Merge branch 'develop' into fix-srd-doc-page

.github/CODEOWNERS

@@ -135,6 +135,7 @@ src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
+src/fix_press_langevin.*  @Bibobu
 
 # tools
 tools/coding_standard/* @akohlmey @rbberger

doc/src/variable.rst

@@ -1183,7 +1183,7 @@ table:
 +--------+------------+------------------------------------------+
 | vector | c_ID       | global vector                            |
 | vector | c_ID[I]    | column of global array                   |
----------+------------+------------------------------------------+
++--------+------------+------------------------------------------+
 | atom   | c_ID       | per-atom vector                          |
 | atom   | c_ID[I]    | column of per-atom array                 |
 +--------+------------+------------------------------------------+
@@ -1247,7 +1247,7 @@ and atom-style variables are listed in the following table:
 +--------+------------+------------------------------------------+
 | vector | f_ID       | global vector                            |
 | vector | f_ID[I]    | column of global array                   |
----------+------------+------------------------------------------+
++--------+------------+------------------------------------------+
 | atom   | f_ID       | per-atom vector                          |
 | atom   | f_ID[I]    | column of per-atom array                 |
 +--------+------------+------------------------------------------+

src/EXTRA-DUMP/dump_yaml.cpp

@@ -24,6 +24,8 @@
 
 using namespace LAMMPS_NS;
 
+static constexpr char special_chars[] = "{}[],&:*#?|-<>=!%@\\";
+
 /* ---------------------------------------------------------------------- */
 DumpYAML::DumpYAML(class LAMMPS *_lmp, int narg, char **args) :
     DumpCustom(_lmp, narg, args), thermo(false)
@@ -67,7 +69,12 @@ void DumpYAML::write_header(bigint ndump)
       const auto &fields = th->get_fields();
 
       thermo_data += "thermo:\n  - keywords: [ ";
-      for (int i = 0; i < nfield; ++i) thermo_data += fmt::format("{}, ", keywords[i]);
+      for (int i = 0; i < nfield; ++i) {
+        if (keywords[i].find_first_of(special_chars) == std::string::npos)
+          thermo_data += fmt::format("{}, ", keywords[i]);
+        else
+          thermo_data += fmt::format("'{}', ", keywords[i]);
+      }
       thermo_data += "]\n  - data: [ ";
 
       for (int i = 0; i < nfield; ++i) {
@@ -107,7 +114,12 @@ void DumpYAML::write_header(bigint ndump)
     if (domain->triclinic) fmt::print(fp, "  - [ {}, {}, {} ]\n", boxxy, boxxz, boxyz);
 
     fmt::print(fp, "keywords: [ ");
-    for (const auto &item : utils::split_words(columns)) fmt::print(fp, "{}, ", item);
+    for (const auto &item : utils::split_words(columns)) {
+      if (item.find_first_of(special_chars) == std::string::npos)
+        fmt::print(fp, "{}, ", item);
+      else
+        fmt::print(fp, "'{}', ", item);
+    }
     fputs(" ]\ndata:\n", fp);
   } else    // reset so that the remainder of the output is not multi-proc
     filewriter = 0;

src/KOKKOS/min_kokkos.cpp

@@ -59,6 +59,9 @@ void MinKokkos::init()
 {
   Min::init();
 
+  if (!fix_minimize->kokkosable)
+    error->all(FLERR,"KOKKOS package requires fix minimize/kk");
+
   fix_minimize_kk = (FixMinimizeKokkos*) fix_minimize;
 }
 

src/KOKKOS/npair_halffull_kokkos.h

@@ -16,7 +16,7 @@
 
 // Trim off
 
-// Newton, no triclinic 
+// Newton, no triclinic
 
 typedef NPairHalffullKokkos<LMPDeviceType,1,0,0> NPairKokkosHalffullNewtonDevice;
 NPairStyle(halffull/newton/kk/device,

src/KOKKOS/npair_kokkos.cpp

@@ -1354,7 +1354,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeGPU(typename Kokkos::TeamP
       other_x[MY_II + 2 * atoms_per_bin] = ztmp;
       other_x[MY_II + 3 * atoms_per_bin] = itype;
       other_x[MY_II + 4 * atoms_per_bin] = radi;
-      if (HalfNeigh && Newton && Tri) { 
+      if (HalfNeigh && Newton && Tri) {
         itag = tag(i);
         other_x[MY_II + 5 * atoms_per_bin] = itag;
       }

src/KOKKOS/pair_snap_kokkos_impl.h

@@ -63,10 +63,6 @@ PairSNAPKokkos<DeviceType, real_type, vector_length>::PairSNAPKokkos(LAMMPS *lmp
   datamask_read = EMPTY_MASK;
   datamask_modify = EMPTY_MASK;
 
-  k_cutsq = tdual_fparams("PairSNAPKokkos::cutsq",atom->ntypes+1,atom->ntypes+1);
-  auto d_cutsq = k_cutsq.template view<DeviceType>();
-  rnd_cutsq = d_cutsq;
-
   host_flag = (execution_space == Host);
 }
 
@@ -546,6 +542,9 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::allocate()
 
   int n = atom->ntypes;
   MemKK::realloc_kokkos(d_map,"PairSNAPKokkos::map",n+1);
+
+  MemKK::realloc_kokkos(k_cutsq,"PairSNAPKokkos::cutsq",n+1,n+1);
+  rnd_cutsq = k_cutsq.template view<DeviceType>();
 }
 
 

src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp

@@ -87,6 +87,7 @@ void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list)
     n = 0;
     neighptr = ipage.vget();
 
+    itag = tag[i];
     itype = type[i];
     xtmp = x[i][0];
     ytmp = x[i][1];

src/balance.cpp

@@ -473,7 +473,7 @@ void Balance::options(int iarg, int narg, char **arg, int sortflag_default)
       }
       iarg += 2+nopt;
 
-    } else if (strcmp(arg[iarg+1],"sort") == 0) {
+    } else if (strcmp(arg[iarg],"sort") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "balance sort", error);
       sortflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;

src/fix_press_langevin.cpp

@@ -46,7 +46,8 @@ enum { ISO, ANISO, TRICLINIC };
 /* ---------------------------------------------------------------------- */
 
 FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), id_press(nullptr), pflag(0), random(nullptr), irregular(nullptr)
+    Fix(lmp, narg, arg), id_temp(nullptr), id_press(nullptr), temperature(nullptr),
+    pressure(nullptr), irregular(nullptr), random(nullptr)
 {
   if (narg < 5) utils::missing_cmd_args(FLERR, "fix press/langevin", error);
 
@@ -62,6 +63,9 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
   allremap = 1;
   pre_exchange_flag = 0;
   flipflag = 1;
+  seed = 111111;
+  pflag = 0;
+  kspace_flag = 0;
 
   p_ltime = 0.0;
 
@@ -239,7 +243,7 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
       t_start = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
       t_stop = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
       seed = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
-      if (seed <= 0.0) error->all(FLERR, "Fix press/langevin temp seed must be > 0");
+      if (seed <= 0) error->all(FLERR, "Fix press/langevin temp seed must be > 0");
       iarg += 4;
     }
 
@@ -349,7 +353,7 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
   // Kinetic contribution will be added by the fix style
 
   id_press = utils::strdup(std::string(id) + "_press");
-  modify->add_compute(fmt::format("{} all pressure NULL virial", id_press));
+  pressure = modify->add_compute(fmt::format("{} all pressure NULL virial", id_press));
   pflag = 1;
 
   // p_fric is alpha coeff from GJF
@@ -482,7 +486,7 @@ void FixPressLangevin::initial_integrate(int /* vflag */)
 
   if (delta != 0.0) delta /= update->endstep - update->beginstep;
   t_target = t_start + delta * (t_stop - t_start);
-  couple_beta(t_target);
+  couple_beta();
 
   dt = update->dt;
 
@@ -492,11 +496,12 @@ void FixPressLangevin::initial_integrate(int /* vflag */)
       displacement = dt * p_deriv[i] * gjfb[i];
       displacement += 0.5 * dt * dt * f_piston[i] * gjfb[i] / p_mass[i];
       displacement += 0.5 * dt * fran[i] * gjfb[i] / p_mass[i];
-      dl = domain->boxhi[i] - domain->boxlo[i];
+      if (i < 3) {
-      if (i < 3)
+        dl = domain->boxhi[i] - domain->boxlo[i];
         dilation[i] = (dl + displacement) / dl;
-      else
+      } else {
         dilation[i] = displacement;
+      }
     }
   }
 }
@@ -527,7 +532,7 @@ void FixPressLangevin::post_force(int /*vflag*/)
   }
 
   couple_pressure();
-  couple_kinetic(t_target);
+  couple_kinetic();
 
   for (int i = 0; i < 6; i++) {
     if (p_flag[i]) {
@@ -594,10 +599,9 @@ void FixPressLangevin::couple_pressure()
 }
 /* ---------------------------------------------------------------------- */
 
-void FixPressLangevin::couple_kinetic(double t_target)
+void FixPressLangevin::couple_kinetic()
 {
   double pk, volume;
-  nktv2p = force->nktv2p;
 
   // kinetic part
 
@@ -607,7 +611,7 @@ void FixPressLangevin::couple_kinetic(double t_target)
     volume = domain->xprd * domain->yprd;
 
   pk = atom->natoms * force->boltz * t_target / volume;
-  pk *= nktv2p;
+  pk *= force->nktv2p;
 
   p_current[0] += pk;
   p_current[1] += pk;
@@ -616,7 +620,7 @@ void FixPressLangevin::couple_kinetic(double t_target)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPressLangevin::couple_beta(double t_target)
+void FixPressLangevin::couple_beta()
 {
   double gamma[6];
   int me = comm->me;
@@ -812,7 +816,7 @@ int FixPressLangevin::modify_param(int narg, char **arg)
     id_press = utils::strdup(arg[1]);
 
     pressure = modify->get_compute_by_id(arg[1]);
-    if (pressure) error->all(FLERR, "Could not find fix_modify pressure compute ID: {}", arg[1]);
+    if (!pressure) error->all(FLERR, "Could not find fix_modify pressure compute ID: {}", arg[1]);
     if (pressure->pressflag == 0)
       error->all(FLERR, "Fix_modify pressure compute {} does not compute pressure", arg[1]);
     return 2;

src/fix_press_langevin.h

@@ -40,10 +40,9 @@ class FixPressLangevin : public Fix {
   int modify_param(int, char **) override;
 
  protected:
-  int dimension, which;
+  int dimension;
   int pstyle, pcouple, allremap;
   int p_flag[6];    // 1 if control P on this dim, 0 if not
-  double nktv2p;
   double t_start, t_stop, t_target;
   double p_fric[6], p_ltime;    // Friction and Langevin charac. time
   double p_alpha[6];
@@ -68,8 +67,8 @@ class FixPressLangevin : public Fix {
   int seed;
 
   void couple_pressure();
-  void couple_kinetic(double);
+  void couple_kinetic();
-  void couple_beta(double);
+  void couple_beta();
   void remap();
 };
 

src/fix_property_atom.cpp

@@ -46,6 +46,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   rmass_flag = 0;
   temperature_flag = 0;
   heatflow_flag = 0;
+  nmax_old = 0;
 
   nvalue = 0;
   values_peratom = 0;
@@ -212,7 +213,6 @@ void FixPropertyAtom::post_constructor()
 {
   // perform initial allocation of atom-based array
 
-  nmax_old = 0;
   grow_arrays(atom->nmax);
 }
 

src/min.cpp

@@ -215,6 +215,9 @@ void Min::setup(int flag)
   }
   update->setupflag = 1;
 
+  if (lmp->kokkos)
+    error->all(FLERR,"KOKKOS package requires Kokkos-enabled min_style");
+
   // setup extra global dof due to fixes
   // cannot be done in init() b/c update init() is before modify init()
 

tools/lammps-gui/CMakeLists.txt

@@ -110,14 +110,15 @@ endif()
 
 # we require Qt 5 and at least version 5.12 at that.
 if(NOT LAMMPS_GUI_USE_QT5)
-  find_package(Qt6 6.2 COMPONENTS Widgets Charts)
+  find_package(Qt6 6.2 QUIET COMPONENTS Widgets Charts)
 endif()
 if(NOT Qt6_FOUND)
   find_package(Qt5 5.12 REQUIRED COMPONENTS Widgets Charts)
-  set(QT_VERSION_MAJOR "5")
+  set(QT_VERSION_MAJOR 5)
 else()
-  set(QT_VERSION_MAJOR "6")
+  set(QT_VERSION_MAJOR 6)
 endif()
+message(STATUS "Using Qt version ${Qt${QT_VERSION_MAJOR}_VERSION} for LAMMPS GUI")
 
 set(PROJECT_SOURCES
   main.cpp
@@ -188,7 +189,7 @@ else()
 endif()
 target_include_directories(lammps-gui PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
 target_compile_definitions(lammps-gui PRIVATE LAMMPS_GUI_VERSION="${PROJECT_VERSION}")
-target_link_libraries(lammps-gui PRIVATE Qt${QT_VERSION_MAJOR}::Widgets Qt${VERSION_MAJOR}::Charts)
+target_link_libraries(lammps-gui PRIVATE Qt${QT_VERSION_MAJOR}::Widgets Qt${QT_VERSION_MAJOR}::Charts)
 if(BUILD_OMP)
   find_package(OpenMP COMPONENTS CXX REQUIRED)
   target_link_libraries(lammps-gui PRIVATE OpenMP::OpenMP_CXX)

tools/lammps-gui/lammpsgui.cpp

@@ -1432,12 +1432,12 @@ void LammpsGui::start_lammps()
     lammps.open(narg, args);
     lammpsstatus->show();
 
-    // must have at least 2 August 2023 version of LAMMPS
+    // must have a version newer than the 2 August 2023 release of LAMMPS
     // TODO: must update this check before next feature release
-    if (lammps.version() < 20230802) {
+    if (lammps.version() <= 20230802) {
         QMessageBox::critical(this, "Incompatible LAMMPS Version",
                               "LAMMPS-GUI version " LAMMPS_GUI_VERSION " requires\n"
-                              "LAMMPS version 2 August 2023 or later");
+                              "a LAMMPS version more recent than 2 August 2023");
         exit(1);
     }