Merge pull request #3020 from akohlmey/collected-small-changes

Collected small changes and fixes

cmake/presets/most.cmake

@@ -48,7 +48,6 @@ set(ALL_PACKAGES
   PHONON
   PLUGIN
   POEMS
-  PYTHON
   QEQ
   REACTION
   REAXFF

doc/src/Howto_github.rst

@@ -141,7 +141,8 @@ unrelated feature, you should switch branches!
    Committing changes to the *develop*, *release*, or *stable* branches
    is strongly discouraged.  While it may be convenient initially, it
    will create more work in the long run.  Various texts and tutorials
-   on using git effectively discuss the motivation for this.
+   on using git effectively discuss the motivation for using feature
+   branches instead.
 
 **After changes are made**
 

doc/src/Install_git.rst

@@ -28,8 +28,9 @@ provides `limited support for subversion clients <svn_>`_.
 
 You can follow the LAMMPS development on 3 different git branches:
 
-* **stable**   :  this branch is updated with every stable release;
-  updates are always "fast forward" merges from *develop*
+* **stable**   :  this branch is updated from the *release* branch with
+  every stable release version and also has selected bug fixes and updates
+  back-ported from the *develop* branch
 * **release**  :  this branch is updated with every patch release;
   updates are always "fast forward" merges from *develop*
 * **develop**  :  this branch follows the ongoing development and
@@ -47,20 +48,22 @@ your machine and "release" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
 between them at any time using "git checkout <branch name>".)
 
-.. note::
+.. admonition:: Saving time and disk space when using ``git clone``
 
    The complete git history of the LAMMPS project is quite large because
    it contains the entire commit history of the project since fall 2006,
-   which includes the time when LAMMPS was managed with subversion. This
-   also includes commits that have added and removed some large files
-   (mostly by accident).  If you do not need access to the entire commit
-   history, you can speed up the "cloning" process and reduce local disk
-   space requirements by using the *--depth* git command line flag thus
-   create a "shallow clone" of the repository that contains only a
-   subset of the git history. Using a depth of 1000 is usually sufficient
-   to include the head commits of the *develop* and the *release* branches.
-   To include the head commit of the *stable* branch you may need a depth
-   of up to 10000.
+   which includes the time when LAMMPS was managed with subversion.
+   This includes a few commits that have added and removed some large
+   files (mostly by accident).  If you do not need access to the entire
+   commit history (most people don't), you can speed up the "cloning"
+   process and reduce local disk space requirements by using the
+   *--depth* git command line flag.  That will create a "shallow clone"
+   of the repository containing only a subset of the git history.  Using
+   a depth of 1000 is usually sufficient to include the head commits of
+   the *develop* and the *release* branches.  To include the head commit
+   of the *stable* branch you may need a depth of up to 10000.  If you
+   later need more of the git history, you can always convert the
+   shallow clone into a "full clone".
 
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with the exception, that

doc/src/Manual_version.rst

@@ -10,23 +10,31 @@ Whenever we fix a bug or update or add a feature, it will be merged into
 the *develop* branch of the git repository.  When a sufficient number of
 changes have accumulated *and* the software passes a set of automated
 tests, we release it in the next *patch* release, which are made every
-few weeks.  Info on patch releases are on `this website page
+few weeks.  The *release* branch of the git repository is updated with
+every such release.  Info on patch releases are on `this website page
 <https://www.lammps.org/bug.html>`_.
 
-Once or twice a year, only bug fixes and small, non-intrusive changes are
-included for a period of time, and the code is subjected to more detailed
+Once or twice a year, we apply only bug fixes and small, non-intrusive
+changes to the *develop* branch and the code is subjected to more detailed
 and thorough testing than the default automated testing.  The latest
-patch release after such a period is then labeled as a *stable* version.
+patch release after such a period is then also labeled as a *stable* version
+and the *stable* branch is updated with it.  Between stable releases
+we occasionally release some updates to the stable release containing
+only bug fixes and updates back-ported from *develop* but no new features
+and update the *stable* branch accordingly.
 
-Each version of LAMMPS contains all the features and bug-fixes up to
-and including its version date.
+Each version of LAMMPS contains all the documented features up to and
+including its version date.
 
 The version date is printed to the screen and logfile every time you
 run LAMMPS. It is also in the file src/version.h and in the LAMMPS
 directory name created when you unpack a tarball.  And it is on the
 first page of the :doc:`manual <Manual>`.
 
-* If you browse the HTML pages on the LAMMPS WWW site, they always
-  describe the most current patch release of LAMMPS.
+* If you browse the HTML pages on the LAMMPS WWW site, they will by
+  default describe the most current patch release version of LAMMPS.
+  In the navigation bar on the bottom left, there is the option to
+  view instead the documentation for the most recent *stable* version
+  or the latest version from the current development branch.
 * If you browse the HTML pages included in your tarball, they
   describe the version you have, which may be older.

doc/src/dump_modify.rst

@@ -710,7 +710,9 @@ default and it can be disabled with the :code:`checksum` keyword.
 
 Restrictions
 """"""""""""
- none
+
+Not all *dump_modify* options can be applied to all dump styles.
+Details are in the discussions of the individual options.
 
 Related commands
 """"""""""""""""

doc/src/pair_granular.rst

@@ -205,7 +205,7 @@ For *damping mass_velocity*, the normal damping is given by:
    \eta_n = \eta_{n0} m_{eff}
 
 Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
-contact model, in units of *mass*\ /\ *time* and
+contact model, in units of 1/\ *time* and
 :math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass.
 Use *damping mass_velocity* to reproduce the damping behavior of
 *pair gran/hooke/\**.

doc/src/pair_lebedeva_z.rst

@@ -26,15 +26,29 @@ Examples
 Description
 """""""""""
 
-The *lebedeva/z* style computes the Lebedeva interaction
-potential as described in :ref:`(Lebedeva et al.) <Leb01>`. An important simplification is made,
-which is to take all normals along the z-axis.
+The *lebedeva/z* pair style computes the Lebedeva interaction potential
+as described in :ref:`(Lebedeva1) <Leb01>` and :ref:`(Lebedeva2)
+<Leb02>`.  An important simplification is made, which is to take all
+normals along the z-axis.
+
+The Lebedeva potential is intended for the description of the interlayer
+interaction between graphene layers.  To perform a realistic simulation,
+this potential must be used in combination with an intralayer potential
+such as :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>`
+facilitated by using pair style :doc:`hybrid/overlay <pair_hybrid>`.  To
+keep the intralayer properties unaffected, the interlayer interaction
+within the same layers should be avoided.  This can be achieved by
+assigning different atom types to atoms of different layers (e.g. 1 and
+2 in the examples above).
+
+Other interactions can be set to zero using pair_style *none*\ .
+
 
 .. math::
 
-   E       = & \frac{1}{2} \sum_i \sum_{i \neq j} V_{ij}\\
+   E       = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij}\\
    V_{ij}  = & B e^{-\alpha(r_{ij} - z_0)} \\
-             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij} e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
+             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij}) e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
              & - A \left(\frac{z_0}{r_ij}\right)^6 + A \left( \frac{z_0}{r_c} \right)^6 \\
    \rho^2_{ij} = & x^2_{ij} + y^2_{ij} \qquad (\mathbf{n_i} \equiv \mathbf{\hat{z}})
 
@@ -43,12 +57,15 @@ Energies are shifted so that they go continuously to zero at the cutoff assuming
 that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast.
 This shift is achieved by the last term in the equation for :math:`V_{ij}` above.
 
-The parameter file (e.g. CC.Lebedeva), is intended for use with metal
-:doc:`units <units>`, with energies in meV. An additional parameter, *S*,
-is available to facilitate scaling of energies.
+The provided parameter file (CC.Lebedeva) contains two sets of parameters.
 
-This potential must be used in combination with hybrid/overlay.
-Other interactions can be set to zero using pair_style *none*\ .
+- The first set (element name "C") is suitable for normal conditions and
+  is taken from :ref:`(Popov1) <Popov>`
+- The second set (element name "C1") is suitable for high-pressure
+  conditions and is taken from :ref:`(Koziol1) <Koziol>`
+
+Both sets contain an additional parameter, *S*, that can be used to
+facilitate scaling of energies and is set to 1.0 by default.
 
 Restrictions
 """"""""""""
@@ -77,4 +94,16 @@ none
 
 .. _Leb01:
 
-**(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+**(Lebedeva1)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+
+.. _Leb02:
+
+**(Lebedeva2)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
+
+.. _Popov:
+
+**(Popov1)** A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
+
+.. _Koziol:
+
+**(Koziol1)** Z. Koziol, G. Gawlik and J. Jagielski, Chinese Phys. B 28, 096101 (2019).

doc/utils/sphinx-config/false_positives.txt

@@ -1125,6 +1125,7 @@ gaussian
 gaussians
 Gaussians
 Gavhane
+Gawlik
 gayberne
 gcc
 gcmc
@@ -1483,6 +1484,7 @@ Izz
 Jacobsen
 Jadhao
 Jadhav
+Jagielski
 jagreat
 Jahn
 Jalalvand
@@ -1609,6 +1611,7 @@ Koslowski
 Kosovan
 Koster
 Kosztin
+Koziol
 Kp
 kradius
 Kraker

potentials/CC.Lebedeva

@@ -1,12 +1,13 @@
-# DATE: 2018-11-28  UNITS: metal  CONTRIBUTOR: Zbigniew Koziol softquake@gmail.com CITATION: Z. Koziol et al.: https://arxiv.org/abs/1803.05162
+# DATE: 2021-11-04  UNITS: metal  CONTRIBUTOR: Zbigniew Koziol softquake@gmail.com CITATION: Z. Koziol et al.: https://arxiv.org/abs/1803.05162
 #
-# Lebedeva Potential. https://doi.org/10.1016/j.physe.2011.07.018
+# Lebedeva potential: https://doi.org/10.1039/C0CP02614J and https://doi.org/10.1016/j.physe.2011.07.018
 
 # Parameters must be in this order as here, otherwise their values may be changed.
+# Energies here are given in meV.
 # The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
 #        A       B           C       z0     alpha   D1      D2       lambda1   lambda2     S
-# These are values according to Levedeva et al
-#C  C   10.510  11.6523.34  35.883  3.34    4.16   -0.86232 0.10049  0.48703   0.46445     1.0
+# These are values according to Lebedeva et al.: https://doi.org/10.1016/j.cplett.2012.03.082
+C  C   10.510  11.652  29.5  3.34    4.16   -0.86232 0.10049  0.48703   0.46445     1.0
 #
 # These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
-C  C    14.558  21.204      1.8     3.198   4.16   -0.862   0.10049  0.6       0.4         1.0
+C1  C1    14.558  21.204      1.8     3.198   4.16   -0.862   0.10049  0.6       0.4         1.0

src/DRUDE/compute_temp_drude.cpp

@@ -89,9 +89,7 @@ void ComputeTempDrude::dof_compute()
   int dim = domain->dimension;
   int *drudetype = fix_drude->drudetype;
 
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  adjust_dof_fix();
 
   bigint dof_core_loc = 0, dof_drude_loc = 0;
   for (int i = 0; i < nlocal; i++) {

src/DRUDE/compute_temp_drude.h

@@ -35,7 +35,6 @@ class ComputeTempDrude : public Compute {
   int modify_param(int, char **);
 
  private:
-  int fix_dof;
   class FixDrude *fix_drude;
   char *id_temp;
   class Compute *temperature;

src/EXTRA-COMPUTE/compute_temp_rotate.h

@@ -43,7 +43,6 @@ class ComputeTempRotate : public Compute {
   double memory_usage();
 
  private:
-  int fix_dof;
   double tfactor, masstotal;
   double **vbiasall;    // stored velocity bias for all atoms
   int maxbias;          // size of vbiasall array

src/MACHDYN/atom_vec_smd.cpp

@@ -115,6 +115,7 @@ void AtomVecSMD::grow_pointers()
   vfrac = atom->vfrac;
   rmass = atom->rmass;
   x0 = atom->x0;
+  x = atom->x;
   radius = atom->radius;
   contact_radius = atom->contact_radius;
   molecule = atom->molecule;
@@ -129,13 +130,11 @@ void AtomVecSMD::grow_pointers()
 /* ----------------------------------------------------------------------
    clear extra forces starting at atom N
    nbytes = # of bytes to clear for a per-atom vector
-   NOTE: does f need to be re-cleared?
 ------------------------------------------------------------------------- */
 
 void AtomVecSMD::force_clear(int n, size_t nbytes)
 {
   memset(&desph[n],0,nbytes);
-  memset(&f[n][0],0,3*nbytes);
 }
 
 /* ----------------------------------------------------------------------

src/MACHDYN/compute_smd_triangle_vertices.cpp

@@ -53,7 +53,7 @@ ComputeSMDTriangleVertices::ComputeSMDTriangleVertices(LAMMPS *lmp, int narg, ch
 /* ---------------------------------------------------------------------- */
 
 ComputeSMDTriangleVertices::~ComputeSMDTriangleVertices() {
-    memory->sfree(outputVector);
+    memory->destroy(outputVector);
 }
 
 /* ---------------------------------------------------------------------- */

src/MACHDYN/pair_smd_ulsph.cpp

@@ -85,7 +85,8 @@ PairULSPH::PairULSPH(LAMMPS *lmp) :
 
 PairULSPH::~PairULSPH() {
         if (allocated) {
-                //printf("... deallocating\n");
+                memory->destroy(setflag);
+                memory->destroy(cutsq);
                 memory->destroy(Q1);
                 memory->destroy(rho0);
                 memory->destroy(eos);

src/fix_deposit.cpp

@@ -569,10 +569,12 @@ void FixDeposit::pre_exchange()
     //   coord is new position of geometric center of mol, not COM
     // FixShake::set_molecule stores shake info for molecule
 
+    if (mode == MOLECULE) {
       if (rigidflag)
         fixrigid->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
       else if (shakeflag)
         fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
+    }
 
     success = 1;
     break;

src/verlet.cpp

@@ -54,7 +54,7 @@ void Verlet::init()
 
   bool do_time_integrate = false;
   for (const auto &fix : modify->get_fix_list())
-    if (fix->time_integrate) do_time_integrate;
+    if (fix->time_integrate) do_time_integrate = true;
 
   if (!do_time_integrate && (comm->me == 0))
     error->warning(FLERR,"No fixes with time integration, atoms won't move");

tools/lammps-shell/.clang-format

@@ -0,0 +1 @@
+../../unittest/.clang-format

tools/lammps-shell/lammps-shell.cpp

@@ -10,8 +10,8 @@
 #include "utils.h"
 
 #include <cstring>
-#include <iostream>
 #include <fstream>
+#include <iostream>
 #include <string>
 #include <vector>
 
@@ -342,14 +342,13 @@ static char *plugin_generator(const char *text, int state)
 {
     const char *subcmd[] = {"load", "unload", "list", "clear", nullptr};
     const char *sub;
-    static std::size_t idx=0, len;
+    static std::size_t idx = 0, len;
     if (!state) idx = 0;
     len = strlen(text);
 
     while ((sub = subcmd[idx]) != nullptr) {
         ++idx;
-        if (strncmp(text,sub,len) == 0)
-            return dupstring(sub);
+        if (strncmp(text, sub, len) == 0) return dupstring(sub);
     }
     return nullptr;
 }
@@ -358,13 +357,12 @@ static char *plugin_style_generator(const char *text, int state)
 {
     const char *styles[] = {"pair", "fix", "command", nullptr};
     const char *s;
-    static std::size_t idx=0, len;
+    static std::size_t idx = 0, len;
     if (!state) idx = 0;
     len = strlen(text);
     while ((s = styles[idx]) != nullptr) {
         ++idx;
-        if (strncmp(text,s,len) == 0)
-            return dupstring(s);
+        if (strncmp(text, s, len) == 0) return dupstring(s);
     }
     return nullptr;
 }
@@ -384,8 +382,7 @@ static char *plugin_name_generator(const char *text, int state)
         lammps_plugin_name(idx, style, name, BUFLEN);
         ++idx;
         if (words[2] == style) {
-            if (strncmp(name, words[3].c_str(), len) == 0)
-                return dupstring(name);
+            if (strncmp(name, words[3].c_str(), len) == 0) return dupstring(name);
         }
     }
     return nullptr;
@@ -527,9 +524,7 @@ static char **cmd_completion(const char *text, int start, int)
         } else if (words.size() == 2) { // expand third word
 
             // these commands have a group name as 3rd word
-            if ((words[0] == "fix")
-                || (words[0] == "compute")
-                || (words[0] == "dump")) {
+            if ((words[0] == "fix") || (words[0] == "compute") || (words[0] == "dump")) {
                 matches = rl_completion_matches(text, group_generator);
             } else if (words[0] == "region") {
                 matches = rl_completion_matches(text, region_generator);
@@ -736,7 +731,7 @@ int main(int argc, char **argv)
     // switch to the user's documents directory.
 
     auto curdir = platform::current_directory();
-    if (utils::strmatch(curdir,"[Ss]ystem32")) {
+    if (utils::strmatch(curdir, "[Ss]ystem32")) {
         std::string docdir = getenv("HOMEDRIVE");
         docdir += getenv("HOMEPATH");
         docdir += "\\Documents";

unittest/CMakeLists.txt

@@ -54,6 +54,10 @@ if(BUILD_MPI)
     set(MPI_TEST_NUM_PROCS 1)
     set(MPI_TEST_WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     cmake_parse_arguments(MPI_TEST "" "NAME;NUM_PROCS;WORKING_DIRECTORY" "COMMAND" ${ARGN})
+    # Do not add test when oversubscribing
+    if(MPI_TEST_NUMPROCS GREATER MPIEXEC_MAX_NUMPROCS)
+      return()
+    endif()
     list(GET MPI_TEST_COMMAND 0 EXECUTABLE)
     list(REMOVE_AT MPI_TEST_COMMAND 0)
     set(ARGS ${MPI_TEST_COMMAND})

unittest/commands/test_groups.cpp

@@ -246,7 +246,7 @@ TEST_F(GroupTest, Molecular)
     ASSERT_DOUBLE_EQ(group->mass(group->find("half")), 40);
     ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->find_region("top")), 10);
     ASSERT_NEAR(group->charge(group->find("top")), 0, 1.0e-14);
-    ASSERT_DOUBLE_EQ(group->charge(group->find("right"), domain->find_region("top")), 0);
+    ASSERT_NEAR(group->charge(group->find("right"), domain->find_region("top")), 0, 1.0e-14);
 
     TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three include xxx"););
 }

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

@@ -14,7 +14,7 @@ post_commands: ! ""
 input_file: in.bilayer
 pair_style: hybrid/overlay lebedeva/z 16.0
 pair_coeff: ! |
-  * * lebedeva/z CC.Lebedeva C C C
+  * * lebedeva/z CC.Lebedeva C1 C1 C1
 extract: ! ""
 natoms: 48
 init_vdwl: 2360.887727742073