Merge branch 'master' of github.com:lammps/lammps

collected various small corrections and updates

doc/src/commands.txt

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

doc/src/dump_nc.txt

@@ -0,0 +1,64 @@
+"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}.
+
+: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.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+

doc/src/fixes.txt

@@ -48,6 +48,7 @@ Fixes :h1
    fix_gld
    fix_gle
    fix_gravity
+   fix_halt
    fix_heat
    fix_imd
    fix_indent

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/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

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

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.

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

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)
 

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;

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,

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();
 

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

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

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) */

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) */

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;

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;
       }

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
 

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;

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;
+}

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);
 

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"

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
 

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,

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 &);
 

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;