Merge branch 'master' into fep

LICENSE

@@ -301,9 +301,8 @@ one line to give the program's name and an idea of what it does.
 Copyright (C) yyyy  name of author
 
 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
+it under the terms of the GNU General Public License version 2 as
-the Free Software Foundation; either version 2 of the License, or (at
+published by the Free Software Foundation.
-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

cmake/CMakeLists.txt

@@ -26,7 +26,14 @@ find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
+option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
+if (LAMMPS_INSTALL_RPATH)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner

doc/src/Build_basics.rst

@@ -526,6 +526,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

doc/src/Howto_cmake.rst

@@ -296,6 +296,8 @@ Some common CMake variables
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
      - root directory of install location for ``make install``  (default: ``$HOME/.local``)
+   * - ``LAMMPS_INSTALL_RPATH``
+     - set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
    * - ``CMAKE_BUILD_TYPE``
      - controls compilation options:
        one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``

doc/src/create_box.rst

@@ -13,7 +13,7 @@ Syntax
 * N = # of atom types to use in this simulation
 * region-ID = ID of region to use as simulation domain
 * zero or more keyword/value pairs may be appended
-* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
+* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
 
   .. parsed-literal::
 

examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep01/in.insertion

@@ -12,7 +12,7 @@ improper_style  class2
 pair_modify     mix sixthpower tail yes
 special_bonds   lj/coul 0 0 1
 
-read_data       data.init_conf_without_heptane
+read_data       data.init_conf_with_heptane
 
 pair_coeff    1    6  lj/class2/coul/long/soft   0.054 4.01 0.0
 pair_coeff    2    6  lj/class2/coul/long/soft   0.054 4.01 0.0
@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep10/in.deletion

@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

python/lammps/core.py

@@ -121,18 +121,16 @@ class lammps(object):
         lib_ext = ".so"
 
     if not self.lib:
-      try:
+      if name:
-        if not name:
+        libpath = join(modpath,"liblammps_%s" % name + lib_ext)
-          self.lib = CDLL(join(modpath,"liblammps" + lib_ext),RTLD_GLOBAL)
       else:
-          self.lib = CDLL(join(modpath,"liblammps_%s" % name + lib_ext),
+        libpath = join(modpath,"liblammps" + lib_ext)
-                          RTLD_GLOBAL)
+      if not os.path.isfile(libpath):
-      except:
+        if name:
-        if not name:
+          libpath = "liblammps_%s" % name + lib_ext
-          self.lib = CDLL("liblammps" + lib_ext,RTLD_GLOBAL)
         else:
-          self.lib = CDLL("liblammps_%s" % name + lib_ext,RTLD_GLOBAL)
+          libpath = "liblammps" + lib_ext
-
+      self.lib = CDLL(libpath,RTLD_GLOBAL)
 
     # declare all argument and return types for all library methods here.
     # exceptions are where the arguments depend on certain conditions and

src/GRANULAR/fix_pour.cpp

@@ -371,6 +371,14 @@ void FixPour::init()
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixPour::setup_pre_exchange()
+{
+  if (ninserted < ninsert) next_reneighbor = update->ntimestep + 1;
+  else next_reneighbor = 0;
+}
+
 /* ----------------------------------------------------------------------
    perform particle insertion
 ------------------------------------------------------------------------- */

src/GRANULAR/fix_pour.h

@@ -30,6 +30,7 @@ class FixPour : public Fix {
   ~FixPour();
   int setmask();
   void init();
+  void setup_pre_exchange();
   void pre_exchange();
   void reset_dt();
   void *extract(const char *, int &);
@@ -63,7 +64,8 @@ class FixPour : public Fix {
 
   int me,nprocs;
   int *recvcounts,*displs;
-  int nfreq,nfirst,ninserted,nper;
+  int nfreq,ninserted,nper;
+  bigint nfirst;
   double lo_current,hi_current;
   tagint maxtag_all,maxmol_all;
   class RanPark *random,*random2;

src/MISC/fix_deposit.cpp

@@ -292,6 +292,14 @@ void FixDeposit::init()
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixDeposit::setup_pre_exchange()
+{
+  if (ninserted < ninsert) next_reneighbor = update->ntimestep+1;
+  else next_reneighbor = 0;
+}
+
 /* ----------------------------------------------------------------------
    perform particle insertion
 ------------------------------------------------------------------------- */
@@ -833,7 +841,7 @@ void FixDeposit::write_restart(FILE *fp)
   double list[5];
   list[n++] = random->state();
   list[n++] = ninserted;
-  list[n++] = nfirst;
+  list[n++] = ubuf(nfirst).d;
   list[n++] = ubuf(next_reneighbor).d;
   list[n++] = ubuf(update->ntimestep).d;
 
@@ -855,10 +863,10 @@ void FixDeposit::restart(char *buf)
 
   seed = static_cast<int>(list[n++]);
   ninserted = static_cast<int>(list[n++]);
-  nfirst = static_cast<int> (list[n++]);
+  nfirst = static_cast<bigint>(ubuf(list[n++]).i);
-  next_reneighbor = (bigint) ubuf(list[n++]).i;
+  next_reneighbor = static_cast<bigint>(ubuf(list[n++]).i);
 
-  bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
+  bigint ntimestep_restart = static_cast<bigint>(ubuf(list[n++]).i);
   if (ntimestep_restart != update->ntimestep)
     error->all(FLERR,"Must not reset timestep when restarting this fix");
 

src/MISC/fix_deposit.h

@@ -30,6 +30,7 @@ class FixDeposit : public Fix {
   ~FixDeposit();
   int setmask();
   void init();
+  void setup_pre_exchange();
   void pre_exchange();
   void write_restart(FILE *);
   void restart(char *);
@@ -54,7 +55,8 @@ class FixDeposit : public Fix {
   class Fix *fixrigid,*fixshake;
   double oneradius;
 
-  int nfirst,ninserted;
+  int ninserted;
+  bigint nfirst;
   tagint maxtag_all,maxmol_all;
   class RanPark *random;
 

src/PYTHON/pair_python.cpp

@@ -49,14 +49,19 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
   python->init();
 
   // add current directory to PYTHONPATH
+
+  PyGILState_STATE gstate = PyGILState_Ensure();
   PyObject *py_path = PySys_GetObject((char *)"path");
   PyList_Append(py_path, PY_STRING_FROM_STRING("."));
 
-  // if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
+  // if LAMMPS_POTENTIALS environment variable is set,
+  // add it to PYTHONPATH as well
+
   const char *potentials_path = getenv("LAMMPS_POTENTIALS");
   if (potentials_path != nullptr) {
     PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
   }
+  PyGILState_Release(gstate);
 }
 
 /* ---------------------------------------------------------------------- */

src/imbalance_time.cpp

@@ -59,16 +59,19 @@ void ImbalanceTime::compute(double *weight)
   // cost = CPU time for relevant timers since last invocation
   // localwt = weight assigned to each owned atom
   // just return if no time yet tallied
+  // we 0.1 seconds as a minimum time to avoid computation of bogus
+  // load balancing weights due to limited timer resolution/precision
 
   double cost = -last;
   cost += timer->get_wall(Timer::PAIR);
   cost += timer->get_wall(Timer::NEIGH);
   cost += timer->get_wall(Timer::BOND);
   cost += timer->get_wall(Timer::KSPACE);
+  cost += 0.1;
 
   double maxcost;
   MPI_Allreduce(&cost,&maxcost,1,MPI_DOUBLE,MPI_MAX,world);
-  if (maxcost <= 0.0) return;
+  if (maxcost <= 0.1) return;
 
   int nlocal = atom->nlocal;
   double localwt = 0.0;

src/main.cpp

@@ -64,9 +64,15 @@ int main(int argc, char **argv)
     exit(1);
   }
 #else
+  try {
     LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
     lammps->input->file();
     delete lammps;
+  } catch(fmt::format_error &fe) {
+    fprintf(stderr,"fmt::format_error: %s\n", fe.what());
+    MPI_Abort(MPI_COMM_WORLD, 1);
+    exit(1);
+  }
 #endif
   MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();

src/utils.cpp

@@ -414,6 +414,9 @@ void utils::bounds(const char *file, int line, const std::string &str,
   }
 
   if (error) {
+    if ((nlo <= 0) || (nhi <=0))
+      error->all(file,line,fmt::format("Invalid range string: {}",str));
+
     if (nlo < nmin)
       error->all(file,line,fmt::format("Numeric index {} is out of bounds"
                                        "({}-{})",nlo,nmin,nmax));
@@ -688,7 +691,7 @@ std::string utils::utf8_subst(const std::string &line)
           out += ' ', i += 2;
       }
     // UTF-8 4-byte character
-    } else if ((in[i] & 0xe8U) == 0xf0U) {
+    } else if ((in[i] & 0xf8U) == 0xf0U) {
       if ((i+3) < len) {
         ;
       }