replace :l,ule and :l,ole with :l :ule or :l :ole
This commit is contained in:
@ -2276,7 +2276,8 @@ molecule diffusion rates. :l
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As input to special functions of "equal-style
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As input to special functions of "equal-style
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variables"_variable.html, like sum() and max(). E.g. to find the
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variables"_variable.html, like sum() and max(). E.g. to find the
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largest cluster or fastest diffusing molecule. :l,ule
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largest cluster or fastest diffusing molecule. :l
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:ule
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Example calculations with chunks :h5
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Example calculations with chunks :h5
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@ -2432,7 +2433,8 @@ package, :ulb,l
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the adiabatic core-shell method, implemented in the
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the adiabatic core-shell method, implemented in the
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"CORESHELL"_#howto_26 package, :l
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"CORESHELL"_#howto_26 package, :l
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the thermalized Drude dipole method, implemented in the
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the thermalized Drude dipole method, implemented in the
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"USER-DRUDE"_#howto_27 package. :l,ule
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"USER-DRUDE"_#howto_27 package. :l
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:ule
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The fluctuating charge method calculates instantaneous charges on
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The fluctuating charge method calculates instantaneous charges on
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interacting atoms based on the electronegativity equalization
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interacting atoms based on the electronegativity equalization
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@ -2739,7 +2741,8 @@ too much. To avoid this, damping at short range can be done by Thole
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functions (for which there are physical grounds). This Thole damping
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functions (for which there are physical grounds). This Thole damping
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is applied to the point charges composing the induced dipole (the
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is applied to the point charges composing the induced dipole (the
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charge of the Drude particle and the opposite charge on the core, not
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charge of the Drude particle and the opposite charge on the core, not
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to the total charge of the core atom). :l,ule
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to the total charge of the core atom). :l
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:ule
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A detailed tutorial covering the usage of Drude induced dipoles in
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A detailed tutorial covering the usage of Drude induced dipoles in
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LAMMPS is "available here"_tutorial_drude.html.
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LAMMPS is "available here"_tutorial_drude.html.
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@ -241,7 +241,8 @@ Our group has also written and released a separate toolkit called
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"Pizza.py"_pizza which provides tools for doing setup, analysis,
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"Pizza.py"_pizza which provides tools for doing setup, analysis,
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plotting, and visualization for LAMMPS simulations. Pizza.py is
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plotting, and visualization for LAMMPS simulations. Pizza.py is
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written in "Python"_python and is available for download from "the
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written in "Python"_python and is available for download from "the
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Pizza.py WWW site"_pizza. :l,ule
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Pizza.py WWW site"_pizza. :l
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:ule
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:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
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:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
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:link(python,http://www.python.org)
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:link(python,http://www.python.org)
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@ -130,7 +130,8 @@ If you add something you think is truly useful and doesn't impact
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LAMMPS performance when it isn't used, send an email to the
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LAMMPS performance when it isn't used, send an email to the
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"developers"_http://lammps.sandia.gov/authors.html. We might be
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"developers"_http://lammps.sandia.gov/authors.html. We might be
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interested in adding it to the LAMMPS distribution. See further
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interested in adding it to the LAMMPS distribution. See further
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details on this at the bottom of this page. :l,ule
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details on this at the bottom of this page. :l
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:ule
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:line
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:line
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:line
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:line
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@ -761,7 +761,8 @@ Add a wrapper method to python/lammps.py for this interface
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function. :l
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function. :l
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You should now be able to invoke the new interface function from a
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You should now be able to invoke the new interface function from a
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Python script. Isn't ctypes amazing? :l,ule
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Python script. Isn't ctypes amazing? :l
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:ule
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:line
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:line
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:line
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:line
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@ -1208,7 +1208,8 @@ Move to the directory where you have saved lmp_win_no-mpi.exe
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(e.g. by typing: cd "Documents"). :l
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(e.g. by typing: cd "Documents"). :l
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At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
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At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
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with the name of your LAMMPS input script. :l,ule
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with the name of your LAMMPS input script. :l
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:ule
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For the MPI version, which allows you to run LAMMPS under Windows on
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For the MPI version, which allows you to run LAMMPS under Windows on
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multiple processors, follow these steps:
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multiple processors, follow these steps:
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@ -1237,7 +1238,8 @@ In this mode, output may not immediately show up on the screen, so if
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your input script takes a long time to execute, you may need to be
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your input script takes a long time to execute, you may need to be
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patient before the output shows up. :l Alternatively, you can still
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patient before the output shows up. :l Alternatively, you can still
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use this executable to run on a single processor by typing something
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use this executable to run on a single processor by typing something
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like: "lmp_win_mpi -in in.lj". :l,ule
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like: "lmp_win_mpi -in in.lj". :l
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:ule
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:line
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:line
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@ -42,7 +42,8 @@ LAMMPS-specific code is in the GPU package. It makes calls to a
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generic GPU library in the lib/gpu directory. This library provides
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generic GPU library in the lib/gpu directory. This library provides
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NVIDIA support as well as more general OpenCL support, so that the
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NVIDIA support as well as more general OpenCL support, so that the
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same functionality can eventually be supported on a variety of GPU
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same functionality can eventually be supported on a variety of GPU
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hardware. :l,ule
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hardware. :l
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:ule
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Here is a quick overview of how to enable and use the GPU package:
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Here is a quick overview of how to enable and use the GPU package:
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@ -245,7 +246,8 @@ regardless of asynchronous CPU calculations. :l
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The output section "GPU Time Info (average)" reports "Max Mem / Proc".
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The output section "GPU Time Info (average)" reports "Max Mem / Proc".
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This is the maximum memory used at one time on the GPU for data
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This is the maximum memory used at one time on the GPU for data
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storage by a single MPI process. :l,ule
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storage by a single MPI process. :l
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:ule
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[Restrictions:]
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[Restrictions:]
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@ -31,7 +31,8 @@ Fixes: nve, npt, nvt, nvt/sllod :l
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Improper Styles: cvff, harmonic :l
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Improper Styles: cvff, harmonic :l
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Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
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Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
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charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
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charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
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K-Space Styles: pppm :l,ule
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K-Space Styles: pppm :l
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:ule
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[Speed-ups to expect:]
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[Speed-ups to expect:]
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@ -70,7 +71,8 @@ For Intel Xeon CPUs:
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Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
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Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
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If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
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If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
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performance. :l
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performance. :l
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"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l,ule
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"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
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:ule
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For Intel Xeon Phi CPUs for simulations without {kspace_style
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For Intel Xeon Phi CPUs for simulations without {kspace_style
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pppm} in the input script :
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pppm} in the input script :
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@ -79,7 +81,8 @@ Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
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Runs should be performed using MCDRAM. :l
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Runs should be performed using MCDRAM. :l
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"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
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"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
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should be added to the LAMMPS command-line. Choice for best
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should be added to the LAMMPS command-line. Choice for best
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performance will depend on the simulation. :l,ule
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performance will depend on the simulation. :l
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:ule
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For Intel Xeon Phi CPUs for simulations with {kspace_style
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For Intel Xeon Phi CPUs for simulations with {kspace_style
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pppm} in the input script:
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pppm} in the input script:
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@ -93,13 +96,15 @@ performance. :l
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export KMP_AFFINITY=none :l
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export KMP_AFFINITY=none :l
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"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
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"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
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-sf intel" added to LAMMPS command-line. Choice for best performance
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-sf intel" added to LAMMPS command-line. Choice for best performance
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will depend on the simulation. :l,ule
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will depend on the simulation. :l
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:ule
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For Intel Xeon Phi coprocessors (Offload):
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For Intel Xeon Phi coprocessors (Offload):
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Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
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Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
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"-pk intel N omp 1" added to command-line where N is the number of
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"-pk intel N omp 1" added to command-line where N is the number of
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coprocessors per node. :l,ule
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coprocessors per node. :l
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:ule
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:line
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:line
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@ -463,7 +468,8 @@ Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Krake
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Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
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Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
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Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l,ule
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Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
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:ule
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@ -381,7 +381,8 @@ When running large number of atoms per GPU, KOKKOS is typically faster
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than the GPU package. :l
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than the GPU package. :l
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When running on Intel Xeon Phi, KOKKOS is not as fast as
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When running on Intel Xeon Phi, KOKKOS is not as fast as
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the USER-INTEL package, which is optimized for that hardware. :l,ule
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the USER-INTEL package, which is optimized for that hardware. :l
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:ule
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See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
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See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
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LAMMPS web site for performance of the KOKKOS package on different
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LAMMPS web site for performance of the KOKKOS package on different
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@ -163,7 +163,8 @@ sometimes be achived by increasing the length of the Coulombic cutoff
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and thus reducing the work done by the long-range solver. Using the
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and thus reducing the work done by the long-range solver. Using the
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"run_style verlet/split"_run_style.html command, which is compatible
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"run_style verlet/split"_run_style.html command, which is compatible
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with the USER-OMP package, is an alternative way to reduce the number
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with the USER-OMP package, is an alternative way to reduce the number
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of MPI tasks assigned to the KSpace calculation. :l,ule
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of MPI tasks assigned to the KSpace calculation. :l
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:ule
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Additional performance tips are as follows:
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Additional performance tips are as follows:
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@ -178,7 +179,8 @@ NOTE: By default, several current MPI implementations use a processor
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affinity setting that restricts each MPI task to a single CPU core.
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affinity setting that restricts each MPI task to a single CPU core.
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Using multi-threading in this mode will force all threads to share the
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Using multi-threading in this mode will force all threads to share the
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one core and thus is likely to be counterproductive. Instead, binding
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one core and thus is likely to be counterproductive. Instead, binding
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MPI tasks to a (multi-core) socket, should solve this issue. :l,ule
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MPI tasks to a (multi-core) socket, should solve this issue. :l
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:ule
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[Restrictions:]
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[Restrictions:]
|
||||||
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|
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@ -108,7 +108,8 @@ variable"_variable.html. :l
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Local values can be reduced by the "compute
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Local values can be reduced by the "compute
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reduce"_compute_reduce.html command, or histogrammed by the "fix
|
reduce"_compute_reduce.html command, or histogrammed by the "fix
|
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ave/histo"_fix_ave_histo.html command, or output by the "dump
|
ave/histo"_fix_ave_histo.html command, or output by the "dump
|
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local"_dump.html command. :l,ule
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local"_dump.html command. :l
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|
:ule
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|
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The results of computes that calculate global quantities can be either
|
The results of computes that calculate global quantities can be either
|
||||||
"intensive" or "extensive" values. Intensive means the value is
|
"intensive" or "extensive" values. Intensive means the value is
|
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@ -130,7 +130,8 @@ variable"_variable.html. :l
|
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|
|
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Local values can be reduced by the "compute
|
Local values can be reduced by the "compute
|
||||||
reduce"_compute_reduce.html command, or histogrammed by the "fix
|
reduce"_compute_reduce.html command, or histogrammed by the "fix
|
||||||
ave/histo"_fix_ave_histo.html command. :l,ule
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ave/histo"_fix_ave_histo.html command. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
See this "howto section"_Section_howto.html#howto_15 for a summary of
|
See this "howto section"_Section_howto.html#howto_15 for a summary of
|
||||||
various LAMMPS output options, many of which involve fixes.
|
various LAMMPS output options, many of which involve fixes.
|
||||||
|
|||||||
@ -61,7 +61,8 @@ It is possible to modify the charges of chosen atom types only,
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instead of scaling all the charges in the system. :ulb,l
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instead of scaling all the charges in the system. :ulb,l
|
||||||
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|
||||||
There is a new option {after} for better compatibility with "fix
|
There is a new option {after} for better compatibility with "fix
|
||||||
ave/time". :l,ule
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ave/time". :l
|
||||||
|
:ule
|
||||||
|
|
||||||
This version is suited for free energy calculations using
|
This version is suited for free energy calculations using
|
||||||
"compute ti"_compute_ti.html or "compute fep"_compute_fep.html.
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"compute ti"_compute_ti.html or "compute fep"_compute_fep.html.
|
||||||
|
|||||||
@ -32,7 +32,8 @@ the components of the total torque applied on the group (around its
|
|||||||
center of mass) are Tx,Ty,Tz :ulb,l
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center of mass) are Tx,Ty,Tz :ulb,l
|
||||||
|
|
||||||
the group would move as a rigid body in the absence of other
|
the group would move as a rigid body in the absence of other
|
||||||
forces. :l,ule
|
forces. :l
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||||||
|
:ule
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||||||
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|
||||||
This command can be used to drive a group of atoms into rotation.
|
This command can be used to drive a group of atoms into rotation.
|
||||||
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|
||||||
|
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@ -19,7 +19,8 @@ type = {thermal} or {two_temperature} or {hardy} or {field} :l
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{two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
|
{two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
|
||||||
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||||
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
|
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
|
||||||
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule
|
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l
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||||||
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:ule
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||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
@ -232,7 +232,8 @@ so Npair = N*(N+1)/2. :l
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|||||||
|
|
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If {type} is set to {full} then each input value is correlated with
|
If {type} is set to {full} then each input value is correlated with
|
||||||
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
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itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
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||||||
Npair = N^2. :l,ule
|
Npair = N^2. :l
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:ule
|
||||||
|
|
||||||
The {ave} keyword determines what happens to the accumulation of
|
The {ave} keyword determines what happens to the accumulation of
|
||||||
correlation samples every {Nfreq} timesteps. If the {ave} setting is
|
correlation samples every {Nfreq} timesteps. If the {ave} setting is
|
||||||
@ -342,7 +343,8 @@ CNN. :l
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|||||||
|
|
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For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
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For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
|
||||||
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
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..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
|
||||||
CNN. :l,ule
|
CNN. :l
|
||||||
|
:ule
|
||||||
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|
||||||
The array values calculated by this fix are treated as intensive. If
|
The array values calculated by this fix are treated as intensive. If
|
||||||
you need to divide them by the number of atoms, you must do this in a
|
you need to divide them by the number of atoms, you must do this in a
|
||||||
|
|||||||
@ -229,7 +229,8 @@ computes the global pressure even if its group is {ATOMS}. This is
|
|||||||
what we want. If we thermostated {ATOMS} using {npt}, the pressure
|
what we want. If we thermostated {ATOMS} using {npt}, the pressure
|
||||||
should be the global one, but the temperature should be only that of
|
should be the global one, but the temperature should be only that of
|
||||||
the cores. That's why the command {fix_modify} should be called in
|
the cores. That's why the command {fix_modify} should be called in
|
||||||
that case. :l,ule
|
that case. :l
|
||||||
|
:ule
|
||||||
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|
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|
||||||
:line
|
:line
|
||||||
|
|||||||
@ -621,7 +621,8 @@ rigid styles for the rigid bodies. :l
|
|||||||
Use "fix press/berendsen"_fix_press_berendsen.html to compute the
|
Use "fix press/berendsen"_fix_press_berendsen.html to compute the
|
||||||
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
|
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
|
||||||
rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any
|
rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any
|
||||||
other thermostat) for the non-rigid particles. :l,ule
|
other thermostat) for the non-rigid particles. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
In all case, the rigid bodies and non-rigid particles both contribute
|
In all case, the rigid bodies and non-rigid particles both contribute
|
||||||
to the global pressure and the box is scaled the same by any of the
|
to the global pressure and the box is scaled the same by any of the
|
||||||
|
|||||||
@ -16,7 +16,8 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
|||||||
temp/berendsen = style name of this fix command :l
|
temp/berendsen = style name of this fix command :l
|
||||||
Tstart,Tstop = desired temperature at start/end of run :l
|
Tstart,Tstop = desired temperature at start/end of run :l
|
||||||
Tstart can be a variable (see below) :pre
|
Tstart can be a variable (see below) :pre
|
||||||
Tdamp = temperature damping parameter (time units) :l,ule
|
Tdamp = temperature damping parameter (time units) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
@ -19,7 +19,8 @@ temp/csvr or temp/csld = style name of this fix command :l
|
|||||||
Tstart,Tstop = desired temperature at start/end of run :l
|
Tstart,Tstop = desired temperature at start/end of run :l
|
||||||
Tstart can be a variable (see below) :pre
|
Tstart can be a variable (see below) :pre
|
||||||
Tdamp = temperature damping parameter (time units) :l
|
Tdamp = temperature damping parameter (time units) :l
|
||||||
seed = random number seed to use for white noise (positive integer) :l,ule
|
seed = random number seed to use for white noise (positive integer) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
@ -18,7 +18,8 @@ N = perform rescaling every N steps :l
|
|||||||
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
|
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
|
||||||
Tstart can be a variable (see below) :pre
|
Tstart can be a variable (see below) :pre
|
||||||
window = only rescale if temperature is outside this window (temperature units) :l
|
window = only rescale if temperature is outside this window (temperature units) :l
|
||||||
fraction = rescale to target temperature by this fraction :l,ule
|
fraction = rescale to target temperature by this fraction :l
|
||||||
|
:ule
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
@ -123,7 +123,8 @@ to freeze a wall or portion of a bio-molecule. :l
|
|||||||
|
|
||||||
When one or more rigid bodies are specified, interactions within each
|
When one or more rigid bodies are specified, interactions within each
|
||||||
body can be turned off to save needless computation. See the "fix
|
body can be turned off to save needless computation. See the "fix
|
||||||
rigid"_fix_rigid.html command for more details. :l,ule
|
rigid"_fix_rigid.html command for more details. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The {exclude type} option turns off the pairwise interaction if one
|
The {exclude type} option turns off the pairwise interaction if one
|
||||||
atom is of type M and the other of type N. M can equal N. The
|
atom is of type M and the other of type N. M can equal N. The
|
||||||
|
|||||||
@ -162,7 +162,8 @@ Line 1: nr, nBOt (nr is the number of divisions the radius is broken
|
|||||||
into for function tables and MUST be a factor of 5; nBOt is the number
|
into for function tables and MUST be a factor of 5; nBOt is the number
|
||||||
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
||||||
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
||||||
formulation, set unused values to 0.0) :l,ule
|
formulation, set unused values to 0.0) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
Following this N lines for e_1-e_N containing p_pi.
|
Following this N lines for e_1-e_N containing p_pi.
|
||||||
|
|
||||||
@ -176,7 +177,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
|
|||||||
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
||||||
Line 3: delta_sigma, delta_pi :l
|
Line 3: delta_sigma, delta_pi :l
|
||||||
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
||||||
the previous section but is interaction type dependent) :l,ule
|
the previous section but is interaction type dependent) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a line for each three body interaction type
|
The next section contains a line for each three body interaction type
|
||||||
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
||||||
@ -185,7 +187,8 @@ Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for
|
|||||||
g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward
|
g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward
|
||||||
contains the full expressions for the constants as functions of
|
contains the full expressions for the constants as functions of
|
||||||
b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l
|
b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l
|
||||||
Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l,ule
|
Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a block for each interaction type for the
|
The next section contains a block for each interaction type for the
|
||||||
phi_ij(r_ij). Each block has nr entries with 5 entries per line.
|
phi_ij(r_ij). Each block has nr entries with 5 entries per line.
|
||||||
@ -196,7 +199,8 @@ Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
|
|||||||
until nr) :l
|
until nr) :l
|
||||||
... :l
|
... :l
|
||||||
Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
|
Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
|
||||||
e_1-e_1 interaction type) :l,ule
|
e_1-e_1 interaction type) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a block for each interaction type for the
|
The next section contains a block for each interaction type for the
|
||||||
beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per
|
beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per
|
||||||
@ -208,7 +212,8 @@ Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9),
|
|||||||
beta_sigma(r10) (this continues until nr) :l
|
beta_sigma(r10) (this continues until nr) :l
|
||||||
... :l
|
... :l
|
||||||
Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3),
|
Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3),
|
||||||
beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l,ule
|
beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a block for each interaction type for
|
The next section contains a block for each interaction type for
|
||||||
beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line.
|
beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line.
|
||||||
@ -219,7 +224,8 @@ Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9),
|
|||||||
beta_pi(r10) (this continues until nr) :l
|
beta_pi(r10) (this continues until nr) :l
|
||||||
... :l
|
... :l
|
||||||
Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4),
|
Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4),
|
||||||
beta_pi(r5) (for the e_1-e_2 interaction type) :l,ule
|
beta_pi(r5) (for the e_1-e_2 interaction type) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a block for each interaction type for the
|
The next section contains a block for each interaction type for the
|
||||||
THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has
|
THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has
|
||||||
@ -231,7 +237,8 @@ Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8),
|
|||||||
THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l
|
THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l
|
||||||
... :l
|
... :l
|
||||||
Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
|
Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
|
||||||
THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l,ule
|
THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a block of N lines for e_1-e_N
|
The next section contains a block of N lines for e_1-e_N
|
||||||
|
|
||||||
@ -266,7 +273,8 @@ into for function tables and MUST be a factor of 5; ntheta is the power of the
|
|||||||
power of the spline used to fit the angular function; nBOt is the number
|
power of the spline used to fit the angular function; nBOt is the number
|
||||||
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
||||||
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
||||||
formulation, set unused values to 0.0) :l,ule
|
formulation, set unused values to 0.0) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
Following this N lines for e_1-e_N containing p_pi.
|
Following this N lines for e_1-e_N containing p_pi.
|
||||||
|
|
||||||
@ -280,7 +288,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
|
|||||||
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
||||||
Line 3: delta_sigma, delta_pi :l
|
Line 3: delta_sigma, delta_pi :l
|
||||||
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
||||||
the previous section but is interaction type dependent) :l,ule
|
the previous section but is interaction type dependent) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a line for each three body interaction type
|
The next section contains a line for each three body interaction type
|
||||||
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
||||||
@ -292,7 +301,8 @@ can contain up to five constants. If the spline has more than five
|
|||||||
terms the second line will contain the remaining constants The
|
terms the second line will contain the remaining constants The
|
||||||
following lines will then contain the constants for the remainaing g0,
|
following lines will then contain the constants for the remainaing g0,
|
||||||
g1, g2... (for e_1-e_1-e_2) and the other three body
|
g1, g2... (for e_1-e_1-e_2) and the other three body
|
||||||
interactions :l,ule
|
interactions :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The rest of the table has the same structure as the previous section
|
The rest of the table has the same structure as the previous section
|
||||||
(see above).
|
(see above).
|
||||||
@ -319,7 +329,8 @@ into for function tables and MUST be a factor of 5; ntheta is the number of
|
|||||||
divisions for the tabulated values of the g angular function; nBOt is the number
|
divisions for the tabulated values of the g angular function; nBOt is the number
|
||||||
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
of divisions for the tabulated values of THETA_(S,ij) :ulb,l
|
||||||
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
Line 2: delta_1-delta_7 (if all are not used in the particular :l
|
||||||
formulation, set unused values to 0.0) :l,ule
|
formulation, set unused values to 0.0) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
Following this N lines for e_1-e_N containing p_pi.
|
Following this N lines for e_1-e_N containing p_pi.
|
||||||
|
|
||||||
@ -333,7 +344,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
|
|||||||
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
Line 2: c_sigma, a_sigma, c_pi, a_pi :l
|
||||||
Line 3: delta_sigma, delta_pi :l
|
Line 3: delta_sigma, delta_pi :l
|
||||||
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
|
||||||
the previous section but is interaction type dependent) :l,ule
|
the previous section but is interaction type dependent) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The next section contains a line for each three body interaction type
|
The next section contains a line for each three body interaction type
|
||||||
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
|
||||||
@ -344,7 +356,8 @@ Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
|
|||||||
until ntheta) :l
|
until ntheta) :l
|
||||||
... :l
|
... :l
|
||||||
Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
|
Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
|
||||||
e_1-e_1-e_2 interaction type) :l,ule
|
e_1-e_1-e_2 interaction type) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The rest of the table has the same structure as the previous section (see above).
|
The rest of the table has the same structure as the previous section (see above).
|
||||||
|
|
||||||
|
|||||||
@ -20,7 +20,8 @@ flag_coul = {long} or {off} :l
|
|||||||
{long} = use Kspace long-range summation for the Coulombic term 1/r
|
{long} = use Kspace long-range summation for the Coulombic term 1/r
|
||||||
{off} = omit the Coulombic term :pre
|
{off} = omit the Coulombic term :pre
|
||||||
cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
|
cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
|
||||||
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
|
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
@ -23,7 +23,8 @@ Kt = elastic constant for tangential contact (force/distance units or pressure u
|
|||||||
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
|
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
|
||||||
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
|
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
|
||||||
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
|
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
|
||||||
dampflag = 0 or 1 if tangential damping force is excluded or included :l,ule
|
dampflag = 0 or 1 if tangential damping force is excluded or included :l
|
||||||
|
:ule
|
||||||
|
|
||||||
NOTE: Versions of LAMMPS before 9Jan09 had different style names for
|
NOTE: Versions of LAMMPS before 9Jan09 had different style names for
|
||||||
granular force fields. This is to emphasize the fact that the
|
granular force fields. This is to emphasize the fact that the
|
||||||
|
|||||||
@ -187,7 +187,8 @@ enabled will not be thermodynamically consistent with the truncated
|
|||||||
force-field that was used. In other words, atoms do not feel any LJ
|
force-field that was used. In other words, atoms do not feel any LJ
|
||||||
pair interactions beyond the cutoff, but the energy and pressure
|
pair interactions beyond the cutoff, but the energy and pressure
|
||||||
reported by the simulation include an estimated contribution from
|
reported by the simulation include an estimated contribution from
|
||||||
those interactions. :l,ule
|
those interactions. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
The {compute} keyword allows pairwise computations to be turned off,
|
The {compute} keyword allows pairwise computations to be turned off,
|
||||||
even though a "pair_style"_pair_style.html is defined. This is not
|
even though a "pair_style"_pair_style.html is defined. This is not
|
||||||
|
|||||||
@ -118,7 +118,8 @@ consistent (dE/dr = -F) over the entire range of r values. LAMMPS
|
|||||||
will warn if this is not the case. :l
|
will warn if this is not the case. :l
|
||||||
|
|
||||||
Use as large an inner cutoff as possible. This avoids fitting splines
|
Use as large an inner cutoff as possible. This avoids fitting splines
|
||||||
to very steep parts of the potential. :l,ule
|
to very steep parts of the potential. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
|||||||
@ -111,7 +111,8 @@ Make sure that your tabulated forces and tabulated energies are consistent
|
|||||||
(dE/dr = -F) along the entire range of r values. :l
|
(dE/dr = -F) along the entire range of r values. :l
|
||||||
|
|
||||||
Use as large an inner cutoff as possible. This avoids fitting splines
|
Use as large an inner cutoff as possible. This avoids fitting splines
|
||||||
to very steep parts of the potential. :l,ule
|
to very steep parts of the potential. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
|||||||
@ -698,7 +698,8 @@ atoms in such a bond. :l
|
|||||||
If you plan to "dump"_dump.html image flags and perform post-analysis
|
If you plan to "dump"_dump.html image flags and perform post-analysis
|
||||||
that will unwrap atom coordinates, it may be important that a
|
that will unwrap atom coordinates, it may be important that a
|
||||||
continued run (restarted from a data file) begins with image flags
|
continued run (restarted from a data file) begins with image flags
|
||||||
that are consistent with the previous run. :l,ule
|
that are consistent with the previous run. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
NOTE: If your system is an infinite periodic crystal with bonds then
|
NOTE: If your system is an infinite periodic crystal with bonds then
|
||||||
it is impossible to have fully consistent image flags. This is because
|
it is impossible to have fully consistent image flags. This is because
|
||||||
|
|||||||
@ -243,7 +243,8 @@ to yz. :l
|
|||||||
|
|
||||||
For style {sphere}, the lattice spacing in dimensions x,y,z are
|
For style {sphere}, the lattice spacing in dimensions x,y,z are
|
||||||
applied to the sphere center x,y,z. The spacing in dimension x is
|
applied to the sphere center x,y,z. The spacing in dimension x is
|
||||||
applied to the sphere radius. :l,ule
|
applied to the sphere radius. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
|||||||
@ -60,7 +60,8 @@ Calculate the portion of per-atom forces resulting from a subset of
|
|||||||
the potential. E.g. compute only Coulombic forces. This can be done
|
the potential. E.g. compute only Coulombic forces. This can be done
|
||||||
by only defining only a Coulombic pair style in the rerun script.
|
by only defining only a Coulombic pair style in the rerun script.
|
||||||
Doing this in the original script would result in different (bad)
|
Doing this in the original script would result in different (bad)
|
||||||
dynamics. :l,ule
|
dynamics. :l
|
||||||
|
:ule
|
||||||
|
|
||||||
Conceptually, using the rerun command is like running an input script
|
Conceptually, using the rerun command is like running an input script
|
||||||
that has a loop in it (see the "next"_next.html and "jump"_jump.html
|
that has a loop in it (see the "next"_next.html and "jump"_jump.html
|
||||||
|
|||||||
@ -332,8 +332,8 @@ For the {thole} pair style the coefficients are
|
|||||||
the atom polarizability in units of cubic length :olb,l
|
the atom polarizability in units of cubic length :olb,l
|
||||||
the screening factor of the Thole function (optional, default value
|
the screening factor of the Thole function (optional, default value
|
||||||
specified by the pair_style command) :l
|
specified by the pair_style command) :l
|
||||||
the cutoff (optional, default value defined by the pair_style command)
|
the cutoff (optional, default value defined by the pair_style command) :l
|
||||||
:l,ole
|
:ole
|
||||||
|
|
||||||
The special neighbors have charge-charge and charge-dipole
|
The special neighbors have charge-charge and charge-dipole
|
||||||
interactions screened by the {coul} factors of the {special_bonds}
|
interactions screened by the {coul} factors of the {special_bonds}
|
||||||
|
|||||||
@ -17,7 +17,8 @@ style = any of the supported "dump styles"_dump.html :l
|
|||||||
file = name of file to write dump info to :l
|
file = name of file to write dump info to :l
|
||||||
dump-args = any additional args needed for a particular "dump style"_dump.html :l
|
dump-args = any additional args needed for a particular "dump style"_dump.html :l
|
||||||
modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l
|
modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l
|
||||||
dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l,ule
|
dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l
|
||||||
|
:ule
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user