 7168 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 262144 ave 262144 max 262144 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:19
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000236988 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 0.001
|
|
||||||
kspace_modify scafacos tolerance energy
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7475646 0 0.50188608 10.44368
|
|
||||||
10 1.5000016 -1.7475671 0 0.50188602 10.44369
|
|
||||||
20 1.4999827 -1.7475388 0 0.50188592 10.443564
|
|
||||||
30 1.4999016 -1.7474173 0 0.5018858 10.443023
|
|
||||||
40 1.4997356 -1.7471685 0 0.50188572 10.441917
|
|
||||||
50 1.4995414 -1.7468771 0 0.5018858 10.440623
|
|
||||||
60 1.4995587 -1.7469027 0 0.50188622 10.440739
|
|
||||||
70 1.5003837 -1.7481389 0 0.50188727 10.446238
|
|
||||||
80 1.5032684 -1.7524625 0 0.50188958 10.465466
|
|
||||||
90 1.5107749 -1.763714 0 0.50189507 10.515502
|
|
||||||
100 1.52919 -1.791306 0 0.50191895 10.638261
|
|
||||||
Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 7247.876 tau/day, 16.777 timesteps/s
|
|
||||||
99.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01
|
|
||||||
Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25
|
|
||||||
Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01
|
|
||||||
Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03
|
|
||||||
Other | | 0.001971 | | | 0.03
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 3584 ave 3584 max 3584 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 65536 ave 65536 max 65536 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:07
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 4 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000361443 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7477245 0 0.50172614 10.443537
|
|
||||||
10 1.5000176 -1.7475898 0 0.50188725 10.443798
|
|
||||||
20 1.5000161 -1.7475262 0 0.50194874 10.443843
|
|
||||||
30 1.4999486 -1.7474019 0 0.50197176 10.443413
|
|
||||||
40 1.4997889 -1.7471525 0 0.50198161 10.442357
|
|
||||||
50 1.4995945 -1.7468614 0 0.50198122 10.441061
|
|
||||||
60 1.499609 -1.7468813 0 0.50198309 10.44116
|
|
||||||
70 1.5004314 -1.7481179 0 0.50197962 10.446638
|
|
||||||
80 1.5033149 -1.7524495 0 0.50197233 10.46585
|
|
||||||
90 1.5108219 -1.7637095 0 0.50197005 10.515883
|
|
||||||
100 1.529239 -1.7913105 0 0.501988 10.638649
|
|
||||||
Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 27571.239 tau/day, 63.822 timesteps/s
|
|
||||||
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03
|
|
||||||
Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65
|
|
||||||
Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02
|
|
||||||
Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06
|
|
||||||
Other | | 0.001859 | | | 0.12
|
|
||||||
|
|
||||||
Nlocal: 256 ave 256 max 256 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2816 ave 2816 max 2816 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 32768 ave 32768 max 32768 min
|
|
||||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.0003438 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7477245 0 0.50172614 10.443537
|
|
||||||
10 1.5000176 -1.7475898 0 0.50188725 10.443798
|
|
||||||
20 1.5000161 -1.7475262 0 0.50194874 10.443843
|
|
||||||
30 1.4999486 -1.7474019 0 0.50197176 10.443413
|
|
||||||
40 1.4997889 -1.7471525 0 0.50198161 10.442357
|
|
||||||
50 1.4995945 -1.7468614 0 0.50198122 10.441061
|
|
||||||
60 1.499609 -1.7468813 0 0.50198309 10.44116
|
|
||||||
70 1.5004314 -1.7481179 0 0.50197962 10.446638
|
|
||||||
80 1.5033149 -1.7524495 0 0.50197233 10.46585
|
|
||||||
90 1.5108219 -1.7637095 0 0.50197005 10.515883
|
|
||||||
100 1.529239 -1.7913105 0 0.501988 10.638649
|
|
||||||
Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 4600.920 tau/day, 10.650 timesteps/s
|
|
||||||
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01
|
|
||||||
Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21
|
|
||||||
Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00
|
|
||||||
Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06
|
|
||||||
Other | | 0.002495 | | | 0.03
|
|
||||||
|
|
||||||
Nlocal: 2048 ave 2048 max 2048 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 7168 ave 7168 max 7168 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 262144 ave 262144 max 262144 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:11
|
|
||||||
|
|
@ -1,102 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.NaCl
|
|
||||||
orthogonal box = (0 0 0) to (1 1 1)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8 atoms
|
|
||||||
|
|
||||||
replicate 8 8 8
|
|
||||||
orthogonal box = (0 0 0) to (8 8 8)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
4096 atoms
|
|
||||||
Time spent = 0.000324488 secs
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance field
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -1.7477245 0 0.50172614 10.443537
|
|
||||||
10 1.5000176 -1.7475898 0 0.50188725 10.443798
|
|
||||||
20 1.5000161 -1.7475262 0 0.50194874 10.443843
|
|
||||||
30 1.4999486 -1.7474019 0 0.50197176 10.443413
|
|
||||||
40 1.4997889 -1.7471525 0 0.50198161 10.442357
|
|
||||||
50 1.4995945 -1.7468614 0 0.50198122 10.441061
|
|
||||||
60 1.499609 -1.7468813 0 0.50198309 10.44116
|
|
||||||
70 1.5004314 -1.7481179 0 0.50197962 10.446638
|
|
||||||
80 1.5033149 -1.7524495 0 0.50197233 10.46585
|
|
||||||
90 1.5108219 -1.7637095 0 0.50197005 10.515883
|
|
||||||
100 1.529239 -1.7913105 0 0.501988 10.638649
|
|
||||||
Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 14973.700 tau/day, 34.661 timesteps/s
|
|
||||||
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02
|
|
||||||
Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51
|
|
||||||
Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01
|
|
||||||
Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06
|
|
||||||
Other | | 0.001645 | | | 0.06
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 3584 ave 3584 max 3584 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 65536 ave 65536 max 65536 min
|
|
||||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 524288
|
|
||||||
Ave neighs/atom = 128
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:03
|
|
||||||
|
|
@ -1,105 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos direct 0.001
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver direct ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417787 0 1.6235721 0.0015678854
|
|
||||||
1 18.780041 -10.770002 0 17.371889 0.016718957
|
|
||||||
2 65.289192 -11.084705 0 86.751149 0.060353634
|
|
||||||
3 121.92987 -7.0625759 0 175.64933 0.11404974
|
|
||||||
4 185.78164 -5.8777512 0 272.51604 0.17462195
|
|
||||||
5 286.36222 -4.382053 0 424.73173 0.26918926
|
|
||||||
6 481.42206 -4.3095567 0 717.1014 0.45274088
|
|
||||||
7 488.59167 -3.8685194 0 728.2861 0.45956866
|
|
||||||
8 497.85287 -3.0417966 0 742.99073 0.46838116
|
|
||||||
9 499.61615 -3.419003 0 745.2558 0.46983345
|
|
||||||
10 502.63684 -2.8360961 0 750.36521 0.47280809
|
|
||||||
11 504.4846 -2.7628105 0 753.20736 0.47462793
|
|
||||||
12 506.54485 -2.8460356 0 756.21142 0.47651441
|
|
||||||
13 508.27211 -2.730935 0 758.91482 0.47813752
|
|
||||||
14 510.57045 -2.6094877 0 762.48033 0.48031431
|
|
||||||
15 513.14798 -2.7150827 0 766.23717 0.48275229
|
|
||||||
16 515.78124 -2.3961811 0 770.50201 0.48526333
|
|
||||||
17 515.70265 -2.2982683 0 770.48215 0.48526617
|
|
||||||
18 515.7081 -2.1515983 0 770.63699 0.48530393
|
|
||||||
19 515.74906 -2.0581436 0 770.79182 0.48530977
|
|
||||||
20 515.70883 -1.8922577 0 770.89742 0.48527105
|
|
||||||
Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 30421.778 tau/day, 70.421 timesteps/s
|
|
||||||
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08
|
|
||||||
Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19
|
|
||||||
Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84
|
|
||||||
Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58
|
|
||||||
Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11
|
|
||||||
Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10
|
|
||||||
Other | | 0.0002506 | | | 0.09
|
|
||||||
|
|
||||||
Nlocal: 500 ave 516 max 484 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 456.5 ave 475 max 438 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 123908 ave 172139 max 75678 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 247817
|
|
||||||
Ave neighs/atom = 247.817
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,105 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos direct 0.001
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver direct ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417787 0 1.6235721 0.0015678854
|
|
||||||
1 18.780041 -10.770002 0 17.371889 0.016718957
|
|
||||||
2 65.289192 -11.084705 0 86.751149 0.060353634
|
|
||||||
3 121.92987 -7.0625759 0 175.64933 0.11404974
|
|
||||||
4 185.78164 -5.8777512 0 272.51604 0.17462195
|
|
||||||
5 286.36222 -4.382053 0 424.73173 0.26918926
|
|
||||||
6 481.42206 -4.3095567 0 717.1014 0.45274088
|
|
||||||
7 488.59167 -3.8685194 0 728.2861 0.45956866
|
|
||||||
8 497.85287 -3.0417966 0 742.99073 0.46838116
|
|
||||||
9 499.61615 -3.419003 0 745.2558 0.46983345
|
|
||||||
10 502.63684 -2.8360961 0 750.36521 0.47280809
|
|
||||||
11 504.4846 -2.7628105 0 753.20736 0.47462793
|
|
||||||
12 506.54485 -2.8460356 0 756.21142 0.47651441
|
|
||||||
13 508.27211 -2.730935 0 758.91482 0.47813752
|
|
||||||
14 510.57045 -2.6094877 0 762.48033 0.48031431
|
|
||||||
15 513.14798 -2.7150827 0 766.23717 0.48275229
|
|
||||||
16 515.78124 -2.3961811 0 770.50201 0.48526333
|
|
||||||
17 515.70265 -2.2982683 0 770.48215 0.48526617
|
|
||||||
18 515.7081 -2.1515983 0 770.63699 0.48530393
|
|
||||||
19 515.74906 -2.0581436 0 770.79182 0.48530977
|
|
||||||
20 515.70883 -1.8922577 0 770.89742 0.48527105
|
|
||||||
Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 97743.448 tau/day, 226.258 timesteps/s
|
|
||||||
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27
|
|
||||||
Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44
|
|
||||||
Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15
|
|
||||||
Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37
|
|
||||||
Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50
|
|
||||||
Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10
|
|
||||||
Other | | 0.0001439 | | | 0.16
|
|
||||||
|
|
||||||
Nlocal: 125 ave 133 max 113 min
|
|
||||||
Histogram: 2 0 0 0 0 1 1 0 2 2
|
|
||||||
Nghost: 773.625 ave 788 max 764 min
|
|
||||||
Histogram: 1 1 2 1 1 0 0 0 1 1
|
|
||||||
Neighs: 30977.1 ave 50690 max 10447 min
|
|
||||||
Histogram: 1 1 1 0 1 1 0 0 2 1
|
|
||||||
|
|
||||||
Total # of neighbors = 247817
|
|
||||||
Ave neighs/atom = 247.817
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,109 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 0.001
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417141 0 1.6235786 0.0015676581
|
|
||||||
1 18.780412 -10.770009 0 17.372438 0.016719188
|
|
||||||
2 65.294131 -11.084501 0 86.758754 0.06035827
|
|
||||||
3 121.92555 -7.0612033 0 175.64423 0.1140457
|
|
||||||
4 185.71165 -5.8781334 0 272.41077 0.17455524
|
|
||||||
5 286.28339 -4.3800108 0 424.61565 0.26911306
|
|
||||||
6 481.28097 -4.3052012 0 716.89433 0.45262045
|
|
||||||
7 487.26022 -3.8672741 0 726.29216 0.45830216
|
|
||||||
8 493.65478 -3.0242687 0 736.71742 0.46443761
|
|
||||||
9 495.66203 -3.4336343 0 739.31592 0.46613014
|
|
||||||
10 498.41831 -2.8837072 0 743.99613 0.46887706
|
|
||||||
11 499.20944 -2.7724783 0 745.29287 0.46966875
|
|
||||||
12 500.97345 -2.8281484 0 747.88057 0.47126462
|
|
||||||
13 507.46412 -2.7752775 0 757.65971 0.47728761
|
|
||||||
14 525.35729 -2.5749814 0 784.67292 0.49422171
|
|
||||||
15 563.9578 -2.9982381 0 842.09253 0.53043696
|
|
||||||
16 645.47602 -2.5519203 0 964.69389 0.60730795
|
|
||||||
17 647.09276 -2.2568468 0 967.41166 0.60891914
|
|
||||||
18 647.12596 -2.2791003 0 967.43915 0.60900309
|
|
||||||
19 647.24862 -2.2495226 0 967.65253 0.60908339
|
|
||||||
20 647.51175 -2.0239179 0 968.27244 0.60932598
|
|
||||||
Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 12321.981 tau/day, 28.523 timesteps/s
|
|
||||||
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03
|
|
||||||
Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00
|
|
||||||
Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55
|
|
||||||
Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27
|
|
||||||
Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06
|
|
||||||
Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05
|
|
||||||
Other | | 0.0002786 | | | 0.04
|
|
||||||
|
|
||||||
Nlocal: 500 ave 509 max 491 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 455.5 ave 467 max 444 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 122171 ave 171834 max 72508 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 244342
|
|
||||||
Ave neighs/atom = 244.342
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,109 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos fmm 0.001
|
|
||||||
kspace_modify scafacos tolerance energy_rel
|
|
||||||
kspace_modify scafacos fmm_tuning 1
|
|
||||||
ScaFaCoS setting fmm inhomogen tuning ...
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver fmm ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417141 0 1.6235786 0.0015676581
|
|
||||||
1 18.780412 -10.770009 0 17.372438 0.016719188
|
|
||||||
2 65.294131 -11.084501 0 86.758754 0.06035827
|
|
||||||
3 121.92555 -7.0612033 0 175.64423 0.1140457
|
|
||||||
4 185.71165 -5.8781334 0 272.41077 0.17455524
|
|
||||||
5 286.28339 -4.3800108 0 424.61565 0.26911306
|
|
||||||
6 481.28097 -4.3052012 0 716.89433 0.45262045
|
|
||||||
7 487.26022 -3.8672741 0 726.29216 0.45830216
|
|
||||||
8 493.65478 -3.0242687 0 736.71742 0.46443761
|
|
||||||
9 495.66203 -3.4336343 0 739.31592 0.46613014
|
|
||||||
10 498.41831 -2.8837072 0 743.99613 0.46887706
|
|
||||||
11 499.20944 -2.7724783 0 745.29287 0.46966875
|
|
||||||
12 500.97345 -2.8281484 0 747.88057 0.47126462
|
|
||||||
13 507.46412 -2.7752775 0 757.65971 0.47728761
|
|
||||||
14 525.35729 -2.5749814 0 784.67292 0.49422171
|
|
||||||
15 563.9578 -2.9982381 0 842.09253 0.53043696
|
|
||||||
16 645.47602 -2.5519203 0 964.69389 0.60730795
|
|
||||||
17 647.09276 -2.2568468 0 967.41166 0.60891914
|
|
||||||
18 647.12596 -2.2791003 0 967.43915 0.60900309
|
|
||||||
19 647.24862 -2.2495226 0 967.65253 0.60908339
|
|
||||||
20 647.51175 -2.0239179 0 968.27244 0.60932598
|
|
||||||
Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 15174.000 tau/day, 35.125 timesteps/s
|
|
||||||
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04
|
|
||||||
Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66
|
|
||||||
Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57
|
|
||||||
Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55
|
|
||||||
Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12
|
|
||||||
Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02
|
|
||||||
Other | | 0.0002268 | | | 0.04
|
|
||||||
|
|
||||||
Nlocal: 125 ave 137 max 111 min
|
|
||||||
Histogram: 1 1 0 0 0 2 2 1 0 1
|
|
||||||
Nghost: 768.875 ave 788 max 761 min
|
|
||||||
Histogram: 4 0 2 0 0 0 1 0 0 1
|
|
||||||
Neighs: 30542.8 ave 48077 max 10011 min
|
|
||||||
Histogram: 1 1 1 0 1 1 0 0 0 3
|
|
||||||
|
|
||||||
Total # of neighbors = 244342
|
|
||||||
Ave neighs/atom = 244.342
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
|
|
@ -1,107 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
1 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance potential
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417787 0 1.6235721 0.0015678854
|
|
||||||
1 18.780041 -10.770002 0 17.371889 0.016718957
|
|
||||||
2 65.289192 -11.084705 0 86.751149 0.060353634
|
|
||||||
3 121.92987 -7.0625759 0 175.64933 0.11404974
|
|
||||||
4 185.78164 -5.8777511 0 272.51603 0.17462194
|
|
||||||
5 286.36221 -4.3820531 0 424.73172 0.26918925
|
|
||||||
6 481.42203 -4.3095567 0 717.10136 0.45274086
|
|
||||||
7 488.59165 -3.8685193 0 728.28607 0.45956865
|
|
||||||
8 497.85288 -3.0417938 0 742.99075 0.46838117
|
|
||||||
9 499.61619 -3.4190063 0 745.25585 0.46983349
|
|
||||||
10 502.63691 -2.8360951 0 750.36531 0.47280815
|
|
||||||
11 504.4847 -2.7628089 0 753.20751 0.47462802
|
|
||||||
12 506.54494 -2.8460319 0 756.21157 0.4765145
|
|
||||||
13 508.2722 -2.7309328 0 758.91497 0.47813761
|
|
||||||
14 510.57053 -2.6094792 0 762.48045 0.48031438
|
|
||||||
15 513.14804 -2.7150819 0 766.23726 0.48275234
|
|
||||||
16 515.78127 -2.3961749 0 770.50206 0.48526336
|
|
||||||
17 515.70267 -2.2982581 0 770.48219 0.48526619
|
|
||||||
18 515.70813 -2.1516075 0 770.63702 0.48530395
|
|
||||||
19 515.74908 -2.0581483 0 770.79185 0.48530979
|
|
||||||
20 515.70881 -1.892235 0 770.89742 0.48527104
|
|
||||||
Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 12320.557 tau/day, 28.520 timesteps/s
|
|
||||||
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03
|
|
||||||
Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95
|
|
||||||
Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64
|
|
||||||
Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24
|
|
||||||
Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06
|
|
||||||
Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04
|
|
||||||
Other | | 0.000288 | | | 0.04
|
|
||||||
|
|
||||||
Nlocal: 500 ave 516 max 484 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 456.5 ave 475 max 438 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
Neighs: 123908 ave 172139 max 75678 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 247817
|
|
||||||
Ave neighs/atom = 247.817
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,107 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance potential
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417787 0 1.6235721 0.0015678854
|
|
||||||
1 18.780041 -10.770002 0 17.371889 0.016718957
|
|
||||||
2 65.289192 -11.084705 0 86.751149 0.060353634
|
|
||||||
3 121.92987 -7.0625759 0 175.64933 0.11404974
|
|
||||||
4 185.78164 -5.8777511 0 272.51603 0.17462194
|
|
||||||
5 286.36221 -4.3820531 0 424.73172 0.26918925
|
|
||||||
6 481.42203 -4.3095567 0 717.10136 0.45274086
|
|
||||||
7 488.59165 -3.8685193 0 728.28607 0.45956865
|
|
||||||
8 497.85288 -3.0417938 0 742.99075 0.46838117
|
|
||||||
9 499.61619 -3.4190063 0 745.25585 0.46983349
|
|
||||||
10 502.63691 -2.8360951 0 750.36531 0.47280815
|
|
||||||
11 504.4847 -2.7628089 0 753.20751 0.47462802
|
|
||||||
12 506.54494 -2.8460319 0 756.21157 0.4765145
|
|
||||||
13 508.2722 -2.7309328 0 758.91497 0.47813761
|
|
||||||
14 510.57053 -2.6094792 0 762.48045 0.48031438
|
|
||||||
15 513.14804 -2.7150819 0 766.23726 0.48275234
|
|
||||||
16 515.78127 -2.3961749 0 770.50206 0.48526336
|
|
||||||
17 515.70267 -2.2982581 0 770.48219 0.48526619
|
|
||||||
18 515.70813 -2.1516075 0 770.63702 0.48530395
|
|
||||||
19 515.74908 -2.0581483 0 770.79185 0.48530979
|
|
||||||
20 515.70881 -1.892235 0 770.89742 0.48527104
|
|
||||||
Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 20210.785 tau/day, 46.784 timesteps/s
|
|
||||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05
|
|
||||||
Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85
|
|
||||||
Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31
|
|
||||||
Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60
|
|
||||||
Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10
|
|
||||||
Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04
|
|
||||||
Other | | 0.0002093 | | | 0.05
|
|
||||||
|
|
||||||
Nlocal: 250 ave 259 max 238 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
||||||
Nghost: 672.25 ave 683 max 663 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
||||||
Neighs: 61954.2 ave 97157 max 25016 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 247817
|
|
||||||
Ave neighs/atom = 247.817
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -1,107 +0,0 @@
|
||||||
LAMMPS (2 Aug 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Point dipoles in a 2d box
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.hammersley_shphere
|
|
||||||
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
||||||
2 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
change_box all boundary f f f
|
|
||||||
|
|
||||||
velocity all create 1.5 49893
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 0
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
# LAMMPS computes pairwise and long-range Coulombics
|
|
||||||
|
|
||||||
#pair_style coul/long 3.0
|
|
||||||
#pair_coeff * *
|
|
||||||
#kspace_style pppm 1.0e-3
|
|
||||||
|
|
||||||
# Scafacos computes entire long-range Coulombics
|
|
||||||
# use dummy pair style to perform atom sorting
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
#fix 2 all scafacos p3m tolerance field 0.001
|
|
||||||
|
|
||||||
kspace_style scafacos p2nfft 0.001
|
|
||||||
kspace_modify scafacos tolerance potential
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Setting up ScaFaCoS with solver p2nfft ...
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 102 102 102
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1.5 -0.62417787 0 1.6235721 0.0015678854
|
|
||||||
1 18.780041 -10.770002 0 17.371889 0.016718957
|
|
||||||
2 65.289192 -11.084705 0 86.751149 0.060353634
|
|
||||||
3 121.92987 -7.0625759 0 175.64933 0.11404974
|
|
||||||
4 185.78164 -5.8777511 0 272.51603 0.17462194
|
|
||||||
5 286.36221 -4.3820531 0 424.73172 0.26918925
|
|
||||||
6 481.42203 -4.3095567 0 717.10136 0.45274086
|
|
||||||
7 488.59165 -3.8685193 0 728.28607 0.45956865
|
|
||||||
8 497.85288 -3.0417938 0 742.99075 0.46838117
|
|
||||||
9 499.61619 -3.4190063 0 745.25585 0.46983349
|
|
||||||
10 502.63691 -2.8360951 0 750.36531 0.47280815
|
|
||||||
11 504.4847 -2.7628089 0 753.20751 0.47462802
|
|
||||||
12 506.54494 -2.8460319 0 756.21157 0.4765145
|
|
||||||
13 508.2722 -2.7309328 0 758.91497 0.47813761
|
|
||||||
14 510.57053 -2.6094792 0 762.48045 0.48031438
|
|
||||||
15 513.14804 -2.7150819 0 766.23726 0.48275234
|
|
||||||
16 515.78127 -2.3961749 0 770.50206 0.48526336
|
|
||||||
17 515.70267 -2.2982581 0 770.48219 0.48526619
|
|
||||||
18 515.70813 -2.1516075 0 770.63702 0.48530395
|
|
||||||
19 515.74908 -2.0581483 0 770.79185 0.48530979
|
|
||||||
20 515.70881 -1.892235 0 770.89742 0.48527104
|
|
||||||
Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 35681.038 tau/day, 82.595 timesteps/s
|
|
||||||
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10
|
|
||||||
Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48
|
|
||||||
Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81
|
|
||||||
Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29
|
|
||||||
Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20
|
|
||||||
Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04
|
|
||||||
Other | | 0.0001938 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 125 ave 133 max 113 min
|
|
||||||
Histogram: 2 0 0 0 0 1 1 0 2 2
|
|
||||||
Nghost: 773.625 ave 788 max 764 min
|
|
||||||
Histogram: 1 1 2 1 1 0 0 0 1 1
|
|
||||||
Neighs: 30977.1 ave 50690 max 10447 min
|
|
||||||
Histogram: 1 1 1 0 1 1 0 0 2 1
|
|
||||||
|
|
||||||
Total # of neighbors = 247817
|
|
||||||
Ave neighs/atom = 247.817
|
|
||||||
Neighbor list builds = 19
|
|
||||||
Dangerous builds = 18
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
|
|
@ -0,0 +1,92 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.cloud_wall
|
||||||
|
orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
300 atoms
|
||||||
|
|
||||||
|
velocity all set 0.0 0.0 0.0 mom no
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
kspace_style scafacos ewald 0.001
|
||||||
|
kspace_modify scafacos tolerance field
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
||||||
|
|
||||||
|
run_style verlet
|
||||||
|
|
||||||
|
#dump simple all custom 1000 id x y z vx vy vz
|
||||||
|
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||||
|
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||||
|
#dump_modify dmpvtk pad 7
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 100
|
||||||
|
Setting up ScaFaCoS with solver ewald ...
|
||||||
|
WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 10 10 10
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
|
||||||
|
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
||||||
|
0 300 0 0 0.49647271 0 0.49647271 0 0
|
||||||
|
10 300 0.13361073 0.015454603 0.47336798 0.023104631 0.49647261 0 0.0046209262
|
||||||
|
20 300 0.26624846 0.062286838 0.40335451 0.093118823 0.49647334 0 0.018623765
|
||||||
|
30 300 0.39882493 0.14309258 0.2825546 0.21392341 0.49647801 0 0.042784682
|
||||||
|
40 300 0.53216863 0.52823732 0.08958779 0.78971479 0.87930258 0 0.15794296
|
||||||
|
50 300 0.66626191 1.1912156 -0.082808834 1.7808674 1.6980585 0 0.35617347
|
||||||
|
60 300 0.80045819 1.3877079 -0.37658402 2.0746234 1.6980393 0 0.41492467
|
||||||
|
70 300 0.93514919 1.7017671 -0.84569366 2.5441418 1.6984482 0 0.50882837
|
||||||
|
80 300 1.0722892 15.128456 -3.370646 22.617042 19.246396 0 4.5234083
|
||||||
|
90 300 1.2106726 41.994547 -2.2024419 62.781847 60.579406 0 12.556369
|
||||||
|
100 300 1.3514247 41.352114 -0.92449496 61.821411 60.896916 0 12.364282
|
||||||
|
Loop time of 1.35144 on 1 procs for 100 steps with 300 atoms
|
||||||
|
|
||||||
|
Performance: 31966.000 tau/day, 73.995 timesteps/s
|
||||||
|
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.718e-05 | 2.718e-05 | 2.718e-05 | 0.0 | 0.00
|
||||||
|
Kspace | 1.3486 | 1.3486 | 1.3486 | 0.0 | 99.79
|
||||||
|
Neigh | 0.0019956 | 0.0019956 | 0.0019956 | 0.0 | 0.15
|
||||||
|
Comm | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.02
|
||||||
|
Output | 0.00013924 | 0.00013924 | 0.00013924 | 0.0 | 0.01
|
||||||
|
Modify | 0.00023341 | 0.00023341 | 0.00023341 | 0.0 | 0.02
|
||||||
|
Other | | 0.000195 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 300 ave 300 max 300 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 374 ave 374 max 374 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2465 ave 2465 max 2465 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2465
|
||||||
|
Ave neighs/atom = 8.21667
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
|
|
@ -0,0 +1,92 @@
|
||||||
|
LAMMPS (27 Nov 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style charge
|
||||||
|
|
||||||
|
read_data data.cloud_wall
|
||||||
|
orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
300 atoms
|
||||||
|
|
||||||
|
velocity all set 0.0 0.0 0.0 mom no
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
kspace_style scafacos ewald 0.001
|
||||||
|
kspace_modify scafacos tolerance field
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
|
||||||
|
|
||||||
|
run_style verlet
|
||||||
|
|
||||||
|
#dump simple all custom 1000 id x y z vx vy vz
|
||||||
|
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
|
||||||
|
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
|
||||||
|
#dump_modify dmpvtk pad 7
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 100
|
||||||
|
Setting up ScaFaCoS with solver ewald ...
|
||||||
|
WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 10 10 10
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
|
||||||
|
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
|
||||||
|
0 300 0 0 0.49647271 0 0.49647271 0 0
|
||||||
|
10 300 0.04107213 0.015454603 0.47336798 0.023104631 0.49647261 0 0.0046209262
|
||||||
|
20 300 0.083310604 0.062286838 0.40335451 0.093118823 0.49647334 0 0.018623765
|
||||||
|
30 300 0.12387085 0.14309258 0.2825546 0.21392341 0.49647801 0 0.042784682
|
||||||
|
40 300 0.1672492 0.52823732 0.08958779 0.78971479 0.87930258 0 0.15794296
|
||||||
|
50 300 0.21049809 1.1912156 -0.082808834 1.7808674 1.6980585 0 0.35617347
|
||||||
|
60 300 0.25216699 1.3877079 -0.37658402 2.0746234 1.6980393 0 0.41492467
|
||||||
|
70 300 0.29355645 1.7017671 -0.84569366 2.5441418 1.6984482 0 0.50882837
|
||||||
|
80 300 0.33713698 15.128456 -3.370646 22.617042 19.246396 0 4.5234083
|
||||||
|
90 300 0.38109112 41.994547 -2.2024419 62.781847 60.579406 0 12.556369
|
||||||
|
100 300 0.4267664 41.352114 -0.92449496 61.821411 60.896916 0 12.364282
|
||||||
|
Loop time of 0.426857 on 4 procs for 100 steps with 300 atoms
|
||||||
|
|
||||||
|
Performance: 101204.784 tau/day, 234.270 timesteps/s
|
||||||
|
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.6689e-05 | 1.8835e-05 | 2.2173e-05 | 0.0 | 0.00
|
||||||
|
Kspace | 0.42368 | 0.42384 | 0.42405 | 0.0 | 99.29
|
||||||
|
Neigh | 0.00040579 | 0.00056726 | 0.00075126 | 0.0 | 0.13
|
||||||
|
Comm | 0.0010395 | 0.0010909 | 0.001189 | 0.2 | 0.26
|
||||||
|
Output | 0.00015545 | 0.00034326 | 0.00090313 | 0.0 | 0.08
|
||||||
|
Modify | 9.8705e-05 | 0.00010544 | 0.00011539 | 0.0 | 0.02
|
||||||
|
Other | | 0.0008868 | | | 0.21
|
||||||
|
|
||||||
|
Nlocal: 75 ave 81 max 70 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 282.5 ave 290 max 274 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Neighs: 616.25 ave 983 max 283 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2465
|
||||||
|
Ave neighs/atom = 8.21667
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue