forgot pair table change

Merge branch 'master' of github.com:lammps/lammps
Merge pull request #229 from akohlmey/small-corrections
2016-10-19 10:47:07 -06:00 · 2016-10-19 08:58:22 -06:00 · 2016-10-19 08:57:54 -06:00 · 2016-10-19 08:56:19 -06:00 · 2016-10-19 10:44:38 -04:00 · 2016-10-19 10:43:25 -04:00
37 changed files with 2973 additions and 76 deletions
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="18 Oct 2016 version">
+<META NAME="docnumber" CONTENT="19 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
-18 Oct 2016 version :c,h4
+19 Oct 2016 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -528,6 +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)

--- a/doc/src/Section_howto.txt
+++ b/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 *)
+char *lammps_commands_list(void *, int, char **)
+char *lammps_commands_concatenated(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.

@ -1891,16 +1901,33 @@ 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
+The lammps_file(), lammps_command(), lammps_commands_list(),
+lammps_commands_concatenated() functions are used to pass one or more
+commands to LAMMPS to execute as if they were coming from an input
+script.
+
+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_multiple() function passes multiple commands in a
+char** list.  The lammps_commands_concatentaed() function passes
+multiple commands concatenated into one long string, separated by
+newline characters.  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.
+
+Via these library 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, interleaving
+the command function calls with operations performed within the
+faller, calls to extract information from LAMMPS, or calls to another
 code's library.

-Other useful functions are also included in library.cpp.  For example:
+The lammps_free() is a clean-up function to free memory that the library
+allocated previously.
+
+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:

 void *lammps_extract_global(void *, char *)
 void *lammps_extract_atom(void *, char *)
@ -1908,27 +1935,37 @@ 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 *)
 int lammps_set_variable(void *, char *, char *)
+double lammps_get_thermo(void *, char *)
 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

-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.
+These functions can extract various global or per-atom quantities from
+LAMMPS as well as values calculated by a compute, fix, or variable.
+The lammps_set_variable() function can set an existing string-style variable
+to a new value, so that subsequent LAMMPS commands can access the
+variable.  The lammps_get_thermo() function returns the current
+value of a thermo keyword.

-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
+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 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 your own 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 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.
+change any LAMMPS data you wish.

 :line

--- a/doc/src/Section_python.txt
+++ b/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 +550,7 @@ 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

 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                     # name = "boxxlo", "nlocal", etc
@ -580,6 +582,8 @@ 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 +603,10 @@ 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:

--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -37,6 +37,7 @@ Commands :h1
   dump_image
   dump_modify
   dump_molfile
+   dump_nc
   echo
   fix
   fix_modify
--- a/doc/src/dump.txt
+++ b/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\[I\]
--- a/doc/src/dump_nc.txt
+++ b/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
+
--- a/doc/src/fix.txt
+++ b/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
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -48,6 +48,7 @@ Fixes :h1
   fix_gld
   fix_gle
   fix_gravity
+   fix_halt
   fix_heat
   fix_imd
   fix_indent
--- a/doc/src/lammps.book
+++ b/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
--- a/doc/src/pair_gauss.txt
+++ b/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
--- a/lib/netcdf/Makefile.lammps
+++ b/lib/netcdf/Makefile.lammps
@ -0,0 +1,19 @@
+# Settings that the LAMMPS build will import when a package using the
+# netCDF library is installed. This tries to automate configuration
+# via the nc-config tool, which is part of the netCDF installation.
+
+netcdf_SYSINC =
+netcdf_SYSLIB =
+netcdf_SYSPATH =
+
+ifneq ($(shell which nc-config 2>> /dev/null),)
+netcdf_SYSINC += -DLMP_HAS_NETCDF $(shell nc-config --cflags)
+netcdf_SYSLIB += $(shell nc-config --libs)
+endif
+
+ifneq ($(shell which ncmpidump 2>> /dev/null),)
+PNETCDF_PATH = $(shell which ncmpidump | sed -e 's,bin/ncmpidump,,')
+netcdf_SYSINC += -DLMP_HAS_PNETCDF -I$(PNETCDF_PATH)/include
+netcdf_SYSLIB += -lpnetcdf
+netcdf_SYSPATH += -L$(PNETCDF_PATH)/lib
+endif
--- a/lib/netcdf/README
+++ b/lib/netcdf/README
@ -0,0 +1,43 @@
+The Makefile.lammps file in this directory is used when building
+LAMMPS with packages that make use of the NetCDF library or its
+parallel version.  The file has several settings needed to compile
+and link LAMMPS with the NetCDF and parallel NetCDF support.
+For any regular NetCDF installation, all required flags should be
+autodetected. Please note that parallel NetCDF support is
+beneficial only when you run on a machine with very many processors
+like an IBM BlueGene or Cray. For most people regular NetCDF
+support should be sufficient and not cause any performance
+penalties.
+
+If you have problems compiling or linking, you may have to set
+the flags manually. There are three makefile variables
+
+1) netcdf_SYSINC
+This is for setting preprocessor options and include file paths.
+Set -DLMP_HAS_NETCDF, if you have NetCDF installed.
+Set -DLMP_HAS_PNETCDF, if you have parallel NetCDF installed.
+You can have either or both defines set. If none of these are
+set, LAMMPS will compile, but the NetCDF enabled functionality
+will not be available.
+In addition you may have to point to the folder with the include
+with -I/path/to/netcdf/include
+
+Example for a Fedora 24 machine with serial NetCDF installed as
+netcdf-devel-4.4.0-3.fc24.x86_64 RPM package:
+
+netcdf_SYSINC = -DLMP_HAS_NETCDF -I/usr/include -I/usr/include/hdf
+
+2) netcdf_SYSLIB
+This is the setting for all required libraries that need to be linked to.
+
+Example for a Fedora 24 machine with serial NetCDF installed as
+netcdf-devel-4.4.0-3.fc24.x86_64 RPM package:
+
+netcdf_SYSLIB = -lnetcdf
+
+3) netcdf_SYSPATH
+This is the setting for the path of directories with the NetCDF libraries.
+Typically, this will be of the form -L/path/to/netcdf/lib
+
+In the example from above, it can be left empty, because the Linux
+distribution provided libraries are installed in a system library location.
--- a/src/.gitignore
+++ b/src/.gitignore
@ -271,6 +271,10 @@
 /dump_custom_vtk.h
 /dump_h5md.cpp
 /dump_h5md.h
+/dump_nc.cpp
+/dump_nc.h
+/dump_nc_mpiio.cpp
+/dump_nc_mpiio.h
 /dump_xtc.cpp
 /dump_xtc.h
 /dump_xyz_mpiio.cpp
--- a/src/Makefile
+++ b/src/Makefile
@ -50,14 +50,14 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \

 PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \
 	   user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
-	   user-intel user-lb user-manifold user-mgpt \
-	   user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
+	   user-intel user-lb user-manifold user-mgpt user-misc user-molfile \
+	   user-nc-dump user-omp user-phonon user-qmmm user-qtb \
 	   user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
 	   user-vtk

 PACKLIB = compress gpu kim kokkos meam mpiio poems python reax voronoi \
 	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
-	  user-qmmm user-quip user-vtk
+	  user-nc-dump user-qmmm user-quip user-smd user-vtk

 PACKALL = $(PACKAGE) $(PACKUSER)

--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@ -795,7 +795,7 @@ void PRD::replicate(int ireplica)

  if (cmode == SINGLE_PROC_DIRECT) {
    MPI_Bcast(atom->x[0],3*atom->nlocal,MPI_DOUBLE,ireplica,comm_replica);
-    MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
+    MPI_Bcast(atom->image,atom->nlocal,MPI_LMP_IMAGEINT,ireplica,comm_replica);
    return;
  }

@ -815,9 +815,9 @@ void PRD::replicate(int ireplica)
      memcpy(imageall,image,nlocal*sizeof(imageint));
    }

-    MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
+    MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,ireplica,comm_replica);
    MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
-    MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
+    MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,ireplica,comm_replica);

    for (i = 0; i < nlocal; i++) {
      m = atom->map(tagall[i]);
@ -844,8 +844,8 @@ void PRD::replicate(int ireplica)
      displacements[i+1] = displacements[i] + counts[i];
    MPI_Gatherv(atom->tag,atom->nlocal,MPI_LMP_TAGINT,
                tagall,counts,displacements,MPI_LMP_TAGINT,0,world);
-    MPI_Gatherv(atom->image,atom->nlocal,MPI_LMP_TAGINT,
-                imageall,counts,displacements,MPI_LMP_TAGINT,0,world);
+    MPI_Gatherv(atom->image,atom->nlocal,MPI_LMP_IMAGEINT,
+                imageall,counts,displacements,MPI_LMP_IMAGEINT,0,world);
    for (i = 0; i < nprocs; i++) counts[i] *= 3;
    for (i = 0; i < nprocs-1; i++)
      displacements[i+1] = displacements[i] + counts[i];
@ -854,13 +854,13 @@ void PRD::replicate(int ireplica)
  }
  
  if (me == 0) {
-    MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
-    MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
+    MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,ireplica,comm_replica);
+    MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,ireplica,comm_replica);
    MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
  }
  
-  MPI_Bcast(tagall,natoms,MPI_INT,0,world);
-  MPI_Bcast(imageall,natoms,MPI_INT,0,world);
+  MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,0,world);
+  MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,0,world);
  MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
  
  double **x = atom->x;
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@ -39,6 +39,7 @@ using namespace MathConst;
 PairGaussCut::PairGaussCut(LAMMPS *lmp) : Pair(lmp)
 {
  respa_enable = 0;
+  writedata = 1;
 }

 /* ---------------------------------------------------------------------- */
@ -96,7 +97,6 @@ void PairGaussCut::compute(int eflag, int vflag)

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
-
      factor_lj = special_lj[sbmask(j)];
      j &= NEIGHMASK;

@ -221,7 +221,21 @@ void PairGaussCut::coeff(int narg, char **arg)

 double PairGaussCut::init_one(int i, int j)
 {
-  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+  if (setflag[i][j] == 0) {
+    hgauss[i][j] = mix_energy(fabs(hgauss[i][i]), fabs(hgauss[j][j]),
+			      fabs(sigmah[i][i]), fabs(sigmah[j][j]));
+
+    // If either of the particles is repulsive (ie, if hgauss > 0),
+    // then the interaction between both is repulsive.
+    double sign_hi = (hgauss[i][i] >= 0.0) ? 1.0 : -1.0;
+    double sign_hj = (hgauss[j][j] >= 0.0) ? 1.0 : -1.0;
+    hgauss[i][j] *= MAX(sign_hi, sign_hj);
+
+    sigmah[i][j] = mix_distance(sigmah[i][i], sigmah[j][j]);
+    rmh[i][j] = mix_distance(rmh[i][i], rmh[j][j]);
+    cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
+  }
+
  pgauss[i][j] = hgauss[i][j] / sqrt(MY_2PI) / sigmah[i][j];

  if (offset_flag) {
@ -334,6 +348,27 @@ void PairGaussCut::read_restart_settings(FILE *fp)
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }

+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairGaussCut::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g %g\n",i,hgauss[i][i],rmh[i][i],sigmah[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairGaussCut::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g %g\n",i,j,hgauss[i][j],rmh[i][j],sigmah[i][j],cut[i][j]);
+}
+
 /* ---------------------------------------------------------------------- */

 double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
--- a/src/USER-MISC/pair_gauss_cut.h
+++ b/src/USER-MISC/pair_gauss_cut.h
@ -42,6 +42,8 @@ class PairGaussCut : public Pair {
  virtual void read_restart(FILE *);
  virtual void write_restart_settings(FILE *);
  virtual void read_restart_settings(FILE *);
+  virtual void write_data(FILE *fp);
+  virtual void write_data_all(FILE *fp);

  virtual double memory_usage();

--- a/src/USER-NC-DUMP/Install.sh
+++ b/src/USER-NC-DUMP/Install.sh
@ -0,0 +1,63 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+for file in *.cpp *.h; do
+  action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*netcdf[^ \t]* //g' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(netcdf_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(netcdf_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(netcdf_SYSPATH) |' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+    # multiline form needed for BSD sed on Macs
+    sed -i -e '4 i \
+include ..\/..\/lib\/netcdf\/Makefile.lammps
+' ../Makefile.package.settings
+
+  fi
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*netcdf[^ \t]* //g' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+  fi
+
+fi
--- a/src/USER-NC-DUMP/README
+++ b/src/USER-NC-DUMP/README
@ -0,0 +1,39 @@
+USER-NC-DUMP
+============
+
+This package provides the nc and (optionally) the nc/mpiio dump styles.
+See the doc page for dump nc or dump nc/mpiio command for how to use them.
+Compiling these dump styles requires having the netCDF library installed
+on your system. See lib/netcdf/README for additional details.
+
+PACKAGE DESCRIPTION
+-------------------
+
+This is a LAMMPS (http://lammps.sandia.gov/) dump style for output into a NetCDF
+database. The database format follows the AMBER NetCDF trajectory convention
+(http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this
+convention. These extension are:
+* A variable "cell_origin" (of dimension "frame", "cell_spatial") that contains
+  the bottom left corner of the simulation cell.
+* Any number of additional variables corresponding to per atom scalar, vector
+  or tensor quantities available within LAMMPS. Tensor quantities are written in
+  Voigt notation. An additional dimension "Voigt" of length 6 is created for
+  this purpose.
+* Possibility to output to an HDF5 database.
+
+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.
+* VMD (http://www.ks.uiuc.edu/Research/vmd/).
+* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+  a NetCDF reader that is not present in the standard distribution of AtomEye.
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka@kit.edu).
+Contact him directly if you have questions.
+
+Lars Pastewka
+Institute for Applied Materials (IAM)
+Karlsruhe Institute of Technology (KIT)
+Kaiserstrasse 12, 76131 Karlsruhe
+e-mail: lars.pastewka@kit.edu
--- a/src/USER-NC-DUMP/dump_nc.cpp
+++ b/src/USER-NC-DUMP/dump_nc.cpp
--- a/src/USER-NC-DUMP/dump_nc.h
+++ b/src/USER-NC-DUMP/dump_nc.h
@ -0,0 +1,143 @@
+/* ======================================================================
+   LAMMPS NetCDF dump style
+   https://github.com/pastewka/lammps-netcdf
+   Lars Pastewka, lars.pastewka@kit.edu
+
+   Copyright (2011-2013) Fraunhofer IWM
+   Copyright (2014) Karlsruhe Institute of Technology
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 2 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+   ====================================================================== */
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+#if defined(LMP_HAS_NETCDF)
+
+#ifdef DUMP_CLASS
+
+DumpStyle(nc,DumpNC)
+
+#else
+
+#ifndef LMP_DUMP_NC_H
+#define LMP_DUMP_NC_H
+
+#include "dump_custom.h"
+
+namespace LAMMPS_NS {
+
+const int NC_FIELD_NAME_MAX = 100;
+const int DUMP_NC_MAX_DIMS  = 100;
+
+class DumpNC : public DumpCustom {
+ public:
+  DumpNC(class LAMMPS *, int, char **);
+  virtual ~DumpNC();
+  virtual void write();
+
+ private:
+  // per-atoms quantities (positions, velocities, etc.)
+  struct nc_perat_t {
+    int dims;                     // number of dimensions
+    int field[DUMP_NC_MAX_DIMS];  // field indices corresponding to the dim.
+    char name[NC_FIELD_NAME_MAX]; // field name
+    int var;                      // NetCDF variable
+
+    bool constant;                // is this property per file (not per frame)
+    int ndumped;                  // number of enties written for this prop.
+  };
+
+  typedef void (DumpNC::*funcptr_t)(void *);
+
+  // per-frame quantities (variables, fixes or computes)
+  struct nc_perframe_t {
+    char name[NC_FIELD_NAME_MAX]; // field name
+    int var;                      // NetCDF variable
+    int type;                     // variable, fix, compute or callback
+    int index;                    // index in fix/compute list
+    funcptr_t compute;            // compute function
+    int dim;                      // dimension
+    char id[NC_FIELD_NAME_MAX];   // variable id
+
+    bigint bigint_data;           // actual data
+    double double_data;           // actual data
+  };
+
+  int framei;                  // current frame index
+  int blocki;                  // current block index
+  int ndata;                   // number of data blocks to expect
+
+  bigint ntotalgr;             // # of atoms
+
+  int n_perat;                 // # of netcdf per-atom properties
+  nc_perat_t *perat;           // per-atom properties
+
+  int n_perframe;              // # of global netcdf (not per-atom) fix props
+  nc_perframe_t *perframe;     // global properties
+
+  bool double_precision;       // write everything as double precision
+
+  bigint n_buffer;             // size of buffer
+  int *int_buffer;             // buffer for passing data to netcdf
+  double *double_buffer;       // buffer for passing data to netcdf
+
+  int ncid;
+
+  int frame_dim;
+  int spatial_dim;
+  int Voigt_dim;
+  int atom_dim;
+  int cell_spatial_dim;
+  int cell_angular_dim;
+  int label_dim;
+
+  int spatial_var;
+  int cell_spatial_var;
+  int cell_angular_var;
+
+  int time_var;
+  int cell_origin_var;
+  int cell_lengths_var;
+  int cell_angles_var;
+
+  virtual void openfile();
+  void closefile();
+  virtual void write_header(bigint);
+  virtual void write_data(int, double *);
+  void write_prmtop();
+
+  virtual int modify_param(int, char **);
+
+  void ncerr(int, const char *, int);
+
+  void compute_step(void *);
+  void compute_elapsed(void *);
+  void compute_elapsed_long(void *);
+};
+
+}
+
+#endif
+#endif
+#endif /* defined(LMP_HAS_NETCDF) */
--- a/src/USER-NC-DUMP/dump_nc_mpiio.cpp
+++ b/src/USER-NC-DUMP/dump_nc_mpiio.cpp
--- a/src/USER-NC-DUMP/dump_nc_mpiio.h
+++ b/src/USER-NC-DUMP/dump_nc_mpiio.h
@ -0,0 +1,140 @@
+/* ======================================================================
+   LAMMPS NetCDF dump style
+   https://github.com/pastewka/lammps-netcdf
+   Lars Pastewka, lars.pastewka@kit.edu
+
+   Copyright (2011-2013) Fraunhofer IWM
+   Copyright (2014) Karlsruhe Institute of Technology
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 2 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+   ====================================================================== */
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+#if defined(LMP_HAS_PNETCDF)
+
+#ifdef DUMP_CLASS
+
+DumpStyle(nc/mpiio,DumpNCMPIIO)
+
+#else
+
+#ifndef LMP_DUMP_NC_MPIIO_H
+#define LMP_DUMP_NC_MPIIO_H
+
+#include "dump_custom.h"
+
+namespace LAMMPS_NS {
+
+const int NC_MPIIO_FIELD_NAME_MAX = 100;
+const int DUMP_NC_MPIIO_MAX_DIMS  = 100;
+
+class DumpNCMPIIO : public DumpCustom {
+ public:
+  DumpNCMPIIO(class LAMMPS *, int, char **);
+  virtual ~DumpNCMPIIO();
+  virtual void write();
+
+ private:
+  // per-atoms quantities (positions, velocities, etc.)
+  struct nc_perat_t {
+    int dims;                           // number of dimensions
+    int field[DUMP_NC_MPIIO_MAX_DIMS];  // field indices corresponding to the dim.
+    char name[NC_MPIIO_FIELD_NAME_MAX]; // field name
+    int var;                            // NetCDF variable
+  };
+
+  typedef void (DumpNCMPIIO::*funcptr_t)(void *);
+
+  // per-frame quantities (variables, fixes or computes)
+  struct nc_perframe_t {
+    char name[NC_MPIIO_FIELD_NAME_MAX]; // field name
+    int var;                            // NetCDF variable
+    int type;                           // variable, fix, compute or callback
+    int index;                          // index in fix/compute list
+    funcptr_t compute;                  // compute function
+    int dim;                            // dimension
+    char id[NC_MPIIO_FIELD_NAME_MAX];   // variable id
+
+    bigint bigint_data;                 // actual data
+    double double_data;                 // actual data
+  };
+
+  int framei;                           // current frame index
+  int blocki;                           // current block index
+  int ndata;                            // number of data blocks to expect
+
+  bigint ntotalgr;                      // # of atoms
+
+  int n_perat;                          // # of netcdf per-atom properties
+  nc_perat_t *perat;                    // per-atom properties
+
+  int n_perframe;                       // # of global netcdf (not per-atom) fix props
+  nc_perframe_t *perframe;              // global properties
+
+  bool double_precision;                // write everything as double precision
+
+  bigint n_buffer;                      // size of buffer
+  int *int_buffer;                      // buffer for passing data to netcdf
+  double *double_buffer;                // buffer for passing data to netcdf
+
+  int ncid;
+
+  int frame_dim;
+  int spatial_dim;
+  int Voigt_dim;
+  int atom_dim;
+  int cell_spatial_dim;
+  int cell_angular_dim;
+  int label_dim;
+
+  int spatial_var;
+  int cell_spatial_var;
+  int cell_angular_var;
+
+  int time_var;
+  int cell_origin_var;
+  int cell_lengths_var;
+  int cell_angles_var;
+
+  virtual void openfile();
+  void closefile();
+  void write_time_and_cell();
+  virtual void write_data(int, double *);
+  void write_prmtop();
+
+  virtual int modify_param(int, char **);
+
+  void ncerr(int, const char *, int);
+
+  void compute_step(void *);
+  void compute_elapsed(void *);
+  void compute_elapsed_long(void *);
+};
+
+}
+
+#endif
+#endif
+#endif /* defined(LMP_HAS_PNETCDF) */
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@ -148,7 +148,7 @@ int ComputeBondLocal::compute_bonds(int flag)
  double vvib,vrotsq;
  double inertia,omegasq;
  double mvv2e;
-  double engpot,engtrans,engvib,engrot,engtot,fbond;
+  double engpot,engtrans,engvib,engrot,fbond;
  double *ptr;

  double **x = atom->x;
--- a/src/dump.cpp
+++ b/src/dump.cpp
@ -874,7 +874,7 @@ void Dump::modify_params(int narg, char **arg)
        format_float_user = NULL;
        // pass format none to child classes which may use it
        // not an error if they don't
-        int n = modify_param(narg-iarg,&arg[iarg]);
+        modify_param(narg-iarg,&arg[iarg]);
        iarg += 2;
        continue;
      }
--- a/src/finish.cpp
+++ b/src/finish.cpp
@ -1,5 +1,5 @@
 /* ----------------------------------------------------------------------
-   LAMMRDS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@ -194,10 +194,8 @@ void FixHalt::post_run()
 double FixHalt::bondmax()
 {
  double **x = atom->x;
-  double **f = atom->f;
  int **bondlist = neighbor->bondlist;
  int nbondlist = neighbor->nbondlist;
-  int nlocal = atom->nlocal;

  int i1,i2;
  double delx,dely,delz,rsq;
--- a/src/info.cpp
+++ b/src/info.cpp
@ -1079,3 +1079,10 @@ bool Info::has_exceptions() const {
  return false;
 #endif
 }
+
+/* ---------------------------------------------------------------------- */
+
+char **Info::get_variable_names(int &num) {
+    num = input->variable->nvar;
+    return input->variable->names;
+}
--- a/src/info.h
+++ b/src/info.h
@ -39,6 +39,8 @@ class Info : protected Pointers {
  bool has_ffmpeg_support() const;
  bool has_exceptions() const;

+  char **get_variable_names(int &num);
+
 private:
  void available_styles(FILE * out, int flags);

--- a/src/lmptype.h
+++ b/src/lmptype.h
@ -89,6 +89,7 @@ typedef int64_t bigint;
 #define MAXBIGINT INT64_MAX

 #define MPI_LMP_TAGINT MPI_INT
+#define MPI_LMP_IMAGEINT MPI_INT
 #define MPI_LMP_BIGINT MPI_LL

 #define TAGINT_FORMAT "%d"
@ -120,6 +121,7 @@ typedef int64_t bigint;
 #define MAXBIGINT INT64_MAX

 #define MPI_LMP_TAGINT MPI_LL
+#define MPI_LMP_IMAGEINT MPI_LL
 #define MPI_LMP_BIGINT MPI_LL

 #define TAGINT_FORMAT "%" PRId64
@ -150,6 +152,7 @@ typedef int bigint;
 #define MAXBIGINT INT_MAX

 #define MPI_LMP_TAGINT MPI_INT
+#define MPI_LMP_IMAGEINT MPI_INT
 #define MPI_LMP_BIGINT MPI_INT

 #define TAGINT_FORMAT "%d"
--- a/src/neigh_derive.cpp
+++ b/src/neigh_derive.cpp
@ -232,8 +232,8 @@ void Neighbor::skip_from_granular(NeighList *list)
 {
  int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
  tagint jtag;
-  int *neighptr,*jlist,*touchptr,*touchptr_skip;
-  double *shearptr,*shearptr_skip;
+  int *neighptr,*jlist,*touchptr;
+  double *shearptr;

  NeighList *listgranhistory;
  int *npartner;
@ -364,8 +364,8 @@ void Neighbor::skip_from_granular_off2on(NeighList *list)
 {
  int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
  tagint itag,jtag;
-  int *neighptr,*jlist,*touchptr,*touchptr_skip;
-  double *shearptr,*shearptr_skip;
+  int *neighptr,*jlist,*touchptr;
+  double *shearptr;

  NeighList *listgranhistory;
  int *npartner;
@ -502,8 +502,8 @@ void Neighbor::skip_from_granular_off2on(NeighList *list)
 void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
 {
  int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
-  tagint itag,jtag;
-  int *surf,*neighptr,*jlist;
+  tagint jtag;
+  int *surf,*jlist;

  NeighList *listgranhistory;
  int *npartner;
@ -571,7 +571,6 @@ void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
    i = ilist_skip[ii];
    itype = type[i];
    if (iskip[itype]) continue;
-    itag = tag[i];

    n = 0;

@ -625,7 +624,6 @@ void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
    i = ilist_skip[ii];
    itype = type[i];
    if (iskip[itype]) continue;
-    itag = tag[i];

    // loop over parent non-skip granular list and optionally its history info

--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@ -34,10 +34,11 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp)
+PairGauss::PairGauss(LAMMPS *lmp) : Pair(lmp)
 {
  nextra = 1;
  pvector = new double[1];
+  writedata = 1;
 }

 /* ---------------------------------------------------------------------- */
@ -187,7 +188,7 @@ void PairGauss::coeff(int narg, char **arg)
    error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

-  int ilo, ihi, jlo, jhi;
+  int ilo,ihi,jlo,jhi;
  force->bounds(arg[0],atom->ntypes,ilo,ihi);
  force->bounds(arg[1],atom->ntypes,jlo,jhi);

@ -204,7 +205,7 @@ void PairGauss::coeff(int narg, char **arg)
      b[i][j] = b_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
-      count++ ;
+      count++;
    }
  }

@ -217,12 +218,27 @@ void PairGauss::coeff(int narg, char **arg)

 double PairGauss::init_one(int i, int j)
 {
+  if (setflag[i][j] == 0) {
+    double sign_bi = (b[i][i] >= 0.0) ? 1.0 : -1.0;
+    double sign_bj = (b[j][j] >= 0.0) ? 1.0 : -1.0;
+    double si = sqrt(0.5/fabs(b[i][i]));
+    double sj = sqrt(0.5/fabs(b[j][j]));
+    double sij = mix_distance(si, sj);
+    b[i][j] = 0.5 / (sij*sij);
+    b[i][j] *= MAX(sign_bi, sign_bj);

-  // This error is triggered when ti is performed on lj/cut tail
-  // in presence of extra atom type for tether sites
-  // "i = 2 j = 1 ERROR: All pair coeffs are not set (pair_gauss.cpp:223)"
-  //  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+    // Negative "a" values are useful for simulating repulsive particles.
+    // If either of the particles is repulsive (a<0), then the
+    // interaction between both is repulsive.
+    double sign_ai = (a[i][i] >= 0.0) ? 1.0 : -1.0;
+    double sign_aj = (a[j][j] >= 0.0) ? 1.0 : -1.0;
+    a[i][j] = mix_energy(fabs(a[i][i]), fabs(a[j][j]), si, sj);
+    a[i][j] *= MIN(sign_ai, sign_aj);

+    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
+  }
+
+  // cutoff correction to energy
  if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);
  else offset[i][j] = 0.0;

@ -260,7 +276,6 @@ void PairGauss::write_restart(FILE *fp)
 void PairGauss::read_restart(FILE *fp)
 {
  read_restart_settings(fp);
-
  allocate();

  int i,j;
@ -309,6 +324,27 @@ void PairGauss::read_restart_settings(FILE *fp)
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }

+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairGauss::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g\n",i,a[i][i],b[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairGauss::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g\n",i,j,a[i][j],b[i][j],cut[i][j]);
+}
+
 /* ---------------------------------------------------------------------- */

 double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
--- a/src/pair_gauss.h
+++ b/src/pair_gauss.h
@ -36,6 +36,8 @@ class PairGauss : public Pair {
  void read_restart(FILE *);
  void write_restart_settings(FILE *);
  void read_restart_settings(FILE *);
+  void write_data(FILE *fp);
+  void write_data_all(FILE *fp);
  double single(int, int, int, int, double, double, double, double &);
  void *extract(const char *, int &);

--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@ -554,7 +554,7 @@ void PairTable::spline_table(Table *tb)

 /* ----------------------------------------------------------------------
   extract attributes from parameter line in table section
-   format of line: N value R/RSQ/BITMAP lo hi FP fplo fphi
+   format of line: N value R/RSQ/BITMAP lo hi FPRIME fplo fphi
   N is required, other params are optional
 ------------------------------------------------------------------------- */

@ -578,7 +578,7 @@ void PairTable::param_extract(Table *tb, char *line)
      tb->rlo = atof(word);
      word = strtok(NULL," \t\n\r\f");
      tb->rhi = atof(word);
-    } else if (strcmp(word,"FP") == 0) {
+    } else if (strcmp(word,"FPRIME") == 0) {
      tb->fpflag = 1;
      word = strtok(NULL," \t\n\r\f");
      tb->fplo = atof(word);
--- a/src/region.cpp
+++ b/src/region.cpp
@ -517,7 +517,6 @@ void Region::set_velocity()

 void Region::velocity_contact(double *vwall, double *x, int ic)
 {
-  Contact c = contact[ic];
  double xc[3];

  vwall[0] = vwall[1] = vwall[2] = 0.0;
--- a/src/version.h
+++ b/src/version.h
@ -1 +1 @@
-#define LAMMPS_VERSION "18 Oct 2016"
+#define LAMMPS_VERSION "19 Oct 2016"
Author	SHA1	Message	Date
Steve Plimpton	9954d5d346	forgot pair table change	2016-10-19 10:47:07 -06:00
Steve Plimpton	3d254780de	Merge branch 'master' of github.com:lammps/lammps	2016-10-19 08:58:22 -06:00
sjplimp	b0cf1ded38	Merge pull request #229 from akohlmey/small-corrections collected various small corrections and updates	2016-10-19 08:57:54 -06:00
sjplimp	0891ed83a5	Merge pull request #228 from akohlmey/correct-prd-for-bigbig make PRD code compatible with -DLAMMPS_BIGBIG	2016-10-19 08:56:19 -06:00
Axel Kohlmeyer	ffb8eb36da	Revert "recognize any word starting with FP as FPRIME style table" This reverts commit `86f5b51133`.	2016-10-19 10:44:38 -04:00
Axel Kohlmeyer	1a10857244	make PRD code compatible with -DLAMMPS_BIGBIG	2016-10-19 10:43:25 -04:00
Axel Kohlmeyer	2634468676	dead code removal	2016-10-19 10:42:02 -04:00
Steve Plimpton	58141e0559	text edit	2016-10-19 08:41:44 -06:00
sjplimp	393337e7cf	Merge pull request #226 from akohlmey/pair-gauss-mixing add mixing support for pair styles gauss and gauss/cut	2016-10-19 08:37:32 -06:00
sjplimp	e0ed218cc4	Merge pull request #224 from akohlmey/get-vars provide an accessor for names of LAMMPS variables	2016-10-19 08:36:52 -06:00
sjplimp	efc7b23bd8	Merge pull request #216 from akohlmey/user-nc-dump USER-NC-DUMP package	2016-10-19 08:33:59 -06:00
Axel Kohlmeyer	566effc9c9	account for new fix halt properly in PDF and online docs	2016-10-19 09:08:20 -04:00
Axel Kohlmeyer	86f5b51133	recognize any word starting with FP as FPRIME style table	2016-10-19 09:05:25 -04:00
Axel Kohlmeyer	ccca642b3a	fix typo	2016-10-19 08:08:52 -04:00
Axel Kohlmeyer	019bc0ba0b	fix typos in Makefile.lammps for NetCDF support	2016-10-19 07:39:03 -04:00
Axel Kohlmeyer	7b7cb297e6	add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data.	2016-10-18 22:26:47 -04:00
Axel Kohlmeyer	5a6dea7a22	Merge branch 'master' into user-nc-dump	2016-10-18 15:36:18 -04:00
Axel Kohlmeyer	27796b431e	avoid distracting error output	2016-10-18 15:32:20 -04:00
Axel Kohlmeyer	6e54443d8c	make plain nc dump style a compile time option as well according to the package author, lars pastewka, some machines may have only parallel netcdf and not the serial netcdf installed. hence both netcdf dump styles neet to be optional depending on the compile time setting in lib/netcdf/Makefile.lammps The makefile has been set up to auto-detect the necessary flags for most regular and correct installations.	2016-10-18 15:11:22 -04:00
Axel Kohlmeyer	2b47fa6653	update Makefile.lammps and add README according to suggestions by lars pastewka	2016-10-18 15:05:30 -04:00
Axel Kohlmeyer	ae77664bdd	forgot to include USER-NC-DUMP in PACKUSER variable	2016-10-18 14:45:25 -04:00
Axel Kohlmeyer	4502d3276b	updated Makefile.lammps for NetCDF support based on suggestions from lars pastewka	2016-10-18 14:45:06 -04:00
Axel Kohlmeyer	c5513c4f75	provide an accessor for names of LAMMPS variables	2016-10-17 19:56:18 -04:00
Axel Kohlmeyer	2e8edbd2b9	USER-SMD was missing from PACKLIB variable	2016-10-12 06:53:37 -04:00
Axel Kohlmeyer	da66c1e649	update #include directives to match current LAMMPS coding conventions	2016-10-12 00:07:52 -04:00
Axel Kohlmeyer	e10ea91c5f	add doc file to toctree	2016-10-11 23:51:42 -04:00
Axel Kohlmeyer	69cb831705	import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by lars pastewka	2016-10-11 23:44:34 -04:00
Axel Kohlmeyer	ecb03dd2df	import lammps-netcdf code as USER-NC-DUMP package	2016-10-11 23:03:18 -04:00