Merge pull request #3309 from akohlmey/collected-small-fixes

More fixes and small changes for the stable release

doc/src/Howto_structured_data.rst

@@ -184,7 +184,7 @@ frame.
 
 .. code-block:: python
 
-   import re, yaml
+   import yaml
    import pandas as pd
 
    try:
@@ -193,7 +193,7 @@ frame.
        from yaml import SafeLoader as Loader
 
    with open("ave.yaml") as f:
-       ave = yaml.load(docs, Loader=Loader)
+       ave = yaml.load(f, Loader=Loader)
 
    keys = ave['keywords']
    df = {}

doc/src/Speed_measure.rst

@@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
 communication occurs for other processors to catch up.  Thus the
 reported times for "Communication" or "Other" may be higher than they
 really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
+use the :doc:`timer sync <timer>` command to obtain synchronized timings.
-LAMMPS, to obtain synchronized timings.

doc/src/read_restart.rst

@@ -11,7 +11,6 @@ Syntax
    read_restart file flag
 
 * file = name of binary restart file to read in
-* flag = remap (optional)
 
 Examples
 """"""""
@@ -19,44 +18,40 @@ Examples
 .. code-block:: LAMMPS
 
    read_restart save.10000
-   read_restart save.10000 remap
    read_restart restart.*
    read_restart restart.*.mpiio
-   read_restart poly.*.% remap
 
 Description
 """""""""""
 
 Read in a previously saved system configuration from a restart file.
 This allows continuation of a previous run.  Details about what
-information is stored (and not stored) in a restart file is given
+information is stored (and not stored) in a restart file is given below.
-below.  Basically this operation will re-create the simulation box
+Basically this operation will re-create the simulation box with all its
-with all its atoms and their attributes as well as some related global
+atoms and their attributes as well as some related global settings, at
-settings, at the point in time it was written to the restart file by a
+the point in time it was written to the restart file by a previous
-previous simulation.  The simulation box will be partitioned into a
+simulation.  The simulation box will be partitioned into a regular 3d
-regular 3d grid of rectangular bricks, one per processor, based on the
+grid of rectangular bricks, one per processor, based on the number of
-number of processors in the current simulation and the settings of the
+processors in the current simulation and the settings of the
 :doc:`processors <processors>` command.  The partitioning can later be
-changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
+changed by the :doc:`balance <balance>` or :doc:`fix balance
-
+<fix_balance>` commands.
-.. note::
-
-   Normally, restart files are written by the
-   :doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
-   so that all atoms in the restart file are inside the simulation box.
-   If this is not the case, the read_restart command will print an error
-   that atoms were "lost" when the file is read.  This error should be
-   reported to the LAMMPS developers so the invalid writing of the
-   restart file can be fixed.  If you still wish to use the restart file,
-   the optional *remap* flag can be appended to the read_restart command.
-   This should avoid the error, by explicitly remapping each atom back
-   into the simulation box, updating image flags for the atom
-   appropriately.
 
 Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
 those produced by the original run had it continued on.
 
+The binary restart file format was not designed with backward, forward,
+or cross-platform compatibility in mind, so the files are only expected
+to be read correctly by the same LAMMPS executable on the same platform.
+Changes to the architecture, compilation settings, or LAMMPS version can
+render a restart file unreadable or it may read the data incorrectly.
+If you want a more portable format, you can use the data file format as
+created by the :doc:`write_data <write_data>` command.  Binary restart
+files can also be converted into a data file from the command line by
+the LAMMPS executable that wrote them using the :ref:`-restart2data
+<restart2data>` command line flag.
+
 Several things can prevent exact restarts due to round-off effects, in
 which case the trajectories in the 2 runs will slowly diverge.  These
 include running on a different number of processors or changing
@@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
 these cases.
 
 Certain fixes will not restart exactly, though they should provide
-statistically similar results.  These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
+statistically similar results.  These include :doc:`fix shake
+<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
 
 Certain pair styles will not restart exactly, though they should
 provide statistically similar results.  This is because the forces
@@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
 :doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
 
 Because restart files are binary, they may not be portable to other
-machines.  In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
+machines.  In this case, you can use the :doc:`-restart command-line
+switch <Run_options>` to convert a restart file to a data file.
 
-Similar to how restart files are written (see the
+Similar to how restart files are written (see the :doc:`write_restart
-:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
+<write_restart>` and :doc:`restart <restart>` commands), the restart
-commands), the restart filename can contain two wild-card characters.
+filename can contain two wild-card characters.  If a "\*" appears in the
-If a "\*" appears in the filename, the directory is searched for all
+filename, the directory is searched for all filenames that match the
-filenames that match the pattern where "\*" is replaced with a timestep
+pattern where "\*" is replaced with a timestep value.  The file with the
-value.  The file with the largest timestep value is read in.  Thus,
+largest timestep value is read in.  Thus, this effectively means, read
-this effectively means, read the latest restart file.  It's useful if
+the latest restart file.  It's useful if you want your script to
-you want your script to continue a run from where it left off.  See
+continue a run from where it left off.  See the :doc:`run <run>` command
-the :doc:`run <run>` command and its "upto" option for how to specify
+and its "upto" option for how to specify the run command so it does not
-the run command so it does not need to be changed either.
+need to be changed either.
 
 If a "%" character appears in the restart filename, LAMMPS expects a
 set of multiple files to exist.  The :doc:`restart <restart>` and
@@ -222,17 +219,17 @@ its calculations in a consistent manner.
 
 .. note::
 
-   There are a handful of commands which can be used before or
+   There are a handful of commands which can be used before or between
-   between runs which may require a system initialization.  Examples
+   runs which may require a system initialization.  Examples include the
-   include the "balance", "displace_atoms", "delete_atoms", "set" (some
+   "balance", "displace_atoms", "delete_atoms", "set" (some options),
-   options), and "velocity" (some options) commands.  This is because
+   and "velocity" (some options) commands.  This is because they can
-   they can migrate atoms to new processors.  Thus they will also discard
+   migrate atoms to new processors.  Thus they will also discard unused
-   unused "state" information from fixes.  You will know the discard has
+   "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
+   relevant fixes and computes (which create fixes) before those
-   are used.
+   commands are used.
 
 Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
 use a fix to store "state" information that persists from timestep to
@@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or
 deleted in various ways, which can affect how their info is stored in
 a restart file.
 
-If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command,
+If bonds (angles, etc) have been turned off by the :doc:`fix shake
-their info will be written to a restart file as if they are turned on.
+<fix_shake>` or :doc:`delete_bonds <delete_bonds>` command, their info
-This means they will need to be turned off again in a new run after
+will be written to a restart file as if they are turned on.  This means
-the restart file is read.
+they will need to be turned off again in a new run after the restart
+file is read.
 
 Bonds that are broken (e.g. by a bond-breaking potential) are written
 to the restart file as broken bonds with a type of 0.  Thus these
 bonds will still be broken when the restart file is read.
 
-Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
+Bonds that have been broken by the :doc:`fix bond/break
-system.  No information about these bonds is written to the restart
+<fix_bond_break>` command have disappeared from the system.  No
-file.
+information about these bonds is written to the restart file.
 
 ----------
 

doc/utils/sphinx-config/false_positives.txt

@@ -2369,6 +2369,7 @@ nopreliminary
 Nord
 norder
 Nordlund
+noremap
 normals
 normx
 normy

examples/COUPLE/fortran2/LAMMPS-wrapper.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@@ -23,6 +23,7 @@
 
 #include <mpi.h>
 #include "LAMMPS-wrapper.h"
+#define LAMMPS_LIB_MPI 1
 #include <library.h>
 #include <lammps.h>
 #include <atom.h>
@@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
 
 int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *size;
-   int icompute = lmp->modify->find_compute(id);
+   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
-   if ( icompute < 0 ) return 0;
+   if (size) return *size;
-   class Compute *compute = lmp->modify->compute[icompute];
+   return 0;
-
-   if ( style == 0 )
-   {
-      if ( !compute->vector_flag )
-         return 0;
-      else
-         return compute->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-         return 0;
-      else
-         return compute->size_local_rows;
-   }
-   else
-      return 0;
 }
 
 void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *tmp;
-   int icompute = lmp->modify->find_compute(id);
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
-   if ( icompute < 0 )
+   if (tmp) *nrows = *tmp;
-   {
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
-      *nrows = 0;
+   if (tmp) *ncols = *tmp;
-      *ncols = 0;
-   }
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_array_rows;
-         *ncols = compute->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !compute->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = compute->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_local_rows;
-         *ncols = compute->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
    return;
 }
 
 int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *size;
-   int ifix = lmp->modify->find_fix(id);
+   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
-   if ( ifix < 0 ) return 0;
+   if (size) return *size;
-   class Fix *fix = lmp->modify->fix[ifix];
+   return 0;
-
-   if ( style == 0 )
-   {
-      if ( !fix->vector_flag )
-         return 0;
-      else
-         return fix->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-         return 0;
-      else
-         return fix->size_local_rows;
-   }
-   else
-      return 0;
 }
 
 void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *tmp;
-   int ifix = lmp->modify->find_fix(id);
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
-   if ( ifix < 0 )
+   if (tmp) *nrows = *tmp;
-   {
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
-      *nrows = 0;
+   if (tmp) *ncols = *tmp;
-      *ncols = 0;
-   }
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_array_rows;
-         *ncols = fix->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !fix->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = fix->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_local_rows;
-         *ncols = fix->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
    return;
-
 }
 
 /* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran2/LAMMPS-wrapper.h

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran2/LAMMPS.F90

@@ -1292,7 +1292,7 @@ contains !! Wrapper functions local to this module {{{1
       Cname = string2Cstring (name)
       Ccount = size(data) / natoms
       if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
             & count to be either 1 or 3')
       Fdata = data
       Cdata = C_loc (Fdata(1))
@@ -1355,7 +1355,7 @@ contains !! Wrapper functions local to this module {{{1
       Cname = string2Cstring (name)
       Ccount = size(data) / ndata
       if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
             & count to be either 1 or 3')
       Fdata = data
       Cdata = C_loc (Fdata(1))

examples/COUPLE/fortran2/Makefile

@@ -14,7 +14,7 @@ CXXLIB = -lstdc++    # replace with your C++ runtime libs
 # Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
 FFLAGS = -O2 -fPIC
 CXXFLAGS = -O2 -fPIC
-CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
+CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
 
 all : liblammps_fortran.a liblammps_fortran.so
 

examples/COUPLE/fortran2/README

@@ -11,9 +11,8 @@ This interface was created by Karl Hammond who you can contact with
 questions:
 
 Karl D. Hammond
-University of Tennessee, Knoxville
+University of Missouri
-karlh at ugcs.caltech.edu
+hammondkd at missouri.edu
-karlh at utk.edu
 
 -------------------------------------
 

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@@ -23,6 +23,7 @@
 
 #include <mpi.h>
 #include "LAMMPS-wrapper.h"
+#define LAMMPS_LIB_MPI 1
 #include <library.h>
 #include <lammps.h>
 #include <atom.h>
@@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
 
 int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *size;
-   int icompute = lmp->modify->find_compute(id);
+   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
-   if ( icompute < 0 ) return 0;
+   if (size) return *size;
-   class Compute *compute = lmp->modify->compute[icompute];
+   return 0;
-
-   if ( style == 0 )
-   {
-      if ( !compute->vector_flag )
-         return 0;
-      else
-         return compute->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-         return 0;
-      else
-         return compute->size_local_rows;
-   }
-   else
-      return 0;
 }
 
 void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *tmp;
-   int icompute = lmp->modify->find_compute(id);
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
-   if ( icompute < 0 )
+   if (tmp) *nrows = *tmp;
-   {
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
-      *nrows = 0;
+   if (tmp) *ncols = *tmp;
-      *ncols = 0;
-   }
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_array_rows;
-         *ncols = compute->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !compute->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = compute->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_local_rows;
-         *ncols = compute->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
    return;
 }
 
 int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *size;
-   int ifix = lmp->modify->find_fix(id);
+   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
-   if ( ifix < 0 ) return 0;
+   if (size) return *size;
-   class Fix *fix = lmp->modify->fix[ifix];
+   return 0;
-
-   if ( style == 0 )
-   {
-      if ( !fix->vector_flag )
-         return 0;
-      else
-         return fix->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-         return 0;
-      else
-         return fix->size_local_rows;
-   }
-   else
-      return 0;
 }
 
 void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int *tmp;
-   int ifix = lmp->modify->find_fix(id);
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
-   if ( ifix < 0 )
+   if (tmp) *nrows = *tmp;
-   {
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
-      *nrows = 0;
+   if (tmp) *ncols = *tmp;
-      *ncols = 0;
-   }
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_array_rows;
-         *ncols = fix->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !fix->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = fix->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_local_rows;
-         *ncols = fix->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
    return;
-
 }
 
 /* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp

@@ -12,8 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
-                          University of Tennessee, Knoxville (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
+    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS.F90

@@ -12,8 +12,8 @@
 !--------------------------------------------------------------------------
 
 !! ------------------------------------------------------------------------
-!   Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+!   Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-!                         University of Tennessee, Knoxville (USA), 2012
+!                         University of Missouri (USA), 2012
 !--------------------------------------------------------------------------
 
 !! LAMMPS, a Fortran 2003 module containing an interface between Fortran

python/lammps/core.py

@@ -188,20 +188,17 @@ class lammps(object):
       [c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
     self.lib.lammps_reset_box.restype = None
 
-    self.lib.lammps_gather_atoms.argtypes = \
+    self.lib.lammps_gather_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_gather_atoms.restype = None
 
-    self.lib.lammps_gather_atoms_concat.argtypes = \
+    self.lib.lammps_gather_atoms_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_gather_atoms_concat.restype = None
 
     self.lib.lammps_gather_atoms_subset.argtypes = \
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_gather_atoms_subset.restype = None
 
-    self.lib.lammps_scatter_atoms.argtypes = \
+    self.lib.lammps_scatter_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_scatter_atoms.restype = None
 
     self.lib.lammps_scatter_atoms_subset.argtypes = \
@@ -211,20 +208,17 @@ class lammps(object):
     self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
     self.lib.lammps_gather_bonds.restype = None
 
-    self.lib.lammps_gather.argtypes = \
+    self.lib.lammps_gather.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_gather.restype = None
 
-    self.lib.lammps_gather_concat.argtypes = \
+    self.lib.lammps_gather_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_gather_concat.restype = None
 
     self.lib.lammps_gather_subset.argtypes = \
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_gather_subset.restype = None
 
-    self.lib.lammps_scatter.argtypes = \
+    self.lib.lammps_scatter.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
-      [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_scatter.restype = None
 
     self.lib.lammps_scatter_subset.argtypes = \
@@ -244,7 +238,8 @@ class lammps(object):
     self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
     self.lib.lammps_neighlist_num_elements.restype  = c_int
 
-    self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
+    self.lib.lammps_neighlist_element_neighbors.argtypes = \
+      [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
     self.lib.lammps_neighlist_element_neighbors.restype  = None
 
     self.lib.lammps_is_running.argtypes = [c_void_p]
@@ -368,11 +363,9 @@ class lammps(object):
             if type(cmdargs[i]) is str:
               cmdargs[i] = cmdargs[i].encode()
           cargs = (c_char_p*narg)(*cmdargs)
-          self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
+          self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, MPI_Comm, c_void_p]
-                                           MPI_Comm, c_void_p]
         else:
-          self.lib.lammps_open.argtypes = [c_int, c_char_p, \
+          self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p]
-                                           MPI_Comm, c_void_p]
 
         self.opened = 1
         comm_ptr = self.MPI._addressof(comm)
@@ -390,8 +383,7 @@ class lammps(object):
             if type(cmdargs[i]) is str:
               cmdargs[i] = cmdargs[i].encode()
           cargs = (c_char_p*narg)(*cmdargs)
-          self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, \
+          self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, c_void_p]
-                                                  c_void_p]
           self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))
         else:
           self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p]
@@ -963,17 +955,14 @@ class lammps(object):
       return ptr
 
     elif ctype == LMP_SIZE_COLS:
-      if cstyle == LMP_STYLE_GLOBAL  \
+      if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL:
-         or cstyle == LMP_STYLE_ATOM \
-         or cstyle == LMP_STYLE_LOCAL:
         self.lib.lammps_extract_compute.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
         return ptr[0]
 
     elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
-      if cstyle == LMP_STYLE_GLOBAL  \
+      if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL:
-         or cstyle == LMP_STYLE_LOCAL:
         self.lib.lammps_extract_compute.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)

python/lammps/numpy_wrapper.py

@@ -165,7 +165,7 @@ class numpy_wrapper:
     """
     value = self.lmp.extract_compute(cid, cstyle, ctype)
 
-    if cstyle in (LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL):
+    if cstyle == LMP_STYLE_GLOBAL:
       if ctype == LMP_TYPE_VECTOR:
         nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_VECTOR)
         return self.darray(value, nrows)
@@ -173,6 +173,13 @@ class numpy_wrapper:
         nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
         ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
         return self.darray(value, nrows, ncols)
+    elif cstyle == LMP_STYLE_LOCAL:
+      nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
+      ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
+      if ncols == 0:
+        return self.darray(value, nrows)
+      else:
+        return self.darray(value, nrows, ncols)
     elif cstyle == LMP_STYLE_ATOM:
       if ctype == LMP_TYPE_VECTOR:
         nlocal = self.lmp.extract_global("nlocal")

src/EXTRA-COMPUTE/compute_stress_cartesian.cpp

@@ -266,7 +266,7 @@ void ComputeStressCartesian::compute_array()
   Pair *pair = force->pair;
   double **cutsq = force->pair->cutsq;
 
-  double xi1, xi2, xj1, xj2;
+  double xi1, xi2;
 
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
@@ -305,9 +305,6 @@ void ComputeStressCartesian::compute_array()
           }
         }
       }
-      xj1 = x[j][dir1];
-      xj2 = x[j][dir2];
-
       delx = x[j][0] - xtmp;
       dely = x[j][1] - ytmp;
       delz = x[j][2] - ztmp;

src/EXTRA-DUMP/dump_yaml.cpp

@@ -124,6 +124,12 @@ void DumpYAML::write_data(int n, double *mybuf)
     }
     fputs("]\n", fp);
   }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpYAML::write_footer()
+{
   fputs("...\n", fp);
 }
 

src/EXTRA-DUMP/dump_yaml.h

@@ -35,6 +35,7 @@ class DumpYAML : public DumpCustom {
   void write() override;
   void write_header(bigint) override;
   void write_data(int, double *) override;
+  void write_footer() override;
 
   int modify_param(int, char **) override;
 };

src/dump.cpp

@@ -517,6 +517,8 @@ void Dump::write()
 
   if (refreshflag) modify->compute[irefresh]->refresh();
 
+  if (filewriter && fp != nullptr) write_footer();
+
   // if file per timestep, close file if I am filewriter
 
   if (multifile) {

src/dump.h

@@ -153,6 +153,8 @@ class Dump : protected Pointers {
   virtual void pack(tagint *) = 0;
   virtual int convert_string(int, double *) { return 0; }
   virtual void write_data(int, double *) = 0;
+  virtual void write_footer() {}
+
   void pbc_allocate();
   double compute_time();
 

src/library.cpp

@@ -1659,14 +1659,18 @@ lists the available options.
      - LMP_TYPE_ARRAY
      - ``double **``
      - Local data array
+   * - LMP_STYLE_LOCAL
+     - LMP_SIZE_VECTOR
+     - ``int *``
+     - Alias for using LMP_SIZE_ROWS
    * - LMP_STYLE_LOCAL
      - LMP_SIZE_ROWS
      - ``int *``
-     - Number of local data rows
+     - Number of local array rows or length of vector
    * - LMP_STYLE_LOCAL
      - LMP_SIZE_COLS
      - ``int *``
-     - Number of local data columns
+     - Number of local array columns, 0 if vector
 
 .. warning::
 
@@ -1749,6 +1753,7 @@ void *lammps_extract_compute(void *handle, const char *id, int style, int type)
       if (type == LMP_TYPE_SCALAR) return (void *) &compute->size_local_rows;  /* for backward compatibility */
       if (type == LMP_TYPE_VECTOR) return (void *) compute->vector_local;
       if (type == LMP_TYPE_ARRAY) return (void *) compute->array_local;
+      if (type == LMP_SIZE_VECTOR) return (void *) &compute->size_local_rows;  /* alias for LMP_SIZE_ROWS */
       if (type == LMP_SIZE_ROWS) return (void *) &compute->size_local_rows;
       if (type == LMP_SIZE_COLS) return (void *) &compute->size_local_cols;
     }

src/read_restart.cpp

@@ -61,9 +61,10 @@ void ReadRestart::command(int narg, char **arg)
 
   // check for remap option
 
-  int remapflag = 0;
+  int remapflag = 1;
   if (narg == 2) {
-    if (strcmp(arg[1],"remap") == 0) remapflag = 1;
+    if (strcmp(arg[1],"noremap") == 0) remapflag = 0;
+    else if (strcmp(arg[1],"remap") == 0) remapflag = 1; // for backward compatibility
     else error->all(FLERR,"Illegal read_restart command");
   }
 
@@ -643,8 +644,7 @@ void ReadRestart::header()
       int dimension = read_int();
       domain->dimension = dimension;
       if (domain->dimension == 2 && domain->zperiodic == 0)
-        error->all(FLERR,
+        error->all(FLERR, "Cannot run 2d simulation with non-periodic Z dimension");
-                   "Cannot run 2d simulation with non-periodic Z dimension");
 
     // read nprocs from restart file, warn if different
 

tools/msi2lmp/src/msi2lmp.c

@@ -66,9 +66,9 @@
 *  The program is started by supplying information at the command prompt
 * according to the usage described below.
 *
-*  USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle}
+*  USAGE: msi2lmp ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle}
 *
-*  -- msi2lmp3 is the name of the executable
+*  -- msi2lmp is the name of the executable
 *  -- ROOTNAME is the base name of the .car and .mdf files
 *  -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)
 *

unittest/force-styles/tests/manybody-pair-pace_product.yaml

@@ -1,7 +1,7 @@
 ---
 lammps_version: 17 Feb 2022
 date_generated: Fri Mar 18 22:17:48 2022
-epsilon: 1e-12
+epsilon: 5e-12
 skip_tests:
 prerequisites: ! |
   pair pace

unittest/force-styles/tests/manybody-pair-pace_recursive.yaml

@@ -1,7 +1,7 @@
 ---
 lammps_version: 10 Mar 2021
 date_generated: Wed Apr  7 19:30:07 2021
-epsilon: 1e-12
+epsilon: 5e-12
 prerequisites: ! |
   pair pace
 pre_commands: ! |

unittest/python/python-commands.py

@@ -1,6 +1,8 @@
 
 import sys,os,unittest,ctypes
-from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
+from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL
+from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
+from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
 
 has_manybody=False
 try:
@@ -311,6 +313,14 @@ create_atoms 1 single &
         self.assertEqual(minval,1.0)
         self.assertEqual(maxval,2.1)
 
+        ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR)
+        ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS)
+        ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS)
+
+        self.assertEqual(ndist1,21)
+        self.assertEqual(ndist2,21)
+        self.assertEqual(ndist3,0)
+
         self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
         self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
         self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1)

unittest/python/python-numpy.py

@@ -93,17 +93,39 @@ class PythonNumpy(unittest.TestCase):
         # TODO
         pass
 
-    def testExtractComputeLocalScalar(self):
-        # TODO
-        pass
-
     def testExtractComputeLocalVector(self):
-        # TODO
+        self.lmp.command("region       box block 0 2 0 2 0 2")
-        pass
+        self.lmp.command("create_box 1 box")
+        self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
+        self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
+        self.lmp.command("mass 1 1.0")
+        self.lmp.command("pair_style lj/cut 1.9")
+        self.lmp.command("pair_coeff 1 1 1.0 1.0")
+        self.lmp.command("compute r0 all pair/local dist")
+        self.lmp.command("run 0 post no")
+        values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR)
+        self.assertEqual(values.ndim, 1)
+        self.assertEqual(values.size, 2)
+        self.assertEqual(values[0], 0.5)
+        self.assertEqual(values[1], 1.5)
 
     def testExtractComputeLocalArray(self):
-        # TODO
+        self.lmp.command("region       box block 0 2 0 2 0 2")
-        pass
+        self.lmp.command("create_box 1 box")
+        self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
+        self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
+        self.lmp.command("mass 1 1.0")
+        self.lmp.command("pair_style lj/cut 1.9")
+        self.lmp.command("pair_coeff 1 1 1.0 1.0")
+        self.lmp.command("compute r0 all pair/local dist dx dy dz")
+        self.lmp.command("run 0 post no")
+        values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY)
+        self.assertEqual(values.ndim, 2)
+        self.assertEqual(values.size, 8)
+        self.assertEqual(values[0,0], 0.5)
+        self.assertEqual(values[0,3], -0.5)
+        self.assertEqual(values[1,0], 1.5)
+        self.assertEqual(values[1,3], 1.5)
 
     def testExtractAtomDeprecated(self):
         self.lmp.command("units lj")