Merge pull request #4446 from jtclemm/small-patches

Miscellaneous small patches

doc/src/Developer_code_design.rst

@@ -203,6 +203,7 @@ processed in the expected order before types are removed from dynamic
 dispatch.
 
 .. admonition:: Important Notes
+   :class: note
 
    In order to be able to detect incompatibilities at compile time and
    to avoid unexpected behavior, it is crucial that all member functions

doc/src/Fortran.rst

@@ -956,6 +956,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
       :f:func:`extract_atom` between runs.
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional arrays returned from :f:func:`extract_atom` will be
       **transposed** from equivalent arrays in C, and they will be indexed
@@ -1068,6 +1069,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    you based on data from the :cpp:class:`Compute` class.
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional arrays returned from :f:func:`extract_compute` will be
       **transposed** from equivalent arrays in C, and they will be indexed
@@ -1326,6 +1328,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :rtype data: polymorphic
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional global, per-atom, or local array data from
       :f:func:`extract_fix` will be **transposed** from equivalent arrays in

doc/src/Howto_barostat.rst

@@ -10,20 +10,21 @@ and/or pressure (P) is specified by the user, and the thermostat or
 barostat attempts to equilibrate the system to the requested T and/or
 P.
 
-Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Two
+Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Three
 barostatting methods are currently available: Nose-Hoover (npt and
-nph) and Berendsen:
+nph), Berendsen, and various linear controllers in deform/pressure:
 
 * :doc:`fix npt <fix_nh>`
 * :doc:`fix npt/sphere <fix_npt_sphere>`
 * :doc:`fix npt/asphere <fix_npt_asphere>`
 * :doc:`fix nph <fix_nh>`
 * :doc:`fix press/berendsen <fix_press_berendsen>`
+* :doc:`fix deform/pressure <fix_deform_pressure>`
 
 The :doc:`fix npt <fix_nh>` commands include a Nose-Hoover thermostat
 and barostat.  :doc:`Fix nph <fix_nh>` is just a Nose/Hoover barostat;
-it does no thermostatting.  Both :doc:`fix nph <fix_nh>` and :doc:`fix press/berendsen <fix_press_berendsen>` can be used in conjunction
-with any of the thermostatting fixes.
+it does no thermostatting.  The fixes :doc:`nph <fix_nh>`, :doc:`press/berendsen <fix_press_berendsen>`, and :doc:`deform/pressure <fix_deform_pressure>`
+can be used in conjunction with any of the thermostatting fixes.
 
 As with the :doc:`thermostats <Howto_thermostat>`, :doc:`fix npt <fix_nh>`
 and :doc:`fix nph <fix_nh>` only use translational motion of the
@@ -44,9 +45,9 @@ a temperature or pressure compute to a barostatting fix.
 .. note::
 
    As with the thermostats, the Nose/Hoover methods (:doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`) perform time integration.
-   :doc:`Fix press/berendsen <fix_press_berendsen>` does NOT, so it should
-   be used with one of the constant NVE fixes or with one of the NVT
-   fixes.
+   :doc:`Fix press/berendsen <fix_press_berendsen>` and :doc:`fix deform/pressure <fix_deform_pressure>`
+   do NOT, so they should be used with one of the constant NVE fixes or with
+   one of the NVT fixes.
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes pressure

doc/src/Install_git.rst

@@ -52,6 +52,7 @@ your machine and "release" is one of the 3 branches listed above.
 between them at any time using "git checkout <branch name>".)
 
 .. admonition:: Saving time and disk space when using ``git clone``
+   :class: note
 
    The complete git history of the LAMMPS project is quite large because
    it contains the entire commit history of the project since fall 2006,

doc/src/pair_mliap.rst

@@ -145,6 +145,7 @@ per line.
 The detail of *nn* module implementation can be found at :ref:`(Yanxon) <Yanxon2020>`.
 
 .. admonition:: Notes on mliappy models
+   :class: note
 
    When the *model* keyword is *mliappy*, if the filename ends in '.pt',
    or '.pth', it will be loaded using pytorch; otherwise, it will be

doc/src/pair_reaxff.rst

@@ -158,11 +158,36 @@ drops to zero.
 Optional keywords *safezone*, *mincap*, and *minhbonds* are used
 for allocating reaxff arrays.  Increasing these values can avoid memory
 problems, such as segmentation faults and bondchk failed errors, that
-could occur under certain conditions. These keywords are not used by
+could occur under certain conditions. These keywords are **not** used by
 the Kokkos version, which instead uses a more robust memory allocation
 scheme that checks if the sizes of the arrays have been exceeded and
 automatically allocates more memory.
 
+.. admonition:: Memory management problems with ReaxFF
+   :class: tip
+
+   The LAMMPS implementation of ReaxFF is adapted from a standalone MD
+   program written in C called `PuReMD
+   <https://github.com/msu-sparta/PuReMD>`_.  It inherits from this code
+   a heuristic memory management that is different from what the rest of
+   LAMMPS uses.  It assumes that a system is dense and already well
+   equilibrated, so that there are no large changes in how many and what
+   types of neighbors atoms have.  However, not all systems are like
+   that, and thus there can be errors or segmentation faults if the
+   system changes too much.  If you run into problems, here are three
+   options to avoid them:
+
+   - Use the KOKKOS version of ReaxFF (KOKKOS is not only for GPUs,
+     but can also be compiled for serial or OpenMP execution) which
+     uses a different memory management approach.
+   - Break down a run command during which memory related errors happen
+     into multiple smaller segments so that the memory management
+     heuristics are re-initialized for each segment before they become
+     invalid.
+   - Increase the values for *safezone*, *mincap*, and *minhbonds* as
+     needed.  This can lead to significant increase of memory consumption
+     through.
+
 The keyword *tabulate* controls the size of interpolation table for
 Lennard-Jones and Coulomb interactions. Tabulation may also be set in the
 control file (see below). If tabulation is set in both the input script and the

examples/PACKAGES/stressprofile/in.flat

@@ -32,7 +32,7 @@ fix             1 all nvt temp 0.7 0.7 0.2
 #dump_modify    3 pad 3
 
 fix 2 all recenter NULL NULL 15 units lattice
-compute p1 all stress/cartesian z 0.5
+compute p1 all stress/cartesian z 0.5 NULL 0
 fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector
 
 thermo          50

examples/multi/in.granular

@@ -1,4 +1,4 @@
-# Big colloid particles and small LJ particles
+# Binary granular system
 
 units           lj
 atom_style      sphere

src/EXTRA-FIX/fix_electron_stopping_fit.cpp

@@ -68,7 +68,8 @@ FixElectronStoppingFit::FixElectronStoppingFit(LAMMPS *lmp, int narg, char **arg
      error->all(FLERR,"Incorrect number of fix electron/stopping/fit arguments");
   }
 
-  scalar_flag = 1;
+  scalar_flag = 1; // intensive total energy loss since start of run
+  extscalar = 0;
   global_freq = 1;
 
   energy_coh_in = new double[atom->ntypes+1];

src/MISC/pair_srp.cpp

@@ -397,10 +397,11 @@ void PairSRP::coeff(int narg, char **arg)
     error->all(FLERR,"PairSRP: Incorrect args for pair coeff");
   if (!allocated) allocate();
 
-  if (btype_str.size() > 0)
+  if (btype_str.size() > 0) {
     btype = utils::expand_type_int(FLERR, btype_str, Atom::BOND, lmp);
     if ((btype > atom->nbondtypes) || (btype <= 0))
       error->all(FLERR,"Invalid bond type {} for pair style srp", btype);
+  }
 
   if (bptype_str.size() > 0)
     bptype = utils::expand_type_int(FLERR, bptype_str, Atom::ATOM, lmp);

src/RHEO/fix_rheo_pressure.cpp

@@ -273,11 +273,13 @@ double FixRHEOPressure::calc_rho(double p, int i)
     error->one(FLERR,
                "Rho calculation from pressure not yet supported for cubic pressure equation");
   } else if (pressure_style[type] == TAITWATER) {
-    rho = pow(7.0 * p + csq[type] * rho0[type], SEVENTH);
+    double tmp = 7.0 * p + csq[type] * rho0[type];
+    rho = pow(MAX(0.0, tmp), SEVENTH);
     rho *= pow(rho0[type], 6.0 * SEVENTH);
     rho *= pow(csq[type], -SEVENTH);
   } else if (pressure_style[type] == TAITGENERAL) {
-    rho = pow(tpower[type] * p + csq[type] * rho0[type], 1.0 / tpower[type]);
+    double tmp = tpower[type] * p + csq[type] * rho0[type];
+    rho = pow(MAX(0.0, tmp), 1.0 / tpower[type]);
     rho *= pow(rho0[type], 1.0 - 1.0 / tpower[type]);
     rho *= pow(csq[type], -1.0 / tpower[type]);
   } else if (pressure_style[type] == IDEAL) {