new library functions

Static analysis fixes

doc/.gitignore

@@ -1 +1,5 @@
 /html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf

doc/Makefile

@@ -8,19 +8,21 @@ VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 
 PYTHON        = $(shell which python3)
+HAS_PYTHON3    = NO
+HAS_VIRTUALENV = NO
 
-ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
-$(error Python3 was not found! Please check README.md for further instructions)
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
+HAS_PYTHON3 = YES
 endif
 
-ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
-$(error virtualenv was not found! Please check README.md for further instructions)
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+HAS_VIRTUALENV = YES
 endif
 
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv
 
 # ------------------------------------------
 
@@ -30,6 +32,7 @@ help:
 	@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 "  epub       create ePUB format manual for e-book readers"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
@@ -61,6 +64,20 @@ html: $(OBJECTS)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
+epub: $(OBJECTS)
+	@mkdir -p epub
+	@rm -f LAMMPS.epub
+	@cp src/JPG/lammps-logo.png epub/
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		deactivate ;\
+	)
+	@mv  epub/LAMMPS.epub .
+	@rm -rf epub
+	@echo "Build finished. The ePUB manual file is created."
+
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \
@@ -109,6 +126,8 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	)
 
 $(VENV):
+	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \

doc/README

@@ -1,13 +1,14 @@
 LAMMPS Documentation
 
 Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files:
+sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
 tools           tools and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
+LAMMPS.epub     Manual in ePUB format
 
 If you downloaded LAMMPS as a tarball from the web site, all these
 directories and files should be included.
@@ -49,6 +50,7 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 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 epub         # generate LAMMPS.epub in ePUB format using Sphinx 
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -92,5 +94,22 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
+[TBA]
 
+----------------
+
+Installing prerequisites for epub build
+
+## ePUB
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi
 

doc/src/Eqs/pair_dpd_conservative.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-$$
-F^C = A \omega_{ij} \qquad \qquad r_{ij} < r_c
-$$
-
-\end{document}

doc/src/Eqs/pair_dpd_energy.tex

@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  du_{i}^{cond} & = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\
+  du_{i}^{mech} & = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - 
+  \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - 
+  \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} \\
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Eqs/pair_dpd_energy_terms.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  \alpha_{ij}^{2} & = & 2k_{B}\kappa_{ij} \\
+  \sigma^{2}_{ij} & = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
+  \Theta_{ij}^{-1} & = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}}) \\
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="11 Oct 2016 version">
+<META NAME="docnumber" CONTENT="27 Oct 2016 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>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-11 Oct 2016 version :c,h4
+27 Oct 2016 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -106,7 +106,7 @@ 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.
+of variable it is; see the "variable"_variable.html 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
@@ -282,78 +282,135 @@ the "minimize"_minimize.html command.  A parallel tempering
 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.
+"next section"_#cmd_5 lists the same commands alphabetically.  The
+next section also includes (long) lists of style options for entries
+that appear in the following categories as a single command (fix,
+compute, pair, etc).  Commands that are added by user packages are not
+included in these categories, but they are in the next section.
 
 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
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html
 
-Atom definition:
+Setup simulation box:
 
-"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
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.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,
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.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,
+"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
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html
 
-Fixes:
+Operations within timestepping (fixes) and diagnositics (computes):
 
-"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
-
-Computes:
-
-"compute"_compute.html, "compute_modify"_compute_modify.html,
-"uncompute"_uncompute.html
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.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
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.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
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html
 
-Miscellaneous:
+Input script control:
 
-"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
+"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,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html
 
 :line
 
@@ -471,6 +528,8 @@ These are additional commands in USER packages, which can be used if
 package"_Section_start.html#start_3.
 
 "dump custom/vtk"_dump_custom_vtk.html,
+"dump nc"_dump_nc.html,
+"dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html :tb(c=3,ea=c)
 
@@ -516,6 +575,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "gcmc"_fix_gcmc.html,
 "gld"_fix_gld.html,
 "gravity (o)"_fix_gravity.html,
+"halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
@@ -618,6 +678,7 @@ package"_Section_start.html#start_3.
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
 "colvars"_fix_colvars.html,
+"dpd/energy"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
@@ -923,6 +984,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
 "vashishta (o)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
 "zbl (go)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

@@ -8116,11 +8116,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPM} :dt
 
@@ -8132,11 +8132,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPMDisp} :dt
 
@@ -8148,11 +8148,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Overflow of allocated fix vector storage} :dt
 

doc/src/Section_howto.txt

@@ -1854,13 +1854,19 @@ internal LAMMPS operations.  Note that LAMMPS classes are defined
 within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
 application.
 
-Library.cpp contains these 5 basic functions:
+Library.cpp contains these functions for creating and destroying an
+instance of LAMMPS and sending it commands to execute.  See the
+documentation in the src/library.cpp file for details:
 
 void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
 void lammps_close(void *)
 int lammps_version(void *)
 void lammps_file(void *, char *)
-char *lammps_command(void *, char *) :pre
+char *lammps_command(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
+void lammps_free(void *) :pre
 
 The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were "command-line
@@ -1880,6 +1886,10 @@ half to the other code and run both codes simultaneously before
 syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
 
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller.  Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialzed if necessary.
+
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
 
@@ -1891,44 +1901,93 @@ changes to the LAMMPS command syntax between versions. The returned
 LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
 20150902) that grows with every new LAMMPS version.
 
-The lammps_file() and lammps_command() functions are used to pass a
-file or string to LAMMPS as if it were an input script or single
-command in an input script.  Thus the calling code can read or
-generate a series of LAMMPS commands one line at a time and pass it
-thru the library interface to setup a problem and then run it,
-interleaving the lammps_command() calls with other calls to extract
-information from LAMMPS, perform its own operations, or call another
-code's library.
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
 
-Other useful functions are also included in library.cpp.  For example:
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages.  The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps_file() function passes the filename of an input script.
+The lammps_command() function passes a single command as a string.
+The lammps_commands_list() function passes multiple commands in a
+char** list.  In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline.  The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls.  See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+Library.cpp also contains these functions for extracting information
+from LAMMPS and setting value within LAMMPS.  Again, see the
+documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
 
 void *lammps_extract_global(void *, char *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
 int lammps_set_variable(void *, char *, char *)
+double lammps_get_thermo(void *, char *) :pre
+
 int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
-void lammps_put_coords(void *, double *) :pre
+void lammps_gather_atoms(void *, double *)
+void lammps_scatter_atoms(void *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre
 
-These can extract various global or per-atom quantities from LAMMPS as
-well as values calculated by a compute, fix, or variable.  The
-"set_variable" function can set an existing string-style variable to a
-new value, so that subsequent LAMMPS commands can access the variable.
-The "get" and "put" operations can retrieve and reset atom
-coordinates.  See the library.cpp file and its associated header file
-library.h for details.
+The extract functions return a pointer to various global or per-atom
+quantities stored in LAMMPS or to values calculated by a compute, fix,
+or variable.  The pointer returned by the extract_global() function
+can be used as a permanent reference to a value which may change.  For
+the other extract functions, the underlying storage may be reallocated
+as LAMMPS runs, so you need to re-call the function to assure a
+current pointer or returned value(s).
 
-The key idea of the library interface is that you can write any
-functions you wish to define how your code talks to LAMMPS and add
-them to src/library.cpp and src/library.h, as well as to the "Python
-interface"_Section_python.html.  The routines you add can access or
-change any LAMMPS data you wish.  The examples/COUPLE and python
-directories have example C++ and C and Python codes which show how a
-driver code can link to LAMMPS as a library, run LAMMPS on a subset of
-processors, grab data from LAMMPS, change it, and put it back into
-LAMMPS.
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.  The lammps_get_thermo() function returns the
+current value of a thermo keyword as a double.
+
+The lammps_get_natoms() function returns the total number of atoms in
+the system and can be used by the caller to allocate space for the
+lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
+gather function collects atom info of the requested type (atom coords,
+types, forces, etc) from all procsesors, orders them by atom ID, and
+returns a full list to each calling processor.  The scatter function
+does the inverse.  It distributes the same kinds of values, 
+passed by the caller, to each atom owned by individual processors.
+
+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities.  It uses the coords of each atom to assign it as a new
+atom to the processor that owns it.  Additional properties for the new
+atoms can be assigned via the lammps_scatter_atoms() or
+lammps_extract_atom() functions.
+
+The examples/COUPLE and python directories have example C++ and C and
+Python codes which show how a driver code can link to LAMMPS as a
+library, run LAMMPS on a subset of processors, grab data from LAMMPS,
+change it, and put it back into LAMMPS.
+
+NOTE: You can write code for additional functions as needed to define
+how your code talks to LAMMPS and add them to src/library.cpp and
+src/library.h, as well as to the "Python
+interface"_Section_python.html.  The added functions can access or
+change any LAMMPS data you wish.
 
 :line
 

doc/src/Section_packages.txt

@@ -1153,6 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@@ -1598,6 +1599,29 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
 
+USER-NC-DUMP package :link(USER-NC-DUMP),h5
+
+Contents: Dump styles for writing NetCDF format files.  NetCDF is a binary,
+portable, self-describing file format on top of HDF5. The file format
+contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
+convention. This package implements a "dump nc"_dump_nc.html command
+and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
+in this format.  See src/USER-NC-DUMP/README for more details.
+
+NetCDF files can be directly visualized with the following tools:
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
+  and all of the above extensions. :ulb,l
+VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
+Contact him directly if you have questions.
+
+:line
+
 USER-OMP package :link(USER-OMP),h5
 
 Supporting info:

doc/src/Section_python.txt

@@ -534,10 +534,11 @@ from lammps import lammps :pre
 These are the methods defined by the lammps module.  If you look at
 the files src/library.cpp and src/library.h you will see that they
 correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program.
+from a C++ or C or Fortran program, and which are described in
+"Section 6.19"_Section_howto.html#howto_19 of the manual.
 
 lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
+                         # 4 optional args are allowed: name, cmdargs, ptr, comm
 lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
 lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
 lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
@@ -549,6 +550,8 @@ version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 20
 
 lmp.file(file)           # run an entire input script, file = "in.lj"
 lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
+lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
+lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20"
 
 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                      # name = "boxxlo", "nlocal", etc
@@ -580,6 +583,8 @@ var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
                                              #        1 = atom-style variable :pre
 
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+value = lmp.get_thermo(name)              # return current value of a thermo keyword
+
 natoms = lmp.get_natoms()                 # total # of atoms as int
 data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
@@ -599,9 +604,10 @@ create an instance of LAMMPS, wrapped in a Python class by the lammps
 Python module, and return an instance of the Python class as lmp.  It
 is used to make all subequent calls to the LAMMPS library.
 
-Additional arguments can be used to tell Python the name of the shared
-library to load or to pass arguments to the LAMMPS instance, the same
-as if LAMMPS were launched from a command-line prompt.
+Additional arguments to lammps() can be used to tell Python the name
+of the shared library to load or to pass arguments to the LAMMPS
+instance, the same as if LAMMPS were launched from a command-line
+prompt.
 
 If the ptr argument is set like this:
 
@@ -626,8 +632,9 @@ lmp2 = lammps()
 lmp1.file("in.file1")
 lmp2.file("in.file2") :pre
 
-The file() and command() methods allow an input script or single
-commands to be invoked.
+The file(), command(), commands_list(), commands_string() methods
+allow an input script, a single command, or multiple commands to be
+invoked.
 
 The extract_global(), extract_atom(), extract_compute(),
 extract_fix(), and extract_variable() methods return values or

doc/src/Section_start.txt

@@ -1601,9 +1601,9 @@ implementations, either by environment variables that specify how to
 order physical processors, or by config files that specify what
 physical processors to assign to each MPI rank.  The -reorder switch
 simply gives you a portable way to do this without relying on MPI
-itself.  See the "processors out"_processors command for how to output
-info on the final assignment of physical processors to the LAMMPS
-simulation domain.
+itself.  See the "processors out"_processors.html command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.
 
 -screen file :pre
 

doc/src/accelerate_intel.txt

@@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used
 efficiently. Although benefits can be seen by launching a MPI task
 for every hardware thread, for multinode simulations, we recommend
 that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
+USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
 "KOKKOS package"_accelerate_kokkos.html. In the example above, up
 to 36X speedups can be observed by using all 36 physical cores with
 LAMMPS. By using all 72 hardware threads, an additional 10-30%
@@ -343,7 +343,7 @@ when using offload.
 
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html". Of course,
+package or the "USER-OMP package"_accelerate_omp.html. Of course,
 this requires that these packages were installed at build time. This
 can performed automatically by using "-sf hybrid intel opt" or
 "-sf hybrid intel omp" command-line options. Alternatively, the "opt"

doc/src/atom_style.txt

@@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner
 points of the triangle).
 
 The {template} style allows molecular topolgy (bonds,angles,etc) to be
-defined via a molecule template using the "molecule"_molecule.txt
+defined via a molecule template using the "molecule"_molecule.html
 command.  The template stores one or more molecules with a single copy
 of the topology info (bonds,angles,etc) of each.  Individual atoms
 only store a template index and template atom to identify which

doc/src/bond_fene.txt

@@ -73,7 +73,7 @@ This bond style can only be used if LAMMPS was built with the
 MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/bond_fene_expand.txt

@@ -76,7 +76,7 @@ This bond style can only be used if LAMMPS was built with the
 MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/commands.txt

@@ -37,6 +37,7 @@ Commands :h1
    dump_image
    dump_modify
    dump_molfile
+   dump_nc
    echo
    fix
    fix_modify

doc/src/compute_fep.txt

@@ -236,7 +236,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]
 
 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_lj_soft_coul_soft"_pair_lj_soft_coul_soft.txt
+"pair_style lj/soft/coul/soft"_pair_lj_soft.html
 
 [Default:]
 

doc/src/compute_orientorder_atom.txt

@@ -15,7 +15,7 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {ql}
+keyword = {cutoff} or {nnn} or {degrees}
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
   {degrees} values = nlvalues, l1, l2,...  :pre
@@ -111,7 +111,7 @@ options.
 
 [Default:]
 
-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
 
 :line
 

doc/src/compute_pe_atom.txt

@@ -72,9 +72,10 @@ compute        peratom all pe/atom
 compute        pe all reduce sum c_peratom
 thermo_style   custom step temp etotal press pe c_pe :pre
 
-NOTE: The per-atom energy does not any Lennard-Jones tail corrections
-invoked by the "pair_modify tail yes"_pair_modify.html command, since
-those are global contributions to the system energy.
+NOTE: The per-atom energy does not include any Lennard-Jones tail
+corrections to the energy added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the
+global system energy.
 
 [Output info:]
 

doc/src/compute_property_local.txt

@@ -78,7 +78,7 @@ defined by the "pair_style"_pair_style.html command for the types of
 the two atoms is used.  For the {radius} setting, the sum of the radii
 of the two particles is used as a cutoff.  For example, this is
 appropriate for granular particles which only interact when they are
-overlapping, as computed by "granular pair styles"_pair_gran.txt.
+overlapping, as computed by "granular pair styles"_pair_gran.html.
 
 If the inputs are bond, angle, etc attributes, the local data is
 generated by looping over all the atoms owned on a processor and

doc/src/compute_stress_atom.txt

@@ -133,6 +133,11 @@ compute        p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
 variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
 thermo_style   custom step temp etotal press v_press :pre
 
+NOTE: The per-atom stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the
+global system pressure.
+
 [Output info:]
 
 This compute calculates a per-atom array with 6 columns, which can be

doc/src/dump.txt

@@ -12,6 +12,7 @@ dump command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
 "dump molfile"_dump_molfile.html command :h3
+"dump nc"_dump_nc.html command :h3
 
 [Syntax:]
 
@@ -43,7 +44,9 @@ args = list of arguments for a particular style :l
 
   {movie} args = discussed on "dump image"_dump_image.html doc page :pre
 
-  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
+  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+
+  {nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
 
   {local} args = list of local attributes
     possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]

doc/src/dump_modify.txt

@@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
      id = sort per-atom lines by atom ID
      N = sort per-atom lines in ascending order by the Nth column
      -N = sort per-atom lines in descending order by the Nth column
-  {thresh} args = attribute operation value
+  {thresh} args = attribute operator value
     attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
-    operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
+    operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
     value = numeric value to compare to, or LAST
     these 3 args can be replaced by the word "none" to turn off thresholding
   {unwrap} arg = {yes} or {no} :pre
@@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
 
 If an atom-style variable is used as the attribute, then it can
 produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparision operation.  Boolean values can
+which may be useful for the comparision operator.  Boolean values can
 be generated by variable formulas that use comparison or Boolean math
 operators or special functions like gmask() and rmask() and grmask().
 See the "variable"_variable.html command doc page for details.
@@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
 E.g. due to reactions and subsequent charge equilibration in a
 reactive force field.
 
-The choice of operations are the usual comparison operators.  The XOR
-operation (exclusive or) is also included as "|^".  In this context,
-XOR means that if either the attribute or value is 0.0 and the other
-is non-zero, then the result is "true" and the threshold criterion is
-met.  Otherwise it is not met.
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "|^".
+In this context, XOR means that if either the attribute or value is
+0.0 and the other is non-zero, then the result is "true" and the
+threshold criterion is met.  Otherwise it is not met.
 
 :line
 

doc/src/dump_nc.txt

@@ -0,0 +1,66 @@
+"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
+
+dump nc command :h3
+dump nc/mpiio command :h3
+
+[Syntax:]
+
+dump ID group-ID nc N file.nc args
+dump ID group-ID nc/mpiio N file.nc args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+{nc} or {nc/mpiio}  = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file.nc = name of file to write to :l
+args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
+
+[Examples:]
+
+dump 1 all nc 100 traj.nc type x y z vx vy vz
+dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
+
+dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format. NetCDF files are binary, portable and
+self-describing.  This dump style will write only one file on the root
+node.  The dump style {nc} uses the "standard NetCDF
+library"_netcdf-home all data is collected on one processor and then
+written to the dump file. Dump style {nc/mpiio} used the "parallel
+NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
+a larger number of processors. Note that 'nc' outputs all atoms sorted
+by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
+
+In addition to per-atom data, also global (i.e. not per atom, but per
+frame) quantities can be included in the dump file. This can be
+variables, output from computes or fixes data prefixed with v_, c_ and
+f_, respectively.  These properties are included via
+"dump_modify"_dump_modify.html {global}.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Restrictions:]
+
+The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
+package.  It is only enabled if LAMMPS was built with that
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info.
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+

doc/src/fix.txt

@@ -190,6 +190,7 @@ of "this page"_Section_commands.html#cmd_5.
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
 "gld"_fix_gcmc.html - generalized Langevin dynamics integrator
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
+"halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "indent"_fix_indent.html - impose force due to an indenter
 "langevin"_fix_langevin.html - Langevin temperature control

doc/src/fix_dpd_energy.txt

@@ -0,0 +1,83 @@
+"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
+
+fix dpd/energy command :h3
+
+[Syntax:]
+
+fix ID group-ID dpd/energy :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+dpd/energy = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all dpd/energy :pre
+
+[Description:]
+
+Perform constant energy dissipative particle dynamics (DPD-E)
+integration.  This fix updates the internal energies for particles in
+the group at each timestep.  It must be used in conjunction with a
+deterministic integrator (e.g. "fix nve"_fix_nve.html) that updates
+the particle positions and velocities.
+
+For fix {dpd/energy}, the particle internal temperature is related to
+the particle internal energy through a mesoparticle equation of state.
+An additional fix must be specified that defines the equation of state
+for each particle, e.g. "fix eos/cv"_fix_eos_cv.html.
+
+This fix must be used with the "pair_style
+dpd/fdt/energy"_pair_style.html command.
+
+Note that numerous variants of DPD can be specified by choosing an
+appropriate combination of the integrator and "pair_style
+dpd/fdt/energy"_pair_style.html command.  DPD under isoenergetic conditions
+can be specified by using fix {dpd/energy}, fix {nve} and pair_style
+{dpd/fdt/energy}.  DPD under isoenthalpic conditions can
+be specified by using fix {dpd/energy}, fix {nph} and pair_style
+{dpd/fdt/energy}.  Examples of each DPD variant are provided in the
+examples/USER/dpd directory.
+
+:line
+
+[Restrictions:]
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This fix must be used with an additional fix that specifies time
+integration, e.g. "fix nve"_fix_nve.html.
+
+The fix {dpd/energy} requires the {dpd} "atom_style"_atom_style.html
+to be used in order to properly account for the particle internal
+energies and temperature.
+
+The fix {dpd/energy} must be used with an additional fix that specifies the
+mesoparticle equation of state for each particle.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html "fix eos/cv"_fix_eos_cv.html
+
+[Default:] none
+
+:line
+
+:link(Lisal)
+[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
+particle dynamics at isothermal, isobaric, isoenergetic, and
+isoenthalpic conditions using Shardlow-like splitting algorithms.",
+J. Chem. Phys., 135, 204105 (2011).
+
+:link(Larentzos)
+[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).

doc/src/fix_halt.txt

@@ -0,0 +1,121 @@
+"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
+
+fix halt command :h3
+
+[Syntax:]
+
+fix ID group-ID halt N attribute operator avalue keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+halt = style name of this fix command :l
+N = check halt condition every N steps :l
+attribute = hstyle or v_name :l
+  hstyle = {bondmax}
+  v_name = name of "equal-style variable"_variable.html :pre
+operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
+avalue = numeric value to compare attribute to :l
+string = text string to print with optional variable names :l
+zero or more keyword/value pairs may be appended :l
+keyword = {error} :l
+  {error} value = {hard} or {soft} or {continue} :pre
+:ule
+
+[Examples:]
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all print 10 v_myCheck != 0 error soft :pre
+
+[Description:]
+
+Check a condition every N steps during a simulation run.  N must be >=
+1.  If the condition is met, exit the run immediately.  In this
+context a "run" can be dynamics or minimization iterations, as
+specified by the "run"_run.html or "minimize"_minimize.html command.
+
+The specified group-ID is ignored by this fix.
+
+The specified {attribute} can be one of the {hstyle} options listed
+above, or an "equal-style variable"_variable.html referenced as
+{v_name}, where "name" is the name of a variable that has been defined
+previously in the input script.
+
+The only {hstyle} option currently implemented is {bondmax}.  This
+will loop over all bonds in the system, compute their current
+lengths, and set {attribute} to the longest bond distance.
+
+Equal-style variables evaluate to a numeric value.  See the
+"variable"_variable.html command for a description.  They calculate
+formulas which can involve mathematical operations, atom properties,
+group properties, thermodynamic properties, global values calculated
+by a "compute"_compute.html or "fix"_fix.html, or references to other
+"variables"_variable.html.  Thus they are a very general means of
+computing some attribute of the current system.  For example, the
+following "bondmax" variable will calculate the same quantity as the
+hstyle = bondmax option.
+
+compute         bdist all bond/local dist
+compute         bmax all reduce max c_bdist
+variable        bondmax equal c_bmax :pre
+
+Thus these two versions of a fix halt command will do the same thing:
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all halt 1 v_bondmax > 1.5 :pre
+
+The version with "bondmax" will just run somewhat faster, due to less
+overhead in computing bond lengths and not storing them in a separate
+compute.
+
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "|^".
+In this context, XOR means that if either the attribute or avalue is
+0.0 and the other is non-zero, then the result is "true".  Otherwise
+it is "false".
+
+The specified {avalue} must be a numeric value.
+
+:line
+
+The optional {error} keyword determines how the current run is halted.
+If its value is {hard}, then LAMMPS will stop with an error message.
+
+If its value is {soft}, LAMMPS will exit the current run, but continue
+to execute subsequent commands in the input script.  However,
+additional "run"_run.html or "minimize"_minimize.html commands will be
+skipped.  For example, this allows a script to output the current
+state of the system, e.g. via a "write_dump"_write_dump.html or
+"write_restart"_write_restart.html command.
+
+If its value is {continue}, the behavior is the same as for {soft},
+except subsequent subsequent "run"_run.html or
+"minimize"_minimize.html commands are executed.  This allows your
+script to remedy the condition that triggered the halt, if necessary.
+Note that you may wish use the "unfix"_unfix.html command on the fix
+halt ID, so that the same condition is not immediately triggered in a
+subsequent run.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"variable"_variable.html
+
+[Default:]
+
+The option defaults are error = hard.

doc/src/fix_phonon.txt

@@ -184,7 +184,7 @@ This fix requires LAMMPS be built with an FFT library.  See the
 [Default:]
 
 The option defaults are sysdim = the same dimemsion as specified by
-the "dimension"_dimension command, and nasr = 20.
+the "dimension"_dimension.html command, and nasr = 20.
 
 :line
 

doc/src/fix_property_atom.txt

@@ -177,7 +177,7 @@ their values.  This means that the values can be output via the "dump
 custom"_dump.html command, accessed by fixes like "fix
 ave/atom"_fix_ave_atom.html, accessed by other computes like "compute
 reduce"_compute_reduce.html, or used in "atom-style
-variables"_variables.
+variables"_variable.html.
 
 For example, these commands will output two new properties to a custom
 dump file:

doc/src/fix_rigid.txt

@@ -620,7 +620,7 @@ rigid styles for the rigid bodies. :l
 
 Use "fix press/berendsen"_fix_press_berendsen.html to compute the
 pressure and change the box dimensions.  Use one of the 4 NVE or 2 NVT
-rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.thml (or any
+rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.html (or any
 other thermostat) for the non-rigid particles. :l
 :ule
 

doc/src/fix_temp_berendsen.txt

@@ -49,6 +49,10 @@ variable, it should be specified as v_name, where name is the variable
 name.  In this case, the variable will be evaluated each timestep, and
 its value used to determine the target temperature.
 
+NOTE: This thermostat will generate an error if the current
+temperature is zero at the end of a timestep.  It cannot rescale a
+zero temperature.
+
 Equal-style variables can specify formulas with various mathematical
 functions, and include "thermo_style"_thermo_style.html command
 keywords for the simulation box parameters and timestep and elapsed

doc/src/fix_temp_rescale.txt

@@ -43,6 +43,10 @@ Rescaling is performed every N timesteps.  The target temperature is a
 ramped value between the {Tstart} and {Tstop} temperatures at the
 beginning and end of the run.
 
+NOTE: This thermostat will generate an error if the current
+temperature is zero at the end of a timestep it is inovoked on.  It
+cannot rescale a zero temperature.
+
 {Tstart} can be specified as an equal-style "variable"_variable.html.
 In this case, the {Tstop} setting is ignored.  If the value is a
 variable, it should be specified as v_name, where name is the variable

doc/src/fix_ti_spring.txt

@@ -104,7 +104,7 @@ the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
 recommended due to its well documented issues with the canonical
 sampling of harmonic degrees of freedom (notice that the {chain}
 option will {NOT} solve this problem). The Langevin thermostat ("fix
-langevin"_fix_langevin.html") correctly thermostats the system and we
+langevin"_fix_langevin.html) correctly thermostats the system and we
 advise its usage with ti/spring command.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]

doc/src/fix_wall_gran.txt

@@ -163,8 +163,8 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 [Related commands:]
 
-"fix move"_fix_move.html, 
-"fix wall/gran/region"_fix_wall_gran_region.html, 
+"fix move"_fix_move.html,
+"fix wall/gran/region"_fix_wall_gran_region.html,
 "pair_style granular"_pair_gran.html
 
 [Default:] none

doc/src/fix_wall_gran_region.txt

@@ -84,7 +84,7 @@ is up to you to ensure that the region location with respect to
 periodic or non-periodic boundaries is specified appropriately via the
 "region"_region.html and "boundary"_boundary.html commands when using
 a region as a wall that bounds particle motion.
- 
+
 NOTE: For primitive regions with sharp corners and/or edges (e.g. a
 block or cylinder), wall/particle forces are computed accurately for
 both interior and exterior regions.  For {union} and {intersect}
@@ -163,16 +163,20 @@ info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-Note that info about region definitions is NOT included in restart
-files.  So you must re-define your region and if it is a moving
-region, define its motion attributes in a way that is consistent with
-the simulation that wrote the restart file.  In particular, if you
-want to change its motion attributes (e.g. its velocity), then you
-should insure the postition/orientation of the region at the initial
-restart timestep is the same as it was on the timestep the restart
-file was written.  If this is not possible, then you may need to
-ignore info in the restart file by defining a new fix wall/gran/region
-command in your restart script (e.g. with a different fix ID).
+NOTE: Information about region definitions is NOT included in restart
+files, as discussed on the "read_restart"_read_restart.html doc page.
+So you must re-define your region and if it is a moving region, define
+its motion attributes in a way that is consistent with the simulation
+that wrote the restart file.  In particular, if you want to change the
+region motion attributes (e.g. its velocity), then you should ensure
+the postition/orientation of the region at the initial restart
+timestep is the same as it was on the timestep the restart file was
+written.  If this is not possible, you may need to ignore info in the
+restart file by defining a new fix wall/gran/region command in your
+restart script, e.g. with a different fix ID.  Or if you want to keep
+the shear history info but discard the region motion information, you
+can use the same fix ID for fix wall/gran/region, but assign it a
+region with a different region ID.
 
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for
@@ -190,7 +194,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]
 
 "fix_move"_fix_move.html,
-"fix wall/gran"_fix_wall_gran.html, 
+"fix wall/gran"_fix_wall_gran.html,
 "fix wall/region"_fix_wall_region.html,
 "pair_style granular"_pair_gran.html,
 "region"_region.html

doc/src/fixes.txt

@@ -32,6 +32,7 @@ Fixes :h1
    fix_drag
    fix_drude
    fix_drude_transform
+   fix_dpd_energy
    fix_dt_reset
    fix_efield
    fix_ehex
@@ -47,6 +48,7 @@ Fixes :h1
    fix_gld
    fix_gle
    fix_gravity
+   fix_halt
    fix_heat
    fix_imd
    fix_indent
@@ -148,6 +150,7 @@ Fixes :h1
    fix_viscous
    fix_wall
    fix_wall_gran
+   fix_wall_gran_region
    fix_wall_piston
    fix_wall_reflect
    fix_wall_region

doc/src/lammps.book

@@ -170,6 +170,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_halt.html
 fix_heat.html
 fix_imd.html
 fix_indent.html

doc/src/minimize.txt

@@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
+NOTE: You can also use the "fix halt"_fix_halt.html command to specify
+a general criterion for exiting a minimization, that is a calculation
+performed on the state of the current system, as defined by an
+"equal-style variable"_variable.html.
+
 For the first criterion, the specified energy tolerance {etol} is
 unitless; it is met when the energy change between successive
 iterations divided by the energy magnitude is less than or equal to

doc/src/neb.txt

@@ -83,9 +83,9 @@ replica.  Conceptually, the non-NEB atoms provide a background force
 field for the NEB atoms.  They can be allowed to move during the NEB
 minimiation procedure (which will typically induce different
 coordinates for non-NEB atoms in different replicas), or held fixed
-using other LAMMPS commands such as "fix setforce"_fix_setforce.  Note
-that the "partition"_partition.html command can be used to invoke a
-command on a subset of the replicas, e.g. if you wish to hold NEB or
+using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
+Note that the "partition"_partition.html command can be used to invoke
+a command on a subset of the replicas, e.g. if you wish to hold NEB or
 non-NEB atoms fixed in only the end-point replicas.
 
 The initial atomic configuration for each of the replicas can be

doc/src/pair_dpd_fdt.txt

@@ -33,78 +33,95 @@ pair_coeff * * 3.0 1.0 0.1 2.5 :pre
 
 [Description:]
 
-Styles {dpd/fdt} and {dpd/fdt/energy} set the fluctuation-dissipation
-theorem parameters and compute the conservative force for dissipative
-particle dynamics (DPD). The conservative force on atom I due to atom
-J is given by
+Styles {dpd/fdt} and {dpd/fdt/energy} compute the force for dissipative
+particle dynamics (DPD) simulations.  The {dpd/fdt} style is used to
+perform DPD simulations under isothermal and isobaric conditions,
+while the {dpd/fdt/energy} style is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal).
+For DPD simulations in general, the force on atom I due to atom J is
+given as a sum of 3 terms
 
-:c,image(Eqs/pair_dpd_conservative.jpg)
+:c,image(Eqs/pair_dpd.jpg)
 
-where the weighting factor, omega_ij, varies between 0 and 1, and is
-chosen to have the following functional form:
+where Fc is a conservative force, Fd is a dissipative force, and Fr is
+a random force.  Rij is a unit vector in the direction Ri - Rj, Vij is
+the vector difference in velocities of the two atoms = Vi - Vj, alpha
+is a Gaussian random number with zero mean and unit variance, dt is
+the timestep size, and w(r) is a weighting factor that varies between
+0 and 1.  Rc is the cutoff.  The weighting factor, omega_ij, varies
+between 0 and 1, and is chosen to have the following functional form:
 
 :c,image(Eqs/pair_dpd_omega.jpg)
 
-where Rij is a unit vector in the direction Ri - Rj, and Rc is the
-cutoff.  Note that alternative definitions of the weighting function
-exist, but would have to be implemented as a separate pair style
-command.
+Note that alternative definitions of the weighting function exist, but
+would have to be implemented as a separate pair style command.
 
-These pair style differ from the other dpd styles in that the
-dissipative and random forces are not computed within the pair style.
-This style can be combined with the "fix shardlow"_fix_shardlow.html
-to perform the stochastic integration of the dissipative and random
-forces through the Shardlow splitting algorithm approach.
+For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma
+to be set equal to sigma*sigma/(2 T), where T is the set point
+temperature specified as a pair style parameter in the above examples.
+The following coefficients must be defined for each pair of atoms types
+via the "pair_coeff"_pair_coeff.html command as in the examples above,
+or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands:
+
+A (force units)
+sigma (force*time^(1/2) units)
+cutoff (distance units) :ul
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
+
+Style {dpd/fdt/energy} is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions.  The fluctuation-dissipation
+theorem defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
+dpdTheta is the average internal temperature for the pair. The particle
+internal temperature is related to the particle internal energy through
+a mesoparticle equation of state (see "fix eos"_fix.html). The
+differential internal conductive and mechanical energies are computed
+within style {dpd/fdt/energy} as:
+
+:c,image(Eqs/pair_dpd_energy.jpg)
+
+where
+
+:c,image(Eqs/pair_dpd_energy_terms.jpg)
+
+Zeta_ij^q is a second Gaussian random number with zero mean and unit
+variance that is used to compute the internal conductive energy. The
+fluctuation-dissipation theorem defines alpha*alpha to be set
+equal to 2*kB*kappa, where kappa is the mesoparticle thermal
+conductivity parameter.   The following coefficients must be defined for
+each pair of atoms types via the "pair_coeff"_pair_coeff.html
+command as in the examples above, or in the data file or restart files
+read by the "read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+A (force units)
+sigma (force*time^(1/2) units)
+kappa (energy*temperature/time units)
+cutoff (distance units) :ul
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
 
 The pairwise energy associated with styles {dpd/fdt} and
 {dpd/fdt/energy} is only due to the conservative force term Fc, and is
 shifted to be zero at the cutoff distance Rc.  The pairwise virial is
 calculated using only the conservative term.
 
-For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma
-to be set equal to sigma*sigma/(2 T), where T is the set point
-temperature specified as a pair style parameter in the above examples.
-This style can be combined with "fix shardlow"_fix_shardlow.html to
-perform DPD simulations under isothermal and isobaric conditions (see
-"(Lisal)"_#Lisal).  The following coefficients must be defined for
-each pair of atoms types via the "pair_coeff"_pair_coeff.html command
-as in the examples above, or in the data file or restart files read by
-the "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-A (force units)
-sigma (force*time^(1/2) units)
-cutoff (distance units) :ul
-
-The last coefficient is optional.  If not specified, the global DPD
-cutoff is used.
-
-For style {dpd/fdt/energy}, the fluctuation-dissipation theorem
-defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
-dpdTheta is the average internal temperature for the pair.
-Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
-equal to 2*kB*kappa, where kappa is the mesoparticle thermal
-conductivity parameter.  This style can be combined with "fix
-shardlow"_fix_shardlow.html to perform DPD simulations under
-isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal).  The
-following coefficients must be defined for each pair of atoms types
-via the "pair_coeff"_pair_coeff.html command as in the examples above,
-or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-A (force units)
-sigma (force*time^(1/2) units)
-kappa (1/time units)
-cutoff (distance units) :ul
-
-The last coefficient is optional.  If not specified, the global DPD
-cutoff is used.
-
-For style {dpd/fdt/energy}, the particle internal temperature is
-related to the particle internal energy through a mesoparticle
-equation of state.  Thus, an an additional "fix eos"_fix.html must be
-specified.
+The forces computed through the {dpd/fdt} and {dpd/fdt/energy} styles
+can be integrated with the velocity-Verlet integration scheme or the
+Shardlow splitting integration scheme described by "(Lisal)"_#Lisal.
+In the cases when these pair styles are combined with the
+"fix shardlow"_fix_shardlow.html, these pair styles differ from the
+other dpd styles in that the dissipative and random forces are split
+from the force calculation and are not computed within the pair style.
+Thus, only the conservative force is computed by the pair style,
+while the stochastic integration of the dissipative and random forces
+are handled through the Shardlow splitting algorithm approach.  The
+Shardlow splitting algorithm is advantageous, especially when
+performing DPD under isoenergetic conditions, as it allows
+significantly larger timesteps to be taken.
 
 :line
 
@@ -132,6 +149,6 @@ energies and temperatures.
 
 :link(Lisal)
 [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
-particle dynamics as isothermal, isobaric, isoenergetic, and
+particle dynamics at isothermal, isobaric, isoenergetic, and
 isoenthalpic conditions using Shardlow-like splitting algorithms.",
 J. Chem. Phys., 135, 204105 (2011).

doc/src/pair_gauss.txt

@@ -106,8 +106,31 @@ more instructions on how to use the accelerated styles effectively.
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
-These pair styles do not support mixing. Thus, coefficients for all
-I,J pairs must be specified explicitly.
+For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
+parameters, and the cutoff distance for these pair styles can be mixed:
+A (energy units)
+sqrt(1/B) (distance units, see below)
+H (energy units)
+sigma_h (distance units)
+r_mh (distance units)
+cutoff (distance units):ul
+
+The default mix value is {geometric}.
+Only {arithmetic} and {geometric} mix values are supported.
+See the "pair_modify" command for details.
+
+The A and H parameters are mixed using the same rules normally
+used to mix the "epsilon" parameter in a Lennard Jones interaction.
+The sigma_h, r_mh, and the cutoff distance are mixed using the same
+rules used to mix the "sigma" parameter in a Lennard Jones interaction.
+The B parameter is converted to a distance (sigma), before mixing
+(using sigma=B^-0.5), and converted back to a coefficient
+afterwards (using B=sigma^2).
+Negative A values are converted to positive A values (using abs(A))
+before mixing, and converted back after mixing
+(by multiplying by sign(Ai)*sign(Aj)).
+This way, if either particle is repulsive (if Ai<0 or Aj<0),
+then the default interaction between both particles will be repulsive.
 
 The {gauss} style does not support the "pair_modify"_pair_modify.html
 shift option. There is no effect due to the Gaussian well beyond the

doc/src/pair_hbond_dreiding.txt

@@ -138,8 +138,8 @@ angle cutoff (degrees) :ul
 A single hydrogen atom type K can be specified, or a wild-card
 asterisk can be used in place of or in conjunction with the K
 arguments to select multiple types as hydrogens.  This takes the form
-"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff command
-doc page for details.
+"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff.html
+command doc page for details.
 
 If the donor flag is {i}, then the atom of type I in the pair_coeff
 command is treated as the donor, and J is the acceptor.  If the donor

doc/src/pair_line_lj.txt

@@ -60,8 +60,8 @@ pair_style command or overridden with an optional argument in the
 pair_coeff command for a type pair as discussed below.  The distance
 between the centers of 2 line segments, or the center of a line
 segment and a point particle, must be less than this distance (plus
-the neighbor skin; see the "neighbor"_neighbor command), for the pair
-of particles to be included in the neighbor list.
+the neighbor skin; see the "neighbor"_neighbor.html command), for
+the pair of particles to be included in the neighbor list.
 
 NOTE: This means that a too-short value for the {cutoff} setting can
 exclude a pair of particles from the neighbor list even if pairs of

doc/src/pair_lubricateU.txt

@@ -119,7 +119,7 @@ of walls (whether moving or stationary) will affect the volume
 fraction available to colloidal particles. This is currently accounted
 for with the following types of walls: "wall/lj93"_fix_wall.html,
 "wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and
-"wall/harmonic_fix_wall.html".  For these wall styles, the correct
+"wall/harmonic"_fix_wall.html.  For these wall styles, the correct
 volume fraction will be used when walls do not coincide with the box
 boundary, as well as when walls move and thereby cause a change in the
 volume fraction. To use these wall styles with pair_style {lubricateU}

doc/src/pair_thole.txt

@@ -180,7 +180,7 @@ package.
 langevin/drude"_fix_langevin_drude.html, "fix
 drude/transform"_fix_drude_transform.html, "compute
 temp/drude"_compute_temp_drude.html
-"pair_style lj/cut/coul/long"_pair_lj_cut_coul_long
+"pair_style lj/cut/coul/long"_pair_lj.html
 
 [Default:] none
 

doc/src/read_data.txt

@@ -431,8 +431,8 @@ Atoms # sphere
 Pair Coeffs # lj/cut :pre
 
 will check if the currently-defined "atom_style"_atom_style.html is
-{sphere}, and the current "pair_style"_pair_style is {lj/cut}.  If
-not, LAMMPS will issue a warning to indicate that the data file
+{sphere}, and the current "pair_style"_pair_style.html is {lj/cut}.
+If not, LAMMPS will issue a warning to indicate that the data file
 section likely does not contain the correct number or type of
 parameters expected for the currently-defined style.
 

doc/src/read_dump.txt

@@ -322,3 +322,6 @@ They are only enabled if LAMMPS was built with that packages.  See the
 
 The option defaults are box = yes, replace = yes, purge = no, trim =
 no, add = no, scaled = no, wrapped = yes, and format = native.
+
+:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
+

doc/src/read_restart.txt

@@ -141,11 +141,11 @@ these settings after the restart file is read.
 "units"_units.html
 "newton bond"_newton.html (see discussion of newton command below)
 "atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort
-"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel
+"comm style"_comm_style.html and "comm_modify"_comm_modify.html settings mode, cutoff, vel
 "timestep"_timestep.html
 simulation box size and shape and "boundary"_boundary.html settings
 atom "group"_group.html definitions
-per-type atom settings such as "mass"_mass.thml
+per-type atom settings such as "mass"_mass.html
 per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)
 force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc)
 force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below)
@@ -197,12 +197,13 @@ was used in the input script that wrote the restart file.
 If a match is found, LAMMPS prints a message indicating that the fix
 is being re-enabled.  If no match is found before the first run or
 minimization is performed by the new script, the "state" information
-for the saved fix is discarded.  LAMMPS will also print a list of
-fixes for which the information is being discarded.  See the doc pages
-for individual fixes for info on which ones can be restarted in this
-manner.  Note that fixes which are created internally by other LAMMPS
-commands (computes, fixes, etc) will have style names which are
-all-capitalized, and IDs which are generated internally.
+for the saved fix is discarded.  At the time the discard occurs,
+LAMMPS will also print a list of fixes for which the information is
+being discarded.  See the doc pages for individual fixes for info on
+which ones can be restarted in this manner.  Note that fixes which are
+created internally by other LAMMPS commands (computes, fixes, etc)
+will have style names which are all-capitalized, and IDs which are
+generated internally.
 
 Likewise, the "computes"_fix.html used for a simulation are not stored
 in the restart file.  This means the new input script should specify
@@ -219,12 +220,16 @@ described in the previous paragraph, so that the compute can continue
 its calculations in a consistent manner.
 
 NOTE: There are a handful of commands which can be used before or
-between runs which require a system initialization.  Examples include
-the "balance", "displace_atoms", and "delete_atoms" commands.  This is
-because they may migrate atoms to new processors.  Thus they will also
-discard unused "state" information from fixes.  This means that, if
-desired, you must re-specify the relevant fixes and computes (which
-create fixes) before those commands are used.
+between runs which may require a system initialization.  Examples
+include the "balance", "displace_atoms", "delete_atoms", "set" (some
+options), and "velocity" (some options) commands.  This is because
+they can migrate atoms to new processors.  Thus they will also discard
+unused "state" information from fixes.  You will know the discard has
+occurred because a list of discarded fixes will be printed to the
+screen and log file, as explained above.  This means that if you wish
+to retain that info in a restarted run, you must re-specify the
+relevant fixes and computes (which create fixes) before those commands
+are used.
 
 Some pair styles, like the "granular pair styles"_pair_gran.html, also
 use a fix to store "state" information that persists from timestep to

doc/src/run.txt

@@ -169,17 +169,17 @@ If the {pre} and {post} options are set to "no" when used with the
 run will print the full timing summary, but these operations will be
 skipped for intermediate runs.
 
-NOTE: You might hope to specify a command that exits the run by
+NOTE: You might wish to specify a command that exits the run by
 jumping out of the loop, e.g.
 
 variable t equal temp
 run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre
 
-Unfortunately this will not currently work.  The run command simply
-executes each command one at a time each time it pauses, then
-continues the run.  You can replace the jump command with a simple
-"quit"_quit.html command and cause LAMMPS to exit during the
-middle of a run when the condition is met.
+However, this will not work.  The run command simply executes each
+command one at a time each time it pauses, then continues the run.
+
+Instead, you should use the "fix halt"_fix_halt.html command, which
+has additional options for how to exit the run.
 
 [Restrictions:]
 
@@ -198,7 +198,7 @@ successive runs to run a simulation for any number of steps (ok, up to
 [Related commands:]
 
 "minimize"_minimize.html, "run_style"_run_style.html,
-"temper"_temper.html
+"temper"_temper.html, "fix halt"_fix_halt.html
 
 [Default:]
 

doc/src/thermo_style.txt

@@ -108,7 +108,7 @@ Style {custom} is the most general setting and allows you to specify
 which of the keywords listed above you want printed on each
 thermodynamic timestep.  Note that the keywords c_ID, f_ID, v_name are
 references to "computes"_compute.html, "fixes"_fix.html, and
-equal-style "variables"_variable.html" that have been defined
+equal-style "variables"_variable.html that have been defined
 elsewhere in the input script or can even be new styles which users
 have added to LAMMPS (see the "Section 10"_Section_modify.html
 section of the documentation).  Thus the {custom} style provides a

doc/src/write_dump.txt

@@ -26,7 +26,7 @@ write_dump all atom dump.atom
 write_dump subgroup atom dump.run.bin
 write_dump all custom dump.myforce.* id type x y vx fx
 write_dump flow custom dump.%.myforce id type c_myF\[3\] v_ke modify sort id
-write_dump all xyz system.xyz modify sort id elements O H
+write_dump all xyz system.xyz modify sort id element O H
 write_dump all image snap*.jpg type type size 960 960 modify backcolor white
 write_dump all image snap*.jpg element element &
    bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &

doc/utils/sphinx-config/conf.py

@@ -276,4 +276,27 @@ texinfo_documents = [
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
+# -- Options for ePUB output ----------------------------------------------
+
+epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
+
+epub_cover = ('lammps-logo.png', '')
+
+epub_description = """
+This is the Manual for the LAMMPS software package.
+
+LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator and 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 author of the code is Steve Plimpton, who can be emailed
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+more information about the code and its uses.
+"""
+
+epub_author = 'The LAMMPS Developers'
+
 

examples/COUPLE/simple/in.lj

@@ -20,4 +20,6 @@ neigh_modify	delay 0 every 20 check no
 
 fix		1 all nve
 
+variable        fx atom fx
+
 run		10

examples/COUPLE/simple/simple.c

@@ -71,8 +71,8 @@ int main(int narg, char **arg)
      (could just send it to proc 0 of comm_lammps and let it Bcast)
      all LAMMPS procs call lammps_command() on the line */
 
-  void *ptr;
-  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
+  void *lmp = NULL;
+  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&lmp);
 
   int n;
   char line[1024];
@@ -85,7 +85,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lammps_command(ptr,line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   /* run 10 more steps
@@ -94,23 +94,72 @@ int main(int narg, char **arg)
      put coords back into LAMMPS
      run a single step with changed coords */
 
-  if (lammps == 1) {
-    lammps_command(ptr,"run 10");
+  double *x = NULL;
+  double *v = NULL;
 
-    int natoms = lammps_get_natoms(ptr);
-    double *x = (double *) malloc(3*natoms*sizeof(double));
-    lammps_gather_atoms(ptr,"x",1,3,x);
+  if (lammps == 1) {
+    lammps_command(lmp,"run 10");
+
+    int natoms = lammps_get_natoms(lmp);
+    x = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"x",1,3,x);
+    v = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
-    lammps_scatter_atoms(ptr,"x",1,3,x);
-    free(x);
+    lammps_scatter_atoms(lmp,"x",1,3,x);
 
-    lammps_command(ptr,"run 1");
+    lammps_command(lmp,"run 1");
   }
 
-  if (lammps == 1) lammps_close(ptr);
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  /* use commands_string() and commands_list() to invoke more commands */
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  /* delete all atoms
+     create_atoms() to create new ones with old coords, vels
+     initial thermo should be same as step 20 */
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = lammps_get_natoms(lmp);
+    type = (int *) malloc(natoms*sizeof(double));
+    int i;
+    for (i = 0; i < natoms; i++) type[i] = 1;
+
+    lammps_command(lmp,"delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_command(lmp,"run 10");
+  }
+
+  if (x) free(x);
+  if (v) free(v);
+  if (type) free(type);
+
+  // close down LAMMPS
+
+  lammps_close(lmp);
 
   /* close down MPI */
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

examples/COUPLE/simple/simple.cpp

@@ -77,7 +77,7 @@ int main(int narg, char **arg)
   // (could just send it to proc 0 of comm_lammps and let it Bcast)
   // all LAMMPS procs call input->one() on the line
   
-  LAMMPS *lmp;
+  LAMMPS *lmp = NULL;
   if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
 
   int n;
@@ -91,7 +91,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lmp->input->one(line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   // run 10 more steps
@@ -100,23 +100,74 @@ int main(int narg, char **arg)
   // put coords back into LAMMPS
   // run a single step with changed coords
 
+  double *x = NULL;
+  double *v = NULL;
+
   if (lammps == 1) {
     lmp->input->one("run 10");
 
     int natoms = static_cast<int> (lmp->atom->natoms);
-    double *x = new double[3*natoms];
+    x = new double[3*natoms];
+    v = new double[3*natoms];
     lammps_gather_atoms(lmp,"x",1,3,x);
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
     lammps_scatter_atoms(lmp,"x",1,3,x);
-    delete [] x;
 
+    // these 2 lines are the same
+
+    // lammps_command(lmp,"run 1");
     lmp->input->one("run 1");
   }
 
-  if (lammps == 1) delete lmp;
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  // use commands_string() and commands_list() to invoke more commands
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  // delete all atoms
+  // create_atoms() to create new ones with old coords, vels
+  // initial thermo should be same as step 20
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = static_cast<int> (lmp->atom->natoms);
+    type = new int[natoms];
+    for (int i = 0; i < natoms; i++) type[i] = 1;
+
+    lmp->input->one("delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lmp->input->one("run 10");
+  }
+
+  delete [] x;
+  delete [] v;
+  delete [] type;
+
+  // close down LAMMPS
+
+  delete lmp;
 
   // close down MPI
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

examples/DIFFUSE/log.13Oct16.msd.2d.g++.8

@@ -0,0 +1,245 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable	x equal 40
+variable	y equal 40
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 40 0 $y -0.1 0.1
+region          simbox block 0 40 0 40 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+  4 by 2 by 1 MPI processor grid
+create_atoms    1 box
+Created 3200 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 53 53 1
+Memory usage per processor = 2.478 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0   -0.5652325   -1.5346995 
+    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
+    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
+    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
+    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
+    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 
+Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3896017.421 tau/day, 9018.559 timesteps/s
+98.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23992    | 0.24608    | 0.25161    |   0.7 | 44.39
+Neigh   | 0.063106   | 0.064417   | 0.066279   |   0.4 | 11.62
+Comm    | 0.072465   | 0.085066   | 0.094837   |   2.3 | 15.34
+Output  | 0.00013208 | 0.00013691 | 0.00014591 |   0.0 |  0.02
+Modify  | 0.11441    | 0.11621    | 0.11769    |   0.3 | 20.96
+Other   |            | 0.04251    |            |       |  7.67
+
+Nlocal:    400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost:    202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs:    2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix		2
+
+# data gathering run
+
+reset_timestep  0
+
+# factor of 4 in 2 variables is for 2d
+
+compute         msd all msd com yes
+variable        twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
+fix             9 all vector 10 c_msd[4]
+variable        fitslope equal slope(f_9)/4/(10*dt)
+
+thermo_style	custom step temp c_msd[4] v_twopoint v_fitslope
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump	        1 all custom 1 tmp.dump id type vx vy vz
+
+#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo          1000
+run	        100000
+Memory usage per processor = 2.853 Mbytes
+Step Temp c_msd[4] v_twopoint v_fitslope 
+       0   0.97069905            0            0        5e+20 
+    1000   0.98138076    4.0484996   0.20242494   0.18046446 
+    2000   0.97606079    9.2121392   0.23030346    0.2091528 
+    3000   0.97924866    14.815034   0.24691721   0.22619184 
+    4000   0.98568451    20.516817   0.25646019   0.23715506 
+    5000   0.97551815     27.33922   0.27339219   0.24709999 
+    6000   0.98482252     34.37734   0.28647782   0.25735178 
+    7000    0.9672559    41.696689   0.29783348   0.26654059 
+    8000    0.9836541    48.340277   0.30212673   0.27440308 
+    9000   0.99087147    56.042692   0.31134828   0.28113047 
+   10000   0.99663166     63.69663   0.31848314   0.28767921 
+   11000   0.97776688    71.144109   0.32338231   0.29344527 
+   12000   0.98246011    78.301774   0.32625739   0.29849471 
+   13000   0.98788732    85.061923   0.32716124    0.3026655 
+   14000   0.96872483      91.1658   0.32559214   0.30601023 
+   15000   0.98955796    97.278388   0.32426129    0.3084275 
+   16000   0.99855196    104.23997    0.3257499   0.31049883 
+   17000   0.98600861    110.66055    0.3254722   0.31220348 
+   18000   0.98696963    116.90111   0.32472531   0.31352676 
+   19000    0.9881192    124.21305   0.32687644   0.31480062 
+   20000   0.98527319    131.09874   0.32774685   0.31596198 
+   21000   0.99015191    137.89263   0.32831579   0.31705324 
+   22000   0.97972418    146.68982   0.33338595   0.31833889 
+   23000   0.98911012     155.1264   0.33723129   0.31979515 
+   24000   0.98810498    162.88634   0.33934653   0.32131187 
+   25000   0.96961962    170.37907   0.34075814   0.32276215 
+   26000   0.99118408    179.26511   0.34474059   0.32427111 
+   27000   0.98515159    185.90764    0.3442734   0.32574529 
+   28000   0.98951677    192.12183   0.34307469   0.32700292 
+   29000    0.9832026    196.99457   0.33964581   0.32799023 
+   30000   0.98449493    203.48475   0.33914124    0.3287171 
+   31000   0.96585993    210.06193   0.33880956   0.32935775 
+   32000   0.98758117    218.94174   0.34209646   0.33001591 
+   33000   0.98875584    225.96489   0.34237104   0.33072947 
+   34000   0.98007229     233.5792   0.34349882    0.3314385 
+   35000   0.98415295    241.98148   0.34568783   0.33216634 
+   36000   0.98101154    250.30876   0.34765106   0.33295272 
+   37000   0.97606878     258.2127   0.34893608   0.33377673 
+   38000   0.97220293    266.40464   0.35053242   0.33459273 
+   39000     0.979783     272.8578   0.34981769   0.33539728 
+   40000   0.98375673    279.87598   0.34984497   0.33609699 
+   41000   0.97506523    288.07676   0.35131312   0.33677708 
+   42000   0.97106749    296.11647    0.3525196   0.33751312 
+   43000   0.97717259    304.46747   0.35403194   0.33823441 
+   44000   0.98541435    312.57228   0.35519578    0.3389771 
+   45000   0.97678287    321.82674   0.35758527   0.33973306 
+   46000   0.98169719    329.78197   0.35845866   0.34051748 
+   47000   0.99471466    337.11283   0.35863066   0.34127239 
+   48000   0.98332437     346.0754    0.3604952   0.34202442 
+   49000   0.98126947    356.11859   0.36338631   0.34282132 
+   50000   0.98809751    365.65248   0.36565248   0.34368171 
+   51000   0.95919516    373.91833   0.36658659   0.34454516 
+   52000   0.98097913    381.26492   0.36660089   0.34538506 
+   53000   0.97774072    388.81031   0.36680218   0.34618232 
+   54000   0.99096915    395.56767   0.36626636    0.3469296 
+   55000   0.97652739    401.72735   0.36520668   0.34760374 
+   56000   0.99185306    407.28834    0.3636503   0.34819906 
+   57000   0.96289342    414.75298    0.3638184   0.34871992 
+   58000   0.97871716    424.69443   0.36611588   0.34927986 
+   59000   0.98637393    433.14205   0.36706953   0.34986296 
+   60000   0.98009845    438.14533   0.36512111   0.35040349 
+   61000   0.99416712    446.08007    0.3656394   0.35088379 
+   62000   0.97612483    450.90846   0.36363585   0.35132647 
+   63000   0.97786531    455.36749   0.36140277   0.35167458 
+   64000   0.99080668    458.04873   0.35785057    0.3519105 
+   65000   0.97952497    461.31241    0.3548557    0.3520506 
+   66000   0.98095955    463.91727   0.35145248   0.35207764 
+   67000   0.98370788       468.93   0.34994776   0.35204043 
+   68000   0.96931818    471.07765   0.34638063   0.35192685 
+   69000   0.98512552    474.59146   0.34390685   0.35174053 
+   70000   0.98065743    478.66071    0.3419005   0.35149002 
+   71000   0.98971283    482.57357   0.33984054   0.35119434 
+   72000   0.99890324    485.32018    0.3370279   0.35084345 
+   73000   0.98649924    490.19497   0.33574998   0.35043722 
+   74000   0.98723422    496.04991   0.33516886   0.35003351 
+   75000    1.0025633     501.6313   0.33442087   0.34962094 
+   76000   0.97859959    505.97813   0.33288035   0.34921013 
+   77000   0.97973006    510.55334   0.33152814    0.3487692 
+   78000    0.9903944    515.06966   0.33017286   0.34830833 
+   79000   0.96847518    518.76483   0.32833217    0.3478214 
+   80000   0.99171112    524.18127   0.32761329   0.34733349 
+   81000   0.97202573    529.09959   0.32660468    0.3468315 
+   82000   0.99368438    535.80271   0.32670897   0.34633058 
+   83000   0.97932483    543.08233   0.32715803   0.34586259 
+   84000   0.99078651    547.57861   0.32593965   0.34540839 
+   85000   0.98973457    552.24581   0.32485048   0.34493584 
+   86000    0.9835873     557.3493   0.32404029   0.34446152 
+   87000   0.97180564    564.93434   0.32467491   0.34400358 
+   88000   0.99743353    571.39837   0.32465817    0.3435667 
+   89000   0.98993437    577.81703   0.32461631    0.3431411 
+   90000    0.9926071    583.39378   0.32410765     0.342724 
+   91000   0.98800458    591.08741    0.3247733   0.34232767 
+   92000   0.98501879    596.10133   0.32396811   0.34193949 
+   93000   0.98810082    604.02652   0.32474544    0.3415681 
+   94000   0.97563748    609.43676   0.32416849     0.341209 
+   95000   0.97283448    615.15754   0.32376713   0.34084828 
+   96000    0.9883071    622.30912   0.32411933   0.34049871 
+   97000   0.97717678    628.84457   0.32414669   0.34016355 
+   98000   0.97190208    634.37377   0.32366009    0.3398341 
+   99000   0.98687379    640.66666   0.32356902   0.33950845 
+  100000   0.97559757    646.96406   0.32348203   0.33919036 
+Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 4505729.040 tau/day, 10429.928 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8572     | 4.9363     | 4.9822     |   1.7 | 51.49
+Neigh   | 1.3583     | 1.376      | 1.3991     |   1.2 | 14.35
+Comm    | 1.5192     | 1.7079     | 1.8264     |   7.2 | 17.81
+Output  | 0.0085125  | 0.0086059  | 0.0089455  |   0.1 |  0.09
+Modify  | 0.77663    | 0.7903     | 0.81378    |   1.3 |  8.24
+Other   |            | 0.7686     |            |       |  8.02
+
+Nlocal:    400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost:    204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs:    2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8

@@ -0,0 +1,246 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable	x equal 40
+variable	y equal 40
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 40 0 $y -0.1 0.1
+region          simbox block 0 40 0 40 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+  4 by 2 by 1 MPI processor grid
+create_atoms    1 box
+Created 3200 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 53 53 1
+Memory usage per processor = 2.478 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0   -0.5652325   -1.5346995 
+    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
+    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
+    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
+    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
+    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 
+Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3873826.669 tau/day, 8967.191 timesteps/s
+99.1% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23784    | 0.24683    | 0.25594    |   1.0 | 44.27
+Neigh   | 0.062975   | 0.06439    | 0.0662     |   0.4 | 11.55
+Comm    | 0.083826   | 0.092564   | 0.1035     |   2.1 | 16.60
+Output  | 0.00011778 | 0.00012615 | 0.00014257 |   0.1 |  0.02
+Modify  | 0.11466    | 0.11648    | 0.1187     |   0.4 | 20.89
+Other   |            | 0.0372     |            |       |  6.67
+
+Nlocal:    400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost:    202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs:    2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix		2
+
+# data gathering run
+
+reset_timestep  0
+
+compute         vacf all vacf
+fix             4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
+
+# factor of 0.5 is for 2d
+
+fix             5 all vector 1 c_vacf[4]
+variable        vacf equal 0.5*dt*trap(f_5)
+
+thermo_style	custom step temp c_vacf[4] v_vacf
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump	        1 all custom 1 tmp.dump id type vx vy vz
+
+#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo          1000
+run	        100000
+Memory usage per processor = 2.853 Mbytes
+Step Temp c_vacf[4] v_vacf 
+       0   0.97069905    1.9407914            0 
+    1000   0.98138076  0.029239763   0.22157396 
+    2000   0.97606079 -0.0015179052   0.23974121 
+    3000   0.97924866 -0.013873067   0.21877575 
+    4000   0.98568451  0.026969065   0.24052934 
+    5000   0.97551815  0.050232557   0.24508207 
+    6000   0.98482252 -0.0018424259   0.25686293 
+    7000    0.9672559  0.018499957   0.27279836 
+    8000    0.9836541 -0.022683127   0.27022734 
+    9000   0.99087147 0.0071767632   0.25267902 
+   10000   0.99663166 -0.011971734    0.2645822 
+   11000   0.97776688   0.01601675   0.27801788 
+   12000   0.98246011 0.0085456779   0.29207728 
+   13000   0.98788732 0.0054252587   0.29148533 
+   14000   0.96872483 0.0087976064   0.29645689 
+   15000   0.98955796 -0.060068996   0.28904116 
+   16000   0.99855196 -0.0066979853   0.24964957 
+   17000   0.98600861  0.021334454   0.23410452 
+   18000   0.98696963  -0.01971883   0.23190572 
+   19000    0.9881192 -0.022828159   0.20882183 
+   20000   0.98527319 -0.0085783561   0.20610922 
+   21000   0.99015191 -0.0061019744   0.20199693 
+   22000   0.97972418  -0.04380952   0.22099864 
+   23000   0.98911012 -0.0031381071   0.19304223 
+   24000   0.98810498  0.023131507   0.18483784 
+   25000   0.96961962 -0.020892151   0.17128259 
+   26000   0.99118408   0.02918818   0.15353531 
+   27000   0.98515159 -0.026417648    0.1457756 
+   28000   0.98951677  0.010372147   0.13321212 
+   29000    0.9832026 0.00058150905   0.13262151 
+   30000   0.98449493 0.0012256712   0.13576655 
+   31000   0.96585993 0.0053021384   0.10734708 
+   32000   0.98758117 -0.011513109   0.11473375 
+   33000   0.98875584 -0.0089140499   0.13003947 
+   34000   0.98007229  0.023423116     0.145185 
+   35000   0.98415295 -0.0078343607   0.16513809 
+   36000   0.98101154  0.025471963    0.1296799 
+   37000   0.97606878 -0.016931612   0.11515595 
+   38000   0.97220293 -0.015288346   0.12046935 
+   39000     0.979783  0.039556949   0.10596988 
+   40000   0.98375673 0.0098704124   0.15651085 
+   41000   0.97506523 -0.029457701   0.14822207 
+   42000   0.97106749 -0.024867475   0.12266294 
+   43000   0.97717259  0.010866403   0.14228602 
+   44000   0.98541435 -0.031545234   0.13017093 
+   45000   0.97678287 -0.011024372   0.11824999 
+   46000   0.98169719  0.011925437    0.1390346 
+   47000   0.99471466 0.0048178625   0.13076123 
+   48000   0.98332437  0.045576305   0.12667585 
+   49000   0.98126947 -0.044123768   0.13582991 
+   50000   0.98809751  0.014296599   0.12323107 
+   51000   0.95919516 -0.0091171161    0.1494511 
+   52000   0.98097913  0.010081012   0.12805794 
+   53000   0.97774072  0.043349117   0.14524942 
+   54000   0.99096915  0.021179196    0.1355801 
+   55000   0.97652739 -0.015118967   0.14955035 
+   56000   0.99185306 0.0018045061   0.16706629 
+   57000   0.96289342 0.0095090659   0.19215008 
+   58000   0.97871716 -0.028989119   0.20370326 
+   59000   0.98637393 0.0067841088   0.21820001 
+   60000   0.98009845  0.011559251   0.24504916 
+   61000   0.99416712 0.0099372548   0.24882366 
+   62000   0.97612483  0.014677063   0.25146482 
+   63000   0.97786531 -0.0047938112   0.26052305 
+   64000   0.99080668  -0.01632121   0.24744267 
+   65000   0.97952497 0.0070583633   0.22323997 
+   66000   0.98095955  0.036296232    0.2151706 
+   67000   0.98370788 -0.0040313363   0.22236193 
+   68000   0.96931818    0.0231486   0.20397659 
+   69000   0.98512552 -0.017450997   0.21854935 
+   70000   0.98065743  0.046916694    0.2080453 
+   71000   0.98971283  0.010974871   0.21628306 
+   72000   0.99890324 -0.023780184   0.23385876 
+   73000   0.98649924  0.012862733   0.23458964 
+   74000   0.98723422 -0.0096252165   0.23873216 
+   75000    1.0025633 -0.070387674    0.2275029 
+   76000   0.97859959 0.0058897922   0.22954358 
+   77000   0.97973006 -0.0082868083   0.25189797 
+   78000    0.9903944 -0.042368536   0.26564349 
+   79000   0.96847518 -0.050630573   0.25344248 
+   80000   0.99171112  0.012126001   0.23257751 
+   81000   0.97202573 -0.029816198   0.27354387 
+   82000   0.99368438  0.030082951   0.27859495 
+   83000   0.97932483 -0.0081664387   0.27409123 
+   84000   0.99078651  0.056610231   0.27593659 
+   85000   0.98973457  0.020424285   0.31002605 
+   86000    0.9835873 -0.0016980943   0.30158255 
+   87000   0.97180564 -0.0051924508   0.27401969 
+   88000   0.99743353 -0.030700753   0.24105471 
+   89000   0.98993437 0.0087866525   0.23913724 
+   90000    0.9926071 -0.014023378   0.24202489 
+   91000   0.98800458  0.033613695    0.2238248 
+   92000   0.98501879   -0.0406599   0.21809043 
+   93000   0.98810082  0.027637634   0.21550897 
+   94000   0.97563748 0.0014112208   0.18954766 
+   95000   0.97283448 0.0093796591   0.17838358 
+   96000    0.9883071  0.033049994   0.18594703 
+   97000   0.97717678   0.01070451   0.19203994 
+   98000   0.97190208  0.015065013   0.20906937 
+   99000   0.98687379 -0.036869401   0.22993959 
+  100000   0.97559757  0.045464091   0.23369283 
+Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 3987213.825 tau/day, 9229.662 timesteps/s
+99.5% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8486     | 4.9469     | 5.0248     |   2.8 | 45.66
+Neigh   | 1.3613     | 1.374      | 1.3916     |   0.8 | 12.68
+Comm    | 1.8181     | 1.9534     | 2.0665     |   5.7 | 18.03
+Output  | 0.016565   | 0.016701   | 0.017039   |   0.1 |  0.15
+Modify  | 1.8395     | 1.9053     | 1.9704     |   2.8 | 17.59
+Other   |            | 0.6383     |            |       |  5.89
+
+Nlocal:    400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost:    204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs:    2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:11

examples/DIFFUSE/log.1Feb14.msd.2d.g++.8

@@ -1,223 +0,0 @@
-LAMMPS (12 Feb 2014)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable	x equal 40
-variable	y equal 40
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 40 0 $y -0.1 0.1
-region          simbox block 0 40 0 40 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
-  4 by 2 by 1 MPI processor grid
-create_atoms    1 box
-Created 3200 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0   -0.5652325   -1.5346995 
-    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
-    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
-    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
-    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
-    5000   0.97069909   -1.5851114            0  -0.61471562   0.90108296 
-Loop time of 0.548328 on 8 procs for 5000 steps with 3200 atoms
-
-Pair  time (%) = 0.242437 (44.2139)
-Neigh time (%) = 0.0589295 (10.7471)
-Comm  time (%) = 0.0797399 (14.5424)
-Outpt time (%) = 0.00014773 (0.0269419)
-Other time (%) = 0.167074 (30.4697)
-
-Nlocal:    400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost:    202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs:    2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix		2
-
-# data gathering run
-
-reset_timestep  0
-
-# factor of 4 in 2 variables is for 2d
-
-compute         msd all msd com yes
-variable        twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
-fix             9 all vector 10 c_msd[4]
-variable        fitslope equal slope(f_9)/4/(10*dt)
-
-thermo_style	custom step temp c_msd[4] v_twopoint v_fitslope
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump	        1 all custom 1 tmp.dump id type vx vy vz
-
-#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo          1000
-run	        100000
-Memory usage per processor = 2.29126 Mbytes
-Step Temp msd[4] twopoint fitslope 
-       0   0.97069909 5.6797985e-31 1.4199496e-25        5e+20 
-    1000   0.98259938     4.018182   0.20090906   0.18018405 
-    2000   0.98866167    9.1771673   0.22942916   0.20819132 
-    3000   0.98066292    14.377973   0.23963287    0.2226381 
-    4000   0.97384109    19.666022   0.24582526   0.23154108 
-    5000   0.97843004    25.570023   0.25570022   0.23873417 
-    6000   0.98703537    31.182236   0.25985196    0.2446473 
-    7000   0.97169186    36.915546   0.26368246   0.24892937 
-    8000    0.9823893    42.723242   0.26702026   0.25284158 
-    9000    0.9998457    49.159596   0.27310886   0.25648405 
-   10000   0.98782869     55.95808   0.27979039   0.26026001 
-   11000   0.99481941    63.387246   0.28812384   0.26436008 
-   12000    0.9760981    70.325901   0.29302458   0.26836823 
-   13000   0.97774297    77.590396    0.2984246    0.2723266 
-   14000   0.96752038    85.055703   0.30377036   0.27627449 
-   15000   0.98697717    92.723433    0.3090781   0.28007928 
-   16000   0.98385955    100.89787   0.31530583   0.28396785 
-   17000    0.9839555    108.44716   0.31896223   0.28772551 
-   18000   0.98000182      115.932   0.32203333   0.29120847 
-   19000   0.96633821    123.99378   0.32629942    0.2945701 
-   20000   0.98641362    131.63233   0.32908082   0.29781576 
-   21000    0.9763779    140.20546   0.33382253   0.30091009 
-   22000   0.97984221     149.3632   0.33946182   0.30410181 
-   23000   0.98384014    157.80278   0.34304952   0.30727461 
-   24000   0.97601102    165.78405   0.34538343   0.31026343 
-   25000   0.99623187     173.8015     0.347603   0.31311142 
-   26000   0.98943691    182.06075   0.35011683   0.31582297 
-   27000   0.98992058    188.30114   0.34870582   0.31827868 
-   28000   0.97957751    196.93202   0.35166432   0.32053702 
-   29000   0.99513582    206.48445   0.35600767   0.32277974 
-   30000   0.99754125     213.2124     0.355354   0.32491307 
-   31000   0.98894929    221.74208   0.35764851   0.32691848 
-   32000     0.973493    229.28872   0.35826363    0.3288054 
-   33000   0.99989261     236.7565   0.35872197   0.33061911 
-   34000   0.97192218    243.57374   0.35819667   0.33225106 
-   35000   0.99711642    250.65118   0.35807311   0.33369124 
-   36000   0.97718259    258.94971   0.35965237   0.33507325 
-   37000   0.98194807    265.83921   0.35924218   0.33634589 
-   38000   0.97195138    272.94984   0.35914453   0.33755459 
-   39000   0.98219017    280.07692   0.35907297   0.33864166 
-   40000   0.98039694     288.4453   0.36055663   0.33967254 
-   41000   0.97621359    295.85108     0.360794    0.3406849 
-   42000   0.97460413    303.13769    0.3608782   0.34161073 
-   43000    0.9799912    312.06356    0.3628646   0.34254857 
-   44000   0.96313376    320.55123   0.36426276   0.34347747 
-   45000   0.97643796    329.68761   0.36631956   0.34443057 
-   46000   0.98641729    338.40463   0.36783111   0.34540729 
-   47000   0.97811939    345.46683    0.3675179   0.34634877 
-   48000   0.99744864    352.87823   0.36758148   0.34720815 
-   49000   0.97480356    362.60002   0.37000002   0.34807624 
-   50000   0.97841509    368.44194   0.36844193   0.34892214 
-   51000   0.97865859    375.44238   0.36808076   0.34966222 
-   52000   0.97415415    382.95453   0.36822551   0.35036495 
-   53000   0.97984491    390.33776   0.36824317   0.35103186 
-   54000   0.99289379     396.4986   0.36712833   0.35162842 
-   55000   0.98606668    403.49336   0.36681214   0.35217399 
-   56000   0.98585489    411.98283   0.36784182   0.35270646 
-   57000   0.98507959    418.14272   0.36679186   0.35321673 
-   58000   0.98030805    423.23791   0.36486026     0.353654 
-   59000   0.98315137    429.40554   0.36390299   0.35400654 
-   60000   0.98762585    437.17376   0.36431146   0.35433653 
-   61000   0.96937507    442.38698   0.36261228    0.3546452 
-   62000   0.97194792    450.91689   0.36364265    0.3549106 
-   63000   0.99877655    460.61733   0.36556931    0.3552122 
-   64000   0.98525211    469.26926   0.36661661   0.35554833 
-   65000    0.9833149    477.52571   0.36732747   0.35589823 
-   66000   0.97191797    485.72618   0.36797438   0.35624251 
-   67000   0.98479592    492.83716   0.36778892   0.35657544 
-   68000   0.98418943    498.90452   0.36684156   0.35688872 
-   69000   0.96953928    507.57013   0.36780444   0.35718476 
-   70000   0.98373337    515.05745   0.36789818   0.35749562 
-   71000   0.98260952    522.33093   0.36783868   0.35778626 
-   72000   0.98906053    527.99215   0.36666121   0.35804724 
-   73000   0.99569597    534.99359   0.36643396   0.35827372 
-   74000   0.97627362    540.94769    0.3655052   0.35847643 
-   75000   0.97276792    546.45533   0.36430355   0.35864641 
-   76000   0.97659072    554.59353   0.36486417   0.35879714 
-   77000    0.9807196    562.96571   0.36556215   0.35896542 
-   78000   0.97398601    571.22804   0.36617182   0.35914269 
-   79000   0.98124212    577.92968   0.36577828   0.35930881 
-   80000   0.98506783    586.73568    0.3667098   0.35948276 
-   81000   0.97926561    596.68206   0.36832226   0.35968089 
-   82000   0.97906184    604.24971   0.36844495   0.35988893 
-   83000   0.96540502     610.7078   0.36789626    0.3600856 
-   84000   0.98726761    619.32703   0.36864704   0.36027536 
-   85000   0.98133061    627.20955   0.36894679    0.3604747 
-   86000   0.99142106    634.68836   0.36900486   0.36067069 
-   87000   0.97917566    641.73186   0.36881141   0.36086497 
-   88000   0.99391197    649.76607   0.36918527   0.36105571 
-   89000   0.98521911    655.50224   0.36825969   0.36123298 
-   90000   0.97419059     664.0397   0.36891095   0.36139717 
-   91000   0.98687774    671.19045   0.36878596   0.36156016 
-   92000   0.97816545    677.37724   0.36813981   0.36171235 
-   93000   0.98734859    684.56734   0.36804696    0.3618463 
-   94000   0.99116168    691.47221   0.36780437   0.36197063 
-   95000   0.99982024    698.01624   0.36737697   0.36208597 
-   96000   0.99232404    703.53179    0.3664228   0.36218818 
-   97000   0.97829693    707.91832   0.36490635   0.36225634 
-   98000   0.99878715    713.77777   0.36417233   0.36230715 
-   99000   0.97026354    717.24468   0.36224478    0.3623226 
-  100000   0.98911409     722.1539   0.36107695   0.36230617 
-Loop time of 9.28795 on 8 procs for 100000 steps with 3200 atoms
-
-Pair  time (%) = 4.87621 (52.5003)
-Neigh time (%) = 1.26444 (13.6138)
-Comm  time (%) = 1.60752 (17.3076)
-Outpt time (%) = 0.00843725 (0.0908408)
-Other time (%) = 1.53135 (16.4875)
-
-Nlocal:    400 ave 410 max 389 min
-Histogram: 1 1 1 0 1 1 0 0 1 2
-Nghost:    205.375 ave 216 max 194 min
-Histogram: 1 0 0 2 2 0 1 0 0 2
-Neighs:    2818 ave 3010 max 2683 min
-Histogram: 2 0 2 0 1 1 0 1 0 1
-
-Total # of neighbors = 22544
-Ave neighs/atom = 7.045
-Neighbor list builds = 12748
-Dangerous builds = 0

examples/DIFFUSE/log.1Feb14.vacf.2d.g++.8

@@ -1,224 +0,0 @@
-LAMMPS (12 Feb 2014)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable	x equal 40
-variable	y equal 40
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 40 0 $y -0.1 0.1
-region          simbox block 0 40 0 40 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
-  4 by 2 by 1 MPI processor grid
-create_atoms    1 box
-Created 3200 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0   -0.5652325   -1.5346995 
-    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
-    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
-    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
-    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
-    5000   0.97069909   -1.5851114            0  -0.61471562   0.90108296 
-Loop time of 0.556362 on 8 procs for 5000 steps with 3200 atoms
-
-Pair  time (%) = 0.242478 (43.5828)
-Neigh time (%) = 0.0590148 (10.6073)
-Comm  time (%) = 0.0862918 (15.51)
-Outpt time (%) = 0.000148952 (0.0267725)
-Other time (%) = 0.168428 (30.2731)
-
-Nlocal:    400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost:    202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs:    2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix		2
-
-# data gathering run
-
-reset_timestep  0
-
-compute         vacf all vacf
-fix             4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
-
-# factor of 0.5 is for 2d
-
-fix             5 all vector 1 c_vacf[4]
-variable        vacf equal 0.5*dt*trap(f_5)
-
-thermo_style	custom step temp c_vacf[4] v_vacf
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump	        1 all custom 1 tmp.dump id type vx vy vz
-
-#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo          1000
-run	        100000
-Memory usage per processor = 2.29126 Mbytes
-Step Temp vacf[4] vacf 
-       0   0.97069909    1.9407915            0 
-    1000   0.98259938  0.068345562   0.21424576 
-    2000   0.98866167  0.028205164   0.24370013 
-    3000   0.98066292  0.008852823   0.27439588 
-    4000   0.97384109  0.011903564    0.3159275 
-    5000   0.97843004  0.019295534   0.33596598 
-    6000   0.98703537   0.01070801   0.34517088 
-    7000   0.97169186 -0.0082938435   0.33784119 
-    8000    0.9823893  0.038402174   0.32756669 
-    9000    0.9998457  0.045317593   0.33379383 
-   10000   0.98782869  0.027148675   0.34751149 
-   11000   0.99481941  0.035783937   0.36009047 
-   12000    0.9760981 -0.0010825507   0.36059769 
-   13000   0.97774297  0.048323885   0.36103752 
-   14000   0.96752038 0.0008189784   0.34988029 
-   15000   0.98697717   -0.0339338   0.35841003 
-   16000   0.98385955   0.03729417   0.36378228 
-   17000    0.9839555 -0.0063931744   0.37486488 
-   18000   0.98000182  0.065439765   0.39975619 
-   19000   0.96633821 0.0034363237   0.39585239 
-   20000   0.98641362    -0.020284   0.39696422 
-   21000    0.9763779  0.013683539   0.36183593 
-   22000   0.97984221 -0.0077108606   0.32642476 
-   23000   0.98384014 -0.030550764   0.32775468 
-   24000   0.97601102 -0.0047287909    0.3294707 
-   25000   0.99623187   0.00653461   0.34586445 
-   26000   0.98943691  -0.05047279    0.3283058 
-   27000   0.98992058  -0.01720223   0.30840611 
-   28000   0.97957751  0.020915942    0.3149002 
-   29000   0.99513582   0.03712206   0.30525251 
-   30000   0.99754125 -0.022509889   0.29511243 
-   31000   0.98894929  0.015289267   0.25586423 
-   32000     0.973493  0.015971435   0.25226411 
-   33000   0.99989261  0.026989142   0.29050941 
-   34000   0.97192218  0.043710515   0.29067058 
-   35000   0.99711642  0.047231436   0.27989734 
-   36000   0.97718259 0.0059969847   0.28843181 
-   37000   0.98194807  0.017440303   0.30325718 
-   38000   0.97195138 -0.040449666   0.29696592 
-   39000   0.98219017 0.0063692991   0.28915832 
-   40000   0.98039694 -0.0038122219   0.24799014 
-   41000   0.97621359  0.012624961    0.2374766 
-   42000   0.97460413   -0.0024187   0.24693474 
-   43000    0.9799912  0.015928618   0.26238505 
-   44000   0.96313376 -0.067284605   0.24397772 
-   45000   0.97643796 -0.0039001998   0.22733962 
-   46000   0.98641729 -0.026949085   0.24167989 
-   47000   0.97811939 -0.050859011    0.2335985 
-   48000   0.99744864 -0.008154229    0.2417371 
-   49000   0.97480356 -0.011051498   0.25474033 
-   50000   0.97841509  -0.00531423   0.25357072 
-   51000   0.97865859  0.067722096   0.25086864 
-   52000   0.97415415  0.015863025    0.2516842 
-   53000   0.97984491  0.021332829   0.28226376 
-   54000   0.99289379   -0.0192578   0.28300764 
-   55000   0.98606668  0.029307891   0.27592186 
-   56000   0.98585489 0.0062922121    0.2687204 
-   57000   0.98507959 -0.0068688582   0.27868708 
-   58000   0.98030805  0.013766115   0.31008116 
-   59000   0.98315137  0.033068034   0.32211415 
-   60000   0.98762585  0.050662295   0.30109082 
-   61000   0.96937507  -0.02797113   0.29968066 
-   62000   0.97194792 -0.0032022157    0.2866526 
-   63000   0.99877655 -0.010154313   0.31701083 
-   64000   0.98525211 -0.020415497   0.31774092 
-   65000    0.9833149 0.0087192442   0.31256891 
-   66000   0.97191797 0.0047184494   0.29880531 
-   67000   0.98479592 -0.010779275     0.294197 
-   68000   0.98418943 -0.035264623   0.29993828 
-   69000   0.96953928 -0.028114432   0.27403611 
-   70000   0.98373337 -0.057363336   0.25554163 
-   71000   0.98260952  0.048742037   0.27102884 
-   72000   0.98906053  0.010799224   0.26908376 
-   73000   0.99569597 -0.0092675754   0.26927752 
-   74000   0.97627362  0.013945821    0.2730712 
-   75000   0.97276792  0.015036012   0.25847255 
-   76000   0.97659072 -0.027078556   0.26783118 
-   77000    0.9807196 -0.044553679   0.25993053 
-   78000   0.97398601 -0.00027444729   0.26127735 
-   79000   0.98124212 -0.012488833   0.27454966 
-   80000   0.98506783 -0.015190822    0.2676633 
-   81000   0.97926561 -0.012755191   0.27046398 
-   82000   0.97906184  0.012564185    0.2835038 
-   83000   0.96540502 -0.007372877   0.29622738 
-   84000   0.98726761  0.021015365   0.32432233 
-   85000   0.98133061  0.020043402    0.3540913 
-   86000   0.99142106  0.025350024   0.36697674 
-   87000   0.97917566 0.0061562414   0.37456288 
-   88000   0.99391197 0.0068565008   0.39150922 
-   89000   0.98521911  0.015500816   0.38121119 
-   90000   0.97419059 0.00037609894   0.34181128 
-   91000   0.98687774 -0.0073221495   0.35316892 
-   92000   0.97816545  0.014057005   0.33181146 
-   93000   0.98734859  0.016570523   0.34546487 
-   94000   0.99116168 -0.0068196043   0.36316635 
-   95000   0.99982024  0.076723346   0.38376316 
-   96000   0.99232404 -0.048534983   0.38369657 
-   97000   0.97829693 0.0041180664   0.38022523 
-   98000   0.99878715 -0.00089133295   0.40289006 
-   99000   0.97026354 -0.0039532716   0.43650647 
-  100000   0.98911409  0.028647976    0.4499919 
-Loop time of 10.5771 on 8 procs for 100000 steps with 3200 atoms
-
-Pair  time (%) = 4.88134 (46.1499)
-Neigh time (%) = 1.2657 (11.9664)
-Comm  time (%) = 1.78371 (16.8638)
-Outpt time (%) = 0.0207323 (0.196011)
-Other time (%) = 2.62565 (24.8239)
-
-Nlocal:    400 ave 410 max 389 min
-Histogram: 1 1 1 0 1 1 0 0 1 2
-Nghost:    205.375 ave 216 max 194 min
-Histogram: 1 0 0 2 2 0 1 0 0 2
-Neighs:    2818 ave 3010 max 2683 min
-Histogram: 2 0 2 0 1 1 0 1 0 1
-
-Total # of neighbors = 22544
-Ave neighs/atom = 7.045
-Neighbor list builds = 12748
-Dangerous builds = 0

examples/KAPPA/log.13Oct16.ehex.g++.8

@@ -1,4 +1,4 @@
-LAMMPS (7 Jun 2016)
+LAMMPS (13 Oct 2016)
 # sample LAMMPS input script for thermal conductivity of liquid LJ
 # use fix ehex to add/subtract energy from 2 regions
 
@@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
      800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
      900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
     1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
-Loop time of 0.878884 on 8 procs for 1000 steps with 8000 atoms
+Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
 
-Performance: 491532.534 tau/day, 1137.807 timesteps/s
+Performance: 485876.777 tau/day, 1124.715 timesteps/s
 99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.48108    | 0.4925     | 0.50422    |   1.0 | 56.04
-Neigh   | 0.23355    | 0.23565    | 0.23888    |   0.4 | 26.81
-Comm    | 0.088565   | 0.10044    | 0.11391    |   2.7 | 11.43
-Output  | 0.00029421 | 0.00031444 | 0.00041795 |   0.2 |  0.04
-Modify  | 0.027427   | 0.032625   | 0.035225   |   1.6 |  3.71
-Other   |            | 0.01735    |            |       |  1.97
+Pair    | 0.48042    | 0.50311    | 0.52772    |   1.9 | 56.59
+Neigh   | 0.22997    | 0.23203    | 0.23466    |   0.3 | 26.10
+Comm    | 0.081187   | 0.10484    | 0.1285     |   4.2 | 11.79
+Output  | 0.00027299 | 0.00028226 | 0.000314   |   0.1 |  0.03
+Modify  | 0.028298   | 0.032276   | 0.037612   |   2.0 |  3.63
+Other   |            | 0.01658    |            |       |  1.86
 
 Nlocal:    1000 ave 1020 max 982 min
 Histogram: 1 0 2 1 0 1 1 1 0 1
@@ -121,7 +121,7 @@ thermo_style    custom step temp c_Thot c_Tcold
 thermo	        1000
 run             10000
 Memory usage per processor = 2.80761 Mbytes
-Step Temp Thot Tcold 
+Step Temp c_Thot c_Tcold 
     1000         1.35     1.431295    1.2955644 
     2000    1.3537291    1.6418772    1.1875127 
     3000    1.3615152    1.6451299    1.1769094 
@@ -133,20 +133,20 @@ Step Temp Thot Tcold
     9000    1.3701136    1.8238424     1.136342 
    10000    1.3563004    1.8059065    1.1547129 
    11000    1.3794051     1.692299    1.0515688 
-Loop time of 10.292 on 8 procs for 10000 steps with 8000 atoms
+Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
 
-Performance: 419743.444 tau/day, 971.628 timesteps/s
-99.5% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 409265.976 tau/day, 947.375 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.1797     | 4.902      | 5.5136     |  25.3 | 47.63
-Neigh   | 2.1913     | 2.4616     | 2.6938     |  14.2 | 23.92
-Comm    | 0.87831    | 1.64       | 2.611      |  56.5 | 15.94
-Output  | 0.00043011 | 0.00063166 | 0.00075626 |   0.5 |  0.01
-Modify  | 0.78531    | 0.92487    | 1.0647     |  10.6 |  8.99
-Other   |            | 0.3628     |            |       |  3.53
+Pair    | 4.1863     | 5.0134     | 5.8326     |  28.0 | 47.50
+Neigh   | 2.1559     | 2.4232     | 2.6516     |  14.2 | 22.96
+Comm    | 0.80561    | 1.8126     | 2.8852     |  58.4 | 17.17
+Output  | 0.00044537 | 0.00064856 | 0.00077057 |   0.5 |  0.01
+Modify  | 0.81915    | 0.94285    | 1.0571     |   9.5 |  8.93
+Other   |            | 0.3628     |            |       |  3.44
 
 Nlocal:    1000 ave 1105 max 883 min
 Histogram: 1 1 2 0 0 0 0 0 2 2
@@ -174,7 +174,7 @@ thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave
 
 run             20000
 Memory usage per processor = 3.0578 Mbytes
-Step Temp Thot Tcold tdiff ave 
+Step Temp c_Thot c_Tcold v_tdiff f_ave 
    11000    1.3794051    1.6903393    1.0515688            0            0 
    12000    1.3799777    1.8004888    1.1032219  -0.63860014            0 
    13000    1.3733605    1.7823094    1.0553582  -0.65827891  -0.65827891 
@@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
    29000    1.3819302    1.8619138    1.0495292  -0.78627491  -0.76680973 
    30000    1.3968366     1.883107    1.1004588  -0.83902548  -0.77082172 
    31000    1.3822489    1.8220413    1.0322271   -0.7550338  -0.76999077 
-Loop time of 22.3319 on 8 procs for 20000 steps with 8000 atoms
+Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
 
-Performance: 386890.255 tau/day, 895.579 timesteps/s
+Performance: 379649.018 tau/day, 878.817 timesteps/s
 99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.4818     | 9.8886     | 12.008     |  66.1 | 44.28
-Neigh   | 4.1157     | 5.0693     | 5.9657     |  38.0 | 22.70
-Comm    | 1.8343     | 4.6586     | 7.8747     | 129.4 | 20.86
-Output  | 0.00095606 | 0.0017744  | 0.0019104  |   0.7 |  0.01
-Modify  | 1.6812     | 1.9319     | 2.2204     |  13.5 |  8.65
-Other   |            | 0.7817     |            |       |  3.50
+Pair    | 7.4811     | 10.102     | 12.63      |  68.7 | 44.39
+Neigh   | 4.0495     | 4.9884     | 5.8366     |  37.8 | 21.92
+Comm    | 1.6695     | 4.9483     | 8.493      | 130.7 | 21.74
+Output  | 0.0010517  | 0.0017769  | 0.0019059  |   0.7 |  0.01
+Modify  | 1.6903     | 1.9371     | 2.2355     |  14.8 |  8.51
+Other   |            | 0.7799     |            |       |  3.43
 
 Nlocal:    1000 ave 1121 max 857 min
 Histogram: 2 0 1 1 0 0 0 0 1 3
@@ -222,4 +222,4 @@ Total # of neighbors = 219898
 Ave neighs/atom = 27.4872
 Neighbor list builds = 3474
 Dangerous builds = 0
-Total wall time: 0:00:33
+Total wall time: 0:00:34

examples/KAPPA/log.13Oct16.heat.g++.8

@@ -1,4 +1,4 @@
-LAMMPS (7 Jun 2016)
+LAMMPS (13 Oct 2016)
 # sample LAMMPS input script for thermal conductivity of liquid LJ
 # use fix heat to add/subtract energy from 2 regions
 
@@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
      800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
      900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
     1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
-Loop time of 0.889036 on 8 procs for 1000 steps with 8000 atoms
+Loop time of 0.872163 on 8 procs for 1000 steps with 8000 atoms
 
-Performance: 485919.613 tau/day, 1124.814 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 495320.223 tau/day, 1146.575 timesteps/s
+99.5% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.47867    | 0.4928     | 0.5006     |   1.0 | 55.43
-Neigh   | 0.23302    | 0.23557    | 0.23833    |   0.3 | 26.50
-Comm    | 0.1001     | 0.11264    | 0.12817    |   2.6 | 12.67
-Output  | 0.00032806 | 0.00034043 | 0.00040531 |   0.1 |  0.04
-Modify  | 0.028788   | 0.031511   | 0.033365   |   0.9 |  3.54
-Other   |            | 0.01618    |            |       |  1.82
+Pair    | 0.48598    | 0.49768    | 0.50892    |   1.1 | 57.06
+Neigh   | 0.22855    | 0.23236    | 0.23463    |   0.5 | 26.64
+Comm    | 0.082584   | 0.093727   | 0.10748    |   2.9 | 10.75
+Output  | 0.0002718  | 0.00028038 | 0.00031757 |   0.1 |  0.03
+Modify  | 0.028934   | 0.031425   | 0.03322    |   0.8 |  3.60
+Other   |            | 0.01668    |            |       |  1.91
 
 Nlocal:    1000 ave 1020 max 982 min
 Histogram: 1 0 2 1 0 1 1 1 0 1
@@ -121,7 +121,7 @@ thermo_style    custom step temp c_Thot c_Tcold
 thermo	        1000
 run             10000
 Memory usage per processor = 2.55761 Mbytes
-Step Temp Thot Tcold 
+Step Temp c_Thot c_Tcold 
     1000         1.35     1.431295    1.2955644 
     2000    1.3518468    1.5562602     1.154905 
     3000    1.3477229    1.5890075    1.2395414 
@@ -133,20 +133,20 @@ Step Temp Thot Tcold
     9000    1.3739201    1.6846211    1.1138829 
    10000    1.3751455    1.8039471    1.1500399 
    11000    1.3716416     1.833336    1.1267278 
-Loop time of 10.488 on 8 procs for 10000 steps with 8000 atoms
+Loop time of 10.3395 on 8 procs for 10000 steps with 8000 atoms
 
-Performance: 411900.216 tau/day, 953.473 timesteps/s
+Performance: 417815.278 tau/day, 967.165 timesteps/s
 99.5% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.138      | 4.9118     | 5.6168     |  26.2 | 46.83
-Neigh   | 2.1715     | 2.4541     | 2.7147     |  14.7 | 23.40
-Comm    | 0.94395    | 1.8449     | 2.9212     |  55.3 | 17.59
-Output  | 0.00043416 | 0.00046757 | 0.00054884 |   0.2 |  0.00
-Modify  | 1.0234     | 1.0946     | 1.2539     |   8.7 | 10.44
-Other   |            | 0.1821     |            |       |  1.74
+Pair    | 4.2189     | 4.9657     | 5.6225     |  25.3 | 48.03
+Neigh   | 2.1359     | 2.4223     | 2.6741     |  14.8 | 23.43
+Comm    | 0.83801    | 1.6773     | 2.6984     |  57.1 | 16.22
+Output  | 0.00042701 | 0.00046191 | 0.00052905 |   0.1 |  0.00
+Modify  | 1.0143     | 1.0895     | 1.1846     |   5.7 | 10.54
+Other   |            | 0.1844     |            |       |  1.78
 
 Nlocal:    1000 ave 1131 max 878 min
 Histogram: 3 1 0 0 0 0 0 1 1 2
@@ -174,7 +174,7 @@ thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave
 
 run             20000
 Memory usage per processor = 2.8078 Mbytes
-Step Temp Thot Tcold tdiff ave 
+Step Temp c_Thot c_Tcold v_tdiff f_ave 
    11000    1.3716416     1.833336    1.1267278            0            0 
    12000    1.3703433    1.7829467    1.1194444  -0.66044316            0 
    13000    1.3686734    1.8334366    1.1193477  -0.71431978  -0.71431978 
@@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
    29000    1.3777555    1.8287284    1.0715132  -0.70375514  -0.74425717 
    30000    1.3821118    1.7382856    1.1078333  -0.79892499  -0.74729427 
    31000    1.3870476    1.8410063    1.1235958  -0.76218423  -0.74807795 
-Loop time of 22.3813 on 8 procs for 20000 steps with 8000 atoms
+Loop time of 22.4057 on 8 procs for 20000 steps with 8000 atoms
 
-Performance: 386036.860 tau/day, 893.604 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 385616.132 tau/day, 892.630 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.4578     | 9.8912     | 11.96      |  64.5 | 44.19
-Neigh   | 4.0721     | 5.0195     | 5.8898     |  36.9 | 22.43
-Comm    | 1.9554     | 4.7393     | 7.8917     | 125.4 | 21.18
-Output  | 0.00099301 | 0.0017841  | 0.0019252  |   0.7 |  0.01
-Modify  | 2.2325     | 2.321      | 2.4866     |   6.5 | 10.37
-Other   |            | 0.4085     |            |       |  1.83
+Pair    | 7.6116     | 10.003     | 12.262     |  64.3 | 44.65
+Neigh   | 4.038      | 4.9528     | 5.8822     |  37.6 | 22.10
+Comm    | 1.6649     | 4.7143     | 7.6339     | 124.9 | 21.04
+Output  | 0.00098443 | 0.0017504  | 0.0018921  |   0.7 |  0.01
+Modify  | 2.1819     | 2.3289     | 2.6598     |  12.6 | 10.39
+Other   |            | 0.4047     |            |       |  1.81
 
 Nlocal:    1000 ave 1134 max 850 min
 Histogram: 2 1 0 1 0 0 0 1 0 3

examples/KAPPA/log.13Oct16.heatflux.g++.8

@@ -0,0 +1,230 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# Green-Kubo method via compute heat/flux and fix ave/correlate
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 10
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+
+variable    p equal 200     # correlation length
+variable    s equal 10      # sample interval
+variable    d equal $p*$s   # dump interval
+variable    d equal 200*$s   
+variable    d equal 200*10   
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
+  2 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 4000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# 1st equilibration run
+
+fix		1 all nvt temp $t $t 0.5
+fix		1 all nvt temp 1.35 $t 0.5
+fix		1 all nvt temp 1.35 1.35 0.5
+thermo		100
+run		1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 14 14 14
+Memory usage per processor = 2.52285 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0996979   -3.1962625 
+     100    1.1997886   -3.7796264            0   -1.9803934    0.4889458 
+     200     1.271238   -3.7354981            0   -1.8291178    0.6873844 
+     300    1.3346808   -3.6942841            0   -1.6927634   0.84332881 
+     400    1.4020848   -3.7118654            0   -1.6092641   0.87670585 
+     500    1.3723622   -3.6917931            0   -1.6337644   0.92172921 
+     600    1.3451676   -3.7281573            0   -1.7109103   0.76029091 
+     700    1.3021567   -3.6876155            0   -1.7348687   0.82721085 
+     800    1.3489121   -3.7082852            0   -1.6854229   0.86438061 
+     900    1.3708803   -3.6966168            0   -1.6408103     0.921415 
+    1000    1.3640742   -3.7075319            0   -1.6619322   0.86651332 
+Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms
+
+Performance: 943316.262 tau/day, 2183.602 timesteps/s
+98.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23307    | 0.24263    | 0.2466     |   1.0 | 52.98
+Neigh   | 0.10661    | 0.11011    | 0.11166    |   0.5 | 24.04
+Comm    | 0.069595   | 0.075354   | 0.087444   |   2.2 | 16.45
+Output  | 0.00028014 | 0.00028831 | 0.00031686 |   0.1 |  0.06
+Modify  | 0.01694    | 0.01904    | 0.021602   |   1.2 |  4.16
+Other   |            | 0.01053    |            |       |  2.30
+
+Nlocal:    500 ave 510 max 479 min
+Histogram: 1 0 0 0 0 2 1 1 0 3
+Nghost:    1519 ave 1539 max 1509 min
+Histogram: 2 0 4 0 0 0 0 1 0 1
+Neighs:    13553.8 ave 14051 max 12567 min
+Histogram: 1 0 0 0 1 0 2 1 1 2
+
+Total # of neighbors = 108430
+Ave neighs/atom = 27.1075
+Neighbor list builds = 155
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# thermal conductivity calculation
+
+reset_timestep  0
+
+compute         myKE all ke/atom
+compute         myPE all pe/atom
+compute         myStress all stress/atom NULL virial
+compute         flux all heat/flux myKE myPE myStress
+variable        Jx equal c_flux[1]/vol
+variable        Jy equal c_flux[2]/vol
+variable        Jz equal c_flux[3]/vol
+
+fix	        1 all nve
+fix             JJ all ave/correlate $s $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 200 $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 200 2000                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+
+variable        scale equal $s*dt/$t/$t/vol
+variable        scale equal 10*dt/$t/$t/vol
+variable        scale equal 10*dt/1.35/$t/vol
+variable        scale equal 10*dt/1.35/1.35/vol
+variable        k11 equal trap(f_JJ[3])*${scale}
+variable        k11 equal trap(f_JJ[3])*4.11522633744856e-06
+variable        k22 equal trap(f_JJ[4])*${scale}
+variable        k22 equal trap(f_JJ[4])*4.11522633744856e-06
+variable        k33 equal trap(f_JJ[5])*${scale}
+variable        k33 equal trap(f_JJ[5])*4.11522633744856e-06
+
+thermo	        $d
+thermo	        2000
+thermo_style    custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
+
+run             100000
+Memory usage per processor = 4.39785 Mbytes
+Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 
+       0         1.35  0.012561273 -0.087295611 -0.037041124  0.014429409   0.69689289   0.12547278 
+    2000    1.3455113 -0.034571206  -0.17570902 -0.057218308   -1.6110148    7.9287556    8.5035767 
+    4000    1.3477761 -0.029528723  0.018790489  0.056107464     7.698411    1.9459053    9.9605272 
+    6000    1.3411436  -0.20281149    0.2184806  0.036024028    4.6533075    1.6223216    3.7246529 
+    8000    1.3561682   0.12038719  0.034930957   0.12173601    4.6450263    1.9032849    2.7566363 
+   10000    1.3397694  -0.14241489  -0.10956496  0.053088086    6.4191535    3.1582257    2.2786677 
+   12000    1.3410756 0.0033462395   0.14337321   0.16381733    5.9663779    1.6774436    1.7442075 
+   14000    1.3484928 0.0080419803 -0.080232102  0.039035519    4.9483626    1.6210893    1.6103343 
+   16000    1.3414836  -0.11063045 -0.031557643  0.032060333    6.1381241     1.438198    1.5831541 
+   18000    1.3488617   0.15908507 -0.021418806  -0.13992507    5.9198613    1.1016464    1.2905478 
+   20000    1.3535727   0.13217689  0.071933521 -0.028452943    6.3746606     1.003194    1.7007101 
+   22000    1.3408534 -0.078953557 -0.0022323663  -0.22979033    5.0105241    1.1489328     1.720847 
+   24000      1.34722  0.074784199 -0.071218632   0.15238165    4.4835452   0.94086945    3.1603615 
+   26000    1.3539218  0.052534363   0.10419096    0.1866213    4.2233104    1.3973253    3.2802881 
+   28000    1.3510105 0.0080425673  -0.03723976   0.20758595     5.261917    1.1931088     3.498831 
+   30000    1.3410807 -0.043957884  0.065683978  0.015386362    4.3815277    1.5000017    3.2237565 
+   32000      1.34766 -0.060481287   0.17142383  0.034367135    4.0974942    1.1637027    3.3771953 
+   34000    1.3417583  -0.10055844  0.050237668   0.06974988    4.1478021    1.0235517    2.9440249 
+   36000    1.3468728   0.09375756  -0.17875264 -0.063513807    4.4412987   0.71084371    3.4316313 
+   38000    1.3496868 -0.038635804     0.117965  0.018050271     4.962332   0.41701129    3.4690212 
+   40000    1.3403452 -0.092158116   0.14432655 -0.062258229    4.9980486    0.3762815    3.1688552 
+   42000    1.3498661  0.085807945  0.010256385 -0.002956898    4.8200626   0.29278287     3.094633 
+   44000    1.3564084  -0.07415163 -0.051327929  -0.18457986    4.7070907    0.3358167    3.0741797 
+   46000    1.3435866 -0.013911463  0.081813372  0.022628846    4.6043718    0.3682401    2.9956189 
+   48000     1.350611  0.036512747  0.080481423  -0.22973181    4.5648715   0.32728516    3.8573343 
+   50000    1.3421783  0.057665789  0.075597141   0.17377918    4.4278473    0.5383886    3.5866168 
+   52000    1.3473497  -0.11159587  -0.09688769   0.19876168    4.3876613   0.43408155    3.4786305 
+   54000    1.3459495  -0.15341705  0.063996148 -0.0038254597    4.8434026   0.62047297     3.445187 
+   56000    1.3545654 -0.082406034  0.089232864 -0.024355614     4.546051    0.7367607    3.3694561 
+   58000    1.3577504  0.082844384  0.019500036  0.073721698    4.4061886    1.4575694    3.2754066 
+   60000     1.348614  -0.16190321 -0.048576343  0.093820555    4.2946463    1.3416919    3.1159234 
+   62000    1.3551143  0.097443296  -0.04420265  -0.25713945    4.1260882    1.2550603     3.063215 
+   64000     1.346239  0.019198575 -0.095746619   0.18383922    4.5691519    1.2615165    2.9935539 
+   66000    1.3535383 -0.0035547901   -0.1753318  0.014025292    4.5371394    1.0740671    2.9362916 
+   68000    1.3421249  -0.18217113  0.077901408   0.04314081    5.1644747    1.0218342    2.9789097 
+   70000    1.3446114  0.029565781  -0.13771336  0.050328878    5.4811405    1.0430806    2.9748623 
+   72000    1.3692655  0.005711741   0.13966773 -0.062638787    5.3033385    1.1040582    2.7599218 
+   74000    1.3405365 -0.054281977  0.038019086 -0.024980877    5.1246258    2.0782965     2.725331 
+   76000    1.3644178  0.040847675 -0.051968108  -0.12259032    5.1218657    1.8504273    2.6804003 
+   78000     1.353792 -0.093663092  0.018784967 -0.073871437     5.025196    1.7789709    2.5339006 
+   80000    1.3520982  -0.09407101  0.010328039 0.0028841073    5.1410049     1.855057    2.6935895 
+   82000    1.3447597  -0.11935066   -0.2184608  0.073543056    5.2645334    1.7883077    4.2012292 
+   84000    1.3712151 -0.064367612  0.021246872 -0.033571866    5.0479674    1.8947341    4.3856536 
+   86000    1.3453867 -0.029842112 -0.042297039   0.05422886    5.0667777    2.0365983    4.4542311 
+   88000    1.3439543  -0.21625828 -0.028119372 -0.010320332    4.9946428    2.3095763    4.3429587 
+   90000    1.3472579  0.058391002  0.037139373   0.03424008    5.0599004    2.8132794    4.4503426 
+   92000     1.361788  0.028891114  0.072799744  -0.12035229    4.8759851    2.5130025    4.2747068 
+   94000    1.3440566  0.043421348  0.049653856 -0.060444094    4.8884081    2.5072981    4.3105221 
+   96000    1.3537566  0.088733517  -0.11449828 -0.049852036    4.8115085    2.4780963    4.2213579 
+   98000    1.3373399   0.25457663 -0.041723778 0.00084565184    4.7163394    2.4100822     4.485536 
+  100000    1.3487502  0.046333889    0.1247351  0.063467467    4.6563279    2.4049358    4.5742925 
+Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms
+
+Performance: 872163.631 tau/day, 2018.897 timesteps/s
+99.6% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.027     | 27.478     | 28.167     |   6.9 | 55.48
+Neigh   | 11.257     | 11.369     | 11.491     |   2.3 | 22.95
+Comm    | 6.6783     | 7.6942     | 8.2758     |  19.3 | 15.53
+Output  | 0.0075166  | 0.024356   | 0.026799   |   4.1 |  0.05
+Modify  | 1.7374     | 1.7617     | 1.7845     |   1.0 |  3.56
+Other   |            | 1.205      |            |       |  2.43
+
+Nlocal:    500 ave 505 max 491 min
+Histogram: 1 0 0 1 0 1 0 2 2 1
+Nghost:    1529.88 ave 1548 max 1508 min
+Histogram: 1 1 0 0 1 1 2 0 0 2
+Neighs:    13569.8 ave 13906 max 13235 min
+Histogram: 1 1 0 1 1 1 1 1 0 1
+
+Total # of neighbors = 108558
+Ave neighs/atom = 27.1395
+Neighbor list builds = 16041
+Dangerous builds = 0
+
+variable        kappa equal (v_k11+v_k22+v_k33)/3.0
+print           "running average conductivity: ${kappa}"
+running average conductivity: 3.8785187495769
+Total wall time: 0:00:50

examples/KAPPA/log.13Oct16.langevin.g++.8

@@ -0,0 +1,245 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# thermostatting 2 regions via fix langevin
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+variable        tlo equal 1.0
+variable        thi equal 1.70
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+#variable        tlo equal 0.3
+#variable        thi equal 1.0
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
+  2 by 1 by 4 MPI processor grid
+create_atoms	1 box
+Created 8000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# heat layers
+
+region          hot block INF INF INF INF 0 1
+region          cold block  INF INF INF INF 10 11
+compute         Thot all temp/region hot
+compute         Tcold all temp/region cold
+
+# 1st equilibration run
+
+fix             1 all nvt temp $t $t 0.5
+fix             1 all nvt temp 1.35 $t 0.5
+fix             1 all nvt temp 1.35 1.35 0.5
+thermo	        100
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 14 14 27
+Memory usage per processor = 2.55761 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
+     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
+     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
+     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
+     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
+     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
+     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
+     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
+     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
+     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
+    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
+Loop time of 0.876399 on 8 procs for 1000 steps with 8000 atoms
+
+Performance: 492926.111 tau/day, 1141.033 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.47963    | 0.4975     | 0.51846    |   1.6 | 56.77
+Neigh   | 0.22878    | 0.23186    | 0.23458    |   0.4 | 26.46
+Comm    | 0.081789   | 0.096763   | 0.11865    |   3.6 | 11.04
+Output  | 0.000247   | 0.00025409 | 0.00028944 |   0.1 |  0.03
+Modify  | 0.02689    | 0.033982   | 0.042612   |   2.9 |  3.88
+Other   |            | 0.01604    |            |       |  1.83
+
+Nlocal:    1000 ave 1020 max 982 min
+Histogram: 1 0 2 1 0 1 1 1 0 1
+Nghost:    2299.5 ave 2331 max 2268 min
+Histogram: 1 1 1 1 0 0 0 3 0 1
+Neighs:    27122 ave 28382 max 26337 min
+Histogram: 2 0 2 1 1 0 0 1 0 1
+
+Total # of neighbors = 216976
+Ave neighs/atom = 27.122
+Neighbor list builds = 162
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# 2nd equilibration run
+
+fix		1 all nve
+fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
+fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 1 1.0 287859 tally yes
+fix_modify      hot temp Thot
+fix_modify      cold temp Tcold
+
+variable        tdiff equal c_Thot-c_Tcold
+thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
+thermo	        1000
+run             10000
+Memory usage per processor = 3.30761 Mbytes
+Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff 
+    1000         1.35     1.431295    1.2955644           -0           -0   0.13573065 
+    2000    1.3593243    1.6602094    1.0898701  -0.13903162   0.14234352   0.57033928 
+    3000    1.3412163    1.6308839    1.0677742   -0.2214765   0.25871329   0.56310968 
+    4000    1.3275359    1.5248034    1.0792345  -0.26908328   0.34211202   0.44556887 
+    5000    1.3230922    1.6266046    1.0523802  -0.33175886   0.43533756    0.5742244 
+    6000    1.3037036    1.6021737    1.0408166   -0.3639815   0.49869333   0.56135712 
+    7000    1.2903225    1.5701119    1.0603548  -0.40000421   0.55547714   0.50975712 
+    8000    1.3050677    1.6420218    1.0221774  -0.46368839   0.60293974   0.61984444 
+    9000    1.2950977    1.7153984    1.0583242  -0.51871512   0.66389344   0.65707419 
+   10000    1.3100216    1.6680668    1.0871293  -0.57485359    0.7161839   0.58093752 
+   11000     1.297052    1.6486494     1.088903  -0.60276081   0.75900024   0.55974633 
+Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms
+
+Performance: 372451.299 tau/day, 862.156 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.0544     | 4.9719     | 5.8426     |  34.5 | 42.87
+Neigh   | 2.0735     | 2.3933     | 2.7208     |  18.8 | 20.63
+Comm    | 0.91559    | 1.9788     | 3.1216     |  70.5 | 17.06
+Output  | 0.0005753  | 0.00068495 | 0.00080419 |   0.3 |  0.01
+Modify  | 1.9354     | 1.9837     | 2.0321     |   2.6 | 17.10
+Other   |            | 0.2705     |            |       |  2.33
+
+Nlocal:    1000 ave 1112 max 841 min
+Histogram: 1 1 0 2 0 0 0 0 1 3
+Nghost:    2294.38 ave 2506 max 2077 min
+Histogram: 2 1 1 0 0 0 0 1 1 2
+Neighs:    27441.9 ave 32651 max 19438 min
+Histogram: 1 1 0 2 0 0 0 0 0 4
+
+Total # of neighbors = 219535
+Ave neighs/atom = 27.4419
+Neighbor list builds = 1674
+Dangerous builds = 0
+
+# thermal conductivity calculation
+# reset langevin thermostats to zero energy accumulation
+
+compute		ke all ke/atom
+variable	temp atom c_ke/1.5
+
+fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
+fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 1 1.0 287859 tally yes
+fix_modify      hot temp Thot
+fix_modify      cold temp Tcold
+
+fix             ave all ave/time 10 100 1000 v_tdiff ave running
+thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
+
+compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
+
+run             20000
+Memory usage per processor = 3.5578 Mbytes
+Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave 
+   11000     1.297052    1.6473904     1.088903           -0           -0   0.55848738            0 
+   12000    1.2792808    1.6043738    1.0658375 -0.012256975   0.04611547   0.53853632   0.54492428 
+   13000    1.2787101    1.7035572    1.1159037 -0.073806664  0.099529002   0.58765348    0.5581748 
+   14000     1.289918    1.4642237    1.1073937  -0.11428779   0.13931657   0.35683005   0.56816328 
+   15000    1.2932964    1.5032665    1.0523148  -0.17247717   0.19001309   0.45095174   0.57436291 
+   16000    1.3025037    1.5424316    1.1185175  -0.22598282   0.22640921   0.42391405   0.56973168 
+   17000    1.3009667    1.5582105    1.0745661  -0.27544101   0.26143452   0.48364439    0.5700118 
+   18000    1.2970255    1.5019842    1.0228322  -0.31195285   0.31203237     0.479152   0.56544644 
+   19000    1.2880631    1.5290587    1.0976483  -0.34645573   0.34243366   0.43141047   0.56338309 
+   20000    1.3119675    1.6284144    1.1102294  -0.40922326   0.39217092   0.51818503   0.56614474 
+   21000    1.2838063    1.6670934   0.97721382  -0.43809329   0.46021572   0.68987962    0.5686161 
+   22000    1.2925041    1.7050682    1.0984963   -0.4871305   0.50520177    0.6065719   0.57226368 
+   23000    1.2746463    1.6388503    1.0286701  -0.51212873   0.56478515    0.6101802   0.57290996 
+   24000    1.2745381    1.7085713    1.1362975  -0.54529463   0.58540408   0.57227375   0.57296767 
+   25000    1.2776401    1.5259253    1.0415158  -0.58389862   0.62623289   0.48440948   0.57386374 
+   26000    1.2661888    1.4760829   0.99145001  -0.62638032   0.68155754   0.48463289   0.57021631 
+   27000    1.2923677    1.6070495    1.0300276  -0.70014343   0.70236265    0.5770219   0.57001637 
+   28000    1.2961449    1.7052335    1.0805793  -0.74856241   0.75775659   0.62465427   0.56927907 
+   29000    1.2969474    1.5520176    1.1249649  -0.78900962   0.79539202   0.42705264   0.56986986 
+   30000    1.2900596    1.6556864    1.0302676  -0.84180996   0.87187683    0.6254189   0.57245841 
+   31000    1.2923209    1.6752068    1.0156911  -0.89036148   0.88285227   0.65951571   0.57358134 
+Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 358418.039 tau/day, 829.671 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.5967     | 9.9644     | 12.189     |  62.9 | 41.34
+Neigh   | 3.9305     | 4.7817     | 5.594      |  34.5 | 19.84
+Comm    | 1.7656     | 4.5624     | 7.6382     | 122.3 | 18.93
+Output  | 0.0011697  | 0.0018933  | 0.0020008  |   0.6 |  0.01
+Modify  | 4.1386     | 4.2107     | 4.3622     |   3.8 | 17.47
+Other   |            | 0.5848     |            |       |  2.43
+
+Nlocal:    1000 ave 1118 max 875 min
+Histogram: 2 1 1 0 0 0 0 0 2 2
+Nghost:    2298.62 ave 2535 max 2063 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27462.4 ave 32904 max 21333 min
+Histogram: 2 2 0 0 0 0 0 0 0 4
+
+Total # of neighbors = 219699
+Ave neighs/atom = 27.4624
+Neighbor list builds = 3340
+Dangerous builds = 0
+Total wall time: 0:00:36

examples/KAPPA/log.13Oct16.mp.g++.8

@@ -0,0 +1,232 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# Muller-Plathe method via fix thermal_conductivity
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
+  2 by 1 by 4 MPI processor grid
+create_atoms	1 box
+Created 8000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# 1st equilibration run
+
+fix		1 all nvt temp $t $t 0.5
+fix		1 all nvt temp 1.35 $t 0.5
+fix		1 all nvt temp 1.35 1.35 0.5
+thermo		100
+run		1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 14 14 27
+Memory usage per processor = 2.55761 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
+     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
+     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
+     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
+     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
+     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
+     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
+     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
+     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
+     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
+    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
+Loop time of 0.875524 on 8 procs for 1000 steps with 8000 atoms
+
+Performance: 493418.774 tau/day, 1142.173 timesteps/s
+99.5% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.48279    | 0.49681    | 0.51174    |   1.2 | 56.74
+Neigh   | 0.22868    | 0.23169    | 0.23454    |   0.4 | 26.46
+Comm    | 0.084792   | 0.098391   | 0.11603    |   3.4 | 11.24
+Output  | 0.00027204 | 0.00027871 | 0.00031137 |   0.1 |  0.03
+Modify  | 0.027863   | 0.032316   | 0.039397   |   2.3 |  3.69
+Other   |            | 0.01605    |            |       |  1.83
+
+Nlocal:    1000 ave 1020 max 982 min
+Histogram: 1 0 2 1 0 1 1 1 0 1
+Nghost:    2299.5 ave 2331 max 2268 min
+Histogram: 1 1 1 1 0 0 0 3 0 1
+Neighs:    27122 ave 28382 max 26337 min
+Histogram: 2 0 2 1 1 0 0 1 0 1
+
+Total # of neighbors = 216976
+Ave neighs/atom = 27.122
+Neighbor list builds = 162
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# 2nd equilibration run
+
+compute		ke all ke/atom
+variable	temp atom c_ke/1.5
+
+fix		1 all nve
+
+compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
+
+fix		3 all thermal/conductivity 10 z 20
+
+variable        tdiff equal f_2[11][3]-f_2[1][3]
+thermo_style	custom step temp epair etotal f_3 v_tdiff
+
+thermo		1000
+run		20000
+Memory usage per processor = 2.8078 Mbytes
+Step Temp E_pair TotEng f_3 v_tdiff 
+    1000         1.35   -3.7100044   -1.6852575            0            0 
+    2000    1.3572899   -3.7210084   -1.6853282    873.12373   0.26058005 
+    3000     1.359979   -3.7268343   -1.6871208    1750.6998   0.40845169 
+    4000    1.3677509   -3.7394553   -1.6880853    2565.8064   0.63828485 
+    5000    1.3742987    -3.750287   -1.6890966    3373.2897   0.70173279 
+    6000    1.3950535   -3.7827674   -1.6904487    4162.6672   0.83210131 
+    7000    1.3843852   -3.7679238   -1.6916056    4947.5882   0.92719731 
+    8000     1.396125   -3.7861373   -1.6922116    5703.4508   0.92426948 
+    9000    1.4135104    -3.812624   -1.6926234    6465.5676    1.0412501 
+   10000    1.4092351   -3.8065359   -1.6929474    7242.2986    1.0772505 
+   11000    1.3966916   -3.7874302   -1.6926547    8007.3229     1.056805 
+   12000    1.4111272   -3.8089829   -1.6925567    8750.8648     1.097621 
+   13000    1.4091888   -3.8074873   -1.6939684    9514.7196    1.0734167 
+   14000    1.4132159   -3.8134636   -1.6939046    10284.269    1.1643391 
+   15000    1.3991348   -3.7928819    -1.694442    11051.851    1.0716016 
+   16000    1.4055537   -3.8013252   -1.6932583    11836.812    1.1506479 
+   17000    1.4127928   -3.8141054   -1.6951811    12626.124    1.1301728 
+   18000    1.4118868   -3.8119733   -1.6944077    13391.631    1.1521394 
+   19000    1.4209268    -3.826811   -1.6956872    14180.009    1.0929393 
+   20000    1.4093812   -3.8083875   -1.6945801    14969.574    1.2113183 
+   21000    1.4202317   -3.8255696   -1.6954884    15735.893     1.161082 
+Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 409982.223 tau/day, 949.033 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.4932     | 10.005     | 12.426     |  70.1 | 47.48
+Neigh   | 4.0592     | 5.0894     | 6.0544     |  41.7 | 24.15
+Comm    | 1.7793     | 5.0312     | 8.5027     | 134.6 | 23.87
+Output  | 0.00058484 | 0.00060964 | 0.0007031  |   0.1 |  0.00
+Modify  | 0.39735    | 0.4211     | 0.43467    |   2.3 |  2.00
+Other   |            | 0.5269     |            |       |  2.50
+
+Nlocal:    1000 ave 1188 max 806 min
+Histogram: 2 1 1 0 0 0 0 0 2 2
+Nghost:    2300.5 ave 2645 max 1963 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27897 ave 37064 max 18367 min
+Histogram: 2 2 0 0 0 0 0 0 0 4
+
+Total # of neighbors = 223176
+Ave neighs/atom = 27.897
+Neighbor list builds = 3537
+Dangerous builds = 0
+
+# thermal conductivity calculation
+# reset fix thermal/conductivity to zero energy accumulation
+
+fix		3 all thermal/conductivity 10 z 20
+
+fix             ave all ave/time 1 1 1000 v_tdiff ave running
+thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave
+
+run		20000
+Memory usage per processor = 3.05853 Mbytes
+Step Temp E_pair TotEng f_3 v_tdiff f_ave 
+   21000    1.4202317   -3.8255696   -1.6954884            0     1.161082     1.161082 
+   22000    1.4090517    -3.808543   -1.6952296    745.83128    1.1780376    1.1695598 
+   23000    1.4261394   -3.8350237    -1.696082    1516.9526    1.1393504      1.15949 
+   24000    1.4103907   -3.8098769   -1.6945553    2290.0213    1.1962529    1.1686807 
+   25000    1.4205929   -3.8266444   -1.6960213    3028.2748    1.1355183    1.1620482 
+   26000    1.4148587   -3.8168728     -1.69485    3788.0858    1.1902606    1.1667503 
+   27000    1.4226648   -3.8297832   -1.6960528    4580.4932    1.2378446    1.1769066 
+   28000    1.4167854   -3.8205958   -1.6956834    5328.2357    1.2038835    1.1802787 
+   29000    1.4208636   -3.8267081   -1.6956791     6077.036    1.1970863    1.1821462 
+   30000     1.420575   -3.8256917   -1.6950955    6840.5407    1.1884497    1.1827766 
+   31000    1.4233235   -3.8318045   -1.6970861    7576.9859    1.2088723    1.1851489 
+   32000     1.418912   -3.8229407   -1.6948388    8319.9854    1.1604002    1.1830865 
+   33000    1.4161289   -3.8211375   -1.6972096    9097.8598    1.1381183    1.1796274 
+   34000    1.3982574   -3.7915345   -1.6944106    9819.5817    1.1809721    1.1797235 
+   35000    1.4211314   -3.8267235   -1.6952929    10604.381     1.157812    1.1782627 
+   36000    1.4181668   -3.8217718   -1.6947876    11332.942    1.1843186    1.1786412 
+   37000    1.4092823   -3.8094817   -1.6958226     12068.55    1.1043391    1.1742705 
+   38000    1.4220481   -3.8278441   -1.6950386    12815.406    1.1996255    1.1756791 
+   39000    1.4146432   -3.8175526   -1.6958531    13565.714     1.149226    1.1742868 
+   40000    1.4088356   -3.8079173    -1.694928    14309.801    1.1710565    1.1741253 
+   41000    1.4058693   -3.8043119   -1.6957716    15067.894    1.1839862    1.1745949 
+Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 391962.361 tau/day, 907.320 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.8314     | 10.063     | 12.978     |  88.0 | 45.65
+Neigh   | 3.8802     | 5.2398     | 6.5269     |  52.7 | 23.77
+Comm    | 1.828      | 5.8112     | 10.14      | 160.2 | 26.36
+Output  | 0.00050211 | 0.00052819 | 0.00060391 |   0.1 |  0.00
+Modify  | 0.39313    | 0.41984    | 0.4453     |   3.3 |  1.90
+Other   |            | 0.5084     |            |       |  2.31
+
+Nlocal:    1000 ave 1188 max 810 min
+Histogram: 2 1 1 0 0 0 0 1 1 2
+Nghost:    2304.5 ave 2648 max 1970 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27885.2 ave 36431 max 18556 min
+Histogram: 2 2 0 0 0 0 0 0 1 3
+
+Total # of neighbors = 223082
+Ave neighs/atom = 27.8852
+Neighbor list builds = 3626
+Dangerous builds = 0
+Total wall time: 0:00:44

examples/KAPPA/log.1Feb14.heatflux.g++.8

@@ -1,208 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# Green-Kubo method via compute heat/flux and fix ave/correlate
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 10
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-
-variable    p equal 200     # correlation length
-variable    s equal 10      # sample interval
-variable    d equal $p*$s   # dump interval
-variable    d equal 200*$s   
-variable    d equal 200*10   
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 10
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
-  2 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 4000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# 1st equilibration run
-
-fix		1 all nvt temp $t $t 0.5
-fix		1 all nvt temp 1.35 $t 0.5
-fix		1 all nvt temp 1.35 1.35 0.5
-thermo		100
-run		1000
-Memory usage per processor = 2.10761 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0996979   -3.1962625 
-     100    1.1997886   -3.7796264            0   -1.9803934    0.4889458 
-     200     1.271238   -3.7354981            0   -1.8291178    0.6873844 
-     300    1.3346808   -3.6942841            0   -1.6927634   0.84332881 
-     400    1.4020848   -3.7118654            0   -1.6092641   0.87670585 
-     500    1.3723622   -3.6917931            0   -1.6337644   0.92172921 
-     600    1.3451676   -3.7281573            0   -1.7109103   0.76029091 
-     700    1.3021567   -3.6876155            0   -1.7348687   0.82721085 
-     800    1.3489121   -3.7082852            0   -1.6854229   0.86438062 
-     900    1.3708803   -3.6966168            0   -1.6408104   0.92141491 
-    1000    1.3640742   -3.7075323            0   -1.6619325   0.86651245 
-Loop time of 0.464189 on 8 procs for 1000 steps with 4000 atoms
-
-Pair  time (%) = 0.235336 (50.6983)
-Neigh time (%) = 0.104871 (22.5922)
-Comm  time (%) = 0.0896717 (19.3179)
-Outpt time (%) = 0.000278324 (0.0599591)
-Other time (%) = 0.0340324 (7.33158)
-
-Nlocal:    500 ave 510 max 479 min
-Histogram: 1 0 0 0 0 2 1 1 0 3
-Nghost:    1519 ave 1539 max 1509 min
-Histogram: 2 0 4 0 0 0 0 1 0 1
-Neighs:    13553.8 ave 14051 max 12567 min
-Histogram: 1 0 0 0 1 0 2 1 1 2
-
-Total # of neighbors = 108430
-Ave neighs/atom = 27.1075
-Neighbor list builds = 155
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# thermal conductivity calculation
-
-reset_timestep  0
-
-compute         myKE all ke/atom
-compute         myPE all pe/atom
-compute         myStress all stress/atom virial
-compute         flux all heat/flux myKE myPE myStress
-variable        Jx equal c_flux[1]/vol
-variable        Jy equal c_flux[2]/vol
-variable        Jz equal c_flux[3]/vol
-
-fix	        1 all nve
-fix             JJ all ave/correlate $s $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 200 $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 200 2000                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-
-variable        scale equal $s*dt/$t/$t/vol
-variable        scale equal 10*dt/$t/$t/vol
-variable        scale equal 10*dt/1.35/$t/vol
-variable        scale equal 10*dt/1.35/1.35/vol
-variable        k11 equal trap(f_JJ[3])*${scale}
-variable        k11 equal trap(f_JJ[3])*4.11522633744856e-06
-variable        k22 equal trap(f_JJ[4])*${scale}
-variable        k22 equal trap(f_JJ[4])*4.11522633744856e-06
-variable        k33 equal trap(f_JJ[5])*${scale}
-variable        k33 equal trap(f_JJ[5])*4.11522633744856e-06
-
-thermo	        $d
-thermo	        2000
-thermo_style    custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
-
-run             100000
-Memory usage per processor = 3.25202 Mbytes
-Step Temp Jx Jy Jz k11 k22 k33 
-       0         1.35  0.012562011 -0.087289131 -0.037038204  0.014431103   0.69678942     0.125453 
-    2000    1.3488448 -0.082686441  -0.05888314   0.15641005    9.6556473    4.8724539    39.132688 
-    4000    1.3506828  0.055310422 -0.038254827 -0.081110393    3.4422239    2.3744865    7.4870977 
-    6000    1.3324005  -0.10634454 -0.011811473  0.024430149    3.6509701    11.111829    2.7413472 
-    8000    1.3465517  -0.13857537 -0.058386681 -0.013220164    6.5578792    6.6188014    3.6355334 
-   10000    1.3454126 -0.044292047 -0.0055045339 -0.051726965    5.6920768    6.5502293    7.8616795 
-   12000    1.3601798   0.18989029 -0.094977713 -0.059726722    5.2989118    8.8331032     7.972481 
-   14000    1.3414287 0.0064865781  0.056749763   0.12775935     4.453589    6.4962925    7.9502167 
-   16000    1.3249032 0.0023833148 0.0074389705  -0.12452498    5.2719354     6.164126    7.9937329 
-   18000    1.3486905   0.24719037  -0.13649854 -0.051766952    3.7849335    5.4803263    6.9701788 
-   20000    1.3572854  0.065005524  0.050772448   0.12768096     3.378611    5.6519702    7.1233623 
-   22000     1.352508 -0.042516792 -0.070285937  -0.03879074    5.4717313    5.4908509    6.7550818 
-   24000    1.3559841 -0.015758535 -0.098318418  0.027238601    6.0025309    5.2571093    6.0763852 
-   26000    1.3442105 -0.047372234  0.036647228 -0.0052159685    6.8263856    4.6880057    6.1674781 
-   28000    1.3522633  0.025172759 -0.016031105   0.12001218    6.3114313    4.1003669    5.7234478 
-   30000    1.3593364 -0.044078855 0.0089521622   0.13278909    5.4296394    3.8944372    5.2946242 
-   32000    1.3412479 -0.013107683 -0.089437735 -0.089978727    5.0171818    4.2838538    6.7869585 
-   34000    1.3490784 -0.069828566 -0.018570411  0.018866428    5.1053455    3.7588109    5.7177159 
-   36000    1.3630314 -0.017768864  0.067999673  0.016212961    5.3345297    3.6547014    5.5137046 
-   38000    1.3564307  0.080792723   0.12705697 0.0023785227    5.1062587    3.6140422    5.5464591 
-   40000    1.3546707 -0.030425013   0.17303248 -0.043210574    4.5874798    3.6033647    5.2304191 
-   42000    1.3549663   0.10109213 -0.056635329  0.047756306    4.1930341    3.4788566    5.3322825 
-   44000    1.3557286 0.0083871709  -0.08039758 0.0060697507    4.8453948    3.7579315    4.9727852 
-   46000    1.3434325  0.048348267  -0.12296683 -0.012320195    4.6106895    3.6890294    4.6654515 
-   48000    1.3520456  0.052909962  0.034221069  0.011730009    4.8097414     3.897061    4.5042484 
-   50000    1.3480467  0.084823081 -0.093901701  0.091139125    4.6836534    3.7687187    4.4227539 
-   52000    1.3473278  -0.12531922 -0.065273509   0.11638381    4.9413341    3.8765808    4.5227649 
-   54000    1.3672128   0.11139848  0.034992201 -0.022009105     4.695476    3.5100821    5.0401349 
-   56000     1.341716   0.12258667 -0.089117615  0.041707151    4.5195052    3.3873269     4.972056 
-   58000     1.359732  0.063106883 -0.026013959 -0.026567969    4.3259743    3.6185582     4.721062 
-   60000    1.3587911   0.05591296  -0.12996822  0.095669495    4.1958916    3.5682633    4.8210022 
-   62000    1.3483527  0.048201166 -0.030400186 -0.018919104    4.0886746    3.7373315    4.8825261 
-   64000    1.3531159  -0.10850158 -0.093503261  0.095145743    3.9415737    3.6946305    4.6787173 
-   66000    1.3534358 0.0070478917  -0.13855333 -0.0028185444     3.989283    3.7940811    4.5848181 
-   68000    1.3509679  -0.17972456  -0.15918151 -0.0092253402    4.1168514     3.689533    4.9348847 
-   70000    1.3496439  0.025102803  -0.12080911 0.0099284856    4.0474517    3.6265752    4.8809921 
-   72000    1.3382578    0.2235088   0.10981254  0.049251118    3.9059236    3.5169408    4.9528845 
-   74000    1.3529223  0.012949328   0.11733173   0.12107899    4.0011677    3.4205986    4.7288624 
-   76000    1.3442459  0.090185942  0.038587691 -0.023131667    3.9854752    3.4013375    4.7967661 
-   78000    1.3423941  0.072006425 -0.009752458  0.058791886      3.87483    3.3898574    5.0306248 
-   80000    1.3501112 -0.041057888  -0.11150244 -0.052369732    3.7648956    3.2969166    4.9549774 
-   82000     1.358605   0.14838249  0.055223984  0.019108344    3.8986959    3.2556248    4.8872754 
-   84000     1.357958 -0.087190849  0.029998974  0.089839797    4.4229469    3.2567955    4.7704664 
-   86000    1.3340187   0.10824995 -0.013149214  0.042146878    3.9867785    3.2596969    4.6510248 
-   88000    1.3428375 -0.033908572  -0.11261352  0.099056349    3.8033502    3.1706434    4.5328732 
-   90000    1.3299574  0.055893064  -0.22127211 -0.042737098    3.7086395     3.118066    4.5709281 
-   92000    1.3488719  0.040126575  0.074080804  0.019410656    3.8714376    3.0342566    4.4798044 
-   94000    1.3621842 -0.087519994  0.028392459  0.047179422    3.7841822    3.1603745    4.3925598 
-   96000    1.3578003  0.081511213 -0.0083540805  0.015204759    3.7117805    3.0610774    4.2886014 
-   98000    1.3477904  -0.13903407    0.1146023  0.059812672    3.7445818     3.284994    4.3000618 
-  100000    1.3583776   0.16015243   0.19139469  0.097636877    3.8265662     3.280556    4.2276263 
-Loop time of 49.3099 on 8 procs for 100000 steps with 4000 atoms
-
-Pair  time (%) = 26.5664 (53.8764)
-Neigh time (%) = 10.8228 (21.9485)
-Comm  time (%) = 8.59585 (17.4323)
-Outpt time (%) = 0.0256916 (0.0521023)
-Other time (%) = 3.29916 (6.69066)
-
-Nlocal:    500 ave 519 max 493 min
-Histogram: 4 1 0 1 0 0 1 0 0 1
-Nghost:    1547 ave 1558 max 1523 min
-Histogram: 1 0 0 0 0 2 1 0 2 2
-Neighs:    13544.8 ave 14633 max 13111 min
-Histogram: 2 1 3 1 0 0 0 0 0 1
-
-Total # of neighbors = 108358
-Ave neighs/atom = 27.0895
-Neighbor list builds = 16041
-Dangerous builds = 0
-
-variable        kappa equal (v_k11+v_k22+v_k33)/3.0
-print           "running average conductivity: ${kappa}"
-running average conductivity: 3.77824951481468

examples/KAPPA/log.1Feb14.langevin.g++.8

@@ -1,215 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# thermostatting 2 regions via fix langevin
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-variable        tlo equal 1.0
-variable        thi equal 1.70
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-#variable        tlo equal 0.3
-#variable        thi equal 1.0
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
-  2 by 1 by 4 MPI processor grid
-create_atoms	1 box
-Created 8000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# heat layers
-
-region          hot block INF INF INF INF 0 1
-region          cold block  INF INF INF INF 10 11
-compute         Thot all temp/region hot
-compute         Tcold all temp/region cold
-
-# 1st equilibration run
-
-fix             1 all nvt temp $t $t 0.5
-fix             1 all nvt temp 1.35 $t 0.5
-fix             1 all nvt temp 1.35 1.35 0.5
-thermo	        100
-run             1000
-Memory usage per processor = 2.14238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
-     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
-     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
-     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
-     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
-     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
-     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
-     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
-     800    1.3419994   -3.7155648            0   -1.7028172   0.82925677 
-     900    1.3562214   -3.6965608            0    -1.662483   0.88908144 
-    1000    1.3732016   -3.7100024            0   -1.6504575   0.83982823 
-Loop time of 0.862126 on 8 procs for 1000 steps with 8000 atoms
-
-Pair  time (%) = 0.482831 (56.0047)
-Neigh time (%) = 0.221903 (25.739)
-Comm  time (%) = 0.104307 (12.0989)
-Outpt time (%) = 0.000301003 (0.0349141)
-Other time (%) = 0.0527841 (6.12256)
-
-Nlocal:    1000 ave 1020 max 982 min
-Histogram: 1 0 2 1 0 1 1 1 0 1
-Nghost:    2299.5 ave 2331 max 2268 min
-Histogram: 1 1 1 1 0 0 0 3 0 1
-Neighs:    27122 ave 28382 max 26337 min
-Histogram: 2 0 2 1 1 0 0 1 0 1
-
-Total # of neighbors = 216976
-Ave neighs/atom = 27.122
-Neighbor list builds = 162
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# 2nd equilibration run
-
-fix		1 all nve
-fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
-fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 1 1.0 287859 tally yes
-fix_modify      hot temp Thot
-fix_modify      cold temp Tcold
-
-variable        tdiff equal c_Thot-c_Tcold
-thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
-thermo	        1000
-run             10000
-Memory usage per processor = 2.60014 Mbytes
-Step Temp Thot Tcold hot cold tdiff 
-    1000         1.35    1.4312938    1.2955632            0            0   0.13573057 
-    2000     1.360018     1.493833     1.108937  -0.12327246    0.1384129   0.38489598 
-    3000    1.3375537    1.6938591    1.0191771  -0.21101663   0.26135778   0.67468203 
-    4000    1.3233024    1.6026443    1.1480306  -0.26177493   0.34439263   0.45461365 
-    5000    1.3107386     1.711679      1.05711  -0.31795111   0.42339093   0.65456895 
-    6000     1.297964    1.6472939   0.95469459  -0.36994548   0.48890072   0.69259932 
-    7000    1.3062638    1.5806629     1.080306  -0.43385121   0.56448283   0.50035689 
-    8000    1.3062755    1.6415159    1.0407288  -0.48697483   0.62125026   0.60078705 
-    9000    1.2850239    1.6253774    1.0574621  -0.50398307   0.66921986   0.56791525 
-   10000    1.3035594    1.5362476    1.0681602  -0.56218263   0.71574454   0.46808735 
-   11000    1.2973176    1.6350179    1.0433547  -0.61814256   0.75532475   0.59166313 
-Loop time of 11.3468 on 8 procs for 10000 steps with 8000 atoms
-
-Pair  time (%) = 4.81454 (42.4309)
-Neigh time (%) = 2.27955 (20.0899)
-Comm  time (%) = 1.88988 (16.6557)
-Outpt time (%) = 0.000712395 (0.00627838)
-Other time (%) = 2.36209 (20.8173)
-
-Nlocal:    1000 ave 1135 max 867 min
-Histogram: 2 0 2 0 0 0 0 2 1 1
-Nghost:    2314.38 ave 2559 max 2067 min
-Histogram: 1 1 2 0 0 0 0 2 0 2
-Neighs:    27392.4 ave 33962 max 20582 min
-Histogram: 2 0 2 0 0 0 0 1 1 2
-
-Total # of neighbors = 219139
-Ave neighs/atom = 27.3924
-Neighbor list builds = 1666
-Dangerous builds = 0
-
-# thermal conductivity calculation
-# reset langevin thermostats to zero energy accumulation
-
-compute		ke all ke/atom
-variable	temp atom c_ke/1.5
-
-fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
-fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 1 1.0 287859 tally yes
-fix_modify      hot temp Thot
-fix_modify      cold temp Tcold
-
-fix             ave all ave/time 10 100 1000 v_tdiff ave running
-thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
-
-fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp 		  file profile.langevin units reduced
-
-run             20000
-Memory usage per processor = 2.60106 Mbytes
-Step Temp Thot Tcold hot cold tdiff ave 
-   11000    1.2973176    1.6350179    1.0433547            0            0   0.59166313            0 
-   12000    1.3039677    1.6419813    1.0477757 -0.046382646  0.056968333    0.5942056   0.59568325 
-   13000    1.3110256    1.5869209    1.0158888 -0.094090387   0.10445821   0.57103213   0.57629599 
-   14000     1.293218    1.6629496    1.1121109  -0.11375822   0.15128701   0.55083862    0.5707904 
-   15000    1.2811676    1.6722435    1.0942864  -0.14415448   0.20239116   0.57795712    0.5695191 
-   16000    1.2791266    1.5765255    1.1007618   -0.2014815    0.2427606   0.47576367   0.56997652 
-   17000    1.2622984    1.6433371    1.0358679  -0.22929967   0.29997963   0.60746917   0.56431552 
-   18000    1.2795857    1.7006846    1.0702476  -0.29495954    0.3304481     0.630437   0.57298103 
-   19000    1.2794851    1.5796065    1.0383562   -0.3325748    0.3825079   0.54125035     0.567257 
-   20000    1.3013271    1.6682287    1.0624636  -0.40206115   0.42100016   0.60576507   0.57276102 
-   21000     1.277446    1.5408233    1.0275158  -0.43012499   0.48360636   0.51330753   0.57340191 
-   22000    1.3031703    1.6370721    1.0356931  -0.51126428   0.52836134   0.60137903   0.57578211 
-   23000    1.2719643    1.4882391   0.98769817  -0.55845167   0.61243478   0.50054093   0.57457152 
-   24000    1.2931956    1.5814171    1.0586513  -0.60691503   0.63563787   0.52276581   0.57294037 
-   25000    1.2846646    1.7006525    1.0209227  -0.64068901   0.67962894   0.67972988   0.57312421 
-   26000    1.2711788    1.6697984   0.99699462  -0.67019827   0.73853772   0.67280381   0.57276936 
-   27000    1.2732777    1.6285951    1.1302554  -0.70566156   0.76748898   0.49833966   0.57255348 
-   28000    1.2831929    1.5938242    1.0977096  -0.75144205   0.81168035   0.49611462   0.57460785 
-   29000    1.2792513    1.4854998    1.0013453  -0.79831201   0.86425474    0.4841545   0.57139895 
-   30000    1.2677402    1.6009684     1.092679  -0.83584426   0.90606945   0.50828948   0.57156924 
-   31000    1.2720929    1.5851445    1.0736744  -0.87730401   0.95644174   0.51147013    0.5717415 
-Loop time of 23.7017 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.6584 (40.7498)
-Neigh time (%) = 4.57821 (19.3159)
-Comm  time (%) = 4.45101 (18.7793)
-Outpt time (%) = 0.00194073 (0.00818813)
-Other time (%) = 5.01215 (21.1468)
-
-Nlocal:    1000 ave 1121 max 880 min
-Histogram: 2 2 0 0 0 0 0 0 2 2
-Nghost:    2281.5 ave 2471 max 2073 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-Neighs:    27428.1 ave 33179 max 21152 min
-Histogram: 2 2 0 0 0 0 0 0 1 3
-
-Total # of neighbors = 219425
-Ave neighs/atom = 27.4281
-Neighbor list builds = 3338
-Dangerous builds = 0

examples/KAPPA/log.1Feb14.mp.g++.8

@@ -1,200 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# Muller-Plathe method via fix thermal_conductivity
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
-  2 by 1 by 4 MPI processor grid
-create_atoms	1 box
-Created 8000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# 1st equilibration run
-
-fix		1 all nvt temp $t $t 0.5
-fix		1 all nvt temp 1.35 $t 0.5
-fix		1 all nvt temp 1.35 1.35 0.5
-thermo		100
-run		1000
-Memory usage per processor = 2.14238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
-     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
-     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
-     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
-     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
-     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
-     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
-     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
-     800    1.3419994   -3.7155648            0   -1.7028172   0.82925677 
-     900    1.3562214   -3.6965608            0    -1.662483   0.88908144 
-    1000    1.3732016   -3.7100024            0   -1.6504575   0.83982823 
-Loop time of 0.862547 on 8 procs for 1000 steps with 8000 atoms
-
-Pair  time (%) = 0.478427 (55.4668)
-Neigh time (%) = 0.220096 (25.517)
-Comm  time (%) = 0.10999 (12.7517)
-Outpt time (%) = 0.00030601 (0.0354775)
-Other time (%) = 0.0537277 (6.22896)
-
-Nlocal:    1000 ave 1020 max 982 min
-Histogram: 1 0 2 1 0 1 1 1 0 1
-Nghost:    2299.5 ave 2331 max 2268 min
-Histogram: 1 1 1 1 0 0 0 3 0 1
-Neighs:    27122 ave 28382 max 26337 min
-Histogram: 2 0 2 1 1 0 0 1 0 1
-
-Total # of neighbors = 216976
-Ave neighs/atom = 27.122
-Neighbor list builds = 162
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# 2nd equilibration run
-
-compute		ke all ke/atom
-variable	temp atom c_ke/1.5
-
-fix		1 all nve
-fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp 		  file profile.mp units reduced
-fix		3 all thermal/conductivity 10 z 20
-
-variable        tdiff equal f_2[11][3]-f_2[1][3]
-thermo_style	custom step temp epair etotal f_3 v_tdiff
-
-thermo		1000
-run		20000
-Memory usage per processor = 2.1433 Mbytes
-Step Temp E_pair TotEng 3 tdiff 
-    1000         1.35   -3.7100024   -1.6852556            0            0 
-    2000    1.3488972    -3.708116   -1.6850231    877.52861   0.25969396 
-    3000    1.3658991    -3.735305   -1.6867124    1757.5984   0.40713773 
-    4000    1.3660888   -3.7368211   -1.6879441     2599.882   0.63176318 
-    5000    1.3702365   -3.7439731   -1.6888753    3417.2012   0.68861496 
-    6000    1.3802047   -3.7607288   -1.6906806    4247.6303    0.8258624 
-    7000    1.3981219   -3.7883507     -1.69143    5036.1985   0.90753031 
-    8000    1.3968279   -3.7880683   -1.6930884    5807.0759   0.99392296 
-    9000    1.3960267   -3.7866214   -1.6928431    6584.6398    1.0833481 
-   10000    1.4067029   -3.8038141   -1.6940234    7372.3357    1.0359437 
-   11000    1.4037578   -3.7984096   -1.6930361    8133.4913    1.0506296 
-   12000    1.4112365   -3.8109671   -1.6943769    8908.2356    1.1033313 
-   13000    1.4066326   -3.8036805   -1.6939953    9674.5783    1.1492152 
-   14000    1.4136249   -3.8155288   -1.6953566    10429.951    1.1101441 
-   15000     1.402741   -3.7983064   -1.6944579    11194.927    1.1163151 
-   16000     1.412565   -3.8138997    -1.695317    11931.815    1.2199073 
-   17000    1.4023686   -3.7975376   -1.6942476    12695.415    1.1800489 
-   18000    1.4200941   -3.8257695   -1.6958947    13456.945    1.1583648 
-   19000    1.4016117   -3.7972936   -1.6951388    14216.201    1.1846518 
-   20000    1.4105524   -3.8113272   -1.6957631    14977.184    1.2831156 
-   21000    1.4068217   -3.8054214   -1.6954526    15739.554     1.147926 
-Loop time of 20.7938 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.73079 (46.7967)
-Neigh time (%) = 4.8843 (23.4893)
-Comm  time (%) = 5.15718 (24.8016)
-Outpt time (%) = 0.000606179 (0.0029152)
-Other time (%) = 1.02088 (4.90955)
-
-Nlocal:    1000 ave 1176 max 820 min
-Histogram: 2 2 0 0 0 0 0 0 2 2
-Nghost:    2318.88 ave 2663 max 1967 min
-Histogram: 3 1 0 0 0 0 0 0 2 2
-Neighs:    27860.2 ave 36167 max 18992 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-
-Total # of neighbors = 222882
-Ave neighs/atom = 27.8603
-Neighbor list builds = 3543
-Dangerous builds = 0
-
-# thermal conductivity calculation
-# reset fix thermal/conductivity to zero energy accumulation
-
-fix		3 all thermal/conductivity 10 z 20
-
-fix             ave all ave/time 1 1 1000 v_tdiff ave running
-thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave
-
-run		20000
-Memory usage per processor = 2.33403 Mbytes
-Step Temp E_pair TotEng 3 tdiff ave 
-   21000    1.4068217   -3.8054214   -1.6954526            0     1.147926     1.147926 
-   22000    1.3967994   -3.7893902    -1.694453     767.0398    1.1920832    1.1700046 
-   23000    1.4170976    -3.822137   -1.6967564    1517.2987    1.1545977     1.164869 
-   24000    1.4202355   -3.8249732   -1.6948862    2277.7333    1.1750006    1.1674019 
-   25000    1.4205956   -3.8264595   -1.6958326    3028.6456     1.168964    1.1677143 
-   26000    1.4105028   -3.8099425   -1.6944527    3771.4445    1.1535799    1.1653586 
-   27000    1.4121218   -3.8137079   -1.6957899     4524.007    1.1582776     1.164347 
-   28000    1.4073732   -3.8055739   -1.6947781    5297.7257    1.1390419    1.1611839 
-   29000    1.3935065   -3.7848004   -1.6948019    6040.6442     1.106954    1.1551583 
-   30000    1.4126276   -3.8136783   -1.6950018    6777.7617     1.122798    1.1519223 
-   31000    1.4220569   -3.8292934   -1.6964746    7529.6983    1.1517202    1.1519039 
-   32000    1.4157206   -3.8184427   -1.6951273    8293.9624    1.1600224    1.1525805 
-   33000    1.4300672   -3.8403564   -1.6955237    9056.1085    1.1581575    1.1530095 
-   34000    1.4114669   -3.8123726   -1.6954368    9827.2549     1.169357    1.1541771 
-   35000    1.4087756   -3.8085583    -1.695659    10582.235     1.254384    1.1608576 
-   36000    1.4071234   -3.8063392    -1.695918    11335.664    1.1886748    1.1625962 
-   37000    1.4150044   -3.8175559   -1.6953146    12067.647    1.1452763    1.1615774 
-   38000    1.4208299   -3.8269499   -1.6959714    12785.237    1.1689649    1.1619878 
-   39000    1.4132869   -3.8147648   -1.6950995    13548.517    1.1134294    1.1594321 
-   40000    1.4071151   -3.8068479   -1.6964391    14307.339    1.1772366    1.1603223 
-   41000    1.4126121   -3.8153948   -1.6967416     15087.11    1.1408062     1.159393 
-Loop time of 21.9152 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.77976 (44.6255)
-Neigh time (%) = 5.01423 (22.8802)
-Comm  time (%) = 6.03064 (27.5181)
-Outpt time (%) = 0.000575513 (0.00262609)
-Other time (%) = 1.08999 (4.97365)
-
-Nlocal:    1000 ave 1167 max 820 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-Nghost:    2292.38 ave 2619 max 1989 min
-Histogram: 4 0 0 0 0 0 0 0 2 2
-Neighs:    27929.9 ave 37820 max 19105 min
-Histogram: 4 0 0 0 0 0 0 0 3 1
-
-Total # of neighbors = 223439
-Ave neighs/atom = 27.9299
-Neighbor list builds = 3624
-Dangerous builds = 0

examples/USER/dpd/README

@@ -1,9 +1,11 @@
 This directory contains input files for DPD simulations under
 isothermal, isoenergetic, isobaric and isoenthalpic conditions.  In
 addition, there is also an example for a reaction DPD simulation under
-isoenergetic conditions.  All the DPD scenarios use the Shardlow
-splitting algorithm to integrate the equations of motion.  The compute
-dpd command is used in the isoenergetic and isenthalpic case to
+isoenergetic conditions.  All the DPD scenarios that are named with 
+*-shardlow use the Shardlow splitting algorithm to integrate the 
+equations of motion.  All the DPD scenarious that are named with  
+*-vv utilize the velocity-Verlet integration scheme.  The compute dpd 
+command is used in the isoenergetic and isenthalpic case to
 demonstrate how one can access the particle internal energies.
 
 

examples/USER/dpd/dpd-shardlow/in.dpd-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
-log             log.dpd
+log             log.dpd-shardlow
 boundary        p p p
 
 units           metal  
@@ -24,4 +24,4 @@ thermo_modify   format float %15.10f
 fix             1 all shardlow
 fix             2 all nve
 
-run             100
+run             100

examples/USER/dpd/dpd-shardlow/log.dpd-shardlow.reference

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
 boundary        p p p
 
 units           metal
@@ -38,7 +36,7 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 12 10 9
-Memory usage per processor = 2.04518 Mbytes
+Memory usage per processor = 2.04718 Mbytes
 Step Temp PotEng KinEng TotEng 
        0  128.6667660382  263.2538386154   16.6148533499  279.8686919654 
        1  128.8781761686  263.2538784644   16.6421529271  279.8960313916 
@@ -46,7 +44,7 @@ Step Temp PotEng KinEng TotEng
        3  129.0944237374  263.2540669039   16.6700771671  279.9241440710 
        4  129.1614377649  263.2542208758   16.6787307477  279.9329516235 
        5  129.5099128271  263.2544124900   16.7237296409  279.9781421309 
-       6  129.4373659799  263.2546219015   16.7143616023  279.9689835038 
+       6  129.4373659800  263.2546219015   16.7143616023  279.9689835038 
        7  129.5468806805  263.2548644992   16.7285033325  279.9833678316 
        8  129.6703137794  263.2551528171   16.7444423578  279.9995951748 
        9  129.7536788486  263.2554888044   16.7552073629  280.0106961673 
@@ -141,20 +139,20 @@ Step Temp PotEng KinEng TotEng
       98  143.3138701934  263.4462347092   18.5062468701  281.9524815793 
       99  143.5996902366  263.4503180925   18.5431550652  281.9934731576 
      100  143.4332992914  263.4544359567   18.5216688552  281.9761048118 
-Loop time of 0.802761 on 1 procs for 100 steps with 1000 atoms
+Loop time of 0.350154 on 1 procs for 100 steps with 1000 atoms
 
-Performance: 10.763 ns/day, 2.230 hours/ns, 124.570 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 24.675 ns/day, 0.973 hours/ns, 285.589 timesteps/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.083614   | 0.083614   | 0.083614   |   0.0 | 10.42
-Neigh   | 0.31261    | 0.31261    | 0.31261    |   0.0 | 38.94
-Comm    | 0.012618   | 0.012618   | 0.012618   |   0.0 |  1.57
-Output  | 0.0033751  | 0.0033751  | 0.0033751  |   0.0 |  0.42
-Modify  | 0.38911    | 0.38911    | 0.38911    |   0.0 | 48.47
-Other   |            | 0.001439   |            |       |  0.18
+Pair    | 0.041961   | 0.041961   | 0.041961   |   0.0 | 11.98
+Neigh   | 0.16181    | 0.16181    | 0.16181    |   0.0 | 46.21
+Comm    | 0.0074215  | 0.0074215  | 0.0074215  |   0.0 |  2.12
+Output  | 0.00099516 | 0.00099516 | 0.00099516 |   0.0 |  0.28
+Modify  | 0.13485    | 0.13485    | 0.13485    |   0.0 | 38.51
+Other   |            | 0.003124   |            |       |  0.89
 
 Nlocal:    1000 ave 1000 max 1000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/USER/dpd/dpd-vv/in.dpd-vv

@@ -0,0 +1,29 @@
+# INPUT FILE FOR DPD_Fluid
+
+log             log.dpd-vv
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd    # atomic atom style can also be used
+read_data       data.dpd
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt 300.0 8.6 245455
+pair_coeff      1 1 0.075 0.022 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             2 all nve
+
+variable        totEnergy equal pe+ke
+
+thermo          10
+thermo_style    custom step temp press pe ke v_totEnergy
+thermo_modify   format float %24.16f
+
+run             1000

examples/USER/dpd/dpd-vv/log.dpd-vv.reference

@@ -0,0 +1,169 @@
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd    # atomic atom style can also be used
+read_data       data.dpd
+  orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10125 atoms
+  reading velocities ...
+  10125 velocities
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt 300.0 8.6 245455
+pair_coeff      1 1 0.075 0.022 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             2 all nve
+
+variable        totEnergy equal pe+ke
+
+thermo          10
+thermo_style    custom step temp press pe ke v_totEnergy
+thermo_modify   format float %24.16f
+
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.6
+  ghost atom cutoff = 10.6
+  binsize = 5.3 -> bins = 25 25 25
+Memory usage per processor = 3.36353 Mbytes
+Step Temp Press PotEng KinEng v_totEnergy 
+       0     301.4391322267262012    1549.5478087303108623    1188.6488072196075336     394.4722035796053206    1583.1210107992128542 
+      10     301.1781716844517973    1472.5220704074272362    1188.7073118945888837     394.1307028613744592    1582.8380147559632860 
+      20     301.3348035346627398    1561.5334938481948939    1188.7674931713575006     394.3356759537763878    1583.1031691251339453 
+      30     301.2401656988171226    1589.1590400358682018    1188.8329522652118158     394.2118300702898637    1583.0447823355016226 
+      40     301.2467282647567117    1612.7005954259220744    1188.8998661625830664     394.2204180390389752    1583.1202842016220984 
+      50     301.3868530330685758    1538.2867560691233848    1188.9661306187101673     394.4037894736757153    1583.3699200923858825 
+      60     301.2473566745931635    1442.8478446697065465    1189.0327863162424364     394.2212403948197448    1583.2540267110621244 
+      70     301.3817325834245366    1449.9468021148002208    1189.0958917710283913     394.3970887011532795    1583.4929804721816708 
+      80     301.6350661579102166    1528.7144337987854215    1189.1603115791012897     394.7286085427540456    1583.8889201218553353 
+      90     301.1547075640817752    1512.1770835959378019    1189.2223449446209997     394.0999970163866237    1583.3223419610076235 
+     100     301.1746038085076975    1564.5706067669673303    1189.2844219062417324     394.1260338329196315    1583.4104557391613071 
+     110     301.2018622721547558    1515.4879381876448861    1189.3504251156646205     394.1617050682420427    1583.5121301839067200 
+     120     301.0009801124808178    1557.0329613835117470    1189.4208319594404202     393.8988247062895880    1583.3196566657300082 
+     130     301.0638502637480656    1548.3634383875796630    1189.4951157625748692     393.9810984539830656    1583.4762142165579917 
+     140     301.0311113459680428    1495.2262845183092850    1189.5675481417179071     393.9382553335690318    1583.5058034752869389 
+     150     300.8177209477242400    1428.8898919254613702    1189.6378084330838192     393.6590063190295155    1583.2968147521132778 
+     160     300.8119775481491160    1570.2720283468329399    1189.7083716809172529     393.6514903357206663    1583.3598620166378623 
+     170     300.9335106840651406    1557.4332901198370109    1189.7769958158935424     393.8105322078843642    1583.5875280237778497 
+     180     300.5874591455081486    1520.5298514112455450    1189.8453389121095825     393.3576788840364884    1583.2030177961460140 
+     190     300.4011803057076122    1519.7398182018539501    1189.9061296006261728     393.1139088603054574    1583.0200384609315734 
+     200     300.2169140033789745    1458.2437505784337191    1189.9657655046762557     392.8727725028986129    1582.8385380075749254 
+     210     300.2545970072604860    1496.2729155341944534    1190.0262935280240981     392.9220856012638592    1582.9483791292880142 
+     220     300.3703364838470407    1606.0230144299605399    1190.0833027226285594     393.0735457187111024    1583.1568484413396618 
+     230     300.2033407044385172    1459.9549740461736747    1190.1416131684936772     392.8550100806698424    1582.9966232491635765 
+     240     300.4842762279440080    1670.3474276721599381    1190.2009109755040299     393.2226506527560446    1583.4235616282601313 
+     250     300.2564573977281270    1557.2460328592953829    1190.2596238049020485     392.9245201634982436    1583.1841439684003490 
+     260     300.0449762246657883    1505.0192578442308786    1190.3199416408031084     392.6477696177504413    1582.9677112585536634 
+     270     300.0116460395994977    1509.1981340752856795    1190.3755696034054381     392.6041527474002351    1582.9797223508057868 
+     280     300.3512486599618114    1518.9752783067131077    1190.4261072017084189     393.0485668253141966    1583.4746740270225018 
+     290     300.3552418223667360    1555.5638176571358144    1190.4711084084597132     393.0537923962660898    1583.5249008047258030 
+     300     300.1459940856700541    1599.6176002364238684    1190.5119834703855304     392.7799645916971940    1583.2919480620826107 
+     310     300.0728060417839629    1641.1130631848714074    1190.5527862243700383     392.6841885431988999    1583.2369747675688814 
+     320     300.2437004299284808    1480.0125150324981860    1190.5921170370866093     392.9078260164519065    1583.4999430535385727 
+     330     300.0598571495680176    1558.1995284077863744    1190.6308838646664299     392.6672432381596991    1583.2981271028261290 
+     340     300.2932457229409806    1504.8291140224332594    1190.6648789420762569     392.9726624587786432    1583.6375414008548432 
+     350     300.0508025680157402    1578.6970748006153826    1190.6930603315840926     392.6553941437470598    1583.3484544753312093 
+     360     300.2273424995200344    1514.2714360556162774    1190.7166098654090547     392.8864195427583468    1583.6030294081674583 
+     370     300.1967941947077634    1511.8859175802745085    1190.7410406890937793     392.8464431235526035    1583.5874838126464965 
+     380     300.4506922864079002    1551.8880937733540577    1190.7641303867108036     393.1787017091508005    1583.9428320958616041 
+     390     300.6154615731481954    1491.6540598720923754    1190.7833472426696062     393.3943236927418070    1584.1776709354114701 
+     400     300.4131888226039564    1518.2806993851902462    1190.8000216950690628     393.1296235622648396    1583.9296452573339593 
+     410     300.2164206099614603    1492.4202869919304248    1190.8161806634459481     392.8721268336147432    1583.6883074970605776 
+     420     299.9241651579524728    1437.1178040001384488    1190.8321211036075056     392.4896726667966504    1583.3217937704041560 
+     430     300.1750324308378595    1592.1759851574131517    1190.8470728579757179     392.8179650328543744    1583.6650378908300354 
+     440     300.3203232687657760    1610.5956304714268299    1190.8532393510404290     393.0080969396641422    1583.8613362907044575 
+     450     300.3593377128640896    1514.2015724302684703    1190.8519495611071761     393.0591524002515484    1583.9111019613587814 
+     460     300.2776675433437958    1593.6798981330243805    1190.8459747756926390     392.9522763901615008    1583.7982511658542535 
+     470     299.8777606563147629    1525.3321416074672925    1190.8391264353913357     392.4289463573695116    1583.2680727927609041 
+     480     300.0893325105251392    1577.2512023261467675    1190.8279401949503153     392.7058155711616223    1583.5337557661118808 
+     490     299.7991035093194228    1480.4333732192599200    1190.8067847458821689     392.3260132780664549    1583.1327980239486806 
+     500     299.9677949259065599    1495.0278787582656150    1190.7825410253908558     392.5467678772936324    1583.3293089026844882 
+     510     300.0900811274784701    1639.6696686241473344    1190.7573430643653865     392.7067952335466430    1583.4641382979120863 
+     520     299.9891246673825549    1600.2278532870598156    1190.7251960532676094     392.5746806106526492    1583.2998766639202586 
+     530     300.1603400289337173    1539.5535066502900463    1190.6928984528919955     392.7987381192410226    1583.4916365721330749 
+     540     300.3076269358370496    1595.8675994337252178    1190.6566703473422422     392.9914821412112360    1583.6481524885534782 
+     550     300.4698674068499713    1466.7075904710529812    1190.6131481694715148     393.2037948414154016    1583.8169430108869165 
+     560     300.7206981383458810    1630.2609903270986251    1190.5710873654240913     393.5320393883253018    1584.1031267537493932 
+     570     300.8610815763000232    1556.2884022342987009    1190.5267109994711063     393.7157493257404326    1584.2424603252115958 
+     580     300.8964633483231523    1554.3498972944137222    1190.4812222884627317     393.7620509637309283    1584.2432732521936032 
+     590     300.9107621433563509    1547.4258400009323395    1190.4362818919200890     393.7807627916996580    1584.2170446836198607 
+     600     301.3417451159046436    1536.4134563739603436    1190.3902887741262475     394.3447599132098844    1584.7350486873360751 
+     610     301.6508989111560481    1593.7194612348341707    1190.3421610929228791     394.7493277540106646    1585.0914888469335438 
+     620     301.5698128071562110    1576.1181463329294274    1190.2920606752038566     394.6432160694121194    1584.9352767446159760 
+     630     301.3274041972169357    1509.2272524137147229    1190.2374741364669717     394.3259929609754408    1584.5634670974422988 
+     640     301.3505920687090907    1592.1600851563935066    1190.1794204537054611     394.3563372984748980    1584.5357577521804160 
+     650     301.5804461741749378    1544.9875554279790322    1190.1204065811848523     394.6571312093886377    1584.7775377905734331 
+     660     301.3626783799006148    1580.4147481776212771    1190.0589205400185620     394.3721538043599821    1584.4310743443784304 
+     670     301.3027587470089088    1570.9258836881758725    1189.9974183012859612     394.2937411926666869    1584.2911594939525912 
+     680     301.1174106753824731    1503.7441951732287180    1189.9385560058665305     394.0511891998194756    1583.9897452056859493 
+     690     301.1637317889510541    1485.4239754399416142    1189.8822999581352633     394.1118063851420743    1583.9941063432772808 
+     700     300.7577284964789897    1497.3081311764312886    1189.8265818908062101     393.5804984150753967    1583.4070803058816637 
+     710     300.7582337772330447    1443.2789996571248139    1189.7722579196470178     393.5811596404810757    1583.3534175601280367 
+     720     300.7789291839182511    1480.1771366249440689    1189.7219401607021609     393.6082422644880126    1583.3301824251902872 
+     730     300.2392032164642046    1573.9469162403461269    1189.6722050348253106     392.9019408293094102    1582.5741458641346071 
+     740     300.1498721141534816    1495.8935024851559774    1189.6232009109407954     392.7850394949790029    1582.4082404059197415 
+     750     299.7668955745960488    1587.0579224766690913    1189.5725329834676813     392.2838650178547937    1581.8563980013225319 
+     760     300.1701246080039596    1476.2647356200661761    1189.5185800849978932     392.8115425100924085    1582.3301225950904154 
+     770     300.0596917060459532    1476.9822776185721978    1189.4588693098098702     392.6670267338517419    1582.1258960436616690 
+     780     300.0000978359947794    1656.0447969129193098    1189.3974011035754756     392.5890404250892516    1581.9864415286647272 
+     790     299.8879395255003146    1498.3733949813793060    1189.3295612656791036     392.4422667279793586    1581.7718279936584622 
+     800     299.5399296208984765    1536.5356907957796011    1189.2608026516975315     391.9868506281461009    1581.2476532798436892 
+     810     299.7477702176125263    1527.7843172708669499    1189.1905997605726952     392.2588370075304169    1581.4494367681031690 
+     820     299.6526441282851465    1520.2339634236550410    1189.1179282568577946     392.1343521810326251    1581.2522804378904766 
+     830     299.7117040573267559    1519.3977355174756667    1189.0462571599482544     392.2116397587276992    1581.2578969186758968 
+     840     299.8248393061855950    1492.9872520312869710    1188.9746922447459383     392.3596919064040662    1581.3343841511500614 
+     850     299.8949042735604280    1548.8768511646294428    1188.9003206285553915     392.4513810041994475    1581.3517016327548390 
+     860     299.8659753723547396    1612.8888123513665960    1188.8228698817265467     392.4135237846624591    1581.2363936663889490 
+     870     299.4869644032468159    1501.1368986196648621    1188.7463971708887129     391.9175387708375524    1580.6639359417263222 
+     880     299.4723145868704819    1610.5504771450589487    1188.6685353091816069     391.8983675859109894    1580.5669028950926531 
+     890     299.4069994806970385    1463.6021272210480220    1188.5912631304522620     391.8128942975925497    1580.4041574280447549 
+     900     299.3089704777128190    1566.2168185333516703    1188.5136206415770630     391.6846106320437571    1580.1982312736208769 
+     910     299.5247041888713397    1495.6606753393330109    1188.4345654328317323     391.9669261754785907    1580.4014916083103799 
+     920     298.9408951189174672    1640.3193219922013668    1188.3550783333537311     391.2029362827487944    1579.5580146161025823 
+     930     299.1796032826329110    1446.8716230397405980    1188.2706215145828992     391.5153168773241532    1579.7859383919071661 
+     940     299.3701987753103708    1492.9872751566551869    1188.1849188108449198     391.7647358012489462    1579.9496546120938092 
+     950     299.2072786172182077    1562.8791943561973312    1188.0966113636363843     391.5515336423407575    1579.6481450059770850 
+     960     299.3656085727831737    1560.6583667351615077    1188.0078929542073638     391.7587289258562464    1579.7666218800636670 
+     970     299.3550703551496781    1470.6811691697550941    1187.9234716336209203     391.7449383011918940    1579.6684099348128711 
+     980     299.3253482475718101    1439.7552468745370788    1187.8461953635626287     391.7060430682316792    1579.5522384317941942 
+     990     299.5720628053319956    1537.8753917835106222    1187.7698518865308870     392.0289010679078388    1579.7987529544386689 
+    1000     299.6565043425953263    1587.6003924665003524    1187.6939067472803799     392.1394037721581185    1579.8333105194385553 
+Loop time of 16.4015 on 1 procs for 1000 steps with 10125 atoms
+
+Performance: 5.268 ns/day, 4.556 hours/ns, 60.970 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.3216     | 5.3216     | 5.3216     |   0.0 | 32.45
+Neigh   | 10.155     | 10.155     | 10.155     |   0.0 | 61.91
+Comm    | 0.49085    | 0.49085    | 0.49085    |   0.0 |  2.99
+Output  | 0.0052254  | 0.0052254  | 0.0052254  |   0.0 |  0.03
+Modify  | 0.1345     | 0.1345     | 0.1345     |   0.0 |  0.82
+Other   |            | 0.2945     |            |       |  1.80
+
+Nlocal:    10125 ave 10125 max 10125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5827 ave 5827 max 5827 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    114808 ave 114808 max 114808 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 114808
+Ave neighs/atom = 11.3391
+Neighbor list builds = 1000
+Dangerous builds not checked
+Total wall time: 0:00:16

examples/USER/dpd/dpde-shardlow/in.dpde-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
-log             log.dpde
+log             log.dpde-shardlow
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpde-vv/in.dpde-vv

@@ -0,0 +1,33 @@
+# INPUT FILE FOR DPD_Fluid
+
+log             log.dpde-vv
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd
+read_data       data.dpd
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt/energy 8.6 245455
+pair_coeff      1 1 0.075 0.022 3.2E-05 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             1 all dpd/energy
+fix             2 all nve
+fix             3 all eos/cv 0.00517041
+
+compute         dpdU all dpd
+
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
+
+thermo          10
+thermo_style    custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
+thermo_modify   format float %24.16f
+
+run             1000

examples/USER/dpd/dpde-vv/log.dpde-vv.reference

@@ -0,0 +1,173 @@
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd
+read_data       data.dpd
+  orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10125 atoms
+  reading velocities ...
+  10125 velocities
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt/energy 8.6 245455
+pair_coeff      1 1 0.075 0.022 3.2E-05 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             1 all dpd/energy
+fix             2 all nve
+fix             3 all eos/cv 0.00517041
+
+compute         dpdU all dpd
+
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
+
+thermo          10
+thermo_style    custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
+thermo_modify   format float %24.16f
+
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.6
+  ghost atom cutoff = 10.6
+  binsize = 5.3 -> bins = 25 25 25
+Memory usage per processor = 3.36353 Mbytes
+Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4] 
+       0     301.4391322267262012    1636.1776395935085020    1188.6488072196075336     394.4722035796053206    7852.5601874986105031    7852.5601874986105031   17288.2413857964347699     299.9999999999841407 
+      10     301.4791572483523510    1486.4422375141198245    1188.7147620806101713     394.5245815119678241    7852.5601874999802021    7852.3731942333779443   17288.1727253259377903     299.9960221120699089 
+      20     301.4275643919337426    1677.9356110821624952    1188.7839634625399867     394.4570655673388728    7852.5601874999938445    7852.3711851933012440   17288.1724017231754260     299.9955485734552099 
+      30     301.2240988054542186    1452.7304951528931269    1188.8550809767796181     394.1908044563202225    7852.5601875000002110    7852.5679666239848302   17288.1740395570850524     299.9988968405210130 
+      40     301.1023506886409677    1527.9758363521380033    1188.9264527568634549     394.0314812537677653    7852.5601874999947540    7852.6574764573806533   17288.1755979680056043     300.0001694462812338 
+      50     301.0409654880461972    1597.1737251233498682    1188.9944523606982330     393.9511507566391515    7852.5601875000029395    7852.6700547249911324   17288.1758453423317405     299.9999653064982681 
+      60     301.2904978886139133    1610.8630327676828529    1189.0651026961211301     394.2776962691256131    7852.5601874999829306    7852.2734988976435488   17288.1764853628737910     299.9919857290491905 
+      70     300.8575037843163500    1489.3259312130880971    1189.1295686642290548     393.7110673208616731    7852.5601874999856591    7852.7707182199101226   17288.1715417049854295     300.0010992278233175 
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+     960     301.6392594677008105    1504.8502165144939227    1187.9439133338105421     394.7340960325207675    7852.5601874999711072    7852.9728807988849439   17288.2110776651898050     299.9711546356286362 
+     970     301.6049535791644303    1514.0198965433548892    1187.9094123369413865     394.6892023276233772    7852.5601874999765641    7853.0497909819878259   17288.2085931465298927     299.9722547114341751 
+     980     301.2982841679705643    1634.1208149125807267    1187.8768454876480973     394.2878856256063500    7852.5601874999856591    7853.4862008383515786   17288.2111194515891839     299.9802110109069986 
+     990     301.2573007350166563    1489.7316698898257528    1187.8432331161868660     394.2342534877078606    7852.5601875000047585    7853.5840096862748396   17288.2216837901723920     299.9819468620868292 
+    1000     301.3195135766228532    1562.6587211933920116    1187.8034267774903583     394.3156670604516307    7852.5601874999356369    7853.5372636956635688   17288.2165450335414789     299.9807651637231629 
+Loop time of 21.3308 on 1 procs for 1000 steps with 10125 atoms
+
+Performance: 4.050 ns/day, 5.925 hours/ns, 46.880 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 10.099     | 10.099     | 10.099     |   0.0 | 47.34
+Neigh   | 10.145     | 10.145     | 10.145     |   0.0 | 47.56
+Comm    | 0.49807    | 0.49807    | 0.49807    |   0.0 |  2.33
+Output  | 0.011203   | 0.011203   | 0.011203   |   0.0 |  0.05
+Modify  | 0.28296    | 0.28296    | 0.28296    |   0.0 |  1.33
+Other   |            | 0.295      |            |       |  1.38
+
+Nlocal:    10125 ave 10125 max 10125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5824 ave 5824 max 5824 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    114682 ave 114682 max 114682 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 114682
+Ave neighs/atom = 11.3266
+Neighbor list builds = 1000
+Dangerous builds not checked
+Total wall time: 0:00:21

examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
-log             log.dpdh
+log             log.dpdh-shardlow
 boundary        p p p
 
 units           metal  # ev, ps
@@ -28,4 +28,4 @@ fix             1 all shardlow
 fix             0 all nph iso 0.0 0.0 1000.0
 fix             2 all eos/cv 0.0005
 
-run             100
+run             100

examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isenthalpic conditions using the VV-SSA integration scheme
 boundary        p p p
 
 units           metal  # ev, ps
@@ -42,123 +40,123 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 22 22 22
-Memory usage per processor = 6.99064 Mbytes
-Step Temp Press Volume PotEng KinEng totEnerg Cella Cellb Cellc 
+Memory usage per processor = 6.48143 Mbytes
+Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
        0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450139999  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431976318  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712041855  129.0000000105  129.0000000105  129.0000000105 
-       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404508591  129.0000000186  129.0000000186  129.0000000186 
-       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007387161  129.0000000291  129.0000000291  129.0000000291 
-       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8591957092  129.0000000420  129.0000000420  129.0000000420 
-       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748634338  129.0000000571  129.0000000571  129.0000000571 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
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+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
+       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404460907  129.0000000186  129.0000000186  129.0000000186 
+       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007377625  129.0000000291  129.0000000291  129.0000000291 
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+       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748577118  129.0000000571  129.0000000571  129.0000000571 
        8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.7987136841  129.0000000746  129.0000000746  129.0000000746 
        9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.2603597641  129.0000000944  129.0000000944  129.0000000944 
-      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706562042  129.0000001166  129.0000001166  129.0000001166 
-      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208293915  129.0000001410  129.0000001410  129.0000001410 
-      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.4788341522  129.0000001678  129.0000001678  129.0000001678 
-      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005035400  129.0000001970  129.0000001970  129.0000001970 
-      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825635910  129.0000002285  129.0000002285  129.0000002285 
-      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.8671445847  129.0000002623  129.0000002623  129.0000002623 
-      16  239.8561894618 2817.7971208197 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.9994983673  129.0000002984  129.0000002984  129.0000002984 
-      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226099014  129.0000003369  129.0000003369  129.0000003369 
-      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627689362  129.0000003777  129.0000003777  129.0000003777 
-      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568042755  129.0000004208  129.0000004208  129.0000004208 
-      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802312851  129.0000004662  129.0000004662  129.0000004662 
-      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758684158  129.0000005140  129.0000005140  129.0000005140 
-      22  240.0487944678 2817.9533849158 2146689.0281647225 2639.8938590354  314.1349838054 6049274086.0571269989  129.0000005642  129.0000005642  129.0000005642 
-      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649221420  129.0000006166  129.0000006166  129.0000006166 
-      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473742.2287292480  129.0000006714  129.0000006714  129.0000006714 
-      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446316.4600133896  129.0000007285  129.0000007285  129.0000007285 
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+      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005025864  129.0000001970  129.0000001970  129.0000001970 
+      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825626373  129.0000002285  129.0000002285  129.0000002285 
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+      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226108551  129.0000003369  129.0000003369  129.0000003369 
+      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627622604  129.0000003777  129.0000003777  129.0000003777 
+      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568052292  129.0000004208  129.0000004208  129.0000004208 
+      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802341461  129.0000004662  129.0000004662  129.0000004662 
+      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758703232  129.0000005140  129.0000005140  129.0000005140 
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+      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649183273  129.0000006166  129.0000006166  129.0000006166 
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       26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621421.8445177078  129.0000007880  129.0000007880  129.0000007880 
-      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916733.3989133835  129.0000008498  129.0000008498  129.0000008498 
-      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935208.5422019958  129.0000009139  129.0000009139  129.0000009139 
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-      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054113.1760234833  129.0000010491  129.0000010491  129.0000010491 
-      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316995.4599857330  129.0000011202  129.0000011202  129.0000011202 
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       32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450731.1168394089  129.0000011936  129.0000011936  129.0000011936 
-      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654857.7432937622  129.0000012694  129.0000012694  129.0000012694 
-      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708863.9733123779  129.0000013475  129.0000013475  129.0000013475 
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-      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110539.1171865463  129.0000015958  129.0000015958  129.0000015958 
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+      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750551.5649127960  129.0000014279  129.0000014279  129.0000014279 
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+      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189778.9386901855  129.0000017730  129.0000017730  129.0000017730 
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       41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423113.2358427048  129.0000019595  129.0000019595  129.0000019595 
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+      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504737.9250564575  129.0000023606  129.0000023606  129.0000023606 
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       47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812612.3391046524  129.0000025751  129.0000025751  129.0000025751 
-      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891706.4922075272  129.0000026859  129.0000026859  129.0000026859 
-      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030804.4275312424  129.0000027990  129.0000027990  129.0000027990 
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-      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233814.9634294510  129.0000030321  129.0000030321  129.0000030321 
-      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392671  317.0201158259 6052415218.9485483170  129.0000031522  129.0000031522  129.0000031522 
-      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076505  317.1470160479 6052541789.1273956299  129.0000032746  129.0000032746  129.0000032746 
-      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459040.6286926270  129.0000033994  129.0000033994  129.0000033994 
-      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513743.7400245667  129.0000035265  129.0000035265  129.0000035265 
-      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605122.2894468307  129.0000036559  129.0000036559  129.0000036559 
-      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753494.0979290009  129.0000037876  129.0000037876  129.0000037876 
-      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765744.6257638931  129.0000039217  129.0000039217  129.0000039217 
-      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920813.0568265915  129.0000040582  129.0000040582  129.0000040582 
-      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116688.6155757904  129.0000041969  129.0000041969  129.0000041969 
+      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891706.4921989441  129.0000026859  129.0000026859  129.0000026859 
+      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030804.4275226593  129.0000027990  129.0000027990  129.0000027990 
+      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220795.1955394745  129.0000029144  129.0000029144  129.0000029144 
+      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233814.9634265900  129.0000030321  129.0000030321  129.0000030321 
+      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392670  317.0201158259 6052415218.9485445023  129.0000031522  129.0000031522  129.0000031522 
+      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506  317.1470160479 6052541789.1274013519  129.0000032746  129.0000032746  129.0000032746 
+      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459040.6286897659  129.0000033994  129.0000033994  129.0000033994 
+      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513743.7400159836  129.0000035265  129.0000035265  129.0000035265 
+      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605122.2894439697  129.0000036559  129.0000036559  129.0000036559 
+      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753494.0979280472  129.0000037876  129.0000037876  129.0000037876 
+      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765744.6257629395  129.0000039217  129.0000039217  129.0000039217 
+      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920813.0568208694  129.0000040582  129.0000040582  129.0000040582 
+      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116688.6155729294  129.0000041969  129.0000041969  129.0000041969 
       61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083306.1403274536  129.0000043380  129.0000043380  129.0000043380 
-      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067724228  129.0000044814  129.0000044814  129.0000044814 
-      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989669800  129.0000046272  129.0000046272  129.0000046272 
-      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937957764  129.0000047752  129.0000047752  129.0000047752 
-      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272642136  129.0000049256  129.0000049256  129.0000049256 
+      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067762375  129.0000044814  129.0000044814  129.0000044814 
+      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989650726  129.0000046272  129.0000046272  129.0000046272 
+      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937871933  129.0000047752  129.0000047752  129.0000047752 
+      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272727966  129.0000049256  129.0000049256  129.0000049256 
       66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349244.9473772049  129.0000050784  129.0000050784  129.0000050784 
-      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180746078  129.0000052335  129.0000052335  129.0000052335 
-      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197113037  129.0000053909  129.0000053909  129.0000053909 
-      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757410049  129.0000055506  129.0000055506  129.0000055506 
-      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483983994  129.0000057127  129.0000057127  129.0000057127 
-      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552757263  129.0000058771  129.0000058771  129.0000058771 
+      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180717468  129.0000052335  129.0000052335  129.0000052335 
+      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197017670  129.0000053909  129.0000053909  129.0000053909 
+      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757400513  129.0000055506  129.0000055506  129.0000055506 
+      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483964920  129.0000057127  129.0000057127  129.0000057127 
+      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552747726  129.0000058771  129.0000058771  129.0000058771 
       72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936535.9274711609  129.0000060439  129.0000060439  129.0000060439 
-      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394662  318.6980246193 6053955553.5090150833  129.0000062130  129.0000062130  129.0000062130 
-      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515878677  129.0000063844  129.0000063844  129.0000063844 
-      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909147263  129.0000065581  129.0000065581  129.0000065581 
-      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254135132  129.0000067342  129.0000067342  129.0000067342 
-      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615215302  129.0000069126  129.0000069126  129.0000069126 
+      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955553.5090074539  129.0000062130  129.0000062130  129.0000062130 
+      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515821457  129.0000063844  129.0000063844  129.0000063844 
+      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909118652  129.0000065581  129.0000065581  129.0000065581 
+      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254154205  129.0000067342  129.0000067342  129.0000067342 
+      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615310669  129.0000069126  129.0000069126  129.0000069126 
       78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541703.5689058304  129.0000070934  129.0000070934  129.0000070934 
-      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218521118  129.0000072765  129.0000072765  129.0000072765 
-      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174270630  129.0000074619  129.0000074619  129.0000074619 
+      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218587875  129.0000072765  129.0000072765  129.0000072765 
+      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
       81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664323807  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710672379  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6738977432  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5362014771  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767993927  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416133881  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536083221  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186370850  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258615494  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803415298  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433105469  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774286270  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882719040  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151643753  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169973373  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910085678  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494358063  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4481058121  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006603241  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.26657 on 1 procs for 100 steps with 10125 atoms
+      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
+      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
+      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
+      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
+      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
+      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
+      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
+      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
+      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
+      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
+      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
+      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
+      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
+      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
+      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
+Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
 
-Performance: 2.025 ns/day, 11.852 hours/ns, 23.438 timesteps/s
+Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s
 99.8% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.40111    | 0.40111    | 0.40111    |   0.0 |  9.40
-Neigh   | 1.4039     | 1.4039     | 1.4039     |   0.0 | 32.90
-Comm    | 0.040107   | 0.040107   | 0.040107   |   0.0 |  0.94
-Output  | 0.012053   | 0.012053   | 0.012053   |   0.0 |  0.28
-Modify  | 2.4038     | 2.4038     | 2.4038     |   0.0 | 56.34
-Other   |            | 0.005648   |            |       |  0.13
+Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
+Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
+Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
+Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
+Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
+Other   |            | 0.03004    |            |       |  0.74
 
 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
-log             log.dpdp
+log             log.dpdp-shardlow
 boundary        p p p
 
 units           metal
@@ -24,4 +24,4 @@ thermo_modify   format float %15.10f
 fix             1 all shardlow
 fix             0 all nph iso 0.0 0.0 1000.0
 
-run             100
+run             100

examples/USER/dpd/dpdp-shardlow/log.dpdp-shardlow.reference

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
 boundary        p p p
 
 units           metal
@@ -38,7 +36,7 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 12 10 9
-Memory usage per processor = 2.04518 Mbytes
+Memory usage per processor = 2.04718 Mbytes
 Step Temp Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc 
        0  128.6667660382 3065.7908751302 204306.2673181506  263.2538386154   16.6148533499  279.8686919654  670.8120681014   66.8305353589   57.8900140312   52.8084103339 
        1  128.8781761640 3065.9340218365 204306.2673289568  263.2538784443   16.6421529266  279.8960313709  670.8576613026   66.8305353600   57.8900140323   52.8084103348 
@@ -48,113 +46,113 @@ Step Temp Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc
        5  129.5099127127 3066.3516291155 204306.2675883183  263.2544119877   16.7237296261  279.9781416138  670.9930244672   66.8305353883   57.8900140568   52.8084103572 
        6  129.4373658155 3066.2979832897 204306.2677071957  263.2546211781   16.7143615811  279.9689827592  670.9770250342   66.8305354013   57.8900140680   52.8084103674 
        7  129.5468804564 3066.3661894656 204306.2678476885  263.2548635146   16.7285033035  279.9833668181  671.0001068740   66.8305354166   57.8900140813   52.8084103795 
-       8  129.6703134859 3066.4427527412 204306.2680097974  263.2551515311   16.7444423199  279.9995938510  671.0260974093   66.8305354343   57.8900140966   52.8084103935 
-       9  129.7536784769 3066.4909380739 204306.2681935228  263.2554871768   16.7552073149  280.0106944917  671.0433428967   66.8305354543   57.8900141139   52.8084104093 
-      10  129.6933330547 3066.4412060161 204306.2683988648  263.2558667340   16.7474148571  280.0032815912  671.0295886589   66.8305354767   57.8900141333   52.8084104270 
+       8  129.6703134859 3066.4427527412 204306.2680097972  263.2551515311   16.7444423199  279.9995938510  671.0260974093   66.8305354343   57.8900140966   52.8084103935 
+       9  129.7536784769 3066.4909380739 204306.2681935227  263.2554871768   16.7552073149  280.0106944917  671.0433428967   66.8305354543   57.8900141139   52.8084104093 
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       11  130.0493626138 3066.6716229532 204306.2686258238  263.2562750927   16.7933892692  280.0496643619  671.1053541603   66.8305355014   57.8900141547   52.8084104465 
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-      14  130.1135600843 3066.6777117324 204306.2694364157  263.2576949083   16.8016791453  280.0593740536  671.1158418322   66.8305355898   57.8900142313   52.8084105164 
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       15  130.6547963417 3067.0283008545 204306.2697498515  263.2582241459   16.8715694622  280.1297936080  671.2309683942   66.8305356240   57.8900142609   52.8084105434 
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-      17  131.2014454974 3067.3641769107 204306.2704415885  263.2594031106   16.9421587513  280.2015618620  671.3455682001   66.8305356994   57.8900143262   52.8084106030 
-      18  131.5359721707 3067.5714631111 204306.2708198917  263.2600649028   16.9853564767  280.2454213795  671.4158611542   66.8305357407   57.8900143620   52.8084106356 
-      19  131.5639681439 3067.5705655906 204306.2712198193  263.2607641517   16.9889716215  280.2497357731  671.4200618636   66.8305357843   57.8900143997   52.8084106700 
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-      24  132.0864187320 3067.8064692879 204306.2735438392  263.2648061201   17.0564361282  280.3212422483  671.5216547458   66.8305360377   57.8900146193   52.8084108703 
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-      27  132.6414561712 3068.0981288018 204306.2751977716  263.2677103029   17.1281086038  280.3958189068  671.6334263968   66.8305362180   57.8900147755   52.8084110128 
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-      30  133.3017656825 3068.4496355722 204306.2770463614  263.2709902617   17.2133749553  280.4843652170  671.7667996729   66.8305364196   57.8900149501   52.8084111721 
-      31  133.2181169549 3068.3592522301 204306.2777058183  263.2721596133   17.2025733211  280.4747329344  671.7456431539   66.8305364915   57.8900150123   52.8084112289 
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-      33  133.5661113072 3068.5225231843 204306.2790896243  263.2746385114   17.2475101397  280.5221486512  671.8138814999   66.8305366424   57.8900151430   52.8084113481 
-      34  133.9344409280 3068.7332886556 204306.2798139751  263.2759490654   17.2950728696  280.5710219350  671.8896325541   66.8305367214   57.8900152115   52.8084114105 
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       47  134.7017020134 3068.6523501535 204306.2911991276  263.2965656113   17.3941499725  280.6907155838  671.9990268961   66.8305379628   57.8900162868   52.8084123914 
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       52  134.9445761663 3068.5364265426 204306.2965514932  263.3063613000   17.4255125267  280.7318738267  672.0254130468   66.8305385464   57.8900167923   52.8084128526 
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       57  135.3024634130 3068.4668168613 204306.3024446515  263.3173015297   17.4717268236  280.7890283533  672.0737023745   66.8305391889   57.8900173489   52.8084133603 
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+      58  135.2521293970 3068.3666950252 204306.3036881768  263.3196055001   17.4652271476  280.7848326476  672.0567417166   66.8305393245   57.8900174664   52.8084134675 
+      59  135.0019308452 3068.1306120627 204306.3049533316  263.3219467372   17.4329187872  280.7548655243  671.9966721947   66.8305394625   57.8900175859   52.8084135765 
+      60  135.3361178986 3068.2878435126 204306.3062401155  263.3243328810   17.4760726571  280.8004055381  672.0622645090   66.8305396028   57.8900177074   52.8084136874 
+      61  135.3139081244 3068.2035774253 204306.3075485286  263.3267589778   17.4732046893  280.7999636671  672.0510797027   66.8305397454   57.8900178310   52.8084138001 
+      62  135.7430205344 3068.4226983441 204306.3088785714  263.3292333495   17.5286163545  280.8578497040  672.1369101433   66.8305398905   57.8900179566   52.8084139147 
+      63  136.0382527386 3068.5500741031 204306.3102302457  263.3317605359   17.5667399503  280.8985004861  672.1938062135   66.8305400378   57.8900180843   52.8084140311 
+      64  136.0795110412 3068.5046583092 204306.3116035512  263.3343072525   17.5720676714  280.9063749238  672.1958919511   66.8305401876   57.8900182140   52.8084141495 
+      65  136.5429104992 3068.7428965120 204306.3129984887  263.3368943008   17.6319068534  280.9688011542  672.2887005078   66.8305403397   57.8900183457   52.8084142696 
+      66  136.6747848955 3068.7560934485 204306.3144150592  263.3395194563   17.6489359109  280.9884553672  672.3100402808   66.8305404941   57.8900184795   52.8084143917 
+      67  136.9345148389 3068.8545703617 204306.3158532631  263.3421896806   17.6824750683  281.0246647490  672.3588099945   66.8305406510   57.8900186154   52.8084145156 
       68  136.5690881694 3068.5302814448 204306.3173130994  263.3448899028   17.6352871991  280.9801771020  672.2729724748   66.8305408101   57.8900187532   52.8084146414 
       69  137.0307072166 3068.7630696250 204306.3187945680  263.3476374865   17.6948964752  281.0425339617  672.3650168515   66.8305409717   57.8900188932   52.8084147690 
-      70  137.1048864397 3068.7333916895 204306.3202976696  263.3504277984   17.7044753039  281.0549031023  672.3736044006   66.8305411356   57.8900190351   52.8084148985 
-      71  137.2866532809 3068.7750522066 204306.3218224040  263.3532577755   17.7279470169  281.0812047925  672.4052214764   66.8305413018   57.8900191791   52.8084150299 
-      72  137.3464916785 3068.7338430357 204306.3233687716  263.3561237403   17.7356740022  281.0917977425  672.4105624778   66.8305414704   57.8900193252   52.8084151631 
-      73  137.4267886898 3068.7058777536 204306.3249367719  263.3590305503   17.7460428263  281.1050733766  672.4202750386   66.8305416414   57.8900194733   52.8084152982 
-      74  137.7032214008 3068.8096995216 204306.3265264053  263.3619634311   17.7817388269  281.1437022580  672.4721461079   66.8305418147   57.8900196234   52.8084154352 
+      70  137.1048864397 3068.7333916895 204306.3202976695  263.3504277984   17.7044753039  281.0549031023  672.3736044006   66.8305411356   57.8900190351   52.8084148985 
+      71  137.2866532809 3068.7750522066 204306.3218224039  263.3532577755   17.7279470169  281.0812047925  672.4052214764   66.8305413018   57.8900191791   52.8084150299 
+      72  137.3464916785 3068.7338430357 204306.3233687715  263.3561237403   17.7356740022  281.0917977425  672.4105624778   66.8305414704   57.8900193252   52.8084151631 
+      73  137.4267886898 3068.7058777536 204306.3249367717  263.3590305503   17.7460428263  281.1050733766  672.4202750386   66.8305416414   57.8900194733   52.8084152982 
+      74  137.7032214008 3068.8096995216 204306.3265264051  263.3619634311   17.7817388269  281.1437022580  672.4721461079   66.8305418147   57.8900196234   52.8084154352 
       75  138.2326481893 3069.0827847254 204306.3281376729  263.3649465758   17.8501041765  281.2150507524  672.5783209650   66.8305419904   57.8900197756   52.8084155740 
-      76  138.4006889617 3069.1105563660 204306.3297705764  263.3679794432   17.8718034302  281.2397828734  672.6065975977   66.8305421684   57.8900199299   52.8084157147 
-      77  138.5404442761 3069.1182683851 204306.3314251151  263.3710629684   17.8898501576  281.2609131260  672.6287144410   66.8305423489   57.8900200861   52.8084158573 
-      78  138.8911793449 3069.2673604038 204306.3331012900  263.3741701271   17.9351408874  281.3093110144  672.6961274554   66.8305425316   57.8900202444   52.8084160017 
-      79  138.9740932597 3069.2343926248 204306.3347991016  263.3773233601   17.9458476345  281.3231709947  672.7057867031   66.8305427167   57.8900204048   52.8084161480 
-      80  139.4197304629 3069.4447568636 204306.3365185503  263.3805326609   18.0033931609  281.3839258218  672.7933700502   66.8305429042   57.8900205672   52.8084162961 
-      81  140.0251352305 3069.7614239791 204306.3382596381  263.3837812869   18.0815696143  281.4653509011  672.9151792214   66.8305430941   57.8900207316   52.8084164461 
-      82  140.4343345655 3069.9447540285 204306.3400223668  263.3870704597   18.1344098865  281.5214803462  672.9946899248   66.8305432863   57.8900208981   52.8084165980 
-      83  140.8339491089 3070.1205252103 204306.3418067376  263.3904045656   18.1860124661  281.5764170317  673.0720440188   66.8305434808   57.8900210667   52.8084167517 
-      84  141.2138258327 3070.2828678237 204306.3436127516  263.3937910919   18.2350662835  281.6288573754  673.1451894287   66.8305436777   57.8900212372   52.8084169073 
-      85  141.4316065757 3070.3348892447 204306.3454404097  263.3972231992   18.2631885036  281.6604117028  673.1833809261   66.8305438770   57.8900214099   52.8084170648 
-      86  141.6165004814 3070.3639126512 204306.3472897122  263.4006984023   18.2870640172  281.6877624195  673.2144361936   66.8305440787   57.8900215845   52.8084172241 
-      87  141.7511192071 3070.3578486993 204306.3491606590  263.4042216826   18.3044474524  281.7086691350  673.2345732314   66.8305442827   57.8900217612   52.8084173853 
-      88  141.8992247234 3070.3595802006 204306.3510532502  263.4077909549   18.3235724488  281.7313634037  673.2574919246   66.8305444890   57.8900219400   52.8084175484 
-      89  142.0700970483 3070.3750740931 204306.3529674859  263.4114074261   18.3456373433  281.7570447694  673.2851527089   66.8305446978   57.8900221208   52.8084177133 
-      90  141.8940825299 3070.1552595577 204306.3549033655  263.4150659370   18.3229084328  281.7379743697  673.2380557076   66.8305449088   57.8900223036   52.8084178801 
-      91  141.9603474040 3070.0979256101 204306.3568608879  263.4187731305   18.3314652746  281.7502384052  673.2430123833   66.8305451223   57.8900224885   52.8084180488 
-      92  142.2257467272 3070.1741170513 204306.3588400532  263.4225144876   18.3657365240  281.7882510116  673.2907445632   66.8305453381   57.8900226755   52.8084182193 
-      93  142.5512734406 3070.2900234935 204306.3608408622  263.4263001648   18.4077720766  281.8340722414  673.3513497860   66.8305455562   57.8900228644   52.8084183917 
-      94  142.6487617290 3070.2508281658 204306.3628633148  263.4301422965   18.4203608255  281.8505031221  673.3627864321   66.8305457768   57.8900230555   52.8084185659 
-      95  142.7997358153 3070.2465681156 204306.3649074110  263.4340465006   18.4398562429  281.8739027435  673.3856467375   66.8305459996   57.8900232485   52.8084187421 
-      96  143.4667389211 3070.5895488558 204306.3669731522  263.4380042392   18.5259869441  281.9639911833  673.5194753590   66.8305462249   57.8900234436   52.8084189200 
-      97  143.4616118167 3070.4774890551 204306.3690605390  263.4420072006   18.5253248766  281.9673320772  673.5085306100   66.8305464525   57.8900236408   52.8084190999 
-      98  143.3138195521 3070.2680530999 204306.3711695705  263.4460419232   18.5062403307  281.9522822539  673.4667779706   66.8305466824   57.8900238400   52.8084192816 
-      99  143.5996384267 3070.3502690101 204306.3733002463  263.4501213575   18.5431483749  281.9932697324  673.5182535421   66.8305469148   57.8900240412   52.8084194652 
-     100  143.4332465710 3070.1261458307 204306.3754525657  263.4542352328   18.5216620473  281.9758972802  673.4723054704   66.8305471495   57.8900242445   52.8084196506 
-Loop time of 0.77396 on 1 procs for 100 steps with 1000 atoms
+      76  138.4006889617 3069.1105563660 204306.3297705762  263.3679794432   17.8718034302  281.2397828734  672.6065975977   66.8305421684   57.8900199299   52.8084157147 
+      77  138.5404442761 3069.1182683851 204306.3314251149  263.3710629684   17.8898501576  281.2609131260  672.6287144410   66.8305423489   57.8900200861   52.8084158573 
+      78  138.8911793449 3069.2673604038 204306.3331012898  263.3741701271   17.9351408874  281.3093110144  672.6961274554   66.8305425316   57.8900202444   52.8084160017 
+      79  138.9740932597 3069.2343926248 204306.3347991015  263.3773233601   17.9458476345  281.3231709947  672.7057867031   66.8305427167   57.8900204048   52.8084161480 
+      80  139.4197304629 3069.4447568636 204306.3365185501  263.3805326609   18.0033931609  281.3839258218  672.7933700502   66.8305429042   57.8900205672   52.8084162961 
+      81  140.0251352305 3069.7614239791 204306.3382596380  263.3837812869   18.0815696143  281.4653509011  672.9151792214   66.8305430941   57.8900207316   52.8084164461 
+      82  140.4343345655 3069.9447540285 204306.3400223666  263.3870704597   18.1344098865  281.5214803462  672.9946899248   66.8305432863   57.8900208981   52.8084165980 
+      83  140.8339491089 3070.1205252103 204306.3418067374  263.3904045656   18.1860124661  281.5764170317  673.0720440188   66.8305434808   57.8900210667   52.8084167517 
+      84  141.2138258327 3070.2828678237 204306.3436127514  263.3937910919   18.2350662835  281.6288573754  673.1451894287   66.8305436777   57.8900212372   52.8084169073 
+      85  141.4316065757 3070.3348892447 204306.3454404095  263.3972231992   18.2631885036  281.6604117028  673.1833809261   66.8305438770   57.8900214099   52.8084170648 
+      86  141.6165004814 3070.3639126512 204306.3472897119  263.4006984023   18.2870640172  281.6877624195  673.2144361936   66.8305440787   57.8900215845   52.8084172241 
+      87  141.7511192071 3070.3578486993 204306.3491606587  263.4042216826   18.3044474524  281.7086691350  673.2345732314   66.8305442827   57.8900217612   52.8084173853 
+      88  141.8992247234 3070.3595802006 204306.3510532499  263.4077909549   18.3235724488  281.7313634037  673.2574919246   66.8305444890   57.8900219400   52.8084175484 
+      89  142.0700970483 3070.3750740931 204306.3529674857  263.4114074261   18.3456373433  281.7570447694  673.2851527089   66.8305446978   57.8900221208   52.8084177133 
+      90  141.8940825299 3070.1552595577 204306.3549033653  263.4150659370   18.3229084328  281.7379743697  673.2380557076   66.8305449088   57.8900223036   52.8084178801 
+      91  141.9603474040 3070.0979256101 204306.3568608877  263.4187731305   18.3314652746  281.7502384052  673.2430123833   66.8305451223   57.8900224885   52.8084180488 
+      92  142.2257467272 3070.1741170513 204306.3588400529  263.4225144876   18.3657365240  281.7882510116  673.2907445632   66.8305453381   57.8900226755   52.8084182193 
+      93  142.5512734406 3070.2900234936 204306.3608408618  263.4263001648   18.4077720766  281.8340722414  673.3513497860   66.8305455562   57.8900228644   52.8084183917 
+      94  142.6487617290 3070.2508281658 204306.3628633145  263.4301422965   18.4203608255  281.8505031221  673.3627864321   66.8305457768   57.8900230555   52.8084185659 
+      95  142.7997358153 3070.2465681156 204306.3649074107  263.4340465006   18.4398562429  281.8739027435  673.3856467375   66.8305459996   57.8900232485   52.8084187421 
+      96  143.4667389211 3070.5895488558 204306.3669731518  263.4380042392   18.5259869441  281.9639911833  673.5194753590   66.8305462249   57.8900234436   52.8084189200 
+      97  143.4616118167 3070.4774890551 204306.3690605387  263.4420072006   18.5253248766  281.9673320772  673.5085306100   66.8305464525   57.8900236408   52.8084190999 
+      98  143.3138195521 3070.2680530999 204306.3711695701  263.4460419232   18.5062403307  281.9522822539  673.4667779706   66.8305466824   57.8900238400   52.8084192816 
+      99  143.5996384267 3070.3502690101 204306.3733002460  263.4501213575   18.5431483749  281.9932697324  673.5182535422   66.8305469148   57.8900240412   52.8084194652 
+     100  143.4332465710 3070.1261458307 204306.3754525654  263.4542352328   18.5216620473  281.9758972802  673.4723054704   66.8305471495   57.8900242445   52.8084196506 
+Loop time of 0.363578 on 1 procs for 100 steps with 1000 atoms
 
-Performance: 11.163 ns/day, 2.150 hours/ns, 129.206 timesteps/s
-99.2% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 23.764 ns/day, 1.010 hours/ns, 275.044 timesteps/s
+99.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.081886   | 0.081886   | 0.081886   |   0.0 | 10.58
-Neigh   | 0.29547    | 0.29547    | 0.29547    |   0.0 | 38.18
-Comm    | 0.012082   | 0.012082   | 0.012082   |   0.0 |  1.56
-Output  | 0.0047195  | 0.0047195  | 0.0047195  |   0.0 |  0.61
-Modify  | 0.37794    | 0.37794    | 0.37794    |   0.0 | 48.83
-Other   |            | 0.001861   |            |       |  0.24
+Pair    | 0.04388    | 0.04388    | 0.04388    |   0.0 | 12.07
+Neigh   | 0.16374    | 0.16374    | 0.16374    |   0.0 | 45.04
+Comm    | 0.0078104  | 0.0078104  | 0.0078104  |   0.0 |  2.15
+Output  | 0.0017376  | 0.0017376  | 0.0017376  |   0.0 |  0.48
+Modify  | 0.14291    | 0.14291    | 0.14291    |   0.0 | 39.31
+Other   |            | 0.003504   |            |       |  0.96
 
 Nlocal:    1000 ave 1000 max 1000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow

@@ -1,6 +1,6 @@
 # Example for running DPD-RX
 
-log             log.dpdrx
+log             log.dpdrx-shardlow
 boundary        p p p
 units           metal  # ev, ps
 atom_style      dpd

examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference

@@ -0,0 +1,120 @@
+boundary        p p p
+units           metal  # ev, ps
+atom_style      dpd
+atom_modify     map array
+fix             4 all rx kinetics.dpdrx none dense lammps_rk4 1
+
+lattice         hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
+Lattice spacing in x,y,z = 11.5218 10.8628 6.65209
+region          box block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_box      2 box
+Created orthogonal box = (0 0 0) to (69.1305 65.1769 39.9125)
+  1 by 1 by 1 MPI processor grid
+region          atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_atoms    1 region atoms
+Created 864 atoms
+
+comm_modify     mode single vel yes
+mass            * 222.12
+
+#Set concentrations
+set             atom * d_rdx 1.00
+  864 settings made for d_rdx
+set             atom * d_h2 0.0
+  864 settings made for d_h2
+set             atom * d_no2 0.0
+  864 settings made for d_no2
+set             atom * d_n2 0.0
+  864 settings made for d_n2
+set             atom * d_hcn 0.0
+  864 settings made for d_hcn
+set             atom * d_no 0.0
+  864 settings made for d_no
+set             atom * d_h2o 0.0
+  864 settings made for d_h2o
+set             atom * d_co 0.0
+  864 settings made for d_co
+set             atom * d_co2 0.0
+  864 settings made for d_co2
+
+#Set the kinetic temperature of the particles
+velocity	all create 2065.0 875661 dist gaussian
+
+#Set the internal temperature of the particles
+set             atom * dpd/theta 2065.00
+  864 settings made for dpd/theta
+
+timestep        0.001
+
+pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
+pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+
+fix             1 all shardlow
+fix             2 all nve
+fix             3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
+
+compute         dpdU all dpd
+compute         dpdUatom all dpd/atom
+compute         crdx all property/atom d_rdx
+
+variable        totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
+
+thermo          1
+thermo_style    custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
+thermo_modify   format float %15.8f flush yes
+
+dump            2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
+dump_modify     2 sort id
+
+run             10
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9 -> bins = 8 8 5
+Memory usage per processor = 6.52436 Mbytes
+Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
+       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810   3841.42393279   3841.42393279      0.00000000   7682.84786557   2065.00000000 
+       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424   3841.42393279   3841.43150665      0.00000000   7682.85543943   2065.20275230 
+       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326   3841.42393279   3841.10925763      0.00000000   7682.53319042   2065.32453473 
+       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499   3841.42393279   3840.81572590      0.00000000   7682.23965869   2065.45336917 
+       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217   3841.42393279   3840.30814872      0.00000000   7681.73208151   2065.52973333 
+       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762   3841.42393279   3840.42386327      0.00000000   7681.84779605   2065.76011517 
+       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169   3841.42393279   3840.39038920      0.00000000   7681.81432198   2065.95399323 
+       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100   3841.42393279   3840.70880989      0.00000000   7682.13274267   2066.23407076 
+       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272   3841.42393279   3840.71463817      0.00000000   7682.13857095   2066.43766287 
+       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480   3841.42393279   3840.71482609      0.00000000   7682.13875887   2066.64001166 
+      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415   3841.42393279   3841.25306673      0.00000000   7682.67699952   2066.97516855 
+Loop time of 0.289778 on 1 procs for 10 steps with 864 atoms
+
+Performance: 2.982 ns/day, 8.049 hours/ns, 34.509 timesteps/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.16405    | 0.16405    | 0.16405    |   0.0 | 56.61
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00066328 | 0.00066328 | 0.00066328 |   0.0 |  0.23
+Output  | 0.037718   | 0.037718   | 0.037718   |   0.0 | 13.02
+Modify  | 0.087281   | 0.087281   | 0.087281   |   0.0 | 30.12
+Other   |            | 7.057e-05  |            |       |  0.02
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2700 ave 2700 max 2700 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    55296 ave 55296 max 55296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 55296
+Ave neighs/atom = 64
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1

@@ -0,0 +1,436 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for viscosity of 2d LJ liquid
+# Einstein form of Green-Kubo
+
+# settings
+
+variable	x equal 20
+variable	y equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+variable    p equal 400     # correlation length
+variable    s equal 5       # sample interval
+variable    d equal $p*$s   # dump interval
+variable    d equal 400*$s   
+variable    d equal 400*5   
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 20 0 $y -0.1 0.1
+region          simbox block 0 20 0 20 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 800 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+# equilibration run
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+thermo          $d
+thermo          2000
+run	        10000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 27 27 1
+Memory usage per processor = 2.47956 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0     -0.56617    -1.535262 
+    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
+    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
+    6000    1.0384014   -1.6029223            0   -0.5658189   0.82862123 
+    8000    1.0035814   -1.5749989            0  -0.57267191    1.1514978 
+   10000    1.0149864   -1.5834783            0  -0.56976064   0.94535991 
+Loop time of 1.69247 on 1 procs for 10000 steps with 800 atoms
+
+Performance: 2552489.906 tau/day, 5908.541 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    | 0.93981    | 0.93981    | 0.93981    |   0.0 | 55.53
+Neigh   | 0.22459    | 0.22459    | 0.22459    |   0.0 | 13.27
+Comm    | 0.028411   | 0.028411   | 0.028411   |   0.0 |  1.68
+Output  | 5.6267e-05 | 5.6267e-05 | 5.6267e-05 |   0.0 |  0.00
+Modify  | 0.4531     | 0.4531     | 0.4531     |   0.0 | 26.77
+Other   |            | 0.04649    |            |       |  2.75
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    262 ave 262 max 262 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5587 ave 5587 max 5587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5587
+Ave neighs/atom = 6.98375
+Neighbor list builds = 1101
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1
+
+unfix		2
+
+# Einstein viscosity calculation
+
+reset_timestep  0
+
+# Define distinct components of symmetric traceless stress tensor
+
+variable         pxy equal pxy
+variable         pxx equal pxx-press
+
+fix              avstress all ave/time $s $p $d v_pxy v_pxx ave one file einstein.dat
+fix              avstress all ave/time 5 $p $d v_pxy v_pxx ave one file einstein.dat
+fix              avstress all ave/time 5 400 $d v_pxy v_pxx ave one file einstein.dat
+fix              avstress all ave/time 5 400 2000 v_pxy v_pxx ave one file einstein.dat
+
+# Diagonal components of SS are larger by factor 2-2/d,
+# which is 4/3 for d=3, but 1 for d=2.
+# See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)
+
+variable         scale equal vol/(2.0*$t*dt*$d)
+variable         scale equal vol/(2.0*1*dt*$d)
+variable         scale equal vol/(2.0*1*dt*2000)
+variable         diagfac equal 2-2/2
+variable         deltasqxy equal (f_avstress[1]*$d*dt)^2
+variable         deltasqxy equal (f_avstress[1]*2000*dt)^2
+variable         deltasqxx equal (f_avstress[2]*$d*dt)^2/${diagfac}
+variable         deltasqxx equal (f_avstress[2]*2000*dt)^2/${diagfac}
+variable         deltasqxx equal (f_avstress[2]*2000*dt)^2/1
+
+# compute mean square displacements as running averages
+
+fix              avdeltasq all ave/time $d 1 $d v_deltasqxy v_deltasqxx ave running
+fix              avdeltasq all ave/time 2000 1 $d v_deltasqxy v_deltasqxx ave running
+fix              avdeltasq all ave/time 2000 1 2000 v_deltasqxy v_deltasqxx ave running
+
+# convert to viscosities
+
+variable         vxy equal f_avdeltasq[1]*${scale}
+variable         vxy equal f_avdeltasq[1]*66.6666666666667
+variable         vxx equal f_avdeltasq[2]*${scale}
+variable         vxx equal f_avdeltasq[2]*66.6666666666667
+
+thermo_style     custom step temp pe press pxy v_vxy v_vxx
+
+run              500000
+Memory usage per processor = 2.47956 Mbytes
+Step Temp PotEng Press Pxy v_vxy v_vxx 
+       0            1   -1.5834783   0.93637929  0.013123478            0            0 
+    2000   0.99103273   -1.5739065   0.96182762  0.032871709   0.41926791   0.38581032 
+    4000    1.0416298   -1.6251611    0.9238985   0.02532039   0.35795442   0.29928221 
+    6000    1.0033402   -1.5867776     1.049074  0.056300627   0.29372872    1.5092739 
+    8000    1.0003681   -1.5843096    1.1886635  0.019361031   0.48384709    1.8517115 
+   10000    1.0195921   -1.6022966    0.9009639 -0.075997173   0.67256908    1.5843784 
+   12000    1.0026283   -1.5853941   0.90425907  -0.10655349   0.60161687    1.3594007 
+   14000    1.0062891   -1.5897213     1.120094  0.078261625   0.97450451    1.2282067 
+   16000   0.97921785   -1.5613249     1.056538  -0.27861922   0.87752053    1.1451558 
+   18000     1.012419   -1.5961271    1.0278053  0.022229371    1.5009689    1.0422023 
+   20000    1.0117709   -1.5948272   0.97722275 0.0075466982    1.3698953   0.99945232 
+   22000    1.0008808   -1.5833286    1.0572608  0.087832931    1.3110237   0.93493793 
+   24000    1.0002975   -1.5837822    1.0118667 -0.068081725    1.2215237   0.93661445 
+   26000   0.98509665   -1.5675621    1.1898824   0.21810836    1.3153554   0.87730504 
+   28000    0.9891689   -1.5722635    1.1456688   0.12141752     1.490948   0.90642777 
+   30000    1.0071582   -1.5908732   0.96554132  0.017641823     1.454491   0.95707045 
+   32000    1.0076807   -1.5909133    1.1047186  0.044265263    1.4451215    0.9167669 
+   34000   0.95874174     -1.54087     1.362955  -0.14025695    1.4687664   0.89946229 
+   36000   0.99528173   -1.5791377    1.0970028 -0.016714523    1.4188568   0.88993465 
+   38000    1.0124371   -1.5952165   0.99493986 -0.041410673    1.3575213   0.94345659 
+   40000    1.0141237   -1.5974959   0.98549019  0.047454345    1.3425092   0.89871657 
+   42000    1.0274867   -1.6103177   0.93801507  0.089635945    1.2942122   0.86538125 
+   44000   0.98700259   -1.5693265   0.94306661 -0.045695708    1.3728992   0.93162122 
+   46000    1.0080948    -1.591735    1.0304791 -0.0046135743    1.3174697   0.89594482 
+   48000   0.97227783   -1.5551815    1.1829894  0.042219544    1.2647775   0.87200134 
+   50000   0.99046716   -1.5732492    1.0095618  0.018697031     1.221817   0.84123547 
+   52000    1.0129697   -1.5965188   0.88794241 -0.045990748    1.1856229    0.9040415 
+   54000    1.0013276   -1.5843748    1.0246693  0.012464296    1.2889061   0.87286599 
+   56000    1.0385716   -1.6218376   0.75426191  -0.04775685    1.2504841   0.84682228 
+   58000    1.0107757   -1.5935394    1.0239619  0.029529278    1.2134635    0.9938075 
+   60000    1.0177033   -1.6004904   0.94723439  -0.16871762    1.2535747    1.0125806 
+   62000    1.0210737   -1.6038196    1.0225179  0.079638703     1.215309   0.98168447 
+   64000    1.0106132   -1.5941352    1.0188777   0.02699431    1.1836603   0.97574934 
+   66000   0.98531307   -1.5684662    1.1224354 -0.0069578014    1.2557176   0.99054037 
+   68000   0.99450728   -1.5785884    1.3016366  0.056607824    1.2198402    1.0305974 
+   70000   0.98874589   -1.5720858    1.0724556 -0.022405835    1.1860738    1.0020293 
+   72000    1.0108814   -1.5935405   0.92375729  -0.12669224    1.1627555   0.97777367 
+   74000    1.0098348   -1.5932383    1.0635024  -0.12956833    1.1387216   0.99028812 
+   76000    1.0089021   -1.5925365   0.98626851  -0.20311631    1.1527717   0.97238965 
+   78000     1.002405   -1.5857268     1.008097 -0.089615503    1.1255136   0.94930557 
+   80000    1.0266582   -1.6095848    1.0493411   0.16631226    1.1416236   0.96066686 
+   82000      1.01242   -1.5953224   0.81710829   0.18713063    1.1208021   0.94504086 
+   84000    1.0262474   -1.6102703    1.1125949 -0.0012088503    1.1685343   0.93574513 
+   86000   0.99599827   -1.5786216    1.0337621 -0.0056500173    1.1619022   0.91502714 
+   88000   0.98713531   -1.5701336    1.0665747  -0.10237303    1.2033676   0.91683937 
+   90000    1.0156011   -1.5996767   0.96906164   0.13894564    1.1877816   0.91164181 
+   92000    1.0306883   -1.6137656   0.78929887 0.0089544803    1.1655216   0.89238295 
+   94000   0.98455669   -1.5668138    1.1917323  0.025629181    1.1415233   0.88999487 
+   96000   0.99528576   -1.5779727    1.1055136  0.020277014    1.1220378     0.884028 
+   98000    1.0504589   -1.6338024   0.99135546 -0.051989636    1.0995983   0.88195356 
+  100000   0.98210335   -1.5653161    1.0867432  0.091525725    1.0788118   0.86708357 
+  102000    1.0316494   -1.6156561    1.1350259  0.072311903    1.0682988   0.85879527 
+  104000    1.0292338   -1.6126651   0.83829357  -0.04098328    1.0674517   0.90910693 
+  106000   0.98153521   -1.5647366    1.0653974 -4.3227008e-05     1.048242   0.91634683 
+  108000    1.0074159   -1.5909608    1.0048635    0.1947269    1.1066118   0.96168226 
+  110000    1.0007684   -1.5838251    1.1603181   0.13820163    1.0869248   0.96825039 
+  112000   0.98637814   -1.5692736    1.0037644  0.049907343    1.0678816   0.95140325 
+  114000   0.99310586    -1.574972    1.0896413 -0.079352378     1.049685   0.95078035 
+  116000   0.98829858   -1.5705137   0.87861443   0.05118496    1.0673701   0.93474367 
+  118000      1.01049   -1.5933529   0.96002545  -0.12320659      1.06809   0.94388888 
+  120000    1.0218378   -1.6050064   0.89637436   0.02750584    1.0507296    0.9721852 
+  122000    1.0263547   -1.6090242   0.95854694 0.0034110405    1.0519885   0.97478734 
+  124000    0.9899202   -1.5732471    1.0492908  -0.13855042    1.0352928   0.95932329 
+  126000   0.98192121   -1.5648602    1.1372352   0.16313842    1.0195242   0.96122299 
+  128000     1.002862   -1.5860432   0.97650147  0.048928455    1.0422628   0.97854238 
+  130000   0.99785761   -1.5808342   0.93146735  0.026478401     1.042581   0.99155317 
+  132000   0.98956541   -1.5724182   0.96523389  -0.10052306     1.027027   0.98847097 
+  134000    1.0019397   -1.5848811    1.0447894   0.13871691     1.016337    0.9846235 
+  136000    1.0321449   -1.6162667    1.1072168  -0.15369414    1.0062486   0.99959003 
+  138000    1.0239483   -1.6070861   0.82920716 -0.011872404   0.99440555   0.98531922 
+  140000    1.0082907   -1.5911532    1.0012771  0.027192581   0.98750923    1.0234574 
+  142000    1.0007865   -1.5839168    1.0399048 -0.096251148    1.0112715    1.0110141 
+  144000    1.0001664   -1.5824827    1.0071962 -0.083449668    1.0100611    1.0191469 
+  146000    1.0202238   -1.6043224    1.0702284 -0.063595518    1.0113284    1.0091825 
+  148000    1.0248683   -1.6088702    1.0227875  0.069198975    1.0099355    1.0038023 
+  150000    1.0127614    -1.595093   0.80897516 0.0044443031     1.002562   0.99323586 
+  152000    1.0028044     -1.58605    1.0857002 -0.059930891   0.99898861   0.98463631 
+  154000    1.0149836    -1.597497   0.82631625  0.085962962   0.98807287   0.97473529 
+  156000   0.99818966   -1.5813132     1.035248 -0.029178797   0.97557066    0.9653792 
+  158000    1.0023756   -1.5858717   0.94465038 -0.056571392    0.9646132   0.95331791 
+  160000   0.99847665   -1.5819798    1.0656894 -0.022026678   0.97680099   0.99699456 
+  162000   0.98084763   -1.5637747    1.2446958  0.097934009   0.96520059   0.99886917 
+  164000   0.98358665   -1.5664883    1.1626742 -0.010830507   0.95857867   0.98697029 
+  166000    1.0176133   -1.6002621   0.91335665  0.054966014   0.97897499    1.0064186 
+  168000    1.0252828   -1.6091158    1.0562376  0.025372153   0.96968537    1.0117261 
+  170000    1.0429701   -1.6246241   0.78042973 -0.088860018   0.98832737    1.0091494 
+  172000    1.0167826   -1.5995939   0.93307169 -0.0028786839   0.97757064    1.0140023 
+  174000    1.0067129   -1.5892333   0.93660255   0.13405338    1.0256516    1.0130713 
+  176000    1.0142368   -1.5969856    1.1376546 -0.039887725    1.0142342    1.0042825 
+  178000    1.0337679   -1.6167973   0.88782002 -0.013087286    1.0196301    1.0360511 
+  180000   0.96700375   -1.5494313    1.2700192  -0.17359042    1.0315247    1.0457286 
+  182000    1.0128669   -1.5958728    1.0325786  -0.11340517    1.0279582    1.0364275 
+  184000    1.0016786   -1.5849657    1.2423822  -0.04019647    1.0270552     1.028752 
+  186000    1.0068219   -1.5892056   0.91016442   0.12827957    1.0222492    1.0326718 
+  188000    1.0111052   -1.5936203   0.84190116   0.11675343    1.0132227    1.0349714 
+  190000    1.0428535   -1.6252876   0.84579508  0.074521906    1.0026939    1.0388207 
+  192000   0.98196941   -1.5644931    1.1089098   0.10878744   0.99394843    1.0299225 
+  194000    1.0060461   -1.5891845    1.0637631 0.0094883212   0.98560308    1.0478014 
+  196000     1.009729   -1.5927481    1.0375371  0.001016821   0.98435144    1.0504309 
+  198000    1.0130466   -1.5961561   0.94423285 -0.065299989   0.97454291    1.0416243 
+  200000   0.99556457    -1.578527    1.0479236 -0.078093695   0.96545375    1.0526692 
+  202000    1.0024053   -1.5849364    1.0110919 -0.011771169    0.9561055    1.0509412 
+  204000    1.0487373   -1.6329308   0.96913936  0.092389554   0.94987394    1.0543579 
+  206000    1.0040089   -1.5867752   0.87055365 -0.0029267837    0.9567723    1.0463902 
+  208000   0.98635833   -1.5695234    1.1193994  0.043854107   0.95068021    1.0683786 
+  210000   0.99172336   -1.5744133    1.0945983 -0.047827928   0.94448675    1.0661744 
+  212000   0.99572889   -1.5790512    1.1375524  -0.19281467   0.94310134    1.0562378 
+  214000    1.0146878   -1.5975136   0.93324057  0.023347328   0.94263065     1.046519 
+  216000   0.99707471   -1.5796874   0.96782693  0.083402848   0.93858777    1.0369438 
+  218000    1.0072021   -1.5896781    0.8155869 -0.094678429    0.9324393    1.0402187 
+  220000   0.99829642   -1.5812727    1.0862336 -0.057344135   0.92566931    1.0397392 
+  222000    1.0214364   -1.6037091    1.0020523 -0.081278441   0.91849564     1.032842 
+  224000    1.0007703    -1.583861    1.1398771 -0.014848249   0.91289746    1.0653713 
+  226000    1.0160887   -1.5986412   0.97725713 -0.061995296   0.92331797    1.0560269 
+  228000    1.0094934   -1.5930023     1.040651 0.0079530479   0.91726191    1.0492381 
+  230000   0.98902579   -1.5714487     1.050377  -0.02091325   0.90947876    1.0601329 
+  232000   0.98365162   -1.5665923    1.1795485  0.007265917   0.90850244    1.0527928 
+  234000   0.98804235   -1.5705815   0.99142023  -0.14096873   0.90260469    1.0522485 
+  236000    1.0111715   -1.5944579    1.0365441   0.03705863   0.89687478    1.0650694 
+  238000     1.028486   -1.6112797   0.77859138   0.03686834   0.88950376    1.0613943 
+  240000    1.0048364   -1.5883043    1.0507628     0.177815   0.88491797    1.0540196 
+  242000    1.0612408   -1.6455438   0.80528323 -0.065846556   0.87805554     1.047094 
+  244000   0.99451698    -1.577672   0.90507771 0.0090582429   0.87117885    1.0414447 
+  246000    1.0215777   -1.6050443   0.88605366 -0.033084099   0.86431702    1.0330488 
+  248000    1.0346251   -1.6179476    1.0266325  0.042180226    0.8640658    1.0319629 
+  250000   0.97725995   -1.5600316   0.99997539  0.046921107   0.85977157    1.0423435 
+  252000    1.0045133   -1.5877785    1.2089315  -0.20100537   0.85362501     1.038709 
+  254000    1.0396556   -1.6230252    0.8806146   0.16822159     0.847332    1.0358375 
+  256000   0.99769832   -1.5808696    1.0692142   0.03603972   0.84086272    1.0290594 
+  258000   0.97543457   -1.5580142    1.0623702  0.076387425   0.83692757    1.0365855 
+  260000   0.99005919   -1.5729678    1.0412698  -0.19142244    0.8306184    1.0329137 
+  262000    1.0014908   -1.5850781    1.0353971   0.10763251   0.82439244    1.0256642 
+  264000    1.0392437   -1.6231176    1.0236348  -0.19905313   0.81842954    1.0180519 
+  266000    1.0110595   -1.5936149     0.943378 -0.055766989   0.81566316    1.0185788 
+  268000    1.0155932   -1.5990965   0.84263415 -0.046929409   0.81998209    1.0239593 
+  270000     1.060652   -1.6449021   0.75643153  -0.10294749   0.81609283    1.0386067 
+  272000    1.0069743   -1.5895439   0.97553062  0.029040039   0.81351378    1.0375075 
+  274000    1.0463214   -1.6293543   0.67594148 -0.0069642173   0.80767486    1.0403024 
+  276000    1.0042636   -1.5875148   0.98929276  -0.12449786   0.80322846    1.0331136 
+  278000   0.97917004   -1.5627321    1.1268906 -0.078323442    0.8102638    1.0318867 
+  280000    1.0082531   -1.5907083    1.0527782 -0.036059017   0.80597557    1.0481782 
+  282000    1.0154843   -1.5985096   0.92086705 -0.068530775   0.80179106     1.073873 
+  284000    1.0098619   -1.5927428     1.036216  0.037750753    0.8112042     1.067422 
+  286000    1.0066095    -1.588402   0.98446812   0.02654871   0.80832515    1.0667938 
+  288000    1.0108484   -1.5932756    0.9938665 0.0014634473   0.80352165     1.080693 
+  290000    1.0084713   -1.5916424   0.97267996  -0.16071115   0.80043111    1.0816066 
+  292000    1.0056589   -1.5888464   0.84166635   0.11872697    0.7982537    1.0747896 
+  294000    1.0209933   -1.6049531    0.9891441  -0.08837825   0.79291613    1.0741692 
+  296000   0.99782768   -1.5811255    1.0931691   0.03252435   0.79104136    1.0866176 
+  298000   0.97158829   -1.5544768    1.0587163 -0.020509263   0.78578918    1.0885357 
+  300000   0.99635509   -1.5797521    1.0508706  -0.13999572   0.79997303    1.0997452 
+  302000    1.0244367   -1.6074122   0.98051456  0.078987418   0.80030881    1.0995395 
+  304000    1.0164691    -1.599263   0.92957417 -0.052090111   0.79628244    1.0931733 
+  306000   0.99640652   -1.5798263    1.0046382  -0.17696034   0.79868947    1.0904769 
+  308000   0.99001053   -1.5729715    1.0661668 -0.040494857   0.79359692    1.0911752 
+  310000    1.0176688   -1.6008189   0.88160706  -0.16255132    0.7885584    1.0842801 
+  312000    1.0030797   -1.5862445    1.1056347    0.2012843   0.78631107    1.0817648 
+  314000    1.0135412   -1.5963385   0.89411346   0.14573277   0.79263889    1.0968231 
+  316000    1.0289246   -1.6116769   0.95183363  -0.13790235   0.78774407     1.104116 
+  318000    1.0272076   -1.6108119    1.0546778  -0.15570037   0.78290345    1.0975264 
+  320000    1.0233555    -1.605886   0.69600824 -0.051301259   0.78829232      1.09266 
+  322000    1.0276771   -1.6115588     1.006656 -0.037166444    0.7929092    1.1049954 
+  324000    1.0009085    -1.583632    1.1030988 -0.045003287   0.78813539    1.0982174 
+  326000   0.99820481   -1.5808746   0.96157265 0.0051561382   0.78352469    1.0927727 
+  328000    1.0034746   -1.5866592    0.9828709   0.04098644   0.78017024    1.1021054 
+  330000    0.9855772   -1.5690259    1.2748992     0.216881   0.77581501    1.1148803 
+  332000    0.9965209   -1.5793357    1.1130749  0.090747874   0.77153933    1.1084502 
+  334000     1.035755   -1.6181093   0.88167554   0.02819393   0.77362798     1.101853 
+  336000   0.99996774    -1.582885    1.0190301  0.063460214    0.7730658    1.1168918 
+  338000   0.99767487   -1.5806236    1.0766267   0.17431208   0.84891175     1.114904 
+  340000    1.0253142   -1.6080987   0.95542815 -0.057965391   0.84475717     1.119315 
+  342000    1.0068098   -1.5893898   0.97259996   0.10715327   0.84600544    1.1134594 
+  344000   0.99340991   -1.5757393    1.0870946 -0.068506912   0.84493383    1.1166996 
+  346000    1.0120696   -1.5950574    1.0131809 -0.053688663   0.85345684    1.1136118 
+  348000    1.0309753   -1.6139898   0.89960386 -0.060363095   0.84882315    1.1073002 
+  350000    1.0037776   -1.5861394    1.0091603   0.02135905   0.84400778    1.1065317 
+  352000   0.98591728   -1.5680629    1.1377659 -0.083236455   0.84339812    1.1002993 
+  354000    1.0080397   -1.5904616   0.80849869   0.00928565     0.839096    1.1021557 
+  356000    1.0580451   -1.6407084   0.75557573 -0.072592855   0.83455195     1.104521 
+  358000     1.030585   -1.6137874    1.0380857 -0.080811662   0.82993805    1.1008832 
+  360000    1.0095237   -1.5931114     1.054976  -0.16712924   0.82622185     1.114334 
+  362000    1.0310879    -1.614041   0.84077595  0.080477352   0.82210684     1.110334 
+  364000    1.0000238   -1.5823394    1.1775906 0.0031139552   0.81775187    1.1202628 
+  366000    1.0190616   -1.6010113   0.92848622 -0.046387272   0.81781978    1.1264338 
+  368000    1.0089574    -1.591851   0.88967276  0.084507509   0.82548053    1.1212356 
+  370000   0.98626285   -1.5690591    1.0389475   0.15747394   0.82583189    1.1154499 
+  372000    1.0179928   -1.6012532   0.95338149 -0.079240909   0.82167358    1.1144564 
+  374000    1.0036723   -1.5864866   0.91169472  0.038159086   0.82140017    1.1085543 
+  376000    1.0059869   -1.5884349   0.90711389 -0.093438168    0.8175783    1.1153576 
+  378000    1.0376167   -1.6201331   0.96969013  -0.11849733   0.81376748    1.1099608 
+  380000   0.98982394   -1.5727352    1.1608252 -0.038393364   0.81568758    1.1079312 
+  382000   0.97137184   -1.5536171   0.96619112 -0.034678175   0.82814609    1.1093848 
+  384000   0.99272978   -1.5762779    1.0509393  0.032343038   0.82443143    1.1102277 
+  386000    1.0100648   -1.5930531   0.96303847   -0.0497874    0.8208917    1.1139354 
+  388000   0.99635597   -1.5791363     1.016829  -0.04531565   0.81880723     1.123366 
+  390000    1.0128857    -1.596226    1.0168535  0.030123764    0.8154196    1.1178207 
+  392000    1.0414799   -1.6256855   0.91612676  0.052204166   0.83525866    1.1123266 
+  394000   0.98112978   -1.5641253    1.0438272 -0.068667673   0.83283911    1.1079269 
+  396000   0.97787678   -1.5598426    1.0131718 -0.033109536   0.82986658    1.1023614 
+  398000    1.0292431   -1.6119808   0.90622851 -0.082576483    0.8257706    1.0998351 
+  400000    1.0026087    -1.585683    1.0275497  0.087158222   0.82322877    1.0977666 
+  402000    1.0163706    -1.598545   0.96588365 -0.029125811   0.81982673    1.0926389 
+  404000    1.0262493   -1.6102647   0.79007094 0.0079598958   0.82007072    1.0907315 
+  406000   0.99487107   -1.5778515   0.83977277  0.066596384   0.81631134    1.0866073 
+  408000    1.0108518   -1.5941246    1.1412871  0.041085191   0.81420279    1.1112395 
+  410000    1.0026966   -1.5853826    1.1125145  0.021404009   0.81421483    1.1075314 
+  412000    1.0027426   -1.5856908    1.1445941   0.10077025   0.81035844    1.1221605 
+  414000    1.0525169   -1.6352976    0.6688189 -0.071885452   0.80922951     1.117048 
+  416000   0.95514842   -1.5380164    1.2198976 -0.020098364   0.81039185    1.1127016 
+  418000   0.99853286    -1.581907     1.040174 -0.043752958   0.83070976    1.1151814 
+  420000   0.96432983   -1.5472735    1.2000605    0.0284884   0.82688067    1.1201892 
+  422000    1.0110338   -1.5937639   0.88925615 -0.0056255993   0.83729353    1.1266963 
+  424000    1.0077925   -1.5914573    1.0625448  0.078586775   0.83465757    1.1235583 
+  426000   0.98743189     -1.57002    1.0888581   0.12563331   0.83275041    1.1193766 
+  428000    1.0112301   -1.5939984   0.91688673   -0.1605337   0.82889693     1.121168 
+  430000    1.0283254   -1.6119787   0.83233694  0.047589962    0.8296882    1.1165262 
+  432000   0.97982409   -1.5625913    1.1875522 -0.060520907    0.8264448    1.1156609 
+  434000    0.9830003   -1.5662434    1.2882445  0.026552191   0.82362897    1.1251296 
+  436000   0.98158695   -1.5642196    1.2184202   0.10011832   0.81988328    1.1202386 
+  438000    1.0174602   -1.6006392   0.98983657  -0.26731543   0.82359277    1.1194173 
+  440000    1.0147922   -1.5986583   0.99723521   0.10312258   0.82668874    1.1166321 
+  442000    1.0185438   -1.6025919   0.95378608  0.032898335    0.8376384    1.1141027 
+  444000   0.97737381   -1.5597895    1.2100163  0.022311362   0.85102822    1.1150521 
+  446000   0.99593648   -1.5791062    1.0999746 -0.041825149   0.85489871    1.1105882 
+  448000    1.0259234   -1.6095208   0.90080955 -0.057452702   0.85131792     1.105654 
+  450000   0.98873973   -1.5717826    1.0019177  -0.14057947   0.84916741    1.1007825 
+  452000    1.0059102   -1.5895389    1.0666545  0.014242262   0.84548682     1.096266 
+  454000   0.99943215   -1.5826409    1.1353551  0.070613563   0.84193028    1.0914609 
+  456000   0.99123683    -1.574133    1.1310395 -0.019958521   0.85786896       1.0872 
+  458000   0.98476743   -1.5685042    1.0628314 -0.024302081   0.86756819    1.0850446 
+  460000    1.0139076   -1.5963225    1.0181222  0.089182002   0.87724533    1.0827991 
+  462000    1.0113822   -1.5955924    1.1739975  -0.10175863   0.89205773    1.0951284 
+  464000    1.0228404    -1.607263    1.0517714 -0.031783966   0.89340123    1.0913457 
+  466000    1.0126934   -1.5964207   0.96656763 -0.015021156   0.89086201    1.0870365 
+  468000    1.0070377   -1.5912579    1.0378727 -0.0077122994   0.88981469    1.0868451 
+  470000   0.99238797   -1.5760561    1.0832266 -0.041876018   0.88670298    1.0888446 
+  472000    1.0169724   -1.6006383   0.90761167  -0.12563948   0.89441625    1.0855102 
+  474000    1.0025279    -1.585529    1.0050948  0.043906331   0.89302764    1.0812461 
+  476000   0.99536702   -1.5780191   0.89444096   0.14592241   0.89683614     1.077964 
+  478000   0.98866565   -1.5720704    1.1754384  0.048623957   0.89407347    1.0917047 
+  480000   0.98572668   -1.5687903   0.90601784  -0.26268845   0.89230666     1.087992 
+  482000     1.014423     -1.59804   0.98209159  0.069121411   0.89149689    1.0836584 
+  484000    1.0090002   -1.5916356    0.9957509  -0.09367221    0.9170021    1.1011703 
+  486000   0.99962993   -1.5834522    1.0977267  -0.15748171   0.91654366    1.0989507 
+  488000   0.98394002   -1.5667132    1.0400853 -0.054203925   0.91811726    1.1150492 
+  490000    1.0216626   -1.6057027   0.95663779 -0.076119485   0.91665173    1.1116068 
+  492000   0.98450357   -1.5677506    1.2970783   -0.1684919   0.91932358    1.1071252 
+  494000     1.022591   -1.6056696   0.82845032  -0.10149084   0.91562447    1.1057524 
+  496000    1.0317595   -1.6157971   0.79413446   0.12970065   0.92063013     1.102386 
+  498000    1.0375923   -1.6219641    1.0063299 0.0090318777   0.94925707    1.1005841 
+  500000     1.009533   -1.5922817   0.92939388  0.051496977   0.95185481    1.0969849 
+Loop time of 70.5997 on 1 procs for 500000 steps with 800 atoms
+
+Performance: 3059502.219 tau/day, 7082.181 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    | 47.621     | 47.621     | 47.621     |   0.0 | 67.45
+Neigh   | 12.109     | 12.109     | 12.109     |   0.0 | 17.15
+Comm    | 1.5187     | 1.5187     | 1.5187     |   0.0 |  2.15
+Output  | 0.0026052  | 0.0026052  | 0.0026052  |   0.0 |  0.00
+Modify  | 6.9725     | 6.9725     | 6.9725     |   0.0 |  9.88
+Other   |            | 2.375      |            |       |  3.36
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    271 ave 271 max 271 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5622 ave 5622 max 5622 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5622
+Ave neighs/atom = 7.0275
+Neighbor list builds = 59121
+Dangerous builds = 0
+
+variable         etaxy equal v_vxy
+variable         etaxx equal v_vxx
+variable         eta equal 0.5*(${etaxy}+${etaxx})
+variable         eta equal 0.5*(0.951854813936217+${etaxx})
+variable         eta equal 0.5*(0.951854813936217+1.09698487634149)
+print            "running average viscosity: ${eta}"
+running average viscosity: 1.02441984513885
+Total wall time: 0:01:12

examples/VISCOSITY/log.13Oct16.gk.2d.g++.1

@@ -0,0 +1,423 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for viscosity of 2d LJ liquid
+# Green-Kubo method via fix ave/correlate
+
+# settings
+
+variable	x equal 20
+variable	y equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+variable    p equal 400     # correlation length
+variable    s equal 5       # sample interval
+variable    d equal $p*$s   # dump interval
+variable    d equal 400*$s   
+variable    d equal 400*5   
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 20 0 $y -0.1 0.1
+region          simbox block 0 20 0 20 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 800 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+# equilibration run
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+thermo          $d
+thermo          2000
+run	        10000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 27 27 1
+Memory usage per processor = 2.47956 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0     -0.56617    -1.535262 
+    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
+    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
+    6000    1.0384014   -1.6029223            0   -0.5658189   0.82862123 
+    8000    1.0035814   -1.5749989            0  -0.57267191    1.1514978 
+   10000    1.0149864   -1.5834783            0  -0.56976064   0.94535991 
+Loop time of 1.68923 on 1 procs for 10000 steps with 800 atoms
+
+Performance: 2557381.154 tau/day, 5919.864 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    | 0.93939    | 0.93939    | 0.93939    |   0.0 | 55.61
+Neigh   | 0.22535    | 0.22535    | 0.22535    |   0.0 | 13.34
+Comm    | 0.028255   | 0.028255   | 0.028255   |   0.0 |  1.67
+Output  | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 |   0.0 |  0.00
+Modify  | 0.44989    | 0.44989    | 0.44989    |   0.0 | 26.63
+Other   |            | 0.0463     |            |       |  2.74
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    262 ave 262 max 262 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5587 ave 5587 max 5587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5587
+Ave neighs/atom = 6.98375
+Neighbor list builds = 1101
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1
+
+unfix		2
+
+# Green-Kubo viscosity calculation
+
+reset_timestep  0
+
+# Define distinct components of symmetric traceless stress tensor
+
+variable         pxy equal pxy
+variable         pxx equal pxx-press
+
+fix              SS all ave/correlate $s $p $d                  v_pxy v_pxx type auto file profile.gk.2d ave running
+fix              SS all ave/correlate 5 $p $d                  v_pxy v_pxx type auto file profile.gk.2d ave running
+fix              SS all ave/correlate 5 400 $d                  v_pxy v_pxx type auto file profile.gk.2d ave running
+fix              SS all ave/correlate 5 400 2000                  v_pxy v_pxx type auto file profile.gk.2d ave running
+
+# Diagonal components of SS are larger by factor 2-2/d,
+# which is 4/3 for d=3, but 1 for d=2.
+# See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)
+
+variable         scale equal 1.0/$t*vol*$s*dt
+variable         scale equal 1.0/1*vol*$s*dt
+variable         scale equal 1.0/1*vol*5*dt
+variable         diagfac equal 2-2/2
+variable         vxy equal trap(f_SS[3])*${scale}
+variable         vxy equal trap(f_SS[3])*33.3333333333333
+variable         vxx equal trap(f_SS[4])*${scale}/${diagfac}
+variable         vxx equal trap(f_SS[4])*33.3333333333333/${diagfac}
+variable         vxx equal trap(f_SS[4])*33.3333333333333/1
+
+thermo_style     custom step temp press pxy v_vxy v_vxx
+
+run              500000
+Memory usage per processor = 2.47956 Mbytes
+Step Temp Press Pxy v_vxy v_vxx 
+       0            1   0.93637929  0.013123478 0.0028704278 3.6139711e-05 
+    2000   0.99103273   0.96182762  0.032871709    1.0973353    1.7302859 
+    4000    1.0416298    0.9238985   0.02532039  -0.51174928    1.3585307 
+    6000    1.0033402     1.049074  0.056300627  -0.52973835    2.1985256 
+    8000    1.0003681    1.1886635  0.019361031   -0.2525203    1.5354203 
+   10000    1.0195921    0.9009639 -0.075997173   0.77178738    1.9426534 
+   12000    1.0026283   0.90425907  -0.10655349   0.59485093    1.4709129 
+   14000    1.0062891     1.120094  0.078261625    1.3430022    1.4154697 
+   16000   0.97921785     1.056538  -0.27861922    1.1095264    1.2162698 
+   18000     1.012419    1.0278053  0.022229371    1.7339307    1.1123441 
+   20000    1.0117709   0.97722275 0.0075466982    1.7749122    1.0704588 
+   22000    1.0008808    1.0572608  0.087832931    1.6516858    1.0614696 
+   24000    1.0002975    1.0118667 -0.068081725    1.4708723    1.0635481 
+   26000   0.98509665    1.1898824   0.21810836    1.5759129     1.101463 
+   28000    0.9891689    1.1456688   0.12141752    1.7952721    1.1441876 
+   30000    1.0071582   0.96554132  0.017641823    1.5696844     1.207463 
+   32000    1.0076807    1.1047186  0.044265263    1.6946819    1.0605558 
+   34000   0.95874174     1.362955  -0.14025695    1.7962468    1.0166685 
+   36000   0.99528173    1.0970028 -0.016714523    1.6378502    1.0580616 
+   38000    1.0124371   0.99493986 -0.041410673    1.5728087    1.0689583 
+   40000    1.0141237   0.98549019  0.047454345    1.5733219    1.0153622 
+   42000    1.0274867   0.93801507  0.089635945    1.5765417   0.99165386 
+   44000   0.98700259   0.94306661 -0.045695708    1.7023399   0.99608779 
+   46000    1.0080948    1.0304791 -0.0046135743     1.738355   0.87443113 
+   48000   0.97227783    1.1829894  0.042219544    1.6953772   0.82755164 
+   50000   0.99046716    1.0095618  0.018697031    1.6358006   0.79907178 
+   52000    1.0129697   0.88794241 -0.045990748    1.6257284    0.8693729 
+   54000    1.0013276    1.0246693  0.012464296     1.711089   0.85652021 
+   56000    1.0385716   0.75426191  -0.04775685    1.6576515   0.80114077 
+   58000    1.0107757    1.0239619  0.029529278      1.62731      1.01175 
+   60000    1.0177033   0.94723439  -0.16871762    1.6492387    1.3267438 
+   62000    1.0210737    1.0225179  0.079638703    1.5703895    1.3460163 
+   64000    1.0106132    1.0188777   0.02699431    1.5335146    1.3032641 
+   66000   0.98531307    1.1224354 -0.0069578014    1.6159073    1.2791611 
+   68000   0.99450728    1.3016366  0.056607824     1.560555    1.2757996 
+   70000   0.98874589    1.0724556 -0.022405835    1.5275425    1.2439185 
+   72000    1.0108814   0.92375729  -0.12669224    1.5118684    1.2223259 
+   74000    1.0098348    1.0635024  -0.12956833    1.4818607    1.2161456 
+   76000    1.0089021   0.98626851  -0.20311631    1.4768989    1.2153601 
+   78000     1.002405     1.008097 -0.089615503    1.4499417    1.1460696 
+   80000    1.0266582    1.0493411   0.16631226    1.4254227    1.1765198 
+   82000      1.01242   0.81710829   0.18713063    1.3872432    1.1213607 
+   84000    1.0262474    1.1125949 -0.0012088503     1.464111    1.1215723 
+   86000   0.99599827    1.0337621 -0.0056500173    1.4658272    1.1000357 
+   88000   0.98713531    1.0665747  -0.10237303    1.5900602    1.0774497 
+   90000    1.0156011   0.96906164   0.13894564    1.5880395    1.1005107 
+   92000    1.0306883   0.78929887 0.0089544803    1.5445295    1.1172449 
+   94000   0.98455669    1.1917323  0.025629181    1.4984833    1.1347838 
+   96000   0.99528576    1.1055136  0.020277014    1.4904339    1.0982899 
+   98000    1.0504589   0.99135546 -0.051989636     1.455444    1.0661495 
+  100000   0.98210335    1.0867432  0.091525725    1.4218731    1.0813261 
+  102000    1.0316494    1.1350259  0.072311903    1.3978862    1.0946066 
+  104000    1.0292338   0.83829357  -0.04098328    1.3809297    1.1853511 
+  106000   0.98153521    1.0653974 -4.3227008e-05    1.3544205    1.2098378 
+  108000    1.0074159    1.0048635    0.1947269    1.3858614    1.2974418 
+  110000    1.0007684    1.1603181   0.13820163    1.3549744    1.3665589 
+  112000   0.98637814    1.0037644  0.049907343    1.3424521    1.3434275 
+  114000   0.99310586    1.0896413 -0.079352378    1.3189065    1.3424599 
+  116000   0.98829858   0.87861443   0.05118496    1.3323643    1.2973572 
+  118000      1.01049   0.96002545  -0.12320659    1.3042553    1.3143529 
+  120000    1.0218378   0.89637436   0.02750584    1.2880273    1.4129925 
+  122000    1.0263547   0.95854694 0.0034110405    1.2998558    1.4125761 
+  124000    0.9899202    1.0492908  -0.13855042    1.2885462    1.4024599 
+  126000   0.98192121    1.1372352   0.16313842    1.2742073    1.3858109 
+  128000     1.002862   0.97650147  0.048928455    1.3089319    1.4032307 
+  130000   0.99785761   0.93146735  0.026478401    1.2798809    1.4133812 
+  132000   0.98956541   0.96523389  -0.10052306    1.2753991    1.4194387 
+  134000    1.0019397    1.0447894   0.13871691    1.2573725    1.4193379 
+  136000    1.0321449    1.1072168  -0.15369414    1.2214357    1.4798406 
+  138000    1.0239483   0.82920716 -0.011872404    1.1990447    1.4537855 
+  140000    1.0082907    1.0012771  0.027192581    1.2017711     1.488733 
+  142000    1.0007865    1.0399048 -0.096251148    1.2255281    1.4836706 
+  144000    1.0001664    1.0071962 -0.083449668     1.188732    1.4747949 
+  146000    1.0202238    1.0702284 -0.063595518    1.1747017     1.457276 
+  148000    1.0248683    1.0227875  0.069198975    1.1641817    1.4482984 
+  150000    1.0127614   0.80897516 0.0044443031    1.1486331    1.4389959 
+  152000    1.0028044    1.0857002 -0.059930891    1.1448366    1.4107488 
+  154000    1.0149836   0.82631625  0.085962962    1.1469054    1.3899228 
+  156000   0.99818966     1.035248 -0.029178797    1.1381571     1.380388 
+  158000    1.0023756   0.94465038 -0.056571392    1.1308549    1.3564606 
+  160000   0.99847665    1.0656894 -0.022026678    1.1397154    1.4343558 
+  162000   0.98084763    1.2446958  0.097934009    1.1180528    1.3973883 
+  164000   0.98358665    1.1626742 -0.010830507    1.1042107    1.3740411 
+  166000    1.0176133   0.91335665  0.054966014    1.1205556    1.3965323 
+  168000    1.0252828    1.0562376  0.025372153    1.1392262    1.4162518 
+  170000    1.0429701   0.78042973 -0.088860018    1.1624209    1.4180095 
+  172000    1.0167826   0.93307169 -0.0028786839    1.1482597    1.4102599 
+  174000    1.0067129   0.93660255   0.13405338    1.1765833    1.3906822 
+  176000    1.0142368    1.1376546 -0.039887725    1.1490071    1.3803357 
+  178000    1.0337679   0.88782002 -0.013087286    1.1537575    1.4217567 
+  180000   0.96700375    1.2700192  -0.17359042    1.1782075    1.4515137 
+  182000    1.0128669    1.0325786  -0.11340517    1.1601019    1.4525292 
+  184000    1.0016786    1.2423822  -0.04019647    1.1535732    1.4506038 
+  186000    1.0068219   0.91016442   0.12827957     1.140122    1.4814336 
+  188000    1.0111052   0.84190116   0.11675343    1.1385292    1.4872393 
+  190000    1.0428535   0.84579508  0.074521906     1.126706    1.5039655 
+  192000   0.98196941    1.1089098   0.10878744    1.1159363    1.4826447 
+  194000    1.0060461    1.0637631 0.0094883212    1.1126571    1.4825394 
+  196000     1.009729    1.0375371  0.001016821     1.104084    1.4675566 
+  198000    1.0130466   0.94423285 -0.065299989    1.0985735    1.4613693 
+  200000   0.99556457    1.0479236 -0.078093695     1.087735    1.4629234 
+  202000    1.0024053    1.0110919 -0.011771169    1.0789047    1.4423084 
+  204000    1.0487373   0.96913936  0.092389554    1.0752111    1.4428081 
+  206000    1.0040089   0.87055365 -0.0029267837    1.0892902    1.4295861 
+  208000   0.98635833    1.1193994  0.043854107    1.0935635    1.4288422 
+  210000   0.99172336    1.0945983 -0.047827928    1.0845738    1.4610522 
+  212000   0.99572889    1.1375524  -0.19281467    1.0820934    1.4492165 
+  214000    1.0146878   0.93324057  0.023347328    1.0666754    1.4359126 
+  216000   0.99707471   0.96782693  0.083402848    1.0567355    1.4261272 
+  218000    1.0072021    0.8155869 -0.094678429    1.0397772    1.4363021 
+  220000   0.99829642    1.0862336 -0.057344135    1.0264114    1.4261186 
+  222000    1.0214364    1.0020523 -0.081278441    1.0259496    1.4104525 
+  224000    1.0007703    1.1398771 -0.014848249    1.0383859    1.4298639 
+  226000    1.0160887   0.97725713 -0.061995296    1.0437407    1.4241759 
+  228000    1.0094934     1.040651 0.0079530479    1.0393089    1.4155728 
+  230000   0.98902579     1.050377  -0.02091325    1.0338013    1.4183238 
+  232000   0.98365162    1.1795485  0.007265917     1.023983      1.42409 
+  234000   0.98804235   0.99142023  -0.14096873    1.0094423    1.4122007 
+  236000    1.0111715    1.0365441   0.03705863    0.9986353    1.3994269 
+  238000     1.028486   0.77859138   0.03686834   0.99615802    1.4123065 
+  240000    1.0048364    1.0507628     0.177815   0.98769158    1.4053338 
+  242000    1.0612408   0.80528323 -0.065846556   0.96795821    1.3983254 
+  244000   0.99451698   0.90507771 0.0090582429   0.95858362    1.3911554 
+  246000    1.0215777   0.88605366 -0.033084099   0.94891089    1.3837671 
+  248000    1.0346251    1.0266325  0.042180226   0.94589414    1.3805736 
+  250000   0.97725995   0.99997539  0.046921107    0.9413025    1.4054541 
+  252000    1.0045133    1.2089315  -0.20100537   0.93463731    1.3855538 
+  254000    1.0396556    0.8806146   0.16822159   0.92217148    1.3836271 
+  256000   0.99769832    1.0692142   0.03603972   0.90825537      1.37561 
+  258000   0.97543457    1.0623702  0.076387425   0.89703273    1.3792596 
+  260000   0.99005919    1.0412698  -0.19142244    0.8920687    1.3587022 
+  262000    1.0014908    1.0353971   0.10763251   0.88126218     1.346977 
+  264000    1.0392437    1.0236348  -0.19905313   0.87431966    1.3383363 
+  266000    1.0110595     0.943378 -0.055766989   0.86561643    1.3383356 
+  268000    1.0155932   0.84263415 -0.046929409   0.87912277    1.3349971 
+  270000     1.060652   0.75643153  -0.10294749   0.87236853    1.3457342 
+  272000    1.0069743   0.97553062  0.029040039   0.84867311    1.3119881 
+  274000    1.0463214   0.67594148 -0.0069642173   0.83557725    1.3142664 
+  276000    1.0042636   0.98929276  -0.12449786     0.834825    1.3009674 
+  278000   0.97917004    1.1268906 -0.078323442   0.84264211     1.302196 
+  280000    1.0082531    1.0527782 -0.036059017   0.83666146    1.3290452 
+  282000    1.0154843   0.92086705 -0.068530775   0.83838607    1.3283441 
+  284000    1.0098619     1.036216  0.037750753   0.83579051    1.3263873 
+  286000    1.0066095   0.98446812   0.02654871   0.82548297    1.3204648 
+  288000    1.0108484    0.9938665 0.0014634473    0.8212407    1.3432121 
+  290000    1.0084713   0.97267996  -0.16071115   0.81647241    1.3116145 
+  292000    1.0056589   0.84166635   0.11872697   0.80604569    1.2982472 
+  294000    1.0209933    0.9891441  -0.08837825    0.7987701    1.2971225 
+  296000   0.99782768    1.0931691   0.03252435    0.7933436    1.3227693 
+  298000   0.97158829    1.0587163 -0.020509263   0.78826707    1.3403092 
+  300000   0.99635509    1.0508706  -0.13999572   0.80661653    1.3636672 
+  302000    1.0244367   0.98051456  0.078987418   0.79690906    1.3579957 
+  304000    1.0164691   0.92957417 -0.052090111   0.78111523    1.3494573 
+  306000   0.99640652    1.0046382  -0.17696034   0.78527471    1.3388528 
+  308000   0.99001053    1.0661668 -0.040494857   0.78802705    1.3391576 
+  310000    1.0176688   0.88160706  -0.16255132   0.77827469     1.328968 
+  312000    1.0030797    1.1056347    0.2012843   0.77588955    1.3216876 
+  314000    1.0135412   0.89411346   0.14573277   0.76605153    1.3369024 
+  316000    1.0289246   0.95183363  -0.13790235   0.76142201    1.3264365 
+  318000    1.0272076    1.0546778  -0.15570037    0.7550118     1.319986 
+  320000    1.0233555   0.69600824 -0.051301259   0.75973858     1.316099 
+  322000    1.0276771     1.006656 -0.037166444   0.77429945    1.3244899 
+  324000    1.0009085    1.1030988 -0.045003287   0.77270822    1.3241261 
+  326000   0.99820481   0.96157265 0.0051561382   0.77066804     1.313479 
+  328000    1.0034746    0.9828709   0.04098644   0.77299241    1.3168281 
+  330000    0.9855772    1.2748992     0.216881   0.76442667    1.3495639 
+  332000    0.9965209    1.1130749  0.090747874   0.75969604    1.3482028 
+  334000     1.035755   0.88167554   0.02819393   0.75757808    1.3424486 
+  336000   0.99996774    1.0190301  0.063460214   0.75227901    1.3506673 
+  338000   0.99767487    1.0766267   0.17431208   0.84059427    1.3246922 
+  340000    1.0253142   0.95542815 -0.057965391   0.83723497    1.3293585 
+  342000    1.0068098   0.97259996   0.10715327   0.83750839     1.326108 
+  344000   0.99340991    1.0870946 -0.068506912   0.82881344    1.3279886 
+  346000    1.0120696    1.0131809 -0.053688663   0.83810272    1.3174796 
+  348000    1.0309753   0.89960386 -0.060363095   0.82821889    1.3105855 
+  350000    1.0037776    1.0091603   0.02135905   0.82421593    1.3062743 
+  352000   0.98591728    1.1377659 -0.083236455   0.82154361    1.3039211 
+  354000    1.0080397   0.80849869   0.00928565    0.8133737    1.2966239 
+  356000    1.0580451   0.75557573 -0.072592855   0.80584322    1.2906508 
+  358000     1.030585    1.0380857 -0.080811662    0.8014706    1.2924957 
+  360000    1.0095237     1.054976  -0.16712924   0.80086617    1.2972352 
+  362000    1.0310879   0.84077595  0.080477352   0.79545805    1.2769439 
+  364000    1.0000238    1.1775906 0.0031139552   0.79173356    1.2839778 
+  366000    1.0190616   0.92848622 -0.046387272   0.79173254    1.3032921 
+  368000    1.0089574   0.88967276  0.084507509   0.81055496    1.3028473 
+  370000   0.98626285    1.0389475   0.15747394   0.81689831    1.2919537 
+  372000    1.0179928   0.95338149 -0.079240909   0.80533945    1.2877439 
+  374000    1.0036723   0.91169472  0.038159086   0.80466471    1.2811106 
+  376000    1.0059869   0.90711389 -0.093438168   0.80486392      1.27755 
+  378000    1.0376167   0.96969013  -0.11849733   0.79690186    1.2849264 
+  380000   0.98982394    1.1608252 -0.038393364   0.79074513    1.2787152 
+  382000   0.97137184   0.96619112 -0.034678175   0.79040338    1.2750988 
+  384000   0.99272978    1.0509393  0.032343038   0.78854414    1.2713176 
+  386000    1.0100648   0.96303847   -0.0497874   0.78404981    1.2846324 
+  388000   0.99635597     1.016829  -0.04531565    0.7787559     1.306903 
+  390000    1.0128857    1.0168535  0.030123764   0.77822522    1.2950826 
+  392000    1.0414799   0.91612676  0.052204166   0.80240996    1.2882927 
+  394000   0.98112978    1.0438272 -0.068667673   0.79384032    1.2811558 
+  396000   0.97787678    1.0131718 -0.033109536   0.79605418    1.2692971 
+  398000    1.0292431   0.90622851 -0.082576483   0.79540751    1.2680355 
+  400000    1.0026087    1.0275497  0.087158222   0.79029414    1.2644206 
+  402000    1.0163706   0.96588365 -0.029125811   0.78663679    1.2595275 
+  404000    1.0262493   0.79007094 0.0079598958   0.78812507    1.2575526 
+  406000   0.99487107   0.83977277  0.066596384   0.78322554    1.2506377 
+  408000    1.0108518    1.1412871  0.041085191   0.78509472    1.2623544 
+  410000    1.0026966    1.1125145  0.021404009   0.78266826    1.2703102 
+  412000    1.0027426    1.1445941   0.10077025   0.77085701    1.2849866 
+  414000    1.0525169    0.6688189 -0.071885452   0.77565161    1.2911903 
+  416000   0.95514842    1.2198976 -0.020098364   0.76998705    1.2873301 
+  418000   0.99853286     1.040174 -0.043752958   0.78683106    1.2936501 
+  420000   0.96432983    1.2000605    0.0284884   0.78718481     1.312678 
+  422000    1.0110338   0.88925615 -0.0056255993   0.79178119    1.3132659 
+  424000    1.0077925    1.0625448  0.078586775   0.77982291    1.3031021 
+  426000   0.98743189    1.0888581   0.12563331   0.77548305    1.2938035 
+  428000    1.0112301   0.91688673   -0.1605337   0.76902093    1.2909986 
+  430000    1.0283254   0.83233694  0.047589962   0.76791923    1.2841707 
+  432000   0.97982409    1.1875522 -0.060520907    0.7726128    1.2775717 
+  434000    0.9830003    1.2882445  0.026552191   0.77474589    1.2727174 
+  436000   0.98158695    1.2184202   0.10011832   0.76992849    1.2604393 
+  438000    1.0174602   0.98983657  -0.26731543   0.77292394    1.2570614 
+  440000    1.0147922   0.99723521   0.10312258   0.77211658    1.2600691 
+  442000    1.0185438   0.95378608  0.032898335   0.79194152    1.2533085 
+  444000   0.97737381    1.2100163  0.022311362   0.78333762    1.2556328 
+  446000   0.99593648    1.0999746 -0.041825149   0.80441311    1.2459874 
+  448000    1.0259234   0.90080955 -0.057452702   0.80038521    1.2398877 
+  450000   0.98873973    1.0019177  -0.14057947   0.79374658    1.2334462 
+  452000    1.0059102    1.0666545  0.014242262   0.78886902    1.2270249 
+  454000   0.99943215    1.1353551  0.070613563   0.78877577    1.2211064 
+  456000   0.99123683    1.1310395 -0.019958521    0.8212975    1.2153723 
+  458000   0.98476743    1.0628314 -0.024302081   0.84754857    1.2111254 
+  460000    1.0139076    1.0181222  0.089182002    0.8711683    1.2012356 
+  462000    1.0113822    1.1739975  -0.10175863   0.87381822    1.2134671 
+  464000    1.0228404    1.0517714 -0.031783966   0.87936192    1.2110218 
+  466000    1.0126934   0.96656763 -0.015021156   0.87512117     1.205325 
+  468000    1.0070377    1.0378727 -0.0077122994   0.87144073     1.210374 
+  470000   0.99238797    1.0832266 -0.041876018   0.87158524    1.2128182 
+  472000    1.0169724   0.90761167  -0.12563948   0.87563801    1.2031687 
+  474000    1.0025279    1.0050948  0.043906331   0.88508792    1.2034718 
+  476000   0.99536702   0.89444096   0.14592241   0.88559122    1.2006404 
+  478000   0.98866565    1.1754384  0.048623957   0.88245402    1.2048067 
+  480000   0.98572668   0.90601784  -0.26268845    0.8766798    1.1959848 
+  482000     1.014423   0.98209159  0.069121411   0.87638162    1.1900047 
+  484000    1.0090002    0.9957509  -0.09367221   0.91979312    1.2095237 
+  486000   0.99962993    1.0977267  -0.15748171   0.91796166    1.1883856 
+  488000   0.98394002    1.0400853 -0.054203925   0.90840814    1.2065249 
+  490000    1.0216626   0.95663779 -0.076119485   0.89955072     1.213275 
+  492000   0.98450357    1.2970783   -0.1684919    0.9028997    1.2128895 
+  494000     1.022591   0.82845032  -0.10149084   0.90006981    1.2103346 
+  496000    1.0317595   0.79413446   0.12970065   0.91240504    1.2079784 
+  498000    1.0375923    1.0063299 0.0090318777   0.91283445     1.209838 
+  500000     1.009533   0.92939388  0.051496977   0.92195746    1.2070306 
+Loop time of 70.8372 on 1 procs for 500000 steps with 800 atoms
+
+Performance: 3049246.649 tau/day, 7058.441 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    | 47.562     | 47.562     | 47.562     |   0.0 | 67.14
+Neigh   | 12.145     | 12.145     | 12.145     |   0.0 | 17.14
+Comm    | 1.5125     | 1.5125     | 1.5125     |   0.0 |  2.14
+Output  | 0.004076   | 0.004076   | 0.004076   |   0.0 |  0.01
+Modify  | 7.2584     | 7.2584     | 7.2584     |   0.0 | 10.25
+Other   |            | 2.355      |            |       |  3.32
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    271 ave 271 max 271 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5622 ave 5622 max 5622 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5622
+Ave neighs/atom = 7.0275
+Neighbor list builds = 59121
+Dangerous builds = 0
+
+variable         etaxy equal v_vxy
+variable         etaxx equal v_vxx
+variable         eta equal 0.5*(${etaxy}+${etaxx})
+variable         eta equal 0.5*(0.921957460954984+${etaxx})
+variable         eta equal 0.5*(0.921957460954984+1.20703060474415)
+print            "running average viscosity: ${eta}"
+running average viscosity: 1.06449403284957
+Total wall time: 0:01:12

examples/VISCOSITY/log.13Oct16.mp.2d.g++.1

@@ -0,0 +1,260 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for viscosity of 2d LJ liquid
+# Muller-Plathe via fix viscosity
+
+# settings
+
+variable	x equal 20
+variable	y equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 20 0 $y -0.1 0.1
+region          simbox block 0 20 0 20 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 800 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 27 27 1
+Memory usage per processor = 2.47956 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0     -0.56617    -1.535262 
+    1000   0.95906897    -1.571142            0  -0.61327189   0.82593948 
+    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
+    3000    1.0429232   -1.5801639            0  -0.53854441     1.157286 
+    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
+    5000    0.9411767   -1.6155061            0  -0.67550589   0.79353873 
+Loop time of 0.860626 on 1 procs for 5000 steps with 800 atoms
+
+Performance: 2509801.057 tau/day, 5809.725 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    | 0.48372    | 0.48372    | 0.48372    |   0.0 | 56.21
+Neigh   | 0.11227    | 0.11227    | 0.11227    |   0.0 | 13.05
+Comm    | 0.014462   | 0.014462   | 0.014462   |   0.0 |  1.68
+Output  | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 |   0.0 |  0.01
+Modify  | 0.22682    | 0.22682    | 0.22682    |   0.0 | 26.35
+Other   |            | 0.02332    |            |       |  2.71
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5583 ave 5583 max 5583 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5583
+Ave neighs/atom = 6.97875
+Neighbor list builds = 551
+Dangerous builds = 0
+
+unfix		2
+
+# turn on Muller-Plathe driving force and equilibrate some more
+
+velocity	all scale $t
+velocity	all scale 1
+
+fix		4 all viscosity 100 x y 20
+
+compute         layers all chunk/atom bin/1d y center 0.05 units reduced
+fix		5 all ave/chunk 20 50 1000 layers vx file profile.mp.2d
+
+# equilibration run
+
+variable	dVx equal f_5[11][3]-f_5[1][3]
+
+thermo          1000
+thermo_style	custom step temp epair etotal press f_4 v_dVx
+run		20000
+Memory usage per processor = 2.72975 Mbytes
+Step Temp E_pair TotEng Press f_4 v_dVx 
+    5000            1   -1.6155061  -0.61675613   0.82878859            0            0 
+    6000   0.99205567   -1.6073706  -0.61655497   0.80256133   -40.441513   0.49442509 
+    7000   0.98076638   -1.5968401   -0.6172997   0.93482147   -74.701801   0.81873121 
+    8000   0.99350602   -1.6093282  -0.61706408    1.0032966   -108.00017    1.0369989 
+    9000    1.0130047   -1.6282491  -0.61651065   0.89200717   -133.06372    1.1272589 
+   10000    1.0016704   -1.6170906  -0.61667231    1.0115493   -164.86086    1.1885507 
+   11000   0.99991137   -1.6160496  -0.61738807   0.95811584   -190.62317    1.3389184 
+   12000   0.96344622   -1.5793561   -0.6171142    1.0416296   -221.40727    1.2111221 
+   13000   0.98692912   -1.6022586  -0.61656313    0.9183328    -250.6677    1.4028399 
+   14000    1.0007815   -1.6169097  -0.61737918   0.85210278    -280.3907    1.3446354 
+   15000   0.99742966   -1.6127263   -0.6165434   0.81573578   -308.44839    1.4070968 
+   16000    0.9955551   -1.6105533  -0.61624268   0.88385735   -336.00553    1.3867041 
+   17000   0.98598927   -1.6016934  -0.61693666    1.0601453   -363.09101    1.3716356 
+   18000    0.9827155   -1.5988654  -0.61737831   0.97685532   -391.14488    1.2259196 
+   19000   0.96881647   -1.5839283   -0.6163228    0.9709967   -418.82566    1.2683115 
+   20000    1.0265924   -1.6430234  -0.61771432   0.66156099   -448.12442    1.0964927 
+   21000    1.0001781   -1.6169267  -0.61799878   0.94637366   -477.11852    1.3532793 
+   22000    1.0014617   -1.6170345  -0.61682461   0.89064741   -503.16769    1.2348173 
+   23000   0.98723824   -1.6033256  -0.61732136   0.95636024   -533.04118     1.309259 
+   24000   0.97802015   -1.5945708  -0.61777318    1.1331272   -560.01862    1.3396892 
+   25000   0.98672719   -1.6025172  -0.61702339    1.0225572   -585.97779    1.5256433 
+Loop time of 2.83606 on 1 procs for 20000 steps with 800 atoms
+
+Performance: 3046484.279 tau/day, 7052.047 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    | 1.9431     | 1.9431     | 1.9431     |   0.0 | 68.52
+Neigh   | 0.48329    | 0.48329    | 0.48329    |   0.0 | 17.04
+Comm    | 0.061027   | 0.061027   | 0.061027   |   0.0 |  2.15
+Output  | 0.00022459 | 0.00022459 | 0.00022459 |   0.0 |  0.01
+Modify  | 0.25409    | 0.25409    | 0.25409    |   0.0 |  8.96
+Other   |            | 0.09429    |            |       |  3.32
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    258 ave 258 max 258 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5583 ave 5583 max 5583 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5583
+Ave neighs/atom = 6.97875
+Neighbor list builds = 2363
+Dangerous builds = 0
+
+# data gathering run
+# reset fix viscosity to zero flux accumulation
+
+unfix		4
+fix		4 all viscosity 100 x y 20
+
+variable	visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
+fix		vave all ave/time 1000 1 1000 v_visc ave running start 26000
+
+thermo_style	custom step temp f_4 v_dVx v_visc f_vave
+
+# only need to run for 10000 steps to make a good 100-frame movie
+
+#dump	        1 all custom 100 dump.mp.2d id type x y z vx
+
+#dump		2 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
+#dump_modify	2 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red
+
+run	        50000
+Memory usage per processor = 2.73047 Mbytes
+Step Temp f_4 v_dVx v_visc f_vave 
+   25000   0.98672719            0    1.5256433           -0            0 
+   26000   0.98401533   -25.559065    1.3332094   0.95855405   0.47927702 
+   27000   0.99050741    -53.17367    1.3419843   0.99057919   0.64971108 
+   28000   0.98153807   -83.114662    1.1794868    1.1744467   0.78089498 
+   29000    1.0204966   -110.22215    1.3360187    1.0312556   0.83096712 
+   30000   0.99625662   -133.82368    1.5944344   0.83931757   0.83235886 
+   31000    1.0151551    -158.7453    1.5031209   0.88008718   0.83917719 
+   32000   0.98303358   -184.40723    1.4652847   0.89893417   0.84664681 
+   33000   0.99939957   -210.86096    1.3135851    1.0032703   0.86404943 
+   34000   0.96853185   -235.91032    1.3291636   0.98604334   0.87624882 
+   35000    1.0054026   -267.07311    1.4280769   0.93507957   0.88159707 
+   36000   0.97047213   -290.05846    1.4030844   0.93967798   0.88643714 
+   37000   0.99339602   -317.88469    1.3395274   0.98879613   0.89431091 
+   38000    1.0095839   -339.72956    1.5081424   0.86639838   0.89231716 
+   39000     1.033396   -365.46114    1.4202859   0.91898285   0.89409487 
+   40000    1.0069829   -391.35939    1.4315171   0.91129289   0.89516975 
+   41000    1.0145044   -417.94062    1.5126265   0.86344149   0.89330338 
+   42000   0.99701243   -442.43582    1.3830081   0.94090688   0.89594802 
+   43000     1.011832   -466.04588     1.514607    0.8547246   0.89377837 
+   44000     1.016323   -494.28239    1.4459083   0.89960277   0.89406959 
+   45000    1.0048565   -518.02843    1.4397428   0.89951556   0.89432892 
+   46000   0.99726082   -546.29139    1.2399161    1.0490176   0.90136022 
+   47000    0.9817128    -579.0368    1.2816209     1.026819   0.90681495 
+   48000   0.99883406   -606.89944    1.3508577   0.97667325   0.90972571 
+   49000    1.0327324   -639.80418     1.227321    1.0860446   0.91677847 
+   50000   0.99442217   -668.69881    1.1824503    1.1310391   0.92501927 
+   51000   0.99412485   -695.56436    1.3288051    1.0066366   0.92804213 
+   52000    1.0368955   -724.06214    1.2921091    1.0377265   0.93195943 
+   53000      1.02122   -749.03672    1.5201682      0.87988   0.93016359 
+   54000    1.0304794   -772.90678    1.3994802    0.9522092   0.93089844 
+   55000    1.0150735   -800.69744    1.2226831    1.0914486   0.93607748 
+   56000    1.0066993   -830.92913    1.4581021   0.91914572   0.93554836 
+   57000   0.99054006   -858.94251    1.3736656   0.97701919   0.93680505 
+   58000    1.0300499   -881.47715    1.5995216   0.83498179   0.93381025 
+   59000   0.99187983   -909.58612    1.4692824   0.91039454   0.93314123 
+   60000    1.0116153   -936.80603     1.372993    0.9747277   0.93429641 
+   61000   0.98778111   -966.36841    1.3911445    0.9648015   0.93512087 
+   62000   0.97796351   -996.15306    1.2818309    1.0501797   0.93814874 
+   63000    1.0241007   -1026.5146    1.3364909    1.0106145   0.94000683 
+   64000    1.0447876   -1051.1752    1.4339955   0.93979412   0.94000152 
+   65000     1.013822   -1078.5189    1.5730359   0.85703609   0.93797797 
+   66000    1.0003625   -1104.7839    1.4374578   0.93727789    0.9379613 
+   67000    1.0411074   -1132.5569    1.4426372   0.93459539   0.93788302 
+   68000    1.0005746   -1162.5849    1.2729721     1.061958   0.94070291 
+   69000    1.0032978   -1189.5061    1.4109135   0.95803997   0.94108818 
+   70000     1.003145   -1215.7498    1.4255228   0.94760543   0.94122986 
+   71000    1.0216551   -1244.4852    1.1329731    1.1939394   0.94660666 
+   72000   0.96169183   -1272.9346    1.1024076    1.2283893   0.95247713 
+   73000   0.96956712   -1298.3657    1.3689638   0.98794738   0.95320101 
+   74000    1.0081417   -1327.5255    1.3483851    1.0046224   0.95422944 
+   75000    1.0315254   -1357.3275    1.4937254    0.9086861   0.95333643 
+Loop time of 7.08146 on 1 procs for 50000 steps with 800 atoms
+
+Performance: 3050218.869 tau/day, 7060.692 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    | 4.8558     | 4.8558     | 4.8558     |   0.0 | 68.57
+Neigh   | 1.2027     | 1.2027     | 1.2027     |   0.0 | 16.98
+Comm    | 0.15117    | 0.15117    | 0.15117    |   0.0 |  2.13
+Output  | 0.00069261 | 0.00069261 | 0.00069261 |   0.0 |  0.01
+Modify  | 0.63608    | 0.63608    | 0.63608    |   0.0 |  8.98
+Other   |            | 0.235      |            |       |  3.32
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    273 ave 273 max 273 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5612 ave 5612 max 5612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5612
+Ave neighs/atom = 7.015
+Neighbor list builds = 5873
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1

@@ -0,0 +1,304 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for viscosity of 2d LJ liquid
+# NEMD via fix deform and fix nvt/sllod
+
+# settings
+
+variable	x equal 20
+variable	y equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+variable	srate equal 2.7 # velocity of top edge
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+# problem setup
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox prism 0 $x 0 $y -0.1 0.1 0.0 0.0 0.0
+region          simbox prism 0 20 0 $y -0.1 0.1 0.0 0.0 0.0
+region          simbox prism 0 20 0 20 -0.1 0.1 0.0 0.0 0.0
+create_box      1 simbox
+Created triclinic box = (0 0 -0.182574) to (36.5148 36.5148 0.182574) with tilt (0 0 0)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 800 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 27 27 1
+Memory usage per processor = 2.47956 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0     -0.56617    -1.535262 
+    1000    0.9455393    -1.573329            0  -0.62897162   0.91884199 
+    2000    1.0359047   -1.6229551            0  -0.58834528   0.96136682 
+    3000    1.0171488   -1.5468681            0  -0.53099077    1.1078235 
+    4000    1.0040221   -1.5977142            0  -0.59494717   0.92428924 
+    5000   0.95883045   -1.6087309            0    -0.651099    0.9201564 
+Loop time of 0.896852 on 1 procs for 5000 steps with 800 atoms
+
+Performance: 2408424.088 tau/day, 5575.056 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    | 0.47349    | 0.47349    | 0.47349    |   0.0 | 52.79
+Neigh   | 0.15355    | 0.15355    | 0.15355    |   0.0 | 17.12
+Comm    | 0.017267   | 0.017267   | 0.017267   |   0.0 |  1.93
+Output  | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 |   0.0 |  0.00
+Modify  | 0.2278     | 0.2278     | 0.2278     |   0.0 | 25.40
+Other   |            | 0.0247     |            |       |  2.75
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    266 ave 266 max 266 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5604 ave 5604 max 5604 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5604
+Ave neighs/atom = 7.005
+Neighbor list builds = 548
+Dangerous builds = 0
+
+unfix  	        1
+unfix		2
+
+# turn on NEMD shear and equilibrate some more
+
+velocity	all scale $t
+velocity	all scale 1
+
+# shear rate defined relative to perpendicular dimension
+
+variable	xyrate equal ${srate}/ly
+variable	xyrate equal 2.7/ly
+
+fix		1 all nvt/sllod temp $t $t 0.1
+fix		1 all nvt/sllod temp 1 $t 0.1
+fix		1 all nvt/sllod temp 1 1 0.1
+fix		2 all deform 1 xy erate ${xyrate} remap v
+fix		2 all deform 1 xy erate 0.0739425452631974 remap v
+
+compute         layers all chunk/atom bin/1d y center 0.05 units reduced
+fix		4 all ave/chunk 20 250 5000 layers vx file profile.nemd.2d
+
+compute		usual all temp
+compute		tilt all temp/deform
+
+thermo          1000
+thermo_style	custom step temp c_usual epair etotal press pxy
+thermo_modify	temp tilt
+run		50000
+Memory usage per processor = 2.74501 Mbytes
+Step Temp c_usual E_pair TotEng Press Pxy 
+    5000    2.2074694            1   -1.6087309   0.59597914    1.6684033  -0.13173628 
+    6000   0.93152386    1.0817401   -1.6660819  -0.73572242   0.68318536 -0.028129339 
+    7000    1.0014344    1.1738041   -1.7011099  -0.70092725    0.6084685  -0.14709751 
+    8000     1.025345      1.29299   -1.7011316  -0.67706829   0.58584918  -0.13492866 
+    9000   0.98439625    1.3014301   -1.6432929  -0.66012715   0.78568164   0.03166088 
+   10000   0.94167448     1.304837   -1.6809777  -0.74048031    0.6767415  0.004807405 
+   11000   0.98264458    1.3309352   -1.6681636  -0.68674728   0.74844384 -0.043997826 
+   12000   0.99403655    1.3580131   -1.6369662   -0.6441722   0.86251493  -0.05441449 
+   13000    1.0396869    1.4466214   -1.6285376  -0.59015033   0.85584533 -0.077842666 
+   14000    1.0356564    1.4337041   -1.6284938  -0.59413198   0.86325196  0.021727401 
+   15000   0.97016374    1.4146903   -1.6551162  -0.68616512   0.78678055 -0.067107584 
+   16000   0.94805836    1.4367742   -1.6338511  -0.68697777    0.8447822  -0.11723973 
+   17000    0.9784648    1.4621496   -1.6203417  -0.64309998   0.93704401 -0.070556149 
+   18000    1.0180917    1.5223337   -1.6393062  -0.62248714   0.81117394  -0.21773149 
+   19000    1.0186815    1.5716289   -1.6471996  -0.62979147   0.71667451 -0.091605896 
+   20000    0.9743659    1.5914706   -1.6150957  -0.64194775   0.94267754 -0.034378699 
+   21000    1.0482265    1.5882157   -1.6319486  -0.58503242   0.86464563  -0.30608617 
+   22000    1.0372488    1.6614229    -1.618808  -0.58285576    0.9619593  0.030218471 
+   23000      1.02322     1.605947   -1.6128071   -0.5908661   0.89153388 -0.054926254 
+   24000   0.99202826    1.6263761   -1.6309182     -0.64013   0.82035209  -0.15760707 
+   25000   0.96842077    1.6079837   -1.6514188   -0.6842086   0.74289154  -0.15054022 
+   26000    1.0131182    1.6599526   -1.6282941  -0.61644236   0.79717592  -0.17392393 
+   27000   0.99274208    1.6992131   -1.6141775   -0.6226763   0.87559226 -0.025698533 
+   28000    1.0124353     1.682322   -1.6350699  -0.62390012   0.81863458  -0.10578616 
+   29000    1.0159913    1.7444965    -1.670694  -0.65597278   0.77422638 -0.074417391 
+   30000   0.95757504    1.6770477   -1.6100645  -0.65368638   0.84900509  -0.13811335 
+   31000    0.9882106    1.7024812   -1.6135646  -0.62658928    0.8819342 -0.0083109839 
+   32000   0.94243022     1.665312   -1.6173333  -0.67608112    1.0312796 -0.087350514 
+   33000   0.97629132     1.804652   -1.6148954  -0.63982441   0.73933894 -0.010842321 
+   34000   0.96053868     1.768861   -1.6201954  -0.66085743   0.80440002 -0.0098573375 
+   35000   0.96192532    1.7951878   -1.5904258  -0.62970292   0.98930679  0.061382767 
+   36000     1.034984     1.835204   -1.5872923  -0.55360202    1.1673704 -0.086610164 
+   37000    1.0109946    1.8695414   -1.5899371  -0.58020627    1.0247304 -0.081320896 
+   38000    1.0189063    1.9299754    -1.591087  -0.57345437    1.0238951  -0.12903934 
+   39000   0.96964269    1.8518181   -1.5939152  -0.62548456     1.064667  -0.12625393 
+   40000   0.93813023    1.8601846   -1.5808497  -0.64389211    1.0739269  -0.21342957 
+   41000      1.01992    1.9192923   -1.6087202  -0.59007511   0.96050424   -0.3264004 
+   42000    1.0243282    1.9429183   -1.5918401  -0.56879229    1.1845661 -0.062971629 
+   43000    1.0696065    2.0074757   -1.5973264  -0.52905692   0.90524954  -0.12923233 
+   44000    1.0338542    1.9624549   -1.6079246  -0.57536268    1.0536815  0.070524993 
+   45000   0.95583069     1.945773   -1.6279372  -0.67330128   0.74985796  -0.17325375 
+   46000   0.99732695     1.966957    -1.631205   -0.6351247   0.77350616   -0.1852725 
+   47000    1.0135329    2.0107676   -1.6049852  -0.59271924   0.87782961  -0.20632054 
+   48000   0.98735917    1.9771245   -1.6053591  -0.61923413   0.92710662 -0.0002501296 
+   49000   0.99618418    1.9493979   -1.6066882  -0.61174922   0.89595133  -0.20337142 
+   50000    1.0651949    2.0467535   -1.6074294  -0.54356601   0.99645561 -0.099150393 
+   51000    1.0559004    2.0710034   -1.5978367  -0.54325617   0.99030671   -0.1841017 
+   52000    1.0083619    2.0399634   -1.5973313   -0.5902299    1.1130916 -0.0079150985 
+   53000    1.0118925    2.0439094   -1.5896233  -0.57899564    1.1640067 -0.053482574 
+   54000    1.0162238    2.0117062   -1.6173202  -0.60236666   0.92299331  -0.13080758 
+   55000    1.0101742    2.0023882   -1.5870609  -0.57814937    1.0166974   -0.2462163 
+Loop time of 12.3385 on 1 procs for 50000 steps with 800 atoms
+
+Performance: 1750615.444 tau/day, 4052.351 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    | 5.0133     | 5.0133     | 5.0133     |   0.0 | 40.63
+Neigh   | 3.262      | 3.262      | 3.262      |   0.0 | 26.44
+Comm    | 0.29422    | 0.29422    | 0.29422    |   0.0 |  2.38
+Output  | 0.0017447  | 0.0017447  | 0.0017447  |   0.0 |  0.01
+Modify  | 3.4226     | 3.4226     | 3.4226     |   0.0 | 27.74
+Other   |            | 0.3447     |            |       |  2.79
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    282 ave 282 max 282 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5602 ave 5602 max 5602 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5602
+Ave neighs/atom = 7.0025
+Neighbor list builds = 11232
+Dangerous builds = 0
+
+# data gathering run
+
+variable	visc equal -pxy/(v_srate/ly)
+fix		vave all ave/time 10 100 1000 v_visc ave running start 56000
+
+thermo_style	custom step temp press pxy v_visc f_vave
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
+thermo_modify	temp tilt
+
+# only need to run for 5400 steps to make a good 100-frame movie
+# set 54K steps above in equil and 5400 here simply to make good movie
+# 54K and 5400 are multiples of box-swap periodicity = 2700 steps
+
+#dump	        1 all custom 50 dump.nemd.2d id type x y z vx
+
+#dump		2 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
+#dump_modify	2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
+
+run		50000
+Memory usage per processor = 2.75392 Mbytes
+Step Temp Press Pxy v_visc f_vave 
+   55000    1.0101742    1.0168023  -0.24961054    3.3757364            0 
+   56000   0.95430669   0.99109494  -0.11503816    1.5557777   0.73512854 
+   57000   0.96493583   0.77019161  0.032071381   -0.4337338   0.69832329 
+   58000     1.043882     1.190321   -0.1948503    2.6351582    0.7662455 
+   59000   0.99522262   0.71653967 -0.056810457    0.7683054   0.87054399 
+   60000    1.0147329    1.0803743  -0.13097761    1.7713431    0.8832817 
+   61000   0.93812211    1.0627199 -0.044643317   0.60375683   0.96513251 
+   62000    1.0107288   0.93643991  -0.07289428   0.98582325   0.99515995 
+   63000    1.0516762     1.206755  -0.12107833     1.637465    1.0476529 
+   64000   0.96288473   0.99015782 -0.040632073   0.54950872    1.0857708 
+   65000   0.96981457    1.1393466  0.081769326   -1.1058495    1.0598383 
+   66000    1.0549734    0.9862292 -0.038519333   0.52093599    1.0631279 
+   67000    1.0597179    1.0849355  0.026292892  -0.35558543    1.0560538 
+   68000    1.0260974   0.95293785  0.049285149  -0.66653304    1.0367987 
+   69000    1.0075299    1.0303201  0.041539329  -0.56177846    1.0467854 
+   70000    1.0622593    1.2021547  -0.20731618    2.8037469    1.0667574 
+   71000   0.99847432    1.0509829  -0.15346894     2.075516    1.0655178 
+   72000   0.97453232   0.97670205  -0.22406814    3.0303006    1.0503175 
+   73000    0.9641619   0.89104495  -0.12889334    1.7431553    1.0532335 
+   74000   0.99089222    1.0444418   0.18074575    -2.444408    1.0546561 
+   75000   0.99756998   0.91703128  -0.21829649    2.9522447     1.065423 
+   76000   0.93605182   0.98651769  -0.20794378    2.8122346    1.0798472 
+   77000   0.94258356   0.95471193  -0.14211735    1.9219969    1.0819944 
+   78000    0.9798062    1.2187257 -0.063527885   0.85915199    1.1001509 
+   79000   0.96451401   0.84225692 -0.025071518   0.33906755    1.0969807 
+   80000   0.95011391    1.0570755  -0.11124947    1.5045394    1.1031908 
+   81000   0.99774906   0.96668849 -0.0053084468  0.071791507    1.1312113 
+   82000   0.98889022    0.8762984  0.071585243  -0.96811981    1.1334001 
+   83000   0.93610495    1.0660717 -0.047681336   0.64484304    1.1299719 
+   84000    1.0072593    1.0286446  -0.21827159     2.951908    1.1400137 
+   85000    1.0128434    1.0894592 -0.094017511    1.2714941    1.1421825 
+   86000    1.0193552   0.99088304 -0.057046347   0.77149558    1.1372979 
+   87000   0.92702641   0.88034638 -0.012355342   0.16709381    1.1311508 
+   88000   0.98946493   0.81515436  0.016806513  -0.22729152    1.1379472 
+   89000   0.99799875    1.0151454 -0.084127501    1.1377415    1.1352016 
+   90000   0.99133716   0.86655201 -0.056333485   0.76185483    1.1447978 
+   91000   0.94330916   0.93345911  -0.12219086    1.6525109    1.1417404 
+   92000   0.94909987    1.0726222  -0.26976121    3.6482544    1.1573797 
+   93000   0.99526745    1.0680147   -0.1142234    1.5447588    1.1646702 
+   94000    1.0018217    1.1512259  -0.19659509    2.6587547    1.1604884 
+   95000    0.9686519    1.0577224 -0.055162686   0.74602092    1.1618973 
+   96000   0.97493046   0.96044751  0.050456814  -0.68237864    1.1574483 
+   97000   0.97351913    1.0981546  -0.16357534    2.2121952    1.1677946 
+   98000    1.0157509   0.97339707  -0.13441353    1.8178105    1.1778369 
+   99000    1.0414889    1.0103719  -0.10696881    1.4466477    1.1823616 
+  100000    1.0249428    1.0036886  -0.27447626    3.7120207    1.1792453 
+  101000   0.96960692   0.94692891 -0.053860891   0.72841544    1.1752286 
+  102000    1.0371247    1.0840917 -0.040114754   0.54251249    1.1644228 
+  103000   0.96769028    1.0471324  -0.07971043    1.0780049    1.1657168 
+  104000   0.96896685    1.0326732  -0.23873693    3.2286815     1.162545 
+  105000    1.0122807   0.97927614 -0.068569604   0.92733627    1.1684457 
+Loop time of 12.8562 on 1 procs for 50000 steps with 800 atoms
+
+Performance: 1680117.354 tau/day, 3889.161 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    | 5.0725     | 5.0725     | 5.0725     |   0.0 | 39.46
+Neigh   | 3.5621     | 3.5621     | 3.5621     |   0.0 | 27.71
+Comm    | 0.31528    | 0.31528    | 0.31528    |   0.0 |  2.45
+Output  | 0.00097895 | 0.00097895 | 0.00097895 |   0.0 |  0.01
+Modify  | 3.5411     | 3.5411     | 3.5411     |   0.0 | 27.54
+Other   |            | 0.3643     |            |       |  2.83
+
+Nlocal:    800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    283 ave 283 max 283 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5585 ave 5585 max 5585 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5585
+Ave neighs/atom = 6.98125
+Neighbor list builds = 12225
+Dangerous builds = 0
+Total wall time: 0:00:26

examples/VISCOSITY/log.13Oct16.wall.2d.g++.1

@@ -0,0 +1,246 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for viscosity of 2d LJ liquid
+# use shearing wall, thermostat via fix langevin
+
+# settings
+
+variable	x equal 20
+variable	y equal 20
+variable	ylo equal -2.5
+variable	yhi equal 23
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+variable	srate equal 2.7
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x ${ylo} ${yhi} -0.1 0.1
+region          simbox block 0 20 ${ylo} ${yhi} -0.1 0.1
+region          simbox block 0 20 -2.5 ${yhi} -0.1 0.1
+region          simbox block 0 20 -2.5 23 -0.1 0.1
+create_box      3 simbox
+Created orthogonal box = (0 -4.56435 -0.182574) to (36.5148 41.9921 0.182574)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 1020 atoms
+
+mass            * 1.0
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+region		lower block INF INF INF 0.0 INF INF
+region		upper block INF INF $y INF INF INF
+region		upper block INF INF 20 INF INF INF
+group		lower region lower
+120 atoms in group lower
+group		upper region upper
+120 atoms in group upper
+set		group lower type 2
+  120 settings made for type
+set		group upper type 3
+  120 settings made for type
+group		wall union lower upper
+240 atoms in group wall
+group		flow subtract all wall
+780 atoms in group flow
+
+velocity        flow create $t 97287
+velocity        flow create 1 97287
+velocity	upper set ${srate} 0.0 0.0 units box
+velocity	upper set 2.7 0.0 0.0 units box
+
+compute		thermal flow temp/partial 0 1 0
+compute		flow flow temp
+
+fix             1 all nve
+fix	        2 flow langevin $t $t 0.1 498094
+fix	        2 flow langevin 1 $t 0.1 498094
+fix	        2 flow langevin 1 1 0.1 498094
+fix_modify      2 temp thermal
+
+fix		3 wall setforce 0.0 0.0 0.0
+
+compute         layers all chunk/atom bin/1d y center 0.05 units reduced
+fix		4 all ave/chunk 20 500 10000 layers vx file profile.wall.2d
+
+fix	        5 all enforce2d
+
+# equilibration run
+
+variable        ybox equal $y*ylat
+variable        ybox equal 20*ylat
+compute		tilt flow temp/ramp vx 0 ${srate} y 0 ${ybox} units box
+compute		tilt flow temp/ramp vx 0 2.7 y 0 ${ybox} units box
+compute		tilt flow temp/ramp vx 0 2.7 y 0 36.5148371670111 units box
+
+thermo          1000
+thermo_style	custom step temp c_tilt epair etotal press pxy
+
+run	        20000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 27 34 1
+Memory usage per processor = 2.7306 Mbytes
+Step Temp c_tilt E_pair TotEng Press Pxy 
+       0    1.1937193    2.1893943   -1.4419854  -0.24943634  -0.78936698  0.014349737 
+    1000    1.3454512    1.9300306   -1.5968842  -0.25275207   0.66766599  -0.14162185 
+    2000    1.4039195    1.7346977   -1.5342235  -0.13168039    1.0083734  0.018811845 
+    3000    1.3945539    1.6038724   -1.5472166  -0.15402987   0.89714673  -0.21459294 
+    4000    1.4507445    1.5640577   -1.5682837  -0.11896142   0.80780492  -0.11602642 
+    5000    1.5081166    1.5260484   -1.4466585  0.059979546    1.5213379   0.15651364 
+    6000     1.471403    1.3275791   -1.5730732  -0.10311276   0.76780953 -0.028043991 
+    7000    1.5811576    1.3851463   -1.5518076  0.027799848    1.0149281  0.004725238 
+    8000    1.5298095    1.3333038    -1.536974 -0.0086643578    1.2325979  -0.11754624 
+    9000    1.5269137     1.253444   -1.5995915 -0.074174772   0.72678912  0.068344793 
+   10000    1.6201621    1.2415469   -1.4659459   0.15262788    1.4780324   0.12762214 
+   11000    1.6422795    1.2595346   -1.5659612  0.074708257    1.0471534 -0.039697954 
+   12000    1.7111306    1.1978075   -1.5685671   0.14088596   0.97371007  0.099889098 
+   13000    1.6871075    1.1495076   -1.4967158   0.18873768    1.3445558 -0.058891196 
+   14000    1.7237433    1.1976445   -1.5857394   0.13631394   0.96603231  0.082195882 
+   15000    1.7080799    1.1550766   -1.4962561   0.21014912    1.3733324  0.062008565 
+   16000    1.7030363    1.1186642   -1.5735945   0.12777215    1.0071474  -0.12038271 
+   17000    1.7442786    1.1134856   -1.5544631   0.18810536   0.98640596  -0.10793154 
+   18000    1.7433517    1.0565945   -1.4702226   0.27141996    1.5983127   -0.1847178 
+   19000    1.7909641     1.071494   -1.5628363   0.22637195    1.0487763  -0.16215298 
+   20000    1.8291721    1.1152277   -1.4955372   0.33184161    1.4404718   0.13157652 
+Loop time of 4.60977 on 1 procs for 20000 steps with 1020 atoms
+
+Performance: 1874278.390 tau/day, 4338.607 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    | 2.2771     | 2.2771     | 2.2771     |   0.0 | 49.40
+Neigh   | 0.77127    | 0.77127    | 0.77127    |   0.0 | 16.73
+Comm    | 0.08461    | 0.08461    | 0.08461    |   0.0 |  1.84
+Output  | 0.00045896 | 0.00045896 | 0.00045896 |   0.0 |  0.01
+Modify  | 1.3487     | 1.3487     | 1.3487     |   0.0 | 29.26
+Other   |            | 0.1277     |            |       |  2.77
+
+Nlocal:    1020 ave 1020 max 1020 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    319 ave 319 max 319 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    6977 ave 6977 max 6977 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6977
+Ave neighs/atom = 6.8402
+Neighbor list builds = 3091
+Dangerous builds = 0
+
+# data gathering run
+
+variable	visc equal -pxy/(v_srate/ly)
+fix		vave all ave/time 1000 1 1000 v_visc ave running
+
+thermo_style	custom step temp pxy v_visc f_vave
+thermo_modify	temp tilt
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+
+# only need to run for 5000 steps to make a good 100-frame movie
+
+#dump	        1 all custom 50 dump.wall.2d id type x y z vx
+
+#dump		2 all image 50 image.*.jpg vx type zoom 1.6 adiam 1.2
+#dump_modify	2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
+
+run		50000
+Memory usage per processor = 2.73133 Mbytes
+Step Temp Pxy v_visc f_vave 
+   20000    1.1152277   0.14873839   -2.5647136   -2.5647136 
+   21000    1.0675243 -0.064336523    1.1093622  -0.72767568 
+   22000    1.1044647 -0.092189802    1.5896396  0.044762746 
+   23000    1.0278193  -0.16030404    2.7641414   0.72460741 
+   24000     1.032998 -0.025162118   0.43387337    0.6664606 
+   25000     1.012257   0.15289388   -2.6363671   0.11598931 
+   26000    1.0678095  -0.15317374    2.6411929   0.47673268 
+   27000   0.99951185 -0.013635884   0.23512515   0.44653174 
+   28000    1.0663423 -0.061009474    1.0519935   0.51380527 
+   29000    1.0753719 -0.037018843   0.63832026   0.52625677 
+   30000    1.0749259 -0.0092916614   0.16021721   0.49298044 
+   31000    1.0171594  -0.14103555    2.4318926   0.65455646 
+   32000    1.0811717  -0.22037237    3.7999068   0.89650648 
+   33000    1.0123567 -0.076368085    1.3168239   0.92652915 
+   34000    1.0923478 -0.017551868   0.30264892   0.88493714 
+   35000    1.0252013 0.0042522796 -0.073322558   0.82504591 
+   36000    1.0205412  -0.17942577    3.0938596   0.95850554 
+   37000     1.016861  -0.15185242    2.6184092    1.0507224 
+   38000    1.0156825 -0.058057333    1.0010894    1.0481101 
+   39000    1.0299458 -0.028138186   0.48519005    1.0199641 
+   40000    1.0109947  0.069370747   -1.1961679   0.91443404 
+   41000   0.99255941  -0.20057649    3.4585639    1.0300763 
+   42000   0.93280953  -0.20797609    3.5861562    1.1412102 
+   43000   0.98040039  0.070643632   -1.2181165    1.0429049 
+   44000     1.001795  -0.06620924    1.1416537    1.0468549 
+   45000   0.96231963  0.028026245  -0.48325983   0.98800432 
+   46000    1.0193639  -0.15553891    2.6819757     1.050744 
+   47000    1.0241202 0.0053565438 -0.092363514    1.0099187 
+   48000    0.9736932   0.12643935   -2.1802085   0.89991435 
+   49000   0.96326617  -0.14719163    2.5380426   0.95451862 
+   50000   0.99008772   0.03563038  -0.61437884   0.90390903 
+   51000    1.0689018  -0.11122259    1.9178243   0.93559388 
+   52000    1.0123467  0.021882959  -0.37733044   0.89580829 
+   53000    1.0075671   0.20840798   -3.5936033   0.76376678 
+   54000   0.97454265 -0.027528034   0.47466913   0.75550684 
+   55000    1.0072632  -0.02991098   0.51575854   0.74884717 
+   56000   0.94706748  -0.29624115     5.108121   0.86666538 
+   57000    1.0411989 -0.043160809   0.74422691   0.86344332 
+   58000    1.0040809   0.10858868   -1.8724074    0.7932933 
+   59000    1.0101096  -0.17512944    3.0197775    0.8489554 
+   60000   0.97394086  0.025630293  -0.44194616      0.81747 
+   61000   0.97631407  -0.21776922    3.7550203   0.88741167 
+   62000    0.9650689 -0.036733674   0.63340305   0.88150449 
+   63000    1.0401136   0.11852825   -2.0437965   0.81502038 
+   64000   0.99261276  -0.20362786    3.5111792   0.87493502 
+   65000    1.0397086 -0.056685607   0.97743658   0.87716332 
+   66000    1.0115793  -0.20411863    3.5196415   0.93338626 
+   67000    1.1243059 -0.086897372    1.4983816   0.94515699 
+   68000    1.0005962  0.081847197   -1.4113008   0.89706602 
+   69000    1.0412065  -0.21375629    3.6858249   0.95284119 
+   70000   0.97952466 -0.060208765    1.0381868   0.95451464 
+Loop time of 11.6259 on 1 procs for 50000 steps with 1020 atoms
+
+Performance: 1857923.682 tau/day, 4300.749 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    | 5.6901     | 5.6901     | 5.6901     |   0.0 | 48.94
+Neigh   | 2.0175     | 2.0175     | 2.0175     |   0.0 | 17.35
+Comm    | 0.21634    | 0.21634    | 0.21634    |   0.0 |  1.86
+Output  | 0.00069594 | 0.00069594 | 0.00069594 |   0.0 |  0.01
+Modify  | 3.3775     | 3.3775     | 3.3775     |   0.0 | 29.05
+Other   |            | 0.3236     |            |       |  2.78
+
+Nlocal:    1020 ave 1020 max 1020 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    332 ave 332 max 332 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    6969 ave 6969 max 6969 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6969
+Ave neighs/atom = 6.83235
+Neighbor list builds = 8088
+Dangerous builds = 0
+Total wall time: 0:00:16

examples/VISCOSITY/log.1Feb14.gk.2d.g++.1

@@ -1,386 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for viscosity of 2d LJ liquid
-# Green-Kubo method via fix ave/correlate
-
-# settings
-
-variable	x equal 20
-variable	y equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-variable    p equal 400     # correlation length
-variable    s equal 5       # sample interval
-variable    d equal $p*$s   # dump interval
-variable    d equal 400*$s   
-variable    d equal 400*5   
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 20 0 $y -0.1 0.1
-region          simbox block 0 20 0 20 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
-  1 by 1 by 1 MPI processor grid
-create_atoms    1 box
-Created 800 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-# equilibration run
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-thermo          $d
-thermo          2000
-run	        10000
-Memory usage per processor = 2.06394 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0     -0.56617    -1.535262 
-    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
-    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
-    6000    1.0384043   -1.6029205            0   -0.5658142   0.82862869 
-    8000    1.0288194   -1.5760462            0  -0.54851284    1.1299693 
-   10000   0.97521893   -1.5752855            0  -0.60128557    1.0982639 
-Loop time of 1.72441 on 1 procs for 10000 steps with 800 atoms
-
-Pair  time (%) = 0.929897 (53.9255)
-Neigh time (%) = 0.203868 (11.8225)
-Comm  time (%) = 0.0357857 (2.07524)
-Outpt time (%) = 5.60284e-05 (0.00324913)
-Other time (%) = 0.554805 (32.1736)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    261 ave 261 max 261 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5617 ave 5617 max 5617 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5617
-Ave neighs/atom = 7.02125
-Neighbor list builds = 1101
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1
-
-unfix		2
-
-# Green-Kubo viscosity calculation
-
-reset_timestep  0
-
-variable         pxy equal pxy
-
-fix              SS all ave/correlate $s $p $d                  v_pxy type auto file profile.gk.2d ave running
-fix              SS all ave/correlate 5 $p $d                  v_pxy type auto file profile.gk.2d ave running
-fix              SS all ave/correlate 5 400 $d                  v_pxy type auto file profile.gk.2d ave running
-fix              SS all ave/correlate 5 400 2000                  v_pxy type auto file profile.gk.2d ave running
-
-variable         scale equal 1.0/$t*vol*$s*dt
-variable         scale equal 1.0/1*vol*$s*dt
-variable         scale equal 1.0/1*vol*5*dt
-variable         v11 equal trap(f_SS[3])*${scale}
-variable         v11 equal trap(f_SS[3])*33.3333333333333
-
-thermo_style     custom step temp press pxy v_v11
-
-run              500000
-Memory usage per processor = 2.06394 Mbytes
-Step Temp Press Pxy v11 
-       0            1    1.1131139 -0.062970733  0.066088554 
-    2000    1.0080895    1.0200888  -0.11243616   -1.2606591 
-    4000   0.99653513    1.0745982 -0.0075361431   -1.2260153 
-    6000     1.015614    1.0288859 -0.045052789    2.2423387 
-    8000    1.0480587    1.0090528  -0.16941968    1.4483022 
-   10000    1.0340413    0.8935734 -0.016265599     1.367264 
-   12000    1.0208142   0.98827028 -0.098494798   0.96391762 
-   14000    1.0063108    1.1900869  0.041555635   0.71920668 
-   16000    1.0104133    1.0341648  -0.08539107   0.87216885 
-   18000    1.0324239   0.78956816 -0.022393354   0.99812938 
-   20000   0.98065939    1.1290253  0.088823616   0.86856675 
-   22000    1.0456522   0.79585972  -0.10649734    1.3811196 
-   24000    1.0120651    1.0552123   0.21725489     1.648588 
-   26000    1.0441983     0.959829 0.0053239549    1.6192642 
-   28000    0.9936521    1.1033308 -0.0013213764    1.4830182 
-   30000    1.0106141    1.0845812  0.048019524    1.3015283 
-   32000    1.0138237   0.96535384  -0.18328359    1.1659494 
-   34000   0.99897229    1.2265577 -0.057168503    1.3064819 
-   36000   0.98508691    1.1289173  -0.18839382    1.5336228 
-   38000    1.0419001   0.79249301  -0.20846158    1.4200528 
-   40000    1.0152017   0.98214979 -0.0067504119    1.3792256 
-   42000    1.0113905    1.0421477 -0.047659129    1.3414456 
-   44000    1.0201365     1.112008   0.01373301    1.3159903 
-   46000     1.018482   0.93142144  -0.10476936    1.3358778 
-   48000    1.0362661   0.77862744 -0.073200405    1.2925615 
-   50000    1.0200063   0.96817572 -0.082635361    1.2477558 
-   52000     1.018602    1.0281262  0.059387055     1.253828 
-   54000    1.0465938   0.78372671  -0.04203004    1.2411918 
-   56000    1.0376258     1.031501 -0.043675881    1.3662686 
-   58000   0.97830162     1.239229  0.033252127    1.2677821 
-   60000   0.99938589    1.2023844   0.05306354     1.191899 
-   62000     1.010291   0.93962979  0.047429505    1.0726624 
-   64000    1.0233048   0.93855809   0.17161686    1.0641676 
-   66000    1.0124208    1.0309115 -0.0040419968    1.0550472 
-   68000   0.98507874    1.0281731 -0.090367158     1.070317 
-   70000    1.0012103    1.0065752   0.11646809    1.2306811 
-   72000    1.0257593   0.94487824  0.047164906    1.2402116 
-   74000   0.99773444    1.0006634  -0.16947105    1.3458531 
-   76000   0.99053502    1.1802621 -0.011315672    1.4050256 
-   78000    1.0266873   0.92896952  0.053862201    1.4183056 
-   80000    1.0181396    1.0028774   -0.1669873    1.3918642 
-   82000    1.0183891    1.0045513   0.12750581    1.3598925 
-   84000    1.0054008    1.1361355   0.11127961    1.3235664 
-   86000    1.0153982    1.0270658  0.032996007     1.244148 
-   88000    1.0089441   0.94065248  -0.14958385    1.2504534 
-   90000    1.0090826   0.96386446   0.04002849      1.19906 
-   92000   0.98701529    1.0170739  0.048669738     1.230085 
-   94000    1.0271895   0.90965645   0.16524668    1.2111807 
-   96000    1.0588564   0.64666046 -0.012052311    1.1865422 
-   98000      1.01362      1.02233  0.015426298     1.198456 
-  100000   0.99253832    1.1498855  -0.11430916    1.1821222 
-  102000    1.0260594    0.8604477 -0.038050842    1.1482599 
-  104000    1.0248424    1.0639555  -0.08295859    1.1390154 
-  106000    1.0069076    1.2491555  0.010334731    1.1352025 
-  108000    1.0350323    0.9938777  0.028015622    1.1395354 
-  110000    1.0090965    1.0811591 -0.069761835    1.1641264 
-  112000   0.98126774    1.2677506   0.03105149    1.1417489 
-  114000    1.0053548      1.05943 -0.053492802    1.1435347 
-  116000    1.0116531    1.1377687   0.08984011    1.1290702 
-  118000    1.0441155   0.94024004  0.069880409    1.1352496 
-  120000   0.99682009    1.1603848  -0.09404725    1.2100588 
-  122000    1.0155742    1.0078645 -0.027651839     1.173532 
-  124000   0.99222072    1.1821546   -0.0308041    1.2037919 
-  126000    1.0405098     1.155637  0.030664374    1.1715576 
-  128000    1.0187941   0.98070733 0.0059064696    1.2064639 
-  130000    1.0399447   0.99686501   0.14875158      1.26474 
-  132000    1.0409005    1.0086593  0.021338889    1.2817848 
-  134000    1.0476219    0.8026445  0.036028195     1.269031 
-  136000    1.0361278   0.82017002   0.12410098    1.2516208 
-  138000    1.0118377     1.017853 -0.051473869    1.2497683 
-  140000    1.0150827    1.0187598 -0.021626098    1.2422255 
-  142000    1.0299632   0.85581133 0.0020789713    1.3028929 
-  144000    1.0299864   0.75409682  0.067708051    1.2807235 
-  146000    1.0300343   0.95486967  -0.12805174    1.2639701 
-  148000   0.99833371    1.0636801 -0.012957113    1.2450247 
-  150000    1.0218031    1.0345594 -0.0076210772     1.238176 
-  152000    1.0166582     1.000406  0.048913573    1.2350809 
-  154000    1.0200436    0.9620376  0.016990704    1.2277908 
-  156000    1.0174714   0.97523697 -0.089095058    1.2333756 
-  158000    1.0057212   0.98373273   0.10571489    1.2207665 
-  160000    1.0116139    1.0531268  0.040970831    1.1908489 
-  162000    1.0141586   0.97503702  -0.12255418    1.1835675 
-  164000   0.96779259    1.1194358   0.17756759    1.1540165 
-  166000    1.0009628    1.1253418  0.050763812     1.141318 
-  168000   0.99014049    1.1155831  -0.14569673    1.1317473 
-  170000    1.0298577   0.98702864 -0.00084160851    1.1904372 
-  172000    1.0202995   0.96163813 0.0045819305    1.1873872 
-  174000    1.0359389   0.89018321  0.011677378    1.1807412 
-  176000    1.0256185    1.0300041   0.02536302    1.1857003 
-  178000    1.0271101    1.0152692  -0.13910986    1.2068771 
-  180000    1.0194759   0.87873048  -0.12169124    1.1850476 
-  182000    1.0319658    1.0033092 -0.095869229    1.1660609 
-  184000    1.0078723    1.2412606 -0.049703306    1.1654829 
-  186000    1.0442603   0.79824994 -0.093218879    1.1463494 
-  188000    1.0004515   0.90810497 -0.048680818    1.1105332 
-  190000     1.000942   0.94373473   0.10613178    1.1009497 
-  192000     1.048449   0.97658358  -0.17712897    1.1263395 
-  194000    1.0290391   0.98531851 -0.012106089    1.0921536 
-  196000    1.0315571    1.1564407  0.057141413    1.0858253 
-  198000    1.0142691    1.0606813  0.029671093    1.0716634 
-  200000    1.0456713   0.84981128   0.11494717    1.0676611 
-  202000    1.0260155    1.0217822 -0.040530429    1.0674862 
-  204000   0.99472169    1.1602851 0.0051321303    1.0579412 
-  206000    1.0014916    1.0461488 0.0060656173    1.0549157 
-  208000    1.0022353    1.0846052  -0.11185825    1.0596996 
-  210000     1.015275    1.0276323 -0.030737448    1.0550317 
-  212000    1.0039546    1.1104646   0.10845813    1.0540841 
-  214000     1.007432     1.024032  -0.11046904    1.0455342 
-  216000   0.99740694     1.140278 -0.065900867     1.048484 
-  218000    1.0237293   0.94527063  -0.20653618    1.0406664 
-  220000    1.0069562    1.1273839 -0.0067054642    1.0387632 
-  222000    1.0342064    1.0131146  0.035157231    1.0296557 
-  224000     1.003096    1.0550729   0.03305911       1.0335 
-  226000    1.0144191    1.0049718  0.042900611    1.0650019 
-  228000    1.0268793   0.90872396  -0.17661877    1.0602896 
-  230000    1.0237908   0.98063448 -0.029475684    1.0685714 
-  232000    1.0069934    1.1044794   0.13426396    1.0662281 
-  234000   0.98863378   0.95248555 -0.024211245    1.0765215 
-  236000    1.0134171    1.0478432  -0.17292923    1.0525098 
-  238000    1.0120921   0.99042234  0.025333354    1.0420108 
-  240000    1.0042316    1.1071855  -0.02061948    1.0468243 
-  242000    1.0086548    1.0773029  -0.10892118    1.0462304 
-  244000    1.0016487    1.0120587  -0.11220572    1.0530018 
-  246000    1.0206702   0.96270397  0.076386758    1.0399964 
-  248000    1.0106322   0.97979007 -0.056885564    1.0285937 
-  250000    1.0521704   0.90240063 -0.098004463    1.0680676 
-  252000    1.0031792    1.1298376  -0.12700293    1.0572962 
-  254000    1.0023361    1.0397687 -0.042138767     1.055246 
-  256000    1.0207399   0.99843942 -0.067694614    1.0678481 
-  258000   0.98874431     1.228494  0.040793426    1.0558317 
-  260000    1.0183455    1.0188006  -0.17725132    1.0629806 
-  262000    1.0018425   0.94317435   0.10076842    1.0548939 
-  264000    1.0166318    0.8436724 -0.056681878    1.0488651 
-  266000    1.0091103    1.0775158  0.028771667    1.0371622 
-  268000    1.0013292   0.95251758 -0.050343862    1.0496861 
-  270000   0.99674492    1.1472622  -0.11346408    1.1092918 
-  272000    1.0049198    1.0673533 -0.064343803    1.0881727 
-  274000    1.0303169   0.97093144 -0.010278759    1.0846913 
-  276000    1.0273615   0.84473644 -0.017151036    1.0688783 
-  278000    1.0127363    1.2089228 -0.039397817    1.0875618 
-  280000   0.98505511    1.1212088  -0.04261016    1.0843387 
-  282000    1.0210332   0.93982023  -0.11219324    1.0790461 
-  284000    1.0157606    1.0203143 0.0002164565    1.0721431 
-  286000    1.0062366    1.0025507  -0.16786234    1.0720064 
-  288000   0.98467873    1.2326624 -0.081203997    1.0660396 
-  290000    1.0099975   0.88882236 -0.031064103    1.0590327 
-  292000    1.0122416    1.0611548 -0.022475529    1.0519549 
-  294000    1.0104116    1.0266518  -0.10512697    1.0414083 
-  296000    1.0034132    1.0427754 -0.014337433    1.0415291 
-  298000    1.0171588   0.92899734   0.10623709    1.0432266 
-  300000    1.0280222    1.0524269  0.079178549    1.0534846 
-  302000     1.035771   0.87031074  0.029223556    1.0548035 
-  304000   0.99817826   0.96586889 -0.092577945     1.051271 
-  306000   0.99961879    1.1082249 -0.079054344    1.0495721 
-  308000    1.0136108    1.0992365  -0.11696242    1.0384906 
-  310000   0.99316114    1.0758087  0.067733542    1.0276102 
-  312000    1.0106481   0.99751609  0.096323719    1.0260196 
-  314000    1.0069421    1.0474061 -0.0071188531    1.0257001 
-  316000    1.0401836   0.81939716 -0.088499972    1.0302389 
-  318000    1.0095707    1.1018438 -0.0069997734    1.0318989 
-  320000    1.0316135     1.003588  0.010687649    1.0262453 
-  322000     1.009186   0.93116391   0.02270494    1.0207195 
-  324000    1.0186856    1.0207355 -0.049273034    1.0315045 
-  326000    1.0496148    0.9479271 -0.019377803    1.0186608 
-  328000    1.0280164   0.83246382 -0.067199824    1.0121899 
-  330000    1.0292958   0.96946051 -0.0067323294    1.0106087 
-  332000    1.0118055   0.94580297   -0.1158678   0.99982007 
-  334000    1.0090884    1.1414243 -0.082638749   0.98931612 
-  336000   0.96668553    1.2041384 0.0042176058   0.98213644 
-  338000    1.0292409   0.91712359  -0.10674714    1.0014886 
-  340000    1.0056353    1.0054878 -0.067790602   0.97639404 
-  342000    1.0105034    1.1000009 -0.065106486   0.98781851 
-  344000    1.0296097   0.97446628  -0.11031518   0.98121512 
-  346000     1.022878    1.0302285 -0.092796664    1.0040982 
-  348000    1.0200294   0.84461432  0.001340607    1.0143357 
-  350000    0.9942428    1.0974217  0.032976965    1.0066948 
-  352000    1.0038173    1.1777572  -0.02105487   0.99841101 
-  354000    1.0363725    1.0742789 -0.068095272   0.99311679 
-  356000    1.0142211   0.93380261  0.011873553   0.98531527 
-  358000   0.99346289    1.2559305   -0.1027067   0.98126142 
-  360000   0.99957906    1.0307272 -0.052751638    1.0043971 
-  362000    1.0196151    1.1349776  -0.09260849    1.0011441 
-  364000    1.0371154   0.88342615   0.12450793   0.99706262 
-  366000     1.014625    1.0304514 -0.027977229    0.9921965 
-  368000    1.0584324   0.83998131  -0.07933342   0.99525213 
-  370000    1.0480268   0.83980605 -0.089536871   0.99539504 
-  372000    1.0124627     1.060244   0.14069432   0.99714731 
-  374000    1.0319035   0.80898054   0.13773298   0.99196179 
-  376000    1.0175987   0.86095756 -0.022196463   0.99034665 
-  378000     1.024277   0.96855584 -0.082372168   0.98711506 
-  380000    1.0309973   0.91266594 -0.0038718874    1.0004437 
-  382000    1.0195474   0.84949163 -0.090011652   0.97877658 
-  384000    1.0127199   0.92573997 -0.047436984   0.99568293 
-  386000    1.0155482    1.0260345  0.058825776    1.0032397 
-  388000    1.0341266    1.0684283  0.042324727    0.9962933 
-  390000     1.015419    1.2043476 -0.065809399   0.98978792 
-  392000   0.99510423    1.0679104    0.1194931   0.98198405 
-  394000   0.99275686    1.1827413  0.064956819    1.0203304 
-  396000    1.0004565    1.1524019  -0.12851079    1.0328568 
-  398000    1.0230487    1.1653679  0.066552948    1.0356753 
-  400000    1.0246668    1.0378562 -0.014987589    1.0388305 
-  402000   0.99713302   0.98996019  -0.12440697    1.0369703 
-  404000    1.0078626    1.0678616   -0.0361031    1.0292353 
-  406000    1.0264278   0.91482461    0.1001659    1.0269674 
-  408000   0.99866487    1.1801482 -0.062540579     1.021615 
-  410000   0.97734309    1.1861242   0.05416943     1.014162 
-  412000    1.0157071    0.9442541   0.22262556    1.0141824 
-  414000   0.98254015    1.2581149  0.015246929    1.0085563 
-  416000    1.0325598   0.90098178  0.041081387    1.0044668 
-  418000    1.0285532   0.82679005  -0.10105529    1.0017654 
-  420000    1.0324223   0.95868597  0.024808094   0.99789922 
-  422000    1.0056928    1.0690554 -0.024850455    1.0197904 
-  424000   0.99482351    1.1228662  0.049501791    1.0272213 
-  426000    1.0222594   0.97941801  -0.11968536    1.0186344 
-  428000    1.0111263    1.1141009    0.1437415    1.0130656 
-  430000   0.98139004    1.0366378  0.067956814    1.0108714 
-  432000   0.98613642    1.0119979  0.041509654    1.0033766 
-  434000    1.0230324   0.86869314  0.055734923    1.0020727 
-  436000    1.0212417    0.8436869 -0.022905431    0.9985587 
-  438000    1.0093302   0.97821341  0.023100883   0.99687144 
-  440000    1.0419272   0.87856473 -0.020071536   0.99762884 
-  442000    1.0172555   0.90164932   0.19704935   0.99904268 
-  444000    1.0399087    1.0051297 -0.022213498   0.99616218 
-  446000    1.0281756    1.0867446 -0.048363674   0.99230925 
-  448000   0.98980118    1.1266212   0.16193455   0.99381525 
-  450000    1.0397066    1.0216642 -0.017946472    1.0119634 
-  452000    1.0148816    1.0709423 -0.072255226    1.0011103 
-  454000   0.97505657    1.1553955 -0.019747328    0.9952685 
-  456000    1.0423127   0.93927199    0.1031593    1.0160711 
-  458000    1.0185738    0.9317795  -0.14238875    1.0212947 
-  460000    1.0254941   0.94237321   0.17279884    1.0176267 
-  462000    1.0331624   0.90556647  -0.17064389    1.0197747 
-  464000    1.0170281   0.98452898  -0.17212408     1.006159 
-  466000    1.0201836    1.0477978 0.0063101913   0.99741201 
-  468000   0.99055758      1.19768  -0.04304958   0.99395064 
-  470000    1.0140337    1.1042576   0.06483947    1.0006513 
-  472000    1.0369845   0.82562513  -0.06621037    1.0320218 
-  474000    1.0149565   0.86550007  0.060011486    1.0723558 
-  476000    1.0056806   0.99384495 -0.069441814    1.0623019 
-  478000    1.0333144   0.91193908 0.0045431056    1.0625281 
-  480000    1.0176402   0.90416174 -0.065787627    1.0534142 
-  482000   0.99406615    1.1281258   0.15969853    1.0526461 
-  484000    1.0119737    1.0284268 -0.020359549    1.0710582 
-  486000   0.98481179      1.08347  0.049797547    1.0738962 
-  488000    1.0444857   0.87660853 0.0011127729    1.0730464 
-  490000    1.0253141   0.92405109  0.070770655    1.0712017 
-  492000    1.0167975   0.88249423   0.12097353    1.0689941 
-  494000   0.96051412    1.3166559 -0.034841104    1.0721439 
-  496000    1.0284614    1.0149666 -0.0055275607    1.0641449 
-  498000    1.0107367    1.0406533 -0.030980028    1.0623882 
-  500000    0.9902026    1.2232023 -0.038731213    1.0606073 
-Loop time of 70.5579 on 1 procs for 500000 steps with 800 atoms
-
-Pair  time (%) = 47.4863 (67.3012)
-Neigh time (%) = 11.1177 (15.7568)
-Comm  time (%) = 1.90226 (2.69603)
-Outpt time (%) = 0.00377345 (0.00534802)
-Other time (%) = 10.0479 (14.2406)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    260 ave 260 max 260 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5611 ave 5611 max 5611 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5611
-Ave neighs/atom = 7.01375
-Neighbor list builds = 59311
-Dangerous builds = 0
-
-variable         eta equal v_v11
-print            "running average viscosity: ${eta}"
-running average viscosity: 1.06060731864499

examples/VISCOSITY/log.1Feb14.mp.2d.g++.1

@@ -1,230 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for viscosity of 2d LJ liquid
-# Muller-Plathe via fix viscosity
-
-# settings
-
-variable	x equal 20
-variable	y equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 20 0 $y -0.1 0.1
-region          simbox block 0 20 0 20 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
-  1 by 1 by 1 MPI processor grid
-create_atoms    1 box
-Created 800 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06394 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0     -0.56617    -1.535262 
-    1000   0.95906897    -1.571142            0  -0.61327189   0.82593948 
-    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
-    3000    1.0429232   -1.5801639            0  -0.53854441     1.157286 
-    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
-    5000   0.94117593   -1.6155055            0  -0.67550602   0.79354126 
-Loop time of 0.858331 on 1 procs for 5000 steps with 800 atoms
-
-Pair  time (%) = 0.46184 (53.8067)
-Neigh time (%) = 0.102345 (11.9237)
-Comm  time (%) = 0.0174992 (2.03875)
-Outpt time (%) = 5.10216e-05 (0.00594428)
-Other time (%) = 0.276596 (32.2248)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    256 ave 256 max 256 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5583 ave 5583 max 5583 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5583
-Ave neighs/atom = 6.97875
-Neighbor list builds = 551
-Dangerous builds = 0
-
-unfix		2
-
-# turn on Muller-Plathe driving force and equilibrate some more
-
-velocity	all scale $t
-velocity	all scale 1
-
-fix		4 all viscosity 100 x y 20
-fix		5 all ave/spatial 20 50 1000 y center 0.05 vx 		  units reduced file profile.mp.2d
-
-# equilibration run
-
-variable	dVx equal f_5[11][3]-f_5[1][3]
-
-thermo          1000
-thermo_style	custom step temp epair etotal press f_4 v_dVx
-run		20000
-WARNING: Fix viscosity comes before fix ave/spatial (../fix_viscosity.cpp:129)
-Memory usage per processor = 2.06486 Mbytes
-Step Temp E_pair TotEng Press 4 dVx 
-    5000            1   -1.6155055  -0.61675549   0.82879159            0            0 
-    6000   0.98687509   -1.6019556   -0.6163141   0.81812957   -40.544054   0.48107738 
-    7000   0.99812635     -1.61413   -0.6172513   0.88049928   -72.131982   0.83982485 
-    8000   0.99508548   -1.6108778  -0.61703621    1.0010053   -105.28099   0.80829601 
-    9000   0.94912106    -1.564488  -0.61655333    1.0184324   -141.59349   0.94800981 
-   10000   0.99258056   -1.6078678  -0.61652794   0.94564321   -171.73806    1.1494339 
-   11000    1.0159215   -1.6317434  -0.61709181   0.92235272   -199.00526    1.1830449 
-   12000    1.0126611   -1.6277928  -0.61639754    0.7688915   -227.93583    1.2636885 
-   13000    1.0122947   -1.6285623  -0.61753296   0.88334788   -258.44565     1.217365 
-   14000    1.0175562   -1.6335087  -0.61722444   0.84125493   -282.91095    1.3683789 
-   15000   0.97750561   -1.5930807  -0.61679697    1.1287326   -313.39632    1.2230677 
-   16000   0.98242425   -1.5980008  -0.61680456   0.91325299   -339.83912    1.2882183 
-   17000     1.008242   -1.6242405  -0.61725887   0.87284759   -365.79175    1.4803679 
-   18000   0.99455824    -1.610205  -0.61688999   0.80190574   -391.57365    1.3145093 
-   19000    1.0075504   -1.6245154  -0.61822443    1.1173911   -419.47456    1.2444018 
-   20000    1.0169723   -1.6334224   -0.6177213    0.8584711   -448.67177    1.2101637 
-   21000   0.98967224   -1.6055692  -0.61713404   0.80442505    -476.9284    1.4306147 
-   22000   0.97813764   -1.5935756  -0.61666068   0.99668957   -501.83621    1.5824584 
-   23000   0.98098823   -1.5963749  -0.61661287    1.1169304   -526.25935    1.4837827 
-   24000    1.0002987   -1.6158635  -0.61681517   0.92338935   -554.31346    1.3408732 
-   25000   0.99862734   -1.6139679  -0.61658884   0.87430158   -582.99367    1.2441321 
-Loop time of 2.75452 on 1 procs for 20000 steps with 800 atoms
-
-Pair  time (%) = 1.86056 (67.5458)
-Neigh time (%) = 0.440814 (16.0033)
-Comm  time (%) = 0.0745592 (2.7068)
-Outpt time (%) = 0.000242233 (0.00879403)
-Other time (%) = 0.378341 (13.7353)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    253 ave 253 max 253 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5598 ave 5598 max 5598 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5598
-Ave neighs/atom = 6.9975
-Neighbor list builds = 2354
-Dangerous builds = 0
-
-# data gathering run
-# reset fix viscosity to zero flux accumulation
-
-unfix		4
-fix		4 all viscosity 100 x y 20
-
-variable	visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
-fix		vave all ave/time 1000 1 1000 v_visc ave running start 26000
-
-thermo_style	custom step temp f_4 v_dVx v_visc f_vave
-
-# only need to run for 10000 steps to make a good 100-frame movie
-
-#dump	        1 all custom 100 dump.mp.2d id type x y z vx
-
-#dump		1 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
-#dump_modify	1 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red
-
-run	        50000
-Memory usage per processor = 2.103 Mbytes
-Step Temp 4 dVx visc vave 
-   25000   0.99862734            0    1.2441321            0            0 
-   26000     1.006121   -29.834985    1.0067717    1.4817155   0.74085773 
-   27000     1.000685    -57.28656    1.3703643    1.0450973   0.84227093 
-   28000    1.0119383   -82.689969    1.5329066    0.8990542   0.85646674 
-   29000     1.005591   -111.52398    1.3679394    1.0190874   0.88899088 
-   30000    0.9780793   -132.09122    1.4693711   0.89896428   0.89065311 
-   31000   0.98954223   -160.54318    1.4144949   0.94582162   0.89853433 
-   32000   0.98452695   -186.95511    1.3592447    0.9824527   0.90902412 
-   33000    1.0137305   -216.75823    1.1667402    1.1611316   0.93703607 
-   34000     1.004699   -243.79453    1.3554751   0.99921723   0.94325418 
-   35000   0.99279233   -272.99034    1.4414031   0.94696042   0.94359111 
-   36000   0.98601686   -296.44885    1.2290954    1.0963305    0.9563194 
-   37000   0.99960393   -327.77258    1.2754827    1.0707469   0.96512151 
-   38000    1.0232092   -354.20371     1.471032   0.92609943   0.96233422 
-   39000    1.0220897   -380.33308    1.4729611   0.92217809   0.95965714 
-   40000     1.003192   -409.96551    1.1486002     1.189754    0.9740382 
-   41000    1.0339239    -441.2471    1.2766924    1.0800543   0.98027444 
-   42000    0.9707256   -469.29726     1.298219    1.0632151   0.98488226 
-   43000     1.012508   -498.86351    1.3419554    1.0326215   0.98739485 
-   44000    1.0104362   -528.29202    1.2868256    1.0803656   0.99204339 
-   45000    1.0031694   -554.14027    1.3431643    1.0314082    0.9939179 
-   46000   0.98757964   -582.17026    1.3410473    1.0336098   0.99572208 
-   47000    1.0329913    -612.8052    1.0693478    1.3024192    1.0090567 
-   48000    1.0040957      -640.38    1.3648753    1.0199689    1.0095114 
-   49000    1.0213711   -667.39045    1.3779353    1.0090436    1.0094927 
-   50000    1.0028765   -693.00523     1.353182    1.0242602    1.0100607 
-   51000    1.0456929   -723.75516    1.3013825    1.0695063    1.0122624 
-   52000   0.98661701    -753.9132    1.1752559    1.1879417    1.0185366 
-   53000    1.0067127   -785.13019    1.0304513    1.3605866    1.0303315 
-   54000    1.0049746   -814.24066    1.3688029    1.0256138    1.0301742 
-   55000   0.99145341   -839.02294    1.5370182   0.90979505     1.026291 
-   56000   0.99330997   -866.91329    1.4290157    0.9784688    1.0247966 
-   57000   0.97297071   -891.05513    1.3697724     1.016427    1.0245429 
-   58000    1.0055628   -915.32616    1.7035058   0.81411979     1.018354 
-   59000   0.97447836   -940.88078    1.4544592   0.95131452    1.0164386 
-   60000   0.97786144   -970.22273    1.3938314   0.99440472    1.0158266 
-   61000    1.0069781   -996.52024    1.2925348    1.0708074    1.0173125 
-   62000   0.99860063   -1024.4668    1.3677043    1.0122178    1.0171785 
-   63000    1.0160002   -1052.8951    1.2909807    1.0731286    1.0186131 
-   64000    1.0075017   -1081.0833    1.4389443   0.96320906     1.017228 
-   65000    1.0128103   -1110.5507    1.3712762    1.0123332    1.0171086 
-   66000   0.99788687    -1138.143    1.1744686    1.1817934    1.0210297 
-   67000   0.99340723   -1165.3818    1.2141024    1.1427037    1.0238593 
-   68000   0.99891442   -1194.3011    1.1838074    1.1730981    1.0272511 
-   69000     1.010782   -1222.8307    1.2890796    1.0779631     1.028378 
-   70000    1.0084059   -1254.3924    1.3961366   0.99830441    1.0277242 
-   71000   0.98457274   -1285.1565    1.3228471     1.055987    1.0283256 
-   72000   0.98997963   -1309.8959    1.3420552    1.0383376    1.0285342 
-   73000   0.99661456   -1338.2166     1.114478    1.2507878    1.0330699 
-   74000   0.98823959   -1367.5535    1.1382114    1.2260136    1.0369288 
-   75000   0.99114295   -1396.3043     1.181084    1.1822226    1.0397777 
-Loop time of 6.87975 on 1 procs for 50000 steps with 800 atoms
-
-Pair  time (%) = 4.64786 (67.5585)
-Neigh time (%) = 1.09953 (15.9821)
-Comm  time (%) = 0.184543 (2.68241)
-Outpt time (%) = 0.000693083 (0.0100742)
-Other time (%) = 0.947126 (13.7669)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    257 ave 257 max 257 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5559 ave 5559 max 5559 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5559
-Ave neighs/atom = 6.94875
-Neighbor list builds = 5873
-Dangerous builds = 0

examples/VISCOSITY/log.1Feb14.nemd.2d.g++.1

@@ -1,271 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for viscosity of 2d LJ liquid
-# NEMD via fix deform and fix nvt/sllod
-
-# settings
-
-variable	x equal 20
-variable	y equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-variable	srate equal 2.7
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-# problem setup
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox prism 0 $y 0 $y -0.1 0.1 0.0 0.0 0.0
-region          simbox prism 0 20 0 $y -0.1 0.1 0.0 0.0 0.0
-region          simbox prism 0 20 0 20 -0.1 0.1 0.0 0.0 0.0
-create_box      1 simbox
-Created triclinic box = (0 0 -0.182574) to (36.5148 36.5148 0.182574) with tilt (0 0 0)
-  1 by 1 by 1 MPI processor grid
-create_atoms    1 box
-Created 800 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06394 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0     -0.56617    -1.535262 
-    1000    0.9455393    -1.573329            0  -0.62897162   0.91884199 
-    2000    1.0359047   -1.6229551            0  -0.58834528   0.96136682 
-    3000    1.0171488   -1.5468681            0  -0.53099077    1.1078235 
-    4000    1.0040221   -1.5977142            0  -0.59494717   0.92428924 
-    5000   0.95883045   -1.6087309            0  -0.65109902   0.92015627 
-Loop time of 0.897984 on 1 procs for 5000 steps with 800 atoms
-
-Pair  time (%) = 0.464335 (51.7087)
-Neigh time (%) = 0.13359 (14.8767)
-Comm  time (%) = 0.0208902 (2.32635)
-Outpt time (%) = 5.31673e-05 (0.00592074)
-Other time (%) = 0.279115 (31.0824)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    266 ave 266 max 266 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5604 ave 5604 max 5604 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5604
-Ave neighs/atom = 7.005
-Neighbor list builds = 548
-Dangerous builds = 0
-
-unfix  	        1
-unfix		2
-
-# turn on NEMD shear and equilibrate some more
-
-velocity	all scale $t
-velocity	all scale 1
-
-variable	xyrate equal ${srate}/lx
-variable	xyrate equal 2.7/lx
-
-fix		1 all nvt/sllod temp $t $t 0.1
-fix		1 all nvt/sllod temp 1 $t 0.1
-fix		1 all nvt/sllod temp 1 1 0.1
-fix		2 all deform 1 xy erate ${xyrate} remap v
-fix		2 all deform 1 xy erate 0.0739425452631974 remap v
-fix		4 all ave/spatial 20 250 5000 y center 0.05 vx 		  units reduced file profile.nemd.2d
-
-compute		usual all temp
-compute		tilt all temp/deform
-
-thermo          1000
-thermo_style	custom step temp c_usual epair etotal press pxy
-thermo_modify	temp tilt
-run		50000
-Memory usage per processor = 2.06486 Mbytes
-Step Temp usual E_pair TotEng Press Pxy 
-    5000    2.2074694            1   -1.6087309   0.59597912    1.6684032  -0.13173614 
-    6000   0.92758142    1.0829648   -1.6587109    -0.732289   0.69434408 -0.040395721 
-    7000   0.95692582    1.2000988   -1.7242343  -0.76850461   0.58119159 -0.078038652 
-    8000    1.0214774     1.223802   -1.6519928  -0.63179227   0.74285068  -0.10278761 
-    9000    1.0293091    1.3122841   -1.6684363  -0.64041383   0.90722071  -0.19178365 
-   10000    1.0445241    1.3788798   -1.6688897  -0.62567124   0.71535783 -0.086951926 
-   11000    1.0023372     1.362187   -1.6622117  -0.66112741   0.71746537  -0.18121663 
-   12000   0.95256804     1.379025   -1.6574208  -0.70604349   0.57745775 -0.040719788 
-   13000    1.0318148    1.4597155   -1.6433202  -0.61279515   0.65027764 -0.093427737 
-   14000    1.0332344    1.4031097   -1.6290961  -0.59715319   0.90536763 0.0020682054 
-   15000    1.0277172    1.5207267   -1.6221988  -0.59576627   0.84609392 -0.0074794989 
-   16000   0.99207101    1.5017016   -1.6247974  -0.63396649   0.92606954  -0.10188984 
-   17000   0.96488503    1.4793873    -1.600228  -0.63654911   0.89923523  -0.14261301 
-   18000   0.99547475    1.5236224    -1.635473  -0.64124255   0.68307708  -0.25098795 
-   19000    1.0323664    1.5855445   -1.6227003  -0.59162439   0.94072356  -0.09360683 
-   20000    1.0180092    1.5842966   -1.6143642  -0.59762743   0.93103828  0.040342848 
-   21000    1.0254077    1.6283785   -1.6301278  -0.60600186   0.87479869  0.044804621 
-   22000   0.97172908    1.5990643   -1.6486056  -0.67809118   0.76887644  0.037405021 
-   23000   0.97049676    1.6076804   -1.6058839  -0.63660024   0.93367017 -0.024871417 
-   24000    1.0026729    1.6776495    -1.622805  -0.62138548    0.8635542 -0.038997148 
-   25000    0.9633361    1.6349825   -1.6404336  -0.67830169   0.76001017   -0.1311218 
-   26000    1.0001388    1.6907443   -1.6004823  -0.60159366   0.81806855  -0.18349721 
-   27000   0.94191819    1.6384271   -1.5965443  -0.65580352   0.95785507 -0.086102432 
-   28000    1.0108584     1.731468   -1.6463325  -0.63673767   0.74516073  -0.19911341 
-   29000    1.0138048    1.7289581   -1.6000006  -0.58746311   0.94740326  0.016609077 
-   30000    1.0050557    1.7572204    -1.599182  -0.59538264    0.8223186  -0.24136602 
-   31000    1.0344558    1.7783254   -1.6122236  -0.57906086    1.1734714  -0.23484979 
-   32000    1.0174318    1.8509241   -1.5854329  -0.56927295   0.81903748 -0.096360108 
-   33000    1.0052704    1.7954794   -1.6076165  -0.60360266   0.98062712  -0.23179974 
-   34000    1.0138726    1.7784382   -1.6535717  -0.64096651   0.79928063    -0.184148 
-   35000    1.0108265    1.7715149   -1.5944308  -0.58486783     0.999611  -0.11864672 
-   36000   0.98516241    1.7509661   -1.6285996  -0.64466861   0.94523235  -0.13010197 
-   37000     0.971965    1.7638125   -1.5746851  -0.60393507    1.2265617 -0.077584507 
-   38000   0.93549343    1.8078749   -1.5840479  -0.64972382    1.0484769  0.031083799 
-   39000    1.0416402    1.8705987   -1.5799828  -0.53964462   0.94816785 -0.0034475262 
-   40000   0.96016973     1.856959   -1.5958952  -0.63692565   0.94610429  -0.18285492 
-   41000    1.0051478    1.8962677   -1.5860155  -0.58212412    1.0946382 -0.068521999 
-   42000    1.0081883    1.8593802   -1.6072469   -0.6003189   0.94320687 -0.041090231 
-   43000   0.98432329    1.8786095   -1.5924866  -0.60939372    1.0486461  -0.12281617 
-   44000    1.0262999    1.9116758   -1.5900042  -0.56498711    1.1223199  0.018952448 
-   45000   0.96577584    1.8870562   -1.6252423  -0.66067367   0.96036779 0.0028994584 
-   46000    1.0245911    1.9444906    -1.613004  -0.58969369   0.99363465 -0.021819492 
-   47000   0.93381748    1.8446233   -1.5772527  -0.64460252    1.0674773  -0.11978723 
-   48000   0.97729437    1.8717878   -1.5711485  -0.59507573    1.1563358  -0.25770589 
-   49000    1.0354354     1.987001   -1.6136701  -0.57952894   0.88244264  0.096378234 
-   50000    1.0094924    1.9808787    -1.612573  -0.60434244   0.94984417  -0.11436064 
-   51000     1.027174    1.9461247   -1.5899623   -0.5640723    1.0198367  0.065037899 
-   52000    1.0281396     2.019881   -1.6005519  -0.57369755    1.0350175 -0.057470252 
-   53000     1.018099    2.0455373   -1.6308565   -0.6140301   0.98344621 -0.095749654 
-   54000    1.0378532    2.0621046   -1.6137201   -0.5771642   0.92484803  -0.20897708 
-   55000   0.94998276    1.9258606   -1.5946282   -0.6458329    1.0304527 -0.061356231 
-Loop time of 11.8921 on 1 procs for 50000 steps with 800 atoms
-
-Pair  time (%) = 4.938 (41.5235)
-Neigh time (%) = 2.88697 (24.2764)
-Comm  time (%) = 0.342039 (2.87619)
-Outpt time (%) = 0.00175095 (0.0147236)
-Other time (%) = 3.72331 (31.3092)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    286 ave 286 max 286 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5610 ave 5610 max 5610 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5610
-Ave neighs/atom = 7.0125
-Neighbor list builds = 11310
-Dangerous builds = 0
-
-# data gathering run
-
-variable	visc equal -pxy/(v_srate/ly)
-fix		vave all ave/time 10 100 1000 v_visc ave running start 56000
-
-thermo_style	custom step temp press pxy v_visc f_vave
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
-thermo_modify	temp tilt
-
-# only need to run for 5400 steps to make a good 100-frame movie
-# set 54K steps above in equil and 5400 here simply to make good movie
-# 54K and 5400 are multiples of box-swap periodicity = 2700 steps
-
-#dump	        1 all custom 50 dump.nemd.2d id type x y z vx
-
-#dump		1 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
-#dump_modify	1 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
-
-run		50000
-Memory usage per processor = 2.10508 Mbytes
-Step Temp Press Pxy visc vave 
-   55000   0.94998276    1.0303592 -0.063500962   0.85878789            0 
-   56000    1.0301515    1.0617767  -0.10024411    1.3557027    1.2310718 
-   57000    1.0250473    1.0794382  -0.32669382    4.4182117    1.2359148 
-   58000   0.98594086    1.1283437    0.0380247  -0.51424657      1.30918 
-   59000    1.0164723    1.0980255 -0.069171978   0.93548279    1.3260744 
-   60000    1.0711985    1.1230358    -0.125773    1.7009558    1.3414067 
-   61000   0.98932053    0.9807511  -0.15097335    2.0417657    1.3671221 
-   62000     0.998341   0.81153573 -0.020326294   0.27489307    1.3670784 
-   63000    1.0718254    1.1974744   -0.1580162    2.1370132    1.3213502 
-   64000    1.0057042    1.0230065  0.034014907  -0.46001807    1.3316618 
-   65000    1.0040774    1.0303633 -0.078600273    1.0629912    1.3072524 
-   66000    1.0382782   0.93946231 -0.043423028   0.58725363    1.2837103 
-   67000    1.0226248   0.98900989 -0.054099059   0.73163642     1.253851 
-   68000   0.96605035    1.2060528  0.011937095  -0.16143744    1.2420174 
-   69000    1.0326968    1.0489439 -0.055891469   0.75587699    1.2551535 
-   70000   0.98367121   0.87910603  -0.16249968    2.1976479    1.2607276 
-   71000      1.02139    1.0729641  0.014510511  -0.19624035    1.2555329 
-   72000   0.95586405   0.82121701  0.016186091  -0.21890092    1.2511372 
-   73000    1.0422537    0.8674772  0.029604958  -0.40037786    1.2700259 
-   74000    1.0249336    1.0985439  -0.13831417    1.8705627    1.2656874 
-   75000   0.98213321   0.88865968  0.045972743  -0.62173601    1.2577007 
-   76000    0.9397546   0.71322157 -0.060283057   0.81526889    1.2699146 
-   77000    1.0063205    1.0310471 -0.065558372   0.88661232    1.2675723 
-   78000   0.96815308    1.1257553  0.025044943  -0.33870816     1.258244 
-   79000     1.039923    1.1557001  -0.16485925    2.2295587    1.2397555 
-   80000    1.0203604   0.88432557 -0.096887682    1.3103103    1.2385055 
-   81000    0.9504362   0.98117588 -0.078463955    1.0611476    1.2476425 
-   82000    0.9959177    1.1195113 -0.013058798   0.17660736    1.2360316 
-   83000    1.0001019   0.90295804  -0.26432373    3.5747177    1.2339827 
-   84000    1.0173461   0.84946561   0.12193823   -1.6490943    1.2473019 
-   85000    1.0325527    1.0523874  0.030626506  -0.41419329    1.2440578 
-   86000   0.94990925    1.0851851  -0.28324305    3.8305829    1.2410903 
-   87000    1.0408269    1.2359016  -0.07443383    1.0066441    1.2404526 
-   88000    1.0006532   0.92603737  -0.20524087    2.7756803    1.2439314 
-   89000   0.99846847   0.94779421 -0.047328236   0.64006771    1.2443818 
-   90000   0.98628639    1.0536216  -0.15876739    2.1471724    1.2354671 
-   91000   0.99478876    1.0885053  -0.17485734    2.3647731    1.2249337 
-   92000    1.0423662   0.95712108  -0.13839217    1.8716176    1.2276722 
-   93000   0.99308815    1.1868657  -0.13322814    1.8017792    1.2254173 
-   94000    0.9835718   0.98339544  -0.10768988    1.4563994     1.224888 
-   95000   0.94438219   0.97622034 -0.068799681   0.93044784    1.2204198 
-   96000    1.0142012    0.9210571  -0.14001612    1.8935799     1.217945 
-   97000   0.99678643    1.2773861 -0.091691808    1.2400413    1.2063637 
-   98000   0.96852646   0.89124039  -0.28173744     3.810221     1.203252 
-   99000   0.97030968    1.0148935  -0.11717859    1.5847249    1.2020913 
-  100000   0.97709835    1.0314408  -0.16108012    2.1784497    1.2019234 
-  101000   0.97653875    1.1948328 -0.085456884    1.1557201    1.2026873 
-  102000   0.97469158    1.0508677 -0.062662919   0.84745418    1.2062227 
-  103000   0.99620509   0.96826158  -0.10181244    1.3769128      1.20325 
-  104000   0.98933536    1.0077017  -0.18015152    2.4363717    1.1999909 
-  105000   0.99627299   0.93278548 -0.099781319    1.3494439    1.2018992 
-Loop time of 12.3598 on 1 procs for 50000 steps with 800 atoms
-
-Pair  time (%) = 5.02156 (40.6281)
-Neigh time (%) = 3.14134 (25.4158)
-Comm  time (%) = 0.36303 (2.93718)
-Outpt time (%) = 0.00100946 (0.00816731)
-Other time (%) = 3.83288 (31.0108)
-
-Nlocal:    800 ave 800 max 800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    256 ave 256 max 256 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5616 ave 5616 max 5616 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5616
-Ave neighs/atom = 7.02
-Neighbor list builds = 12247
-Dangerous builds = 0