doc page sync with SVN

Collected small changes and bugfixes

.gitignore

@@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

bench/Cu_u3.eam

@@ -1,4 +1,4 @@
-Cu functions (universal 3)
+DATE: 2007-06-11 CONTRIBUTOR: Stephen Foiles, foiles@sandia.gov CITATION: Foiles et al, Phys Rev B, 33, 7983 (1986) COMMENT: Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
    29     63.550         3.6150    FCC
   500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
   0.                     -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01

bench/FERMI/README

@@ -16,53 +16,88 @@ lmp_linux_double
 The precision (single, mixed, double) refers to the GPU and USER-CUDA
 pacakge precision.  See the README files in the lib/gpu and lib/cuda
 directories for instructions on how to build the packages with
-different precisions.  The doc/Section_accelerate.html file also has a
-summary description.
+different precisions.  The GPU and USER-CUDA sub-sections of the
+doc/Section_accelerate.html file also describes this process.
+
+Make.py -d ~/lammps -j 16 -p #all orig -m linux -o cpu -a exe
+Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt -a exe
+Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp -a exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=double arch=20 -o gpu_double -a libs exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=mixed arch=20 -o gpu_mixed -a libs exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=single arch=20 -o gpu_single -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=double arch=20 -o cuda_double -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=mixed arch=20 -o cuda_mixed -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=single arch=20 -o cuda_single -a libs exe
+Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu -a exe
+Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp -a exe
+Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
+        -m cuda -o kokkos_cuda -a exe
+
+Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
+        -gpu mode=double arch=20 -cuda mode=double arch=20 -m linux \
+        -o all -a libs exe
+
+Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
+        -kokkos cuda arch=20 -gpu mode=double arch=20 \
+        -cuda mode=double arch=20 -m cuda -o all_cuda -a libs exe
 
 ------------------------------------------------------------------------
 
-If the script has "cpu" in its name, it is meant to be run in CPU-only
-mode (without using the GPU or USER-CUDA styles).  For example:
+To run on just CPUs (without using the GPU or USER-CUDA styles),
+do something like the following:
 
-mpirun -np 1 ../lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mpirun -np 12 ../lmp_linux_double -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
+mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
+mpirun -np 12 lmp_linux_double -v x 16 -v y 16 -v z 16 -v t 100 < in.eam
 
 The "xyz" settings determine the problem size.  The "t" setting
 determines the number of timesteps.
 
+These mpirun commands run on a single node.  To run on multiple
+nodes, scale up the "-np" setting.
+
 ------------------------------------------------------------------------
 
-If the script has "gpu" in its name, it is meant to be run using
-the GPU package.  For example:
+To run with the GPU package, do something like the following:
 
-mpirun -np 12 ../lmp_linux_single -sf gpu -v g 1 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.gpu
-
-mpirun -np 8 ../lmp_linux_mixed -sf gpu -v g 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.gpu
+mpirun -np 12 lmp_linux_single -sf gpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj
+mpirun -np 8 lmp_linux_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.eam
 
 The "xyz" settings determine the problem size.  The "t" setting
 determines the number of timesteps.  The "np" setting determines how
-many MPI tasks per compute node the problem will run on, and the "g"
-setting determines how many GPUs per compute node the problem will run
-on, i.e. 1 or 2 in this case.  Note that you can use more MPI tasks
-than GPUs (both per compute node) with the GPU package.
+many MPI tasks (per node) the problem will run on.  The numeric
+argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
+is the default.  Note that you can use more MPI tasks than GPUs (per
+node) with the GPU package.
+
+These mpirun commands run on a single node.  To run on multiple nodes,
+scale up the "-np" setting, and control the number of MPI tasks per
+node via a "-ppn" setting.
 
 ------------------------------------------------------------------------
 
-If the script has "cuda" in its name, it is meant to be run using
-the USER-CUDA package.  For example:
+To run with the USER-CUDA package, do something like the following:
 
-mpirun -np 1 ../lmp_linux_single -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-
-mpirun -np 2 ../lmp_linux_double -c on -sf cuda -v g 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam.cuda
+mpirun -np 1 lmp_linux_single -c on -sf cuda -v x 16 -v y 16 -v z 16 -v t 100 < in.lj
+mpirun -np 2 lmp_linux_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam
 
 The "xyz" settings determine the problem size.  The "t" setting
 determines the number of timesteps.  The "np" setting determines how
-many MPI tasks per compute node the problem will run on, and the "g"
-setting determines how many GPUs per compute node the problem will run
-on, i.e. 1 or 2 in this case.  For the USER-CUDA package, the number
-of MPI tasks and GPUs (both per compute node) must be equal.
+many MPI tasks (per node) the problem will run on.  The numeric
+argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
+is the default.  Note that the number of MPI tasks must equal the
+number of GPUs (both per node) with the USER-CUDA package.
+
+These mpirun commands run on a single node.  To run on multiple nodes,
+scale up the "-np" setting, and control the number of MPI tasks per
+node via a "-ppn" setting.
 
 ------------------------------------------------------------------------
 
-If the script has "titan" in its name, it was run on the Titan supercomputer
-at ORNL.
+If the script has "titan" in its name, it was run on the Titan
+supercomputer at ORNL.

bench/FERMI/in.eam.cuda

@@ -1,29 +0,0 @@
-# bulk Cu lattice
-
-# set variable g = 1/2 for 1/2 GPUs
-
-if "$g == 1" then "package cuda gpu/node 1"
-if "$g == 2" then "package cuda gpu/node 2"
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		$t

bench/FERMI/in.eam.gpu

@@ -1,31 +0,0 @@
-# bulk Cu lattice
-
-# newton off is required for GPU package
-# set variable g = 1/2 for 1/2 GPUs
-
-newton          off
-if "$g == 1" then "package gpu force/neigh 0 0 1"
-if "$g == 2" then "package gpu force/neigh 0 1 1"
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		$t

bench/FERMI/in.lj.cuda

@@ -1,27 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set variable g = 1/2 for 1/2 GPUs
-
-if "$g == 1" then "package cuda gpu/node 1"
-if "$g == 2" then "package cuda gpu/node 2"
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/FERMI/in.lj.gpu

@@ -1,29 +0,0 @@
-# 3d Lennard-Jones melt
-
-# newton off is required for GPU package
-# set variable g = 1/2 for 1/2 GPUs
-
-newton          off
-if "$g == 1" then "package gpu force/neigh 0 0 1"
-if "$g == 2" then "package gpu force/neigh 0 1 1"
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/FERMI/in.rhodo.cuda

@@ -1,35 +0,0 @@
-# Rhodopsin model
-
-# set variable g = 1/2 for 1/2 GPUs
-
-if "$g == 1" then "package cuda gpu/node 1"
-if "$g == 2" then "package cuda gpu/node 2"
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-#atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-thermo_style    multi 
-timestep        2.0
-
-run		$t

bench/FERMI/in.rhodo.gpu

@@ -1,37 +0,0 @@
-# Rhodopsin model
-
-# newton off is required for GPU package
-# set variable g = 1/2 for 1/2 GPUs
-
-newton          off
-if "$g == 1" then "package gpu force/neigh 0 0 1"
-if "$g == 2" then "package gpu force/neigh 0 1 1"
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-thermo_style    multi 
-timestep        2.0
-
-run		$t

bench/KEPLER/Makefile.omp

@@ -7,7 +7,7 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 CC =		icc
-CCFLAGS =	-O3 -openmp -ansi-alias
+CCFLAGS =	-O3 -openmp -restrict -ansi-alias
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 

bench/KEPLER/Makefile.opt

@@ -7,7 +7,7 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 CC =		icc
-CCFLAGS =	-O
+CCFLAGS =	-O -restrict
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 

bench/KEPLER/README

@@ -17,7 +17,7 @@ openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37.
 ------------------------------------------------------------------------
 
 You can, of course, build LAMMPS yourself with any of the accelerator
-packages for your platform.
+packages installed for your platform.
 
 The build.py script will build LAMMPS for the various accelerlator
 packages using the Makefile.* files in this dir, which you can edit if
@@ -50,22 +50,19 @@ directory when the script finishes each build.
 
 ------------------------------------------------------------------------
 
-The in.* files have settings for the benchmark appopriate to each
-accelerator package.  Many of them, including the problem size,
-and number of timsteps, must be set as command-line arguments
-when the input script is run.
-
-------------------------------------------------------------------------
+The in.* files can be run with any of the accelerator packages,
+if you specify the appropriate command-line switches.  These
+include switches to set the problem size and number of timesteps
+to run.
 
 The run*.sh scripts have sample mpirun commands for running the input
 scripts on a single node or on multiple nodes for the strong and weak
 scaling results shown on the benchmark web page.  These scripts are
 provided for illustration purposes, to show what command-line
-arguments are used with each accelerator package, in combination with
-settings in the input scripts themselves.
+arguments are used with each accelerator package.
 
 Note that we generate these run scripts, either for interactive or
-batch submission, via Python scripts which produce a long list of runs
-to exercise a combination of options.  To perform a quick benchmark
-calculation on your platform, you will typically only want to run a
-few commands out of any of the run*.sh scripts.
+batch submission, via Python scripts which often produces a long list
+of runs to exercise a combination of options.  To perform a quick
+benchmark calculation on your platform, you will typically only want
+to run a few commands out of any of the run*.sh scripts.

bench/KEPLER/build.py

@@ -76,11 +76,11 @@ def build_cuda(precision,arch):
 # main program
 # convert target keywords into target flags
 
-cpu = opt = omp = 0
-gpu_double = gpu_mixed = gpu_single = 0
-cuda_double = cuda_mixed = cuda_single = 0
-intel_cpu = intel_phi = 0
-kokkos_omp = kokkos_phi = kokkos_cuda = 0
+  cpu = opt = omp = 0
+gpu = gpu_double = gpu_mixed = gpu_single = 0
+cuda = cuda_double = cuda_mixed = cuda_single = 0
+intel = intel_cpu = intel_phi = 0
+kokkos = kokkos_omp = kokkos_phi = kokkos_cuda = 0
   
 targets = sys.argv[1:]
 for target in targets:
@@ -90,20 +90,26 @@ for target in targets:
   elif target == "gpu/double": gpu_double = 1
   elif target == "gpu/mixed": gpu_mixed = 1
   elif target == "gpu/single": gpu_single = 1
-  elif target == "gpu": gpu_double = gpu_mixed = gpu_single = 1
+  elif target == "gpu": gpu = 1
   elif target == "cuda/double": cuda_double = 1
   elif target == "cuda/mixed": cuda_mixed = 1
   elif target == "cuda/single": cuda_single = 1
-  elif target == "cuda": cuda_double = cuda_mixed = cuda_single = 1
+  elif target == "cuda": cuda = 1
   elif target == "intel/cpu": intel_cpu = 1
   elif target == "intel/phi": intel_phi = 1
-  elif target == "intel": intel_cpu = intel_phi = 1
+  elif target == "intel": intel = 1
   elif target == "kokkos/omp": kokkos_omp = 1
   elif target == "kokkos/phi": kokkos_phi = 1
   elif target == "kokkos/cuda": kokkos_cuda = 1
-  elif target == "kokkos": kokkos_omp = kokkos_phi = kokkos_cuda = 1
+  elif target == "kokkos": kokkos = 1
+  elif target == "all": cpu = omp = gpu = cuda = intel = kokkos = 1
   else: print "Target",target,"is unknown"
 
+if gpu: gpu_double = gpu_mixed = gpu_single = 1
+if cuda: cuda_double = cuda_mixed = cuda_single = 1
+if intel: intel_cpu = intel_phi = 1
+if kokkos: kokkos_omp = kokkos_phi = kokkos_cuda = 1
+
 # CPU
 
 if cpu:

bench/KEPLER/in.lj.cuda

@@ -1,26 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set number of GPUs
-
-package         cuda gpu/node $g
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.gpu

@@ -1,29 +0,0 @@
-# 3d Lennard-Jones melt
-
-# newton off is required for GPU package
-# set number of GPUs
-
-newton          off
-if "$g == 1" then "package gpu force/neigh 0 0 1"
-if "$g == 2" then "package gpu force/neigh 0 1 1"
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.intel.cpu

@@ -1,26 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set precision for USER-INTEL package
-
-package         intel 1 $a balance 0.0
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.kokkos.cuda

@@ -1,29 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set neighlist style and comm mode
-
-package         kokkos neigh full comm/exchange $c comm/forward $c
-newton          off
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-# set neighbor bins to cutoff + skin
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no binsize 2.8
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.kokkos.omp

@@ -1,26 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set neighlist style and comm mode
-
-package         kokkos neigh $n comm/exchange $c comm/forward $c
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.omp

@@ -1,26 +0,0 @@
-# 3d Lennard-Jones melt
-
-# set number of threads per MPI task
-
-package         omp $h
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/in.lj.opt

@@ -1,22 +0,0 @@
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/KEPLER/run_cpu.sh

@@ -1,434 +1,29 @@
 #!/bin/bash
 #SBATCH -N 1 --time=12:00:00
 
-mpirun -N 1 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.1
-mpirun -N 1 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.1
-mpirun -N 1 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.1
-mpirun -N 1 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.1
-mpirun -N 1 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.1
-mpirun -N 1 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.1
-mpirun -N 1 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.1
-mpirun -N 1 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.1
-mpirun -N 1 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.1
-mpirun -N 1 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.1
-mpirun -N 1 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.1
-mpirun -N 1 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.1
-mpirun -N 1 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.1
+mpirun -np 1 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.1
 
-mpirun -N 2 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.2
-mpirun -N 2 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.2
-mpirun -N 2 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.2
-mpirun -N 2 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.2
-mpirun -N 2 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.2
-mpirun -N 2 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.2
-mpirun -N 2 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.2
-mpirun -N 2 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.2
-mpirun -N 2 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.2
-mpirun -N 2 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.2
-mpirun -N 2 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.2
-mpirun -N 2 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.2
-mpirun -N 2 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.2
+mpirun -np 2 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.2
 
-mpirun -N 3 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.3
-mpirun -N 3 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.3
-mpirun -N 3 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.3
-mpirun -N 3 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.3
-mpirun -N 3 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.3
-mpirun -N 3 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.3
-mpirun -N 3 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.3
-mpirun -N 3 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.3
-mpirun -N 3 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.3
-mpirun -N 3 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.3
-mpirun -N 3 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.3
-mpirun -N 3 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.3
-mpirun -N 3 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.3
+mpirun -np 4 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.4
 
-mpirun -N 4 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.4
-mpirun -N 4 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.4
-mpirun -N 4 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.4
-mpirun -N 4 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.4
-mpirun -N 4 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.4
-mpirun -N 4 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.4
-mpirun -N 4 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.4
-mpirun -N 4 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.4
-mpirun -N 4 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.4
-mpirun -N 4 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.4
-mpirun -N 4 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.4
-mpirun -N 4 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.4
-mpirun -N 4 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.4
+mpirun -np 6 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.6
 
-mpirun -N 5 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.5
-mpirun -N 5 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.5
-mpirun -N 5 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.5
-mpirun -N 5 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.5
-mpirun -N 5 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.5
-mpirun -N 5 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.5
-mpirun -N 5 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.5
-mpirun -N 5 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.5
-mpirun -N 5 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.5
-mpirun -N 5 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.5
-mpirun -N 5 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.5
-mpirun -N 5 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.5
-mpirun -N 5 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.5
+mpirun -np 8 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.8
 
-mpirun -N 6 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.6
-mpirun -N 6 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.6
-mpirun -N 6 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.6
-mpirun -N 6 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.6
-mpirun -N 6 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.6
-mpirun -N 6 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.6
-mpirun -N 6 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.6
-mpirun -N 6 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.6
-mpirun -N 6 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.6
-mpirun -N 6 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.6
-mpirun -N 6 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.6
-mpirun -N 6 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.6
-mpirun -N 6 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.6
+mpirun -np 10 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.10
 
-mpirun -N 7 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.7
-mpirun -N 7 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.7
-mpirun -N 7 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.7
-mpirun -N 7 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.7
-mpirun -N 7 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.7
-mpirun -N 7 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.7
-mpirun -N 7 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.7
-mpirun -N 7 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.7
-mpirun -N 7 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.7
-mpirun -N 7 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.7
-mpirun -N 7 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.7
-mpirun -N 7 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.7
-mpirun -N 7 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.7
+mpirun -np 12 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.12
 
-mpirun -N 8 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.8
-mpirun -N 8 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.8
-mpirun -N 8 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.8
-mpirun -N 8 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.8
-mpirun -N 8 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.8
-mpirun -N 8 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.8
-mpirun -N 8 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.8
-mpirun -N 8 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.8
-mpirun -N 8 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.8
-mpirun -N 8 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.8
-mpirun -N 8 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.8
-mpirun -N 8 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.8
-mpirun -N 8 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.8
+mpirun -np 14 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.14
 
-mpirun -N 9 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.9
-mpirun -N 9 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.9
-mpirun -N 9 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.9
-mpirun -N 9 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.9
-mpirun -N 9 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.9
-mpirun -N 9 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.9
-mpirun -N 9 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.9
-mpirun -N 9 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.9
-mpirun -N 9 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.9
-mpirun -N 9 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.9
-mpirun -N 9 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.9
-mpirun -N 9 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.9
-mpirun -N 9 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.9
-
-mpirun -N 10 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.10
-mpirun -N 10 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.10
-mpirun -N 10 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.10
-mpirun -N 10 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.10
-mpirun -N 10 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.10
-mpirun -N 10 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.10
-mpirun -N 10 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.10
-mpirun -N 10 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.10
-mpirun -N 10 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.10
-mpirun -N 10 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.10
-mpirun -N 10 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.10
-mpirun -N 10 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.10
-mpirun -N 10 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.10
-
-mpirun -N 11 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.11
-mpirun -N 11 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.11
-mpirun -N 11 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.11
-mpirun -N 11 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.11
-mpirun -N 11 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.11
-mpirun -N 11 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.11
-mpirun -N 11 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.11
-mpirun -N 11 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.11
-mpirun -N 11 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.11
-mpirun -N 11 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.11
-mpirun -N 11 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.11
-mpirun -N 11 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.11
-mpirun -N 11 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.11
-
-mpirun -N 12 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.12
-mpirun -N 12 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.12
-mpirun -N 12 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.12
-mpirun -N 12 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.12
-mpirun -N 12 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.12
-mpirun -N 12 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.12
-mpirun -N 12 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.12
-mpirun -N 12 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.12
-mpirun -N 12 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.12
-mpirun -N 12 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.12
-mpirun -N 12 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.12
-mpirun -N 12 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.12
-mpirun -N 12 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.12
-
-mpirun -N 13 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.13
-mpirun -N 13 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.13
-mpirun -N 13 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.13
-mpirun -N 13 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.13
-mpirun -N 13 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.13
-mpirun -N 13 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.13
-mpirun -N 13 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.13
-mpirun -N 13 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.13
-mpirun -N 13 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.13
-mpirun -N 13 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.13
-mpirun -N 13 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.13
-mpirun -N 13 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.13
-mpirun -N 13 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.13
-
-mpirun -N 14 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.14
-mpirun -N 14 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.14
-mpirun -N 14 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.14
-mpirun -N 14 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.14
-mpirun -N 14 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.14
-mpirun -N 14 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.14
-mpirun -N 14 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.14
-mpirun -N 14 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.14
-mpirun -N 14 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.14
-mpirun -N 14 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.14
-mpirun -N 14 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.14
-mpirun -N 14 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.14
-mpirun -N 14 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.14
-
-mpirun -N 15 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.15
-mpirun -N 15 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.15
-mpirun -N 15 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.15
-mpirun -N 15 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.15
-mpirun -N 15 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.15
-mpirun -N 15 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.15
-mpirun -N 15 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.15
-mpirun -N 15 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.15
-mpirun -N 15 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.15
-mpirun -N 15 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.15
-mpirun -N 15 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.15
-mpirun -N 15 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.15
-mpirun -N 15 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.15
-
-mpirun -N 16 ./lmp_cpu -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2K.16
-mpirun -N 16 ./lmp_cpu -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4K.16
-mpirun -N 16 ./lmp_cpu -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8K.16
-mpirun -N 16 ./lmp_cpu -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.16K.16
-mpirun -N 16 ./lmp_cpu -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.32K.16
-mpirun -N 16 ./lmp_cpu -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.64K.16
-mpirun -N 16 ./lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.128K.16
-mpirun -N 16 ./lmp_cpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.256K.16
-mpirun -N 16 ./lmp_cpu -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.512K.16
-mpirun -N 16 ./lmp_cpu -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.1024K.16
-mpirun -N 16 ./lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.2048K.16
-mpirun -N 16 ./lmp_cpu -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.4096K.16
-mpirun -N 16 ./lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cpu
-mv log.lammps log.28Jun14.lj.cpu.8192K.16
+mpirun -np 16 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.16

bench/KEPLER/run_cuda.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -N 1 lmp_cuda_double -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.double.128K.1
+
+mpirun -N 2 lmp_cuda_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.double.128K.2
+
+mpirun -N 1 lmp_cuda_mixed -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.mixed.128K.1
+
+mpirun -N 2 lmp_cuda_mixed -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.mixed.128K.2
+
+mpirun -N 1 lmp_cuda_single -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.single.128K.1
+
+mpirun -N 2 lmp_cuda_single -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.single.128K.2

bench/KEPLER/run_intel_cpu.sh

@@ -1,83 +1,83 @@
 #!/bin/bash
 #SBATCH -N 1 --time=12:00:00
 
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.2K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.4K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.8K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.16K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.32K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.64K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.128K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.256K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.512K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.1024K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.2048K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.4096K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.single.8192K.16
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.1
 
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.2K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.4K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.8K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.16K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.32K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.64K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.128K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.256K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.512K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.1024K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.2048K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.4096K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 3 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.mixed.8192K.16
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.2
 
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.2K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.4K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.8K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.16K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.32K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.64K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.128K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.256K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.512K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.1024K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.2048K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.4096K.16
-mpirun -np 16 lmp_intel_cpu -sf intel -v a 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.intel.cpu
-mv log.lammps log.28Jun14.lj.intel.cpu.double.8192K.16
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.16
+
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.1
+
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.2
+
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.16
+
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.1
+
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.2
+
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.16

bench/KEPLER/run_kokkos_cuda.sh

@@ -1,650 +1,74 @@
 #!/bin/bash
 #SBATCH -N 1 --time=12:00:00
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.1
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 1 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.1
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.1
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.2
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 2 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.2
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.2
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.3
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 3 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.3
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.3
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.4
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 4 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.4
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.4
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.5
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 5 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.5
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 6 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 6 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 7 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 8 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 9 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 10 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 11 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.12
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 12 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.12
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 12 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.12
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.13
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 13 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.13
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 13 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.13
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.14
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.14
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.14
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.14
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 14 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.14
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 14 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.14
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.15
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 15 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.15
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 15 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.15
 
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.1.16
-mpirun -np 1 ./lmp_kokkos_cuda -k on g 1 t 16 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.1.16
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 16 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.16
 
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.1024K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.2.1
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 1 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.2.1
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.1
 
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.2K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.4K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.16K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.32K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.64K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.128K.2.2
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.256K.2.2
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 2 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
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+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.2
 
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 3 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 3 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 4 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 4 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 4 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 5 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 5 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 6 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 6 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 6 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.2.6
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 7 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 7 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.2.7
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-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 8 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.cuda
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-mv log.lammps log.28Jun14.lj.kokkos.cuda.4096K.2.8
-mpirun -np 2 ./lmp_kokkos_cuda -k on g 2 t 8 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.cuda
-mv log.lammps log.28Jun14.lj.kokkos.cuda.8192K.2.8
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.8

bench/KEPLER/run_kokkos_omp.sh

@@ -1,137 +1,17 @@
 #!/bin/bash
 #SBATCH -N 1 --time=12:00:00
 
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.16K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.32K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.64K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.128K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.256K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.512K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.1024K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4096K.1.8
-mpirun -np 1 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8192K.1.8
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 16 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.1.16
 
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.16K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.32K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.64K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.128K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.256K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.512K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.1024K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4096K.2.8
-mpirun -np 2 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 8 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8192K.2.8
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 8 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.2.8
 
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.16K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.32K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.64K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.128K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.256K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.512K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.1024K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4096K.4.4
-mpirun -np 4 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 4 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8192K.4.4
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 4 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.4.4
 
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.16K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.32K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.64K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.128K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.256K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.512K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.1024K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.4096K.8.2
-mpirun -np 8 -bind-to socket -map-by socket -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 2 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omp
-mv log.lammps log.28Jun14.lj.kokkos.omp.8192K.8.2
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 2 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.8.2
 
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.2K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.4K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.8K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.16K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.32K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.64K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.128K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.256K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.512K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.1024K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.4096K.16.1
-mpirun -np 16 -bind-to core -map-by core -x KMP_AFFINITY=scatter ./lmp_kokkos_omp -k on t 1 -sf kk -v c device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.kokkos.omphalf
-mv log.lammps log.28Jun14.lj.kokkos.omp.8192K.16.1
+mpirun -np half -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half newton on comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.16.1

bench/KEPLER/run_omp.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_omp -sf omp -pk omp 16 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.1.16
+
+mpirun -np 2 lmp_omp -sf omp -pk omp 8 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.2.8
+
+mpirun -np 4 lmp_omp -sf omp -pk omp 4 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.4.4
+
+mpirun -np 8 lmp_omp -sf omp -pk omp 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.8.2
+
+mpirun -np 16 lmp_omp -sf omp -pk omp 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.16.1

bench/KEPLER/run_opt.sh

@@ -1,29 +1,29 @@
 #!/bin/bash
 #SBATCH -N 1 --time=12:00:00
 
-mpirun -np 16 lmp_opt -sf opt -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.2K.16
-mpirun -np 16 lmp_opt -sf opt -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.4K.16
-mpirun -np 16 lmp_opt -sf opt -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.8K.16
-mpirun -np 16 lmp_opt -sf opt -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.16K.16
-mpirun -np 16 lmp_opt -sf opt -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.32K.16
-mpirun -np 16 lmp_opt -sf opt -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.64K.16
-mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.128K.16
-mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.256K.16
-mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.512K.16
-mpirun -np 16 lmp_opt -sf opt -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.1024K.16
-mpirun -np 16 lmp_opt -sf opt -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.2048K.16
-mpirun -np 16 lmp_opt -sf opt -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.4096K.16
-mpirun -np 16 lmp_opt -sf opt -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.opt
-mv log.lammps log.28Jun14.lj.opt.8192K.16
+mpirun -np 1 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.1
+
+mpirun -np 2 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.2
+
+mpirun -np 4 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.4
+
+mpirun -np 6 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.6
+
+mpirun -np 8 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.8
+
+mpirun -np 10 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.10
+
+mpirun -np 12 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.12
+
+mpirun -np 14 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.14
+
+mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.16

bench/KEPLER/run_strong.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 16 --time=12:00:00
+
+mpirun -npernode 16 lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cpu.2048K.16.16
+
+mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.omp.2048K.16.1.16
+
+mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cuda.2048K.2.16
+
+mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.gpu.2048K.2.14.16
+
+mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.2.1.16
+
+mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.16.1.16

bench/KEPLER/run_user_cuda.sh

@@ -1,164 +0,0 @@
-#!/bin/bash
-#SBATCH -N 1 --time=12:00:00
-
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.2K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.4K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.8K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.16K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.32K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.64K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.128K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.256K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.512K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.1024K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.2048K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.4096K.1
-mpirun -N 1 ./lmp_cuda_double -c on -sf cuda -v g 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.8192K.1
-
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.2K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.4K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.8K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.16K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.32K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.64K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.128K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.256K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.512K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.1024K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.2048K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.4096K.2
-mpirun -N 2 ./lmp_cuda_double -c on -sf cuda -v g 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.double.8192K.2
-
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.2K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.4K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.8K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.16K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.32K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.64K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.128K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.256K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.512K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.1024K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.2048K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.4096K.1
-mpirun -N 1 ./lmp_cuda_mixed -c on -sf cuda -v g 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.8192K.1
-
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.2K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.4K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.8K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.16K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.32K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.64K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.128K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.256K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.512K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.1024K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.2048K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.4096K.2
-mpirun -N 2 ./lmp_cuda_mixed -c on -sf cuda -v g 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.mixed.8192K.2
-
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.2K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.4K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.8K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.16K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.32K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.64K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.128K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.256K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.512K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.1024K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.2048K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.4096K.1
-mpirun -N 1 ./lmp_cuda_single -c on -sf cuda -v g 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.8192K.1
-
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 8 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.2K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 8 -v y 8 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.4K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 8 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.8K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.16K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 16 -v y 16 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.32K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 16 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.64K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.128K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.256K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.512K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 64 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.1024K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.2048K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 64 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.4096K.2
-mpirun -N 2 ./lmp_cuda_single -c on -sf cuda -v g 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj.cuda
-mv log.lammps log.28Jun14.lj.cuda.single.8192K.2

bench/KEPLER/run_user_omp.sh

@@ -1,137 +0,0 @@
-#!/bin/bash
-#SBATCH -N 1 --time=12:00:00
-
-mpirun -bind-to none -N 1 ./lmp_omp -v x 8 -v y 8 -v z 8 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 8 -v y 8 -v z 16 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 8 -v y 16 -v z 16 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 16 -v y 16 -v z 16 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.16K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 16 -v y 16 -v z 32 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.32K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 16 -v y 32 -v z 32 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.64K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 32 -v y 32 -v z 32 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.128K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 32 -v y 32 -v z 64 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.256K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 32 -v y 64 -v z 64 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.512K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 64 -v y 64 -v z 64 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.1024K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 64 -v y 64 -v z 128 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2048K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 64 -v y 128 -v z 128 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4096K.1.16
-mpirun -bind-to none -N 1 ./lmp_omp -v x 128 -v y 128 -v z 128 -v t 100 -v h 16 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8192K.1.16
-
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 8 -v y 8 -v z 8 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 8 -v y 8 -v z 16 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 8 -v y 16 -v z 16 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 16 -v y 16 -v z 16 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.16K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 16 -v y 16 -v z 32 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.32K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 16 -v y 32 -v z 32 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.64K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 32 -v y 32 -v z 32 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.128K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 32 -v y 32 -v z 64 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.256K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 32 -v y 64 -v z 64 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.512K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 64 -v y 64 -v z 64 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.1024K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 64 -v y 64 -v z 128 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2048K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 64 -v y 128 -v z 128 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4096K.2.8
-mpirun -bind-to socket -N 2 ./lmp_omp -v x 128 -v y 128 -v z 128 -v t 100 -v h 8 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8192K.2.8
-
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 8 -v y 8 -v z 8 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 8 -v y 8 -v z 16 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 8 -v y 16 -v z 16 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 16 -v y 16 -v z 16 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.16K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 16 -v y 16 -v z 32 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.32K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 16 -v y 32 -v z 32 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.64K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 32 -v y 32 -v z 32 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.128K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 32 -v y 32 -v z 64 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.256K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 32 -v y 64 -v z 64 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.512K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 64 -v y 64 -v z 64 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.1024K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 64 -v y 64 -v z 128 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2048K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 64 -v y 128 -v z 128 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4096K.4.4
-mpirun -bind-to socket -N 4 ./lmp_omp -v x 128 -v y 128 -v z 128 -v t 100 -v h 4 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8192K.4.4
-
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 8 -v y 8 -v z 8 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 8 -v y 8 -v z 16 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 8 -v y 16 -v z 16 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 16 -v y 16 -v z 16 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.16K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 16 -v y 16 -v z 32 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.32K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 16 -v y 32 -v z 32 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.64K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 32 -v y 32 -v z 32 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.128K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 32 -v y 32 -v z 64 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.256K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 32 -v y 64 -v z 64 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.512K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 64 -v y 64 -v z 64 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.1024K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 64 -v y 64 -v z 128 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2048K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 64 -v y 128 -v z 128 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4096K.8.2
-mpirun -bind-to socket -N 8 ./lmp_omp -v x 128 -v y 128 -v z 128 -v t 100 -v h 2 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8192K.8.2
-
-mpirun -bind-to core -N 16 ./lmp_omp -v x 8 -v y 8 -v z 8 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 8 -v y 8 -v z 16 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 8 -v y 16 -v z 16 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 16 -v y 16 -v z 16 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.16K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 16 -v y 16 -v z 32 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.32K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 16 -v y 32 -v z 32 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.64K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 32 -v y 32 -v z 32 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.128K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 32 -v y 32 -v z 64 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.256K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 32 -v y 64 -v z 64 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.512K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 64 -v y 64 -v z 64 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.1024K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 64 -v y 64 -v z 128 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.2048K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 64 -v y 128 -v z 128 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.4096K.16.1
-mpirun -bind-to core -N 16 ./lmp_omp -v x 128 -v y 128 -v z 128 -v t 100 -v h 1 -sf omp < in.lj.omp
-mv log.lammps log.28Jun14.lj.omp.8192K.16.1

bench/KEPLER/run_weak.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 16 --time=12:00:00
+
+mpirun -npernode 16 lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cpu.512K.16.16
+
+mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.omp.512K.16.1.16
+
+mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cuda.512K.2.16
+
+mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.gpu.512K.2.14.16
+
+mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.2.1.16
+
+mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.omp.512K.16.1.16

bench/POTENTIALS/in.dpd

@@ -2,7 +2,7 @@
 
 units		lj
 atom_style	atomic
-communicate	single vel yes
+comm_modify     mode single vel yes
 
 lattice		fcc 3.0
 region		box block 0 20 0 20 0 20

bench/README

@@ -15,7 +15,7 @@ the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
 
 The remainder of this file refers to the 5 problems in the top-level
 of this directory and how to run them on CPUs, either in serial or
-parallel.  The directories have their own README files which you
+parallel.  The sub-directories have their own README files which you
 should refer to before running those scripts.
 
 ----------------------------------------------------------------------
@@ -71,33 +71,49 @@ integration
 
 ----------------------------------------------------------------------
 
+Here is a src/Make.py command which will perform a parallel build of a
+LAMMPS executable "lmp_mpi" with all the packages needed by all the
+examples.  This assumes you have an MPI installed on your machine so
+that "mpicxx" can be used as the wrapper compiler.  It also assumes
+you have an Intel compiler to use as the base compiler.  You can leave
+off the "-cc mpi wrap=icc" switch if that is not the case.  You can
+also leave off the "-fft fftw3" switch if you do not have the FFTW
+(v3) installed as an FFT package, in which case the default KISS FFT
+library will be used.
+
+cd src
+Make.py -j 16 -p none molecule manybody kspace granular rigid orig \
+  -cc mpi wrap=icc -fft fftw3 -a file mpi
+
+----------------------------------------------------------------------
+
 Here is how to run each problem, assuming the LAMMPS executable is
-named lmp_foo, and you are using the mpirun command to launch parallel
+named lmp_mpi, and you are using the mpirun command to launch parallel
 runs:
 
 Serial (one processor runs):
 
-lmp_foo < in.lj
-lmp_foo < in.chain
-lmp_foo < in.eam
-lmp_foo < in.chute
-lmp_foo < in.rhodo
+lmp_mpi < in.lj
+lmp_mpi < in.chain
+lmp_mpi < in.eam
+lmp_mpi < in.chute
+lmp_mpi < in.rhodo
 
 Parallel fixed-size runs (on 8 procs in this case):
 
-mpirun -np 8 lmp_foo < in.lj
-mpirun -np 8 lmp_foo < in.chain
-mpirun -np 8 lmp_foo < in.eam
-mpirun -np 8 lmp_foo < in.chute
-mpirun -np 8 lmp_foo < in.rhodo
+mpirun -np 8 lmp_mpi < in.lj
+mpirun -np 8 lmp_mpi < in.chain
+mpirun -np 8 lmp_mpi < in.eam
+mpirun -np 8 lmp_mpi < in.chute
+mpirun -np 8 lmp_mpi < in.rhodo
 
 Parallel scaled-size runs (on 16 procs in this case):
 
-mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.lj
-mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.chain.scaled
-mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.eam
-mpirun -np 16 lmp_foo -var x 4 -var y 4 < in.chute.scaled
-mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.lj
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.chain.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.eam
+mpirun -np 16 lmp_mpi -var x 4 -var y 4 < in.chute.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
 
 For each of the scaled-size runs you must set 3 variables as -var
 command line switches.  The variables x,y,z are used in the input

bench/in.chute

@@ -5,7 +5,7 @@ units		lj
 atom_style	sphere
 boundary	p p fs
 newton		off
-communicate	single vel yes
+comm_modify	vel yes
 
 read_data	data.chute
 

bench/in.chute.scaled

@@ -8,7 +8,7 @@ units		lj
 atom_style	sphere
 boundary	p p fs
 newton		off
-communicate	single vel yes
+comm_modify	vel yes
 
 read_data	data.chute
 

bench/log.15Feb16.chain.fixed.icc.1

@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 11.5189 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
+Loop time of 0.978585 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 105948.895 tau/day, 102.188 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.19562    | 0.19562    | 0.19562    |   0.0 | 19.99
+Bond    | 0.087475   | 0.087475   | 0.087475   |   0.0 |  8.94
+Neigh   | 0.44861    | 0.44861    | 0.44861    |   0.0 | 45.84
+Comm    | 0.032932   | 0.032932   | 0.032932   |   0.0 |  3.37
+Output  | 0.00010395 | 0.00010395 | 0.00010395 |   0.0 |  0.01
+Modify  | 0.19413    | 0.19413    | 0.19413    |   0.0 | 19.84
+Other   |            | 0.01972    |            |       |  2.02
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9493 ave 9493 max 9493 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    155873 ave 155873 max 155873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 155873
+Ave neighs/atom = 4.87103
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.chain.fixed.icc.4

@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 3.91518 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
+Loop time of 0.271187 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 382319.453 tau/day, 368.749 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.048621   | 0.050076   | 0.051229   |   0.4 | 18.47
+Bond    | 0.022254   | 0.022942   | 0.023567   |   0.3 |  8.46
+Neigh   | 0.11873    | 0.11881    | 0.11887    |   0.0 | 43.81
+Comm    | 0.019066   | 0.021357   | 0.024297   |   1.3 |  7.88
+Output  | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 |   0.1 |  0.02
+Modify  | 0.048737   | 0.050198   | 0.051231   |   0.4 | 18.51
+Other   |            | 0.007751   |            |       |  2.86
+
+Nlocal:    8000 ave 8030 max 7974 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    4177 ave 4191 max 4160 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:    38995.8 ave 39169 max 38852 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 155983
+Ave neighs/atom = 4.87447
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chain.scaled.icc.4

@@ -0,0 +1,94 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+units		lj
+atom_style	bond
+atom_modify	map hash
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  126720 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 89 89 45
+Memory usage per processor = 12.8735 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
+Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 85764.410 tau/day, 82.720 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.21738    | 0.23306    | 0.23926    |   1.9 | 19.28
+Bond    | 0.094536   | 0.10196    | 0.10534    |   1.4 |  8.43
+Neigh   | 0.52311    | 0.52392    | 0.52519    |   0.1 | 43.34
+Comm    | 0.090161   | 0.10022    | 0.12557    |   4.7 |  8.29
+Output  | 0.00012207 | 0.00017327 | 0.00019598 |   0.2 |  0.01
+Modify  | 0.19662    | 0.20262    | 0.20672    |   0.8 | 16.76
+Other   |            | 0.04694    |            |       |  3.88
+
+Nlocal:    32000 ave 32015 max 31983 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    9492 ave 9522 max 9432 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs:    155837 ave 156079 max 155506 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 623349
+Ave neighs/atom = 4.86991
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.chute.fixed.icc.1

@@ -0,0 +1,80 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 15.567 Mbytes
+Step Atoms KinEng 1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.550482 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1569.534 tau/day, 181.659 timesteps/s
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.33849    | 0.33849    | 0.33849    |   0.0 | 61.49
+Neigh   | 0.040353   | 0.040353   | 0.040353   |   0.0 |  7.33
+Comm    | 0.018023   | 0.018023   | 0.018023   |   0.0 |  3.27
+Output  | 0.00020385 | 0.00020385 | 0.00020385 |   0.0 |  0.04
+Modify  | 0.13155    | 0.13155    | 0.13155    |   0.0 | 23.90
+Other   |            | 0.02186    |            |       |  3.97
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 115133
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chute.fixed.icc.4

@@ -0,0 +1,80 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 6.81783 Mbytes
+Step Atoms KinEng 1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.13141 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 6574.833 tau/day, 760.976 timesteps/s
+99.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.062505   | 0.067      | 0.07152    |   1.5 | 50.99
+Neigh   | 0.010041   | 0.0101     | 0.010178   |   0.1 |  7.69
+Comm    | 0.012347   | 0.012895   | 0.013444   |   0.5 |  9.81
+Output  | 6.3896e-05 | 0.00010294 | 0.00014091 |   0.3 |  0.08
+Modify  | 0.031802   | 0.032348   | 0.032897   |   0.3 | 24.62
+Other   |            | 0.008965   |            |       |  6.82
+
+Nlocal:    8000 ave 8008 max 7992 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    2439 ave 2450 max 2428 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    29500.5 ave 30488 max 28513 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 118002
+Ave neighs/atom = 3.68756
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chute.scaled.icc.4

@@ -0,0 +1,90 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+variable	x index 1
+variable	y index 1
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+replicate	$x $y 1
+replicate	2 $y 1
+replicate	2 2 1
+  orthogonal box = (0 0 0) to (80 40 37.2922)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+3648 atoms in group bottom
+group		active subtract all bottom
+124352 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 146 73 68
+Memory usage per processor = 15.7007 Mbytes
+Step Atoms KinEng 1 Volume 
+       0   128000    3136556.5    6404.5051    119335.13 
+     100   128000    3137168.3    6284.3873    119338.83 
+Loop time of 0.906913 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 952.683 tau/day, 110.264 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.51454    | 0.53094    | 0.55381    |   2.0 | 58.54
+Neigh   | 0.042597   | 0.043726   | 0.045801   |   0.6 |  4.82
+Comm    | 0.063027   | 0.064657   | 0.067367   |   0.7 |  7.13
+Output  | 0.00024891 | 0.00059718 | 0.00086498 |   1.0 |  0.07
+Modify  | 0.16508    | 0.17656    | 0.1925     |   2.6 | 19.47
+Other   |            | 0.09043    |            |       |  9.97
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 460532
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.eam.fixed.icc.1

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 10.2238 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 5.90097 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2121     | 5.2121     | 5.2121     |   0.0 | 88.33
+Neigh   | 0.58212    | 0.58212    | 0.58212    |   0.0 |  9.86
+Comm    | 0.030392   | 0.030392   | 0.030392   |   0.0 |  0.52
+Output  | 0.00023389 | 0.00023389 | 0.00023389 |   0.0 |  0.00
+Modify  | 0.060871   | 0.060871   | 0.060871   |   0.0 |  1.03
+Other   |            | 0.01527    |            |       |  0.26
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19909 ave 19909 max 19909 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.15Feb16.eam.fixed.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 5.09629 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 1.58019 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3617     | 1.366      | 1.3723     |   0.4 | 86.45
+Neigh   | 0.15123    | 0.15232    | 0.15374    |   0.2 |  9.64
+Comm    | 0.033429   | 0.041275   | 0.047066   |   2.7 |  2.61
+Output  | 0.00011301 | 0.0001573  | 0.000211   |   0.3 |  0.01
+Modify  | 0.014694   | 0.015085   | 0.015421   |   0.2 |  0.95
+Other   |            | 0.005342   |            |       |  0.34
+
+Nlocal:    8000 ave 8008 max 7993 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9130.25 ave 9138 max 9122 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    301946 ave 302392 max 301360 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.eam.scaled.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 49 49 25
+Memory usage per processor = 10.1402 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -453120            0   -426647.73    18704.012 
+      50    779.50001   -439457.02            0   -426560.06    52355.276 
+     100    797.97828   -439764.76            0   -426562.07     51474.74 
+Loop time of 6.46849 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.581      | 5.5997     | 5.6265     |   0.8 | 86.57
+Neigh   | 0.65287    | 0.658      | 0.66374    |   0.5 | 10.17
+Comm    | 0.075706   | 0.11015    | 0.13655    |   7.2 |  1.70
+Output  | 0.00026488 | 0.00028312 | 0.00029302 |   0.1 |  0.00
+Modify  | 0.069607   | 0.072407   | 0.074555   |   0.7 |  1.12
+Other   |            | 0.02794    |            |       |  0.43
+
+Nlocal:    32000 ave 32092 max 31914 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    19910 ave 19997 max 19818 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 4829126
+Ave neighs/atom = 37.7275
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.15Feb16.lj.fixed.icc.1

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 8.21387 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 2.26309 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 19088.920 tau/day, 44.187 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9341     | 1.9341     | 1.9341     |   0.0 | 85.46
+Neigh   | 0.2442     | 0.2442     | 0.2442     |   0.0 | 10.79
+Comm    | 0.024158   | 0.024158   | 0.024158   |   0.0 |  1.07
+Output  | 0.00011611 | 0.00011611 | 0.00011611 |   0.0 |  0.01
+Modify  | 0.053222   | 0.053222   | 0.053222   |   0.0 |  2.35
+Other   |            | 0.007258   |            |       |  0.32
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.15Feb16.lj.fixed.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 4.09506 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.640733 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 67422.779 tau/day, 156.071 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.49487    | 0.51733    | 0.5322     |   1.9 | 80.74
+Neigh   | 0.061131   | 0.063685   | 0.065433   |   0.6 |  9.94
+Comm    | 0.02457    | 0.042349   | 0.069598   |   8.1 |  6.61
+Output  | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 |   0.0 |  0.01
+Modify  | 0.012961   | 0.013863   | 0.014491   |   0.5 |  2.16
+Other   |            | 0.003448   |            |       |  0.54
+
+Nlocal:    8000 ave 8037 max 7964 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9007.5 ave 9050 max 8968 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:    300708 ave 305113 max 297203 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00

bench/log.15Feb16.lj.scaled.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 48 48 24
+Memory usage per processor = 8.13678 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
+     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
+Loop time of 2.57914 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 16749.768 tau/day, 38.773 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.042      | 2.1092     | 2.1668     |   3.1 | 81.78
+Neigh   | 0.23982    | 0.24551    | 0.25233    |   1.0 |  9.52
+Comm    | 0.067088   | 0.13887    | 0.22681    |  15.7 |  5.38
+Output  | 0.00013185 | 0.00021666 | 0.00027108 |   0.4 |  0.01
+Modify  | 0.060348   | 0.071269   | 0.077063   |   2.5 |  2.76
+Other   |            | 0.01403    |            |       |  0.54
+
+Nlocal:    32000 ave 32060 max 31939 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    19630.8 ave 19681 max 19562 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 4807797
+Ave neighs/atom = 37.5609
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.15Feb16.rhodo.fixed.icc.1

@@ -0,0 +1,121 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 41070 25600
+Neighbor list info ...
+  1 neighbor list requests
+  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 = 10 13 13
+Memory usage per processor = 91.7487 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =     17.6362 (sec) ----------------
+TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+Volume   =    308031.5639 
+---------------- Step      100 ----- CPU =     35.9089 (sec) ----------------
+TotEng   =    -25290.7593 KinEng   =     21592.0117 Temp     =       301.0920 
+PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
+E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_coul   =    206659.2326 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 25.731     | 25.731     | 25.731     |   0.0 | 71.66
+Bond    | 1.2771     | 1.2771     | 1.2771     |   0.0 |  3.56
+Kspace  | 3.2094     | 3.2094     | 3.2094     |   0.0 |  8.94
+Neigh   | 4.4538     | 4.4538     | 4.4538     |   0.0 | 12.40
+Comm    | 0.068507   | 0.068507   | 0.068507   |   0.0 |  0.19
+Output  | 0.00025916 | 0.00025916 | 0.00025916 |   0.0 |  0.00
+Modify  | 1.1417     | 1.1417     | 1.1417     |   0.0 |  3.18
+Other   |            | 0.027      |            |       |  0.08
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    47958 ave 47958 max 47958 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12028107
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:37

bench/log.15Feb16.rhodo.fixed.icc.4

@@ -0,0 +1,121 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 13230 6400
+Neighbor list info ...
+  1 neighbor list requests
+  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 = 10 13 13
+Memory usage per processor = 36.629 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =      4.7461 (sec) ----------------
+TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+Volume   =    308031.5639 
+---------------- Step      100 ----- CPU =      9.6332 (sec) ----------------
+TotEng   =    -25290.7591 KinEng   =     21592.0117 Temp     =       301.0920 
+PotEng   =    -46882.7708 E_bond   =      2567.9807 E_angle  =     10781.9408 
+E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.4364     | 6.5993     | 6.7208     |   4.7 | 68.51
+Bond    | 0.30755    | 0.32435    | 0.35704    |   3.4 |  3.37
+Kspace  | 0.92248    | 1.0782     | 1.2597     |  13.0 | 11.19
+Neigh   | 1.1669     | 1.1672     | 1.1675     |   0.0 | 12.12
+Comm    | 0.094674   | 0.098065   | 0.10543    |   1.4 |  1.02
+Output  | 0.00015521 | 0.00016224 | 0.00018215 |   0.1 |  0.00
+Modify  | 0.32982    | 0.34654    | 0.35365    |   1.6 |  3.60
+Other   |            | 0.01943    |            |       |  0.20
+
+Nlocal:    8000 ave 8143 max 7933 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    22733.5 ave 22769 max 22693 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 12028107
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:10

bench/log.15Feb16.rhodo.scaled.icc.4

@@ -0,0 +1,142 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+atom_modify	map hash
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  110892 bonds
+  161868 angles
+  227316 dihedrals
+  4136 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  6468 = # of size 2 clusters
+  14532 = # of size 3 clusters
+  2988 = # of size 4 clusters
+  16932 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248593
+  grid = 48 60 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0359793
+  estimated relative force accuracy = 0.00010835
+  using double precision FFTs
+  3d grid and FFT values/proc = 41615 25920
+Neighbor list info ...
+  1 neighbor list requests
+  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 = 19 26 13
+Memory usage per processor = 95.5339 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
+PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
+E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
+E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -142.3092 
+Volume   =   1231980.1340 
+---------------- Step       50 ----- CPU =     18.7806 (sec) ----------------
+TotEng   =   -101320.2677 KinEng   =     86003.4837 Temp     =       299.8118 
+PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
+E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
+E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
+Volume   =   1232126.1855 
+---------------- Step      100 ----- CPU =     38.3684 (sec) ----------------
+TotEng   =   -101158.1849 KinEng   =     86355.6149 Temp     =       301.0393 
+PotEng   =   -187513.7998 E_bond   =     10272.0693 E_angle  =     43128.6454 
+E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
+E_coul   =    825583.7122 E_long   =  -1080572.5667 Press    =        15.2151 
+Volume   =   1232535.8423 
+Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 26.205     | 26.538     | 26.911     |   5.0 | 69.17
+Bond    | 1.298      | 1.3125     | 1.3277     |   1.0 |  3.42
+Kspace  | 3.7099     | 4.0992     | 4.4422     |  13.3 | 10.68
+Neigh   | 4.6137     | 4.6144     | 4.615      |   0.0 | 12.03
+Comm    | 0.21398    | 0.21992    | 0.22886    |   1.2 |  0.57
+Output  | 0.00030518 | 0.00031543 | 0.00033307 |   0.1 |  0.00
+Modify  | 1.5066     | 1.5232     | 1.5388     |   1.0 |  3.97
+Other   |            | 0.06051    |            |       |  0.16
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    47957 ave 47957 max 47957 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 48112472
+Ave neighs/atom = 375.879
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:39

bench/log.1Feb14.chain.fixed.linux.1

@@ -1,63 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 11.5156 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
-Loop time of 1.00129 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.201344 (20.1083)
-Bond  time (%) = 0.0870376 (8.69251)
-Neigh time (%) = 0.45714 (45.6549)
-Comm  time (%) = 0.0338521 (3.38083)
-Outpt time (%) = 0.000102043 (0.0101911)
-Other time (%) = 0.221819 (22.1532)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    9493 ave 9493 max 9493 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    155873 ave 155873 max 155873 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 155873
-Ave neighs/atom = 4.87103
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chain.fixed.linux.4

@@ -1,63 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 4.85536 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
-Loop time of 0.274804 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.0507675 (18.4741)
-Bond  time (%) = 0.0225385 (8.20169)
-Neigh time (%) = 0.121537 (44.2269)
-Comm  time (%) = 0.0207262 (7.54219)
-Outpt time (%) = 8.74996e-05 (0.0318408)
-Other time (%) = 0.0591468 (21.5233)
-
-Nlocal:    8000 ave 8030 max 7974 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    4177 ave 4191 max 4160 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Neighs:    38995.8 ave 39169 max 38852 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 155983
-Ave neighs/atom = 4.87447
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chain.scaled.linux.4

@@ -1,79 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units		lj
-atom_style	bond
-atom_modify	map hash
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  126720 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 13.4806 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
-Loop time of 1.16627 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 0.224354 (19.2369)
-Bond  time (%) = 0.0961447 (8.24378)
-Neigh time (%) = 0.510646 (43.7846)
-Comm  time (%) = 0.0876382 (7.5144)
-Outpt time (%) = 0.000156462 (0.0134156)
-Other time (%) = 0.24733 (21.207)
-
-Nlocal:    32000 ave 32015 max 31983 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    9492 ave 9522 max 9432 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs:    155837 ave 156079 max 155506 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-
-Total # of neighbors = 623349
-Ave neighs/atom = 4.86991
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chute.fixed.linux.1

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 21.4184 Mbytes
-Step Atoms KinEng 1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.540977 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.330571 (61.1064)
-Neigh time (%) = 0.0416589 (7.70067)
-Comm  time (%) = 0.018239 (3.3715)
-Outpt time (%) = 0.000189066 (0.034949)
-Other time (%) = 0.150319 (27.7865)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 115133
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.chute.fixed.linux.4

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 10.7034 Mbytes
-Step Atoms KinEng 1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.133553 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.0669281 (50.1135)
-Neigh time (%) = 0.01061 (7.9444)
-Comm  time (%) = 0.0142241 (10.6505)
-Outpt time (%) = 9.28044e-05 (0.0694888)
-Other time (%) = 0.041698 (31.2221)
-
-Nlocal:    8000 ave 8008 max 7992 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    2439 ave 2450 max 2428 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    29500.5 ave 30488 max 28513 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 118002
-Ave neighs/atom = 3.68756
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.chute.scaled.linux.4

@@ -1,75 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-variable	x index 1
-variable	y index 1
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-replicate	$x $y 1
-replicate	2 $y 1
-replicate	2 2 1
-  orthogonal box = (0 0 0) to (80 40 37.2923)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-3648 atoms in group bottom
-group		active subtract all bottom
-124352 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 22.3334 Mbytes
-Step Atoms KinEng 1 Volume 
-       0   128000    3136556.5    6404.5051    119335.13 
-     100   128000    3137168.3    6284.3873    119338.83 
-Loop time of 0.862817 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 0.518524 (60.0966)
-Neigh time (%) = 0.0441293 (5.11455)
-Comm  time (%) = 0.057479 (6.66178)
-Outpt time (%) = 0.000286222 (0.0331729)
-Other time (%) = 0.242399 (28.0939)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 460532
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.eam.fixed.linux.1

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Memory usage per processor = 15.3727 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 5.93175 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 5.20741 (87.7887)
-Neigh time (%) = 0.618579 (10.4283)
-Comm  time (%) = 0.0310862 (0.524064)
-Outpt time (%) = 0.000214815 (0.00362144)
-Other time (%) = 0.0744634 (1.25533)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19909 ave 19909 max 19909 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0

bench/log.1Feb14.eam.fixed.linux.4

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Memory usage per processor = 4.92441 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 1.57335 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 1.35199 (85.9304)
-Neigh time (%) = 0.160176 (10.1806)
-Comm  time (%) = 0.0413526 (2.62832)
-Outpt time (%) = 0.000119448 (0.00759193)
-Other time (%) = 0.0197157 (1.2531)
-
-Nlocal:    8000 ave 8008 max 7993 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9130.25 ave 9138 max 9122 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    301946 ave 302392 max 301360 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0

bench/log.1Feb14.eam.scaled.linux.4

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Memory usage per processor = 15.2891 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -453120            0   -426647.73    18704.012 
-      50    779.50001   -439457.02            0   -426560.06    52355.276 
-     100    797.97828   -439764.76            0   -426562.07     51474.74 
-Loop time of 6.55459 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 5.63064 (85.9037)
-Neigh time (%) = 0.698691 (10.6596)
-Comm  time (%) = 0.123277 (1.88077)
-Outpt time (%) = 0.000314116 (0.00479231)
-Other time (%) = 0.101672 (1.55115)
-
-Nlocal:    32000 ave 32092 max 31914 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    19910 ave 19997 max 19818 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 4829126
-Ave neighs/atom = 37.7275
-Neighbor list builds = 14
-Dangerous builds = 0

bench/log.1Feb14.lj.fixed.linux.1

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Memory usage per processor = 13.2266 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 2.26599 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 1.92891 (85.1244)
-Neigh time (%) = 0.252641 (11.1493)
-Comm  time (%) = 0.0243704 (1.07549)
-Outpt time (%) = 0.000110865 (0.00489256)
-Other time (%) = 0.059957 (2.64596)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19657 ave 19657 max 19657 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.lj.fixed.linux.4

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Memory usage per processor = 4.31282 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 0.628341 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.505093 (80.3851)
-Neigh time (%) = 0.0659957 (10.5032)
-Comm  time (%) = 0.0406293 (6.46611)
-Outpt time (%) = 8.43406e-05 (0.0134227)
-Other time (%) = 0.016539 (2.63216)
-
-Nlocal:    8000 ave 8037 max 7964 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9007.5 ave 9050 max 8968 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs:    300708 ave 305113 max 297203 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.lj.scaled.linux.4

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Memory usage per processor = 13.1495 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
-     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
-Loop time of 2.54147 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 2.08305 (81.9623)
-Neigh time (%) = 0.258072 (10.1545)
-Comm  time (%) = 0.116279 (4.57528)
-Outpt time (%) = 0.000139415 (0.00548562)
-Other time (%) = 0.0839326 (3.30252)
-
-Nlocal:    32000 ave 32060 max 31939 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost:    19630.8 ave 19681 max 19562 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-
-Total # of neighbors = 4807797
-Ave neighs/atom = 37.5609
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.rhodo.fixed.linux.1

@@ -1,109 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 41070 25600
-Memory usage per processor = 139.238 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =     17.8100 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =     36.2348 (sec) ----------------
-TotEng   =    -25290.7592 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 26.0418 (71.8696)
-Bond  time (%) = 1.26644 (3.4951)
-Kspce time (%) = 3.24933 (8.96742)
-Neigh time (%) = 4.47968 (12.3629)
-Comm  time (%) = 0.0700378 (0.193289)
-Outpt time (%) = 0.000230074 (0.000634953)
-Other time (%) = 1.12729 (3.11108)
-
-FFT time (% of Kspce) = 0.276809 (8.51896)
-FFT Gflps 3d (1d only) = 1.87746 3.23903
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    47958 ave 47958 max 47958 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 12028107
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

bench/log.1Feb14.rhodo.fixed.linux.4

@@ -1,109 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 13230 6400
-Memory usage per processor = 54.595 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =      4.7061 (sec) ----------------
-TotEng   =    -25330.0829 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =      9.5889 (sec) ----------------
-TotEng   =    -25290.7592 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 9.58898 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 6.62576 (69.0976)
-Bond  time (%) = 0.317414 (3.31019)
-Kspce time (%) = 1.04771 (10.9262)
-Neigh time (%) = 1.15891 (12.0859)
-Comm  time (%) = 0.0844751 (0.88096)
-Outpt time (%) = 0.00015074 (0.00157201)
-Other time (%) = 0.354558 (3.69756)
-
-FFT time (% of Kspce) = 0.0967343 (9.23289)
-FFT Gflps 3d (1d only) = 5.37243 12.7459
-
-Nlocal:    8000 ave 8143 max 7933 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost:    22733.5 ave 22769 max 22693 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 12028107
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

bench/log.1Feb14.rhodo.scaled.linux.4

@@ -1,130 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-atom_modify	map hash
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  110892 bonds
-  161868 angles
-  227316 dihedrals
-  4136 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  6468 = # of size 2 clusters
-  14532 = # of size 3 clusters
-  2988 = # of size 4 clusters
-  16932 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248593
-  grid = 48 60 36
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0359793
-  estimated relative force accuracy = 0.00010835
-  using double precision FFTs
-  3d grid and FFT values/proc = 41615 25920
-Memory usage per processor = 146.358 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
-PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
-E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
-E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -142.3092 
-Volume   =   1231980.1340 
----------------- Step       50 ----- CPU =     18.9852 (sec) ----------------
-TotEng   =   -101320.2676 KinEng   =     86003.4837 Temp     =       299.8118 
-PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
-E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
-E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
-Volume   =   1232126.1855 
----------------- Step      100 ----- CPU =     38.9161 (sec) ----------------
-TotEng   =   -101158.1853 KinEng   =     86355.6148 Temp     =       301.0393 
-PotEng   =   -187513.8001 E_bond   =     10272.0693 E_angle  =     43128.6453 
-E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
-E_coul   =    825583.7120 E_long   =  -1080572.5667 Press    =        15.2151 
-Volume   =   1232535.8423 
-Loop time of 38.9162 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 27.1908 (69.8701)
-Bond  time (%) = 1.30758 (3.35999)
-Kspce time (%) = 3.99359 (10.262)
-Neigh time (%) = 4.65272 (11.9557)
-Comm  time (%) = 0.216829 (0.557168)
-Outpt time (%) = 0.000280738 (0.000721391)
-Other time (%) = 1.55441 (3.99426)
-
-FFT time (% of Kspce) = 0.448314 (11.2258)
-FFT Gflps 3d (1d only) = 5.34183 11.5795
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    47957 ave 47957 max 47957 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 48112472
-Ave neighs/atom = 375.879
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

doc/.gitignore

@@ -0,0 +1 @@
+

doc/Eqs/fix_ti_rs_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \lambda F_{\text{int}}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_spring_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
-$$
-
-\end{document}

doc/Eqs/improper_umbrella.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=\frac{1}{2}K\left( \frac{1+cos\omega_0}{sin\omega_0}\right) ^2 \left( cos\omega - cos\omega_0\right) \qquad \omega_0 \neq 0^o
-$$
-
-$$
-E=K\left( 1-cos\omega\right)  \qquad \omega_0 = 0^o
-$$
-
-\end{document}

doc/Makefile

@@ -0,0 +1,126 @@
+# Makefile for LAMMPS documentation
+
+SHELL 	      = /bin/bash
+SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+BUILDDIR      = /tmp/lammps-docs-$(SHA1)
+RSTDIR        = $(BUILDDIR)/rst
+VENV          = $(BUILDDIR)/docenv
+TXT2RST       = $(VENV)/bin/txt2rst
+
+PYTHON        = $(shell which python3)
+
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
+$(error Python3 was not found! Please check README.md for further instructions)
+endif
+
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
+$(error virtualenv was not found! Please check README.md for further instructions)
+endif
+
+SOURCES=$(wildcard src/*.txt)
+OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+
+.PHONY: help clean-all clean html pdf old venv
+
+# ------------------------------------------
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       create HTML doc pages in html dir"
+	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  clean      remove all intermediate RST files"
+	@echo "  clean-all  reset the entire build environment"
+	@echo "  txt2html   build txt2html tool"
+
+# ------------------------------------------
+
+clean-all:
+	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+
+clean:
+	rm -rf $(RSTDIR)
+
+html: $(OBJECTS)
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		deactivate ;\
+	)
+	-rm html/searchindex.js
+	@rm -rf html/_sources
+	@rm -rf html/PDF
+	@rm -rf html/USER
+	@cp -r src/PDF html/PDF
+	@cp -r src/USER html/USER
+	@rm -rf html/PDF/.[sg]*
+	@rm -rf html/USER/.[sg]*
+	@rm -rf html/USER/*/.[sg]*
+	@rm -rf html/USER/*/*.[sg]*
+	@echo "Build finished. The HTML pages are in doc/html."
+
+pdf: utils/txt2html/txt2html.exe
+	@(\
+		cd src; \
+		../utils/txt2html/txt2html.exe -b *.txt; \
+		htmldoc --batch lammps.book;          \
+		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q $$s lammps.book || \
+			echo doc file $$s missing in src/lammps.book; done; \
+		rm *.html; \
+		cd Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
+	)
+
+old: utils/txt2html/txt2html.exe
+	@rm -rf old
+	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
+	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
+	  mv *.html ../old; \
+	  cp Eqs/*.jpg ../old/Eqs; \
+	  cp JPG/* ../old/JPG; \
+	  cp PDF/* ../old/PDF;
+
+fetch:
+	@rm -rf html_www Manual_www.pdf Developer_www.pdf
+	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
+	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
+	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
+	@tar xzf lammps-doc.tar.gz
+	@rm -f lammps-doc.tar.gz
+
+txt2html: utils/txt2html/txt2html.exe
+
+# ------------------------------------------
+
+utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
+	g++ -O -Wall -o $@ $<
+
+$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
+	@(\
+		mkdir -p $(RSTDIR) ; \
+		. $(VENV)/bin/activate ;\
+		txt2rst $< > $@ ;\
+		deactivate ;\
+	)
+
+$(VENV):
+	@( \
+		virtualenv -p $(PYTHON) $(VENV); \
+		. $(VENV)/bin/activate; \
+		pip install Sphinx; \
+		pip install sphinxcontrib-images; \
+		deactivate;\
+	)
+
+$(TXT2RST): $(VENV)
+	@( \
+		. $(VENV)/bin/activate; \
+		(cd utils/converters;\
+		python setup.py develop);\
+		deactivate;\
+	)

doc/Manual.html

@@ -1,428 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Sep 2014 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H1></H1>
-
-<CENTER><H3>LAMMPS Documentation 
-</H3></CENTER>
-<CENTER><H4>5 Sep 2014 version 
-</H4></CENTER>
-<H4>Version info: 
-</H4>
-<P>The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
-the WWW site</A>.  Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-</P>
-<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. 
-
-<LI>If you browse the HTML doc pages included in your tarball, they
-describe the version you have. 
-
-<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
-about once per month.  This is because it is large, and we don't want
-it to be part of every patch. 
-
-<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.  
-</UL>
-<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-</P>
-<P>LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers.  It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
-</P>
-<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
-http://lammps.sandia.gov has more information about the code and its
-uses.
-</P>
-
-
-
-
-<HR>
-
-<P>The LAMMPS documentation is organized into the following sections.  If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
-</P>
-<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
-page</A> at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-</P>
-<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
-<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>
-</P>
-<OL><LI><A HREF = "Section_intro.html">Introduction</A> 
-
-<UL>  1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A> 
-<BR>
-  1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A> 
-<BR>
-  1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A> 
-<BR>
-  1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A> 
-<BR>
-  1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A> 
-<BR></UL>
-<LI><A HREF = "Section_start.html">Getting started</A> 
-
-<UL>  2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A> 
-<BR>
-  2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A> 
-<BR>
-  2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A> 
-<BR>
-  2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A> 
-<BR>
-  2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A> 
-<BR>
-  2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A> 
-<BR>
-  2.7 <A HREF = "Section_start.html#start_7">Command-line options</A> 
-<BR>
-  2.8 <A HREF = "Section_start.html#start_8">Screen output</A> 
-<BR>
-  2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A> 
-<BR></UL>
-<LI><A HREF = "Section_commands.html">Commands</A> 
-
-<UL>  3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A> 
-<BR>
-  3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A> 
-<BR>
-  3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A> 
-<BR>
-  3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A> 
-<BR>
-  3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A> 
-<BR></UL>
-<LI><A HREF = "Section_packages.html">Packages</A> 
-
-<UL>  4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A> 
-<BR>
-  4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A> 
-<BR></UL>
-<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A> 
-
-<UL>  5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A> 
-<BR>
-  5.2 <A HREF = "Section_accelerate.html#acc_2">General strategies</A> 
-<BR>
-  5.3 <A HREF = "Section_accelerate.html#acc_3">Packages with optimized styles</A> 
-<BR>
-  5.4 <A HREF = "Section_accelerate.html#acc_4">OPT package</A> 
-<BR>
-  5.5 <A HREF = "Section_accelerate.html#acc_5">USER-OMP package</A> 
-<BR>
-  5.6 <A HREF = "Section_accelerate.html#acc_6">GPU package</A> 
-<BR>
-  5.7 <A HREF = "Section_accelerate.html#acc_7">USER-CUDA package</A> 
-<BR>
-  5.8 <A HREF = "Section_accelerate.html#acc_8">KOKKOS package</A> 
-<BR>
-  5.9 <A HREF = "Section_accelerate.html#acc_9">USER-INTEL package</A> 
-<BR>
-  5.10 <A HREF = "acc_10">Comparison of GPU and USER-CUDA packages</A> 
-<BR></UL>
-<LI><A HREF = "Section_howto.html">How-to discussions</A> 
-
-<UL>  6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A> 
-<BR>
-  6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A> 
-<BR>
-  6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A> 
-<BR>
-  6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A> 
-<BR>
-  6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A> 
-<BR>
-  6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A> 
-<BR>
-  6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A> 
-<BR>
-  6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A> 
-<BR>
-  6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A> 
-<BR>
-  6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A> 
-<BR>
-  6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A> 
-<BR>
-  6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A> 
-<BR>
-  6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A> 
-<BR>
-  6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A> 
-<BR>
-  6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> 
-<BR>
-  6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A> 
-<BR>
-  6.17 <A HREF = "Section_howto.html#howto_17">Walls</A> 
-<BR>
-  6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A> 
-<BR>
-  6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A> 
-<BR>
-  6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A> 
-<BR>
-  6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A> 
-<BR>
-  6.22 <A HREF = "howto_22">Calculating a diffusion coefficient</A> 
-<BR></UL>
-<LI><A HREF = "Section_example.html">Example problems</A> 
-
-<LI><A HREF = "Section_perf.html">Performance & scalability</A> 
-
-<LI><A HREF = "Section_tools.html">Additional tools</A> 
-
-<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A> 
-
-<UL>  10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A> 
-<BR>
-  10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A> 
-<BR>
-  10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A> 
-<BR>
-  10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A> 
-<BR>
-  10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A> 
-<BR>
-  10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A> 
-<BR>
-  10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A> 
-<BR>
-  10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A> 
-<BR>
-  10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A> 
-<BR>
-  10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A> 
-<BR>
-  10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A> 
-<BR>
-  10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A> 
-<BR>
-  10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A> 
-<BR>
-  10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A> 
-<BR>
-  10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A> 
-<BR></UL>
-<LI><A HREF = "Section_python.html">Python interface</A> 
-
-<UL>  11.1 <A HREF = "Section_python.html#py_1">Building LAMMPS as a shared library</A> 
-<BR>
-  11.2 <A HREF = "Section_python.html#py_2">Installing the Python wrapper into Python</A> 
-<BR>
-  11.3 <A HREF = "Section_python.html#py_3">Extending Python with MPI to run in parallel</A> 
-<BR>
-  11.4 <A HREF = "Section_python.html#py_4">Testing the Python-LAMMPS interface</A> 
-<BR>
-  11.5 <A HREF = "Section_python.html#py_5">Using LAMMPS from Python</A> 
-<BR>
-  11.6 <A HREF = "Section_python.html#py_6">Example Python scripts that use LAMMPS</A> 
-<BR></UL>
-<LI><A HREF = "Section_errors.html">Errors</A> 
-
-<UL>  12.1 <A HREF = "Section_errors.html#err_1">Common problems</A> 
-<BR>
-  12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A> 
-<BR>
-  12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A> 
-<BR></UL>
-<LI><A HREF = "Section_history.html">Future and history</A> 
-
-<UL>  13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A> 
-<BR>
-  13.2 <A HREF = "Section_history.html#hist_2">Past versions</A> 
-<BR></UL>
-
-</OL>
-
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doc/Manual.txt

@@ -1,262 +0,0 @@
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Sep 2014 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-<H1></H1>
-
-LAMMPS Documentation :c,h3
-5 Sep 2014 version :c,h4
-
-Version info: :h4
-
-The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on "this page of
-the WWW site"_bug.  Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-
-If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. :ulb,l
-
-If you browse the HTML doc pages included in your tarball, they
-describe the version you have. :l
-
-The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
-about once per month.  This is because it is large, and we don't want
-it to be part of every patch. :l
-
-There is also a "Developer.pdf"_Developer.pdf file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.  :ule,l
-
-LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-
-LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers.  It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
-
-The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The "LAMMPS WWW Site"_lws at
-http://lammps.sandia.gov has more information about the code and its
-uses.
-
-:link(bug,http://lammps.sandia.gov/bug.html)
-:link(sjp,http://www.sandia.gov/~sjplimp)
-
-:line
-
-The LAMMPS documentation is organized into the following sections.  If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
-
-Once you are familiar with LAMMPS, you may want to bookmark "this
-page"_Section_commands.html#comm at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://www.easysw.com/htmldoc
-
-"Introduction"_Section_intro.html :olb,l
-  1.1 "What is LAMMPS"_intro_1 :ulb,b
-  1.2 "LAMMPS features"_intro_2 :b
-  1.3 "LAMMPS non-features"_intro_3 :b
-  1.4 "Open source distribution"_intro_4 :b
-  1.5 "Acknowledgments and citations"_intro_5 :ule,b
-"Getting started"_Section_start.html :l
-  2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
-  2.2 "Making LAMMPS"_start_2 :b
-  2.3 "Making LAMMPS with optional packages"_start_3 :b
-  2.4 "Building LAMMPS via the Make.py script"_start_4 :b
-  2.5 "Building LAMMPS as a library"_start_5 :b
-  2.6 "Running LAMMPS"_start_6 :b
-  2.7 "Command-line options"_start_7 :b
-  2.8 "Screen output"_start_8 :b
-  2.9 "Tips for users of previous versions"_start_9 :ule,b
-"Commands"_Section_commands.html :l
-  3.1 "LAMMPS input script"_cmd_1 :ulb,b
-  3.2 "Parsing rules"_cmd_2 :b
-  3.3 "Input script structure"_cmd_3 :b
-  3.4 "Commands listed by category"_cmd_4 :b
-  3.5 "Commands listed alphabetically"_cmd_5 :ule,b
-"Packages"_Section_packages.html :l
-  4.1 "Standard packages"_pkg_1 :ulb,b
-  4.2 "User packages"_pkg_2 :ule,b
-"Accelerating LAMMPS performance"_Section_accelerate.html :l
-  5.1 "Measuring performance"_acc_1 :ulb,b
-  5.2 "General strategies"_acc_2 :b
-  5.3 "Packages with optimized styles"_acc_3 :b
-  5.4 "OPT package"_acc_4 :b
-  5.5 "USER-OMP package"_acc_5 :b
-  5.6 "GPU package"_acc_6 :b
-  5.7 "USER-CUDA package"_acc_7 :b
-  5.8 "KOKKOS package"_acc_8 :b
-  5.9 "USER-INTEL package"_acc_9 :b
-  5.10 "Comparison of GPU and USER-CUDA packages"_acc_10 :ule,b
-"How-to discussions"_Section_howto.html :l
-  6.1 "Restarting a simulation"_howto_1 :ulb,b
-  6.2 "2d simulations"_howto_2 :b
-  6.3 "CHARMM and AMBER force fields"_howto_3 :b
-  6.4 "Running multiple simulations from one input script"_howto_4 :b
-  6.5 "Multi-replica simulations"_howto_5 :b
-  6.6 "Granular models"_howto_6 :b
-  6.7 "TIP3P water model"_howto_7 :b
-  6.8 "TIP4P water model"_howto_8 :b
-  6.9 "SPC water model"_howto_9 :b
-  6.10 "Coupling LAMMPS to other codes"_howto_10 :b
-  6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
-  6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
-  6.13 "NEMD simulations"_howto_13 :b
-  6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
-  6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
-  6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
-  6.17 "Walls"_howto_17 :b
-  6.18 "Elastic constants"_howto_18 :b
-  6.19 "Library interface to LAMMPS"_howto_19 :b
-  6.20 "Calculating thermal conductivity"_howto_20 :b
-  6.21 "Calculating viscosity"_howto_21 :b
-  6.22 "Calculating a diffusion coefficient"_howto_22 :ule,b
-"Example problems"_Section_example.html :l
-"Performance & scalability"_Section_perf.html :l
-"Additional tools"_Section_tools.html :l
-"Modifying & extending LAMMPS"_Section_modify.html :l
-  10.1 "Atom styles"_mod_1 :ulb,b
-  10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
-  10.3 "Compute styles"_mod_3 :b
-  10.4 "Dump styles"_mod_4 :b
-  10.5 "Dump custom output options"_mod_5 :b
-  10.6 "Fix styles"_mod_6 :b
-  10.7 "Input script commands"_mod_7 :b
-  10.8 "Kspace computations"_mod_8 :b
-  10.9 "Minimization styles"_mod_9 :b
-  10.10 "Pairwise potentials"_mod_10 :b
-  10.11 "Region styles"_mod_11 :b
-  10.12 "Body styles"_mod_12 :b
-  10.13 "Thermodynamic output options"_mod_13 :b
-  10.14 "Variable options"_mod_14 :b
-  10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
-"Python interface"_Section_python.html :l
-  11.1 "Building LAMMPS as a shared library"_py_1 :ulb,b
-  11.2 "Installing the Python wrapper into Python"_py_2 :b
-  11.3 "Extending Python with MPI to run in parallel"_py_3 :b
-  11.4 "Testing the Python-LAMMPS interface"_py_4 :b
-  11.5 "Using LAMMPS from Python"_py_5 :b
-  11.6 "Example Python scripts that use LAMMPS"_py_6 :ule,b
-"Errors"_Section_errors.html :l
-  12.1 "Common problems"_err_1 :ulb,b
-  12.2 "Reporting bugs"_err_2 :b
-  12.3 "Error & warning messages"_err_3 :ule,b
-"Future and history"_Section_history.html :l
-  13.1 "Coming attractions"_hist_1 :ulb,b
-  13.2 "Past versions"_hist_2 :ule,b
-:ole
-
-:link(intro_1,Section_intro.html#intro_1)
-:link(intro_2,Section_intro.html#intro_2)
-:link(intro_3,Section_intro.html#intro_3)
-:link(intro_4,Section_intro.html#intro_4)
-:link(intro_5,Section_intro.html#intro_5)
-
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-:link(start_9,Section_start.html#start_9)
-
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
-:link(pkg_1,Section_packages.html#pkg_1)
-:link(pkg_2,Section_packages.html#pkg_2)
-
-:link(acc_1,Section_accelerate.html#acc_1)
-:link(acc_2,Section_accelerate.html#acc_2)
-:link(acc_3,Section_accelerate.html#acc_3)
-:link(acc_4,Section_accelerate.html#acc_4)
-:link(acc_5,Section_accelerate.html#acc_5)
-:link(acc_6,Section_accelerate.html#acc_6)
-:link(acc_7,Section_accelerate.html#acc_7)
-:link(acc_8,Section_accelerate.html#acc_8)
-:link(acc_9,Section_accelerate.html#acc_9)
-
-:link(howto_1,Section_howto.html#howto_1)
-:link(howto_2,Section_howto.html#howto_2)
-:link(howto_3,Section_howto.html#howto_3)
-:link(howto_4,Section_howto.html#howto_4)
-:link(howto_5,Section_howto.html#howto_5)
-:link(howto_6,Section_howto.html#howto_6)
-:link(howto_7,Section_howto.html#howto_7)
-:link(howto_8,Section_howto.html#howto_8)
-:link(howto_9,Section_howto.html#howto_9)
-:link(howto_10,Section_howto.html#howto_10)
-:link(howto_11,Section_howto.html#howto_11)
-:link(howto_12,Section_howto.html#howto_12)
-:link(howto_13,Section_howto.html#howto_13)
-:link(howto_14,Section_howto.html#howto_14)
-:link(howto_15,Section_howto.html#howto_15)
-:link(howto_16,Section_howto.html#howto_16)
-:link(howto_17,Section_howto.html#howto_17)
-:link(howto_18,Section_howto.html#howto_18)
-:link(howto_19,Section_howto.html#howto_19)
-:link(howto_20,Section_howto.html#howto_20)
-:link(howto_21,Section_howto.html#howto_21)
-
-:link(mod_1,Section_modify.html#mod_1)
-:link(mod_2,Section_modify.html#mod_2)
-:link(mod_3,Section_modify.html#mod_3)
-:link(mod_4,Section_modify.html#mod_4)
-:link(mod_5,Section_modify.html#mod_5)
-:link(mod_6,Section_modify.html#mod_6)
-:link(mod_7,Section_modify.html#mod_7)
-:link(mod_8,Section_modify.html#mod_8)
-:link(mod_9,Section_modify.html#mod_9)
-:link(mod_10,Section_modify.html#mod_10)
-:link(mod_11,Section_modify.html#mod_11)
-:link(mod_12,Section_modify.html#mod_12)
-:link(mod_13,Section_modify.html#mod_13)
-:link(mod_14,Section_modify.html#mod_14)
-:link(mod_15,Section_modify.html#mod_15)
-
-:link(py_1,Section_python.html#py_1)
-:link(py_2,Section_python.html#py_2)
-:link(py_3,Section_python.html#py_3)
-:link(py_4,Section_python.html#py_4)
-:link(py_5,Section_python.html#py_5)
-:link(py_6,Section_python.html#py_6)
-
-:link(err_1,Section_errors.html#err_1)
-:link(err_2,Section_errors.html#err_2)
-:link(err_3,Section_errors.html#err_3)
-
-:link(hist_1,Section_history.html#hist_1)
-:link(hist_2,Section_history.html#hist_2)
-
-</BODY>

doc/README

@@ -0,0 +1,53 @@
+Generation of LAMMPS Documentation
+
+The generation of all documentation is managed by the Makefile in this
+dir.
+
+----------------
+
+Options:
+
+make html         # generate HTML in html dir using Sphinx
+make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
+                  #   in this dir via htmldoc and pdflatex
+make old          # generate old-style HTML pages in old dir via txt2html
+make fetch        # fetch HTML doc pages and 2 PDF files from web site
+                  #   as a tarball and unpack into html dir and 2 PDFs
+make clean        # remove intermediate RST files created by HTML build
+make clean-all    # remove entire build folder and any cached data
+
+----------------
+
+Installing prerequisites for HTML build
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed.  Here are instructions for common setups:
+
+# Ubuntu
+
+sudo apt-get install python-virtualenv
+
+# Fedora (up to version 21)
+# Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+sudo yum install python3-virtualenv
+
+# Fedora (since version 22)
+
+sudo dnf install python3-virtualenv
+
+# MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from
+https://www.python.org and install it.  This will install both Python
+3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.

doc/Scripts/correlate.py

@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-"""
-  function: 
-    parse the block of thermo data in a lammps logfile and perform auto- and 
-    cross correlation of the specified column data.  The total sum of the 
-    correlation is also computed which can be converted to an integral by 
-    multiplying by the timestep. 
-  output:
-    standard output contains column data for the auto- & cross correlations 
-    plus the total sum of each. Note, only the upper triangle of the 
-    correlation matrix is computed.
-  usage: 
-    correlate.py [-c col] <-c col2> <-s max_correlation_time>  [logfile] 
-"""
-import sys
-import re
-import array
-
-# parse command line
-
-maxCorrelationTime = 0
-cols = array.array("I")
-nCols = 0
-args = sys.argv[1:]
-index = 0
-while index < len(args):
-  arg = args[index]
-  index += 1
-  if   (arg == "-c"):
-    cols.append(int(args[index])-1)
-    nCols += 1
-    index += 1
-  elif (arg == "-s"):
-    maxCorrelationTime = int(args[index])
-    index += 1
-  else :
-    filename = arg
-if (nCols < 1): raise RuntimeError, 'no data columns requested'
-data = [array.array("d")]
-for s in range(1,nCols)  : data.append( array.array("d") )
-
-# read data block from log file
-
-start = False
-input = open(filename)
-nSamples = 0
-pattern = re.compile('\d')
-line = input.readline()
-while line :
-  columns = line.split()
-  if (columns and pattern.match(columns[0])) :
-    for i in range(nCols): 
-      data[i].append( float(columns[cols[i]]) )
-    nSamples += 1
-    start = True
-  else :
-     if (start) : break
-  line = input.readline()
-print "# read :",nSamples," samples of ", nCols," data"
-if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
- 
-# correlate and integrate
-
-correlationPairs = []
-for i in range(0,nCols):
-  for j in range(i,nCols): # note only upper triangle of the correlation matrix
-    correlationPairs.append([i,j])
-header = "# "
-for k in range(len(correlationPairs)):
-  i = str(correlationPairs[k][0]+1)
-  j = str(correlationPairs[k][1]+1)
-  header += " C"+i+j+" sum_C"+i+j
-print header
-nCorrelationPairs = len(correlationPairs)
-sum = [0.0] * nCorrelationPairs
-for s in range(maxCorrelationTime)  :
-  correlation = [0.0] * nCorrelationPairs
-  nt = nSamples-s
-  for t in range(0,nt)  :
-    for p in range(nCorrelationPairs):
-      i = correlationPairs[p][0]
-      j = correlationPairs[p][1]
-      correlation[p] += data[i][t]*data[j][s+t]
-  output = ""
-  for p in range(0,nCorrelationPairs):
-    correlation[p] /= nt
-    sum[p] += correlation[p]
-    output += str(correlation[p]) + " " + str(sum[p]) + " "
-  print output

doc/Section_commands.html

@@ -1,642 +0,0 @@
-<HTML>
-<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>3. Commands 
-</H3>
-<P>This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-</P>
-3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
-3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
-3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
-3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
-3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
-
-<HR>
-
-<HR>
-
-<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script 
-</H4>
-<P>LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-</P>
-<P>In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-</P>
-<P>(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-</P>
-<PRE>timestep 0.5 
-run      100 
-run      100 
-</PRE>
-<P>does something different than this sequence:
-</P>
-<PRE>run      100 
-timestep 0.5 
-run      100 
-</PRE>
-<P>In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-</P>
-<P>(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-</P>
-<P>(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-<A HREF = "read_data.html">read_data</A> command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the <A HREF = "processors.html">processors</A> and
-<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-</P>
-<P>Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  <A HREF = "Section_errors.html">This section</A> gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-</P>
-<HR>
-
-<A NAME = "cmd_2"></A><H4>3.2 Parsing rules 
-</H4>
-<P>Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-</P>
-<P>Here is how each line in the input script is parsed by LAMMPS:
-</P>
-<P>(1) If the last printable character on the line is a "&" character
-(with no surrounding quotes), the command is assumed to continue on
-the next line.  The next line is concatenated to the previous line by
-removing the "&" character and newline.  This allows long commands to
-be continued across two or more lines.
-</P>
-<P>(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-</P>
-<P>(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).  
-</P>
-<P>If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus ${myTemp} and $x refer to variable names "myTemp" and
-"x".
-</P>
-<P>How the variable is converted to a text string depends on what style
-of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-</P>
-<P>As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an <A HREF = "variable.html">equal-style variable</A>.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-</P>
-<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete 
-</PRE>
-<P>can be replaced by 
-</P>
-<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE 
-</PRE>
-<P>so that you do not have to define (or discard) a temporary variable X.
-</P>
-<P>Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-</P>
-<PRE>variable        a equal 2
-variable        b2 equal 4
-print           "B2 = ${b$a}" 
-</PRE>
-<P>Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-<A HREF = "variable.html">equal-style variable</A>.
-</P>
-<P>See the <A HREF = "variable.html">variable</A> command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-</P>
-<P>(4) The line is broken into "words" separated by whitespace (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-</P>
-<P>(5) The first word is the command name.  All successive words in the
-line are arguments.
-</P>
-<P>(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either double or single quotes.  A long single
-argument enclosed in quotes can even span multiple lines if the "&"
-character is used, as described above.  E.g.
-</P>
-<PRE>print "Volume = $v"
-print 'Volume = $v'
-variable a string "red green blue &
-                   purple orange cyan"
-if "$<I>steps</I> > 1000" then quit 
-</PRE>
-<P>The quotes are removed when the single argument is stored internally.
-</P>
-<P>See the <A HREF = "dump_modify.html">dump modify format</A> or <A HREF = "print.html">print</A> or
-<A HREF = "if.html">if</A> commands for examples.  A "#" or "$" character that is
-between quotes will not be treated as a comment indicator in (2) or
-substituted for as a variable in (3). 
-</P>
-<P>IMPORTANT NOTE: If the argument is itself a command that requires a
-quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
-<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then the double and
-single quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-</P>
-<HR>
-
-<H4><A NAME = "cmd_3"></A>3.3 Input script structure 
-</H4>
-<P>This section describes the structure of a typical LAMMPS input script.
-The "examples" directory in the LAMMPS distribution contains many
-sample input scripts; the corresponding problems are discussed in
-<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
-WWW Site</A>.
-</P>
-<P>A LAMMPS input script typically has 4 parts:
-</P>
-<OL><LI>Initialization
-<LI>Atom definition
-<LI>Settings
-<LI>Run a simulation 
-</OL>
-<P>The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all the
-commands need only be used if a non-default value is desired.
-</P>
-<P>(1) Initialization
-</P>
-<P>Set parameters that need to be defined before atoms are created or
-read-in from a file.
-</P>
-<P>The relevant commands are <A HREF = "units.html">units</A>,
-<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
-<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
-<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
-</P>
-<P>If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
-<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
-<A HREF = "improper_style.html">improper_style</A>.
-</P>
-<P>(2) Atom definition
-</P>
-<P>There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the <A HREF = "read_data.html">read_data</A> or
-<A HREF = "read_restart.html">read_restart</A> commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
-<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "create_atoms.html">create_atoms</A>.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-<A HREF = "replicate.html">replicate</A> command.
-</P>
-<P>(3) Settings
-</P>
-<P>Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-</P>
-<P>Force field coefficients are set by these commands (they can also be
-set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
-<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
-<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
-<A HREF = "improper_coeff.html">improper_coeff</A>,
-<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
-<A HREF = "special_bonds.html">special_bonds</A>.
-</P>
-<P>Various simulation parameters are set by these commands:
-<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
-<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
-<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
-<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
-</P>
-<P>Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The <A HREF = "fix.html">fix</A> command comes in many flavors.
-</P>
-<P>Various computations can be specified for execution during a
-simulation using the <A HREF = "compute.html">compute</A>,
-<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
-commands.
-</P>
-<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
-and <A HREF = "restart.html">restart</A> commands.
-</P>
-<P>(4) Run a simulation
-</P>
-<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
-command.  Energy minimization (molecular statics) is performed using
-the <A HREF = "minimize.html">minimize</A> command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-<A HREF = "temper.html">temper</A> command.
-</P>
-<HR>
-
-<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category 
-</H4>
-<P>This section lists all LAMMPS commands, grouped by category.  The
-<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-</P>
-<P>Initialization:
-</P>
-<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
-<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
-<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
-</P>
-<P>Atom definition:
-</P>
-<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
-<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
-<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
-</P>
-<P>Force fields:
-</P>
-<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
-<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
-<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
-<A HREF = "dihedral_style.html">dihedral_style</A>,
-<A HREF = "improper_coeff.html">improper_coeff</A>,
-<A HREF = "improper_style.html">improper_style</A>,
-<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
-<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
-<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
-<A HREF = "special_bonds.html">special_bonds</A>
-</P>
-<P>Settings:
-</P>
-<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
-<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
-<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
-<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
-<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
-</P>
-<P>Fixes:
-</P>
-<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
-</P>
-<P>Computes:
-</P>
-<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
-<A HREF = "uncompute.html">uncompute</A>
-</P>
-<P>Output:
-</P>
-<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
-<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
-<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
-<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
-<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
-<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
-</P>
-<P>Actions:
-</P>
-<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
-<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
-<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
-<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
-</P>
-<P>Miscellaneous:
-</P>
-<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
-<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
-<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
-<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
-</P>
-<HR>
-
-<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands 
-</H4>
-<P>This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands.  The <A HREF = "#cmd_4">previous
-section</A> lists the same commands, grouped by category.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "comm_modify.html">comm_modify</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "comm_style.html">comm_style</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional commands in USER packages, which can be used if
-<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Fix styles 
-</H4>
-<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions of each style
-or click on the style itself for a full description.  Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the <A HREF = "Section_accelerate.html">appropriate accelerated package</A>.
-This is indicated by additional letters in parenthesis: c = USER-CUDA,
-g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce (c)</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce (c)</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d (c)</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze (c)</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity (co)</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin (k)</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (o)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (co)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (co)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional fix styles in USER packages, which can be used if
-<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Compute styles 
-</H4>
-<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
-each style or click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional compute styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Pair_style potentials 
-</H4>
-<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
-potentials.  Click on the style itself for a full description.  Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/dsf (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgot)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy (cgot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgio)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgo)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (co)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgo)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgo)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (co)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (co)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (o)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional pair styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd (o)</A></TD><TD ><A HREF = "pair_edip.html">edip (o)</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Bond_style potentials 
-</H4>
-<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
-potentials.  Click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "bond_none.html">none</A></TD><TD ><A HREF = "bond_hybrid.html">hybrid</A></TD><TD ><A HREF = "bond_class2.html">class2 (o)</A></TD><TD ><A HREF = "bond_fene.html">fene (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_fene_expand.html">fene/expand (o)</A></TD><TD ><A HREF = "bond_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "bond_morse.html">morse (o)</A></TD><TD ><A HREF = "bond_nonlinear.html">nonlinear (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_quartic.html">quartic (o)</A></TD><TD ><A HREF = "bond_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional bond styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift (o)</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Angle_style potentials 
-</H4>
-<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
-angle potentials.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_none.html">none</A></TD><TD ><A HREF = "angle_hybrid.html">hybrid</A></TD><TD ><A HREF = "angle_charmm.html">charmm (o)</A></TD><TD ><A HREF = "angle_class2.html">class2 (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_cosine.html">cosine (o)</A></TD><TD ><A HREF = "angle_cosine_delta.html">cosine/delta (o)</A></TD><TD ><A HREF = "angle_cosine_periodic.html">cosine/periodic (o)</A></TD><TD ><A HREF = "angle_cosine_squared.html">cosine/squared (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "angle_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional angle styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_cosine_shift.html">cosine/shift (o)</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "angle_dipole.html">dipole (o)</A></TD><TD ><A HREF = "angle_fourier.html">fourier (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_fourier_simple.html">fourier/simple (o)</A></TD><TD ><A HREF = "angle_quartic.html">quartic (o)</A></TD><TD ><A HREF = "angle_sdk.html">sdk</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Dihedral_style potentials 
-</H4>
-<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
-of dihedral potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "dihedral_none.html">none</A></TD><TD ><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD ><A HREF = "dihedral_charmm.html">charmm (o)</A></TD><TD ><A HREF = "dihedral_class2.html">class2 (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dihedral_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "dihedral_helix.html">helix (o)</A></TD><TD ><A HREF = "dihedral_multi_harmonic.html">multi/harmonic (o)</A></TD><TD ><A HREF = "dihedral_opls.html">opls (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional dihedral styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier (o)</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic (o)</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Improper_style potentials 
-</H4>
-<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
-of improper potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "improper_none.html">none</A></TD><TD ><A HREF = "improper_hybrid.html">hybrid</A></TD><TD ><A HREF = "improper_class2.html">class2 (o)</A></TD><TD ><A HREF = "improper_cvff.html">cvff (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "improper_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "improper_umbrella.html">umbrella (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional improper styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq (o)</A></TD><TD ><A HREF = "improper_fourier.html">fourier (o)</A></TD><TD ><A HREF = "improper_ring.html">ring (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Kspace solvers 
-</H4>
-<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
-Kspace solvers.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald (o)</A></TD><TD ><A HREF = "kspace_style.html">ewald/disp</A></TD><TD ><A HREF = "kspace_style.html">msm (o)</A></TD><TD ><A HREF = "kspace_style.html">msm/cg (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm (cgo)</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg (o)</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/tip4p (o)</A> 
-</TD></TR></TABLE></DIV>
-
-</HTML>

doc/Section_commands.txt

@@ -1,989 +0,0 @@
-"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-3. Commands :h3
-
-This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-
-3.1 "LAMMPS input script"_#cmd_1
-3.2 "Parsing rules"_#cmd_2
-3.3 "Input script structure"_#cmd_3
-3.4 "Commands listed by category"_#cmd_4
-3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
-
-:line
-:line
-
-3.1 LAMMPS input script :link(cmd_1),h4
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5 
-run      100 
-run      100 :pre
-
-does something different than this sequence:
-
-run      100 
-timestep 0.5 
-run      100 :pre
-
-In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  "This section"_Section_errors.html gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-
-:line
-
-3.2 Parsing rules :link(cmd_2),h4
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here is how each line in the input script is parsed by LAMMPS:
-
-(1) If the last printable character on the line is a "&" character
-(with no surrounding quotes), the command is assumed to continue on
-the next line.  The next line is concatenated to the previous line by
-removing the "&" character and newline.  This allows long commands to
-be continued across two or more lines.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).  
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by 
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by whitespace (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name.  All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either double or single quotes.  A long single
-argument enclosed in quotes can even span multiple lines if the "&"
-character is used, as described above.  E.g.
-
-print "Volume = $v"
-print 'Volume = $v'
-variable a string "red green blue &
-                   purple orange cyan"
-if "${steps} > 1000" then quit :pre
-
-The quotes are removed when the single argument is stored internally.
-
-See the "dump modify format"_dump_modify.html or "print"_print.html or
-"if"_if.html commands for examples.  A "#" or "$" character that is
-between quotes will not be treated as a comment indicator in (2) or
-substituted for as a variable in (3). 
-
-IMPORTANT NOTE: If the argument is itself a command that requires a
-quoted argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then the double and
-single quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-
-:line
-
-3.3 Input script structure :h4,link(cmd_3)
-
-This section describes the structure of a typical LAMMPS input script.
-The "examples" directory in the LAMMPS distribution contains many
-sample input scripts; the corresponding problems are discussed in
-"Section_example"_Section_example.html, and animated on the "LAMMPS
-WWW Site"_lws.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all the
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command.  Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
-:line
-
-3.4 Commands listed by category :link(cmd_4),h4
-
-This section lists all LAMMPS commands, grouped by category.  The
-"next section"_#cmd_5 lists the same commands alphabetically.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-
-Initialization:
-
-"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
-"boundary"_boundary.html, "dimension"_dimension.html,
-"newton"_newton.html, "processors"_processors.html, "units"_units.html
-
-Atom definition:
-
-"create_atoms"_create_atoms.html, "create_box"_create_box.html,
-"lattice"_lattice.html, "read_data"_read_data.html,
-"read_dump"_read_dump.html, "read_restart"_read_restart.html,
-"region"_region.html, "replicate"_replicate.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
-"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html, "pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html
-
-Settings:
-
-"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html,
-"min_modify"_min_modify.html, "min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
-
-Fixes:
-
-"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
-
-Computes:
-
-"compute"_compute.html, "compute_modify"_compute_modify.html,
-"uncompute"_uncompute.html
-
-Output:
-
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
-"restart"_restart.html, "thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
-"undump"_undump.html, "write_data"_write_data.html,
-"write_dump"_write_dump.html, "write_restart"_write_restart.html
-
-Actions:
-
-"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
-"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
-"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
-
-Miscellaneous:
-
-"clear"_clear.html, "echo"_echo.html, "if"_if.html,
-"include"_include.html, "jump"_jump.html, "label"_label.html,
-"log"_log.html, "next"_next.html, "print"_print.html,
-"shell"_shell.html, "variable"_variable.html
-
-:line
-
-3.5 Individual commands :h4,link(cmd_5),link(comm)
-
-This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands.  The "previous
-section"_#cmd_4 lists the same commands, grouped by category.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
-"dump movie"_dump_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"molecule"_molecule.html,
-"neb"_neb.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"group2ndx"_group2ndx.html :tb(c=1,ea=c)
-
-:line
-
-Fix styles :h4
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description.  Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Section_accelerate.html.
-This is indicated by additional letters in parenthesis: c = USER-CUDA,
-g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce (c)"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"aveforce (c)"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/spatial"_fix_ave_spatial.html,
-"ave/time"_fix_ave_time.html,
-"balance"_fix_balance.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"deform"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"enforce2d (c)"_fix_enforce2d.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"freeze (c)"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gravity (co)"_fix_gravity.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"langevin (k)"_fix_langevin.html,
-"lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
-"move"_fix_move.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (o)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (co)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (cko)"_fix_nve.html,
-"nve/asphere"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/body"_fix_nve_body.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (co)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/sllod (o)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/fcc"_fix_orient_fcc.html,
-"planeforce"_fix_planeforce.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom"_fix_property_atom.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (c)"_fix_setforce.html,
-"shake (c)"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"temp/berendsen (c)"_fix_temp_berendsen.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale (c)"_fix_temp_rescale.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous (c)"_fix_viscous.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"colvars"_fix_colvars.html,
-"imd"_fix_imd.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"meso/stationary"_fix_meso_stationary.html,
-"nph/eff"_fix_nh_eff.html,
-"npt/eff"_fix_nh_eff.html,
-"nve/eff"_fix_nve_eff.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"phonon"_fix_phonon.html,
-"qeq/reax"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"reax/c/bonds"_fix_reax_bonds.html,
-"reax/c/species"_fix_reaxc_species.html,
-"smd"_fix_smd.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/rs"_fix_ti_rs.html,
-"ti/spring"_fix_ti_spring.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h4
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"angle/local"_compute_angle_local.html,
-"atom/molecule"_compute_atom_molecule.html,
-"body/local"_compute_body_local.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/molecule"_compute_com_molecule.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"displace/atom"_compute_displace_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/molecule"_compute_gyration_molecule.html,
-"heat/flux"_compute_heat_flux.html,
-"improper/local"_compute_improper_local.html,
-"inertia/molecule"_compute_inertia_molecule.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/molecule"_compute_msd_molecule.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe (c)"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure (c)"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/molecule"_compute_property_molecule.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna.html,
-"snad/atom"_compute_sna.html,
-"snav/atom"_compute_sna.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (c)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/com"_compute_temp_com.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/partial (c)"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html,
-"vacf"_compute_vacf.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"ackland/atom"_compute_ackland_atom.html,
-"basal/atom"_compute_basal_atom.html,
-"fep"_compute_fep.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"meso_e/atom"_compute_meso_e_atom.html,
-"meso_rho/atom"_compute_meso_rho_atom.html,
-"meso_t/atom"_compute_meso_t_atom.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h4
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials.  Click on the style itself for a full description.  Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_pair_none.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (o)"_pair_airebo.html,
-"beck (go)"_pair_beck.html,
-"body"_pair_body.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/long (cgo)"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (cgo)"_pair_buck.html,
-"buck/coul/cut (cgo)"_pair_buck.html,
-"buck/coul/long (cgo)"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (go)"_pair_coul.html,
-"coul/dsf (go)"_pair_coul.html,
-"coul/long (go)"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/wolf (o)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (cgot)"_pair_eam.html,
-"eam/alloy (cgot)"_pair_eam.html,
-"eam/fs (cgot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (co)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj (o)"_pair_line_lj.html,
-"lj/charmm/coul/charmm (co)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (co)"_pair_charmm.html,
-"lj/charmm/coul/long (cgio)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/class2 (cgo)"_pair_class2.html,
-"lj/class2/coul/cut (co)"_pair_class2.html,
-"lj/class2/coul/long (cgo)"_pair_class2.html,
-"lj/cut (cgikot)"_pair_lj.html,
-"lj/cut/coul/cut (cgko)"_pair_lj.html,
-"lj/cut/coul/debye (cgo)"_pair_lj.html,
-"lj/cut/coul/dsf (go)"_pair_lj.html,
-"lj/cut/coul/long (cgikot)"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (cgo)"_pair_lj_expand.html,
-"lj/gromacs (cgo)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (co)"_pair_gromacs.html,
-"lj/long/coul/long (o)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (co)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (cgo)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam (o)"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (cgot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"reax"_pair_reax.html,
-"rebo (o)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (cgo)"_pair_sw.html,
-"table (gko)"_pair_table.html,
-"tersoff (co)"_pair_tersoff.html,
-"tersoff/mod (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (o)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj (o)"_pair_tri_lj.html,
-"yukawa (go)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (o)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"awpmd/cut"_pair_awpmd.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"eam/cd (o)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"eff/cut"_pair_eff.html,
-"gauss/cut"_pair_gauss.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/sdk (go)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"lj/sf (o)"_pair_lj_sf.html,
-"meam/spline"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"reax/c"_pair_reax_c.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h4
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials.  Click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_bond_none.html,
-"hybrid"_bond_hybrid.html,
-"class2 (o)"_bond_class2.html,
-"fene (o)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"harmonic (o)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h4
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_angle_none.html,
-"hybrid"_angle_hybrid.html,
-"charmm (o)"_angle_charmm.html,
-"class2 (o)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (o)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h4
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (o)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
-"harmonic (o)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (o)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h4
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_improper_none.html,
-"hybrid"_improper_hybrid.html,
-"class2 (o)"_improper_class2.html,
-"cvff (o)"_improper_cvff.html,
-"harmonic (o)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h4
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (cgo)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)