Merge pull request lammps#4164 from akohlmey/collected-small-changes

Collected small changes and fixes

python/lammps/core.py

@@ -376,12 +376,16 @@ def __init__(self,name='',cmdargs=None,ptr=None,comm=None):
         narg = 0
         cargs = None
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*(narg+1))(*cmdargs)
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
           cargs[narg] = None
           self.lib.lammps_open.argtypes = [c_int, c_char_p*(narg+1), MPI_Comm, c_void_p]
         else:
@@ -397,12 +401,16 @@ def __init__(self,name='',cmdargs=None,ptr=None,comm=None):
           self.comm = self.MPI.COMM_WORLD
         self.opened = 1
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*(narg+1))(*cmdargs)
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
           cargs[narg] = None
           self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*(narg+1), c_void_p]
           self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))

src/EXTRA-COMPUTE/compute_stress_cartesian.cpp

@@ -386,7 +386,7 @@ void ComputeStressCartesian::compute_array()
         if (tag[i] > tag[j]) {
           if ((tag[i] + tag[j]) % 2 == 0) continue;
         } else if (tag[i] < tag[j]) {
-          if ((tag[i] < tag[j]) % 2 == 1) continue;
+          if ((tag[i] + tag[j]) % 2 == 1) continue;
         }
       }
 

src/EXTRA-FIX/fix_deform_pressure.cpp

@@ -114,7 +114,6 @@ FixDeformPressure::FixDeformPressure(LAMMPS *lmp, int narg, char **arg) :
         if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix deform/pressure erate/rescale", error);
         set[index].style = ERATERS;
         set[index].rate = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
-        iarg += 3;
         i += 3;
       } else error->all(FLERR, "Illegal fix deform/pressure command: {}", arg[iarg + 1]);
 

src/ML-PACE/pair_pace.h

@@ -52,7 +52,7 @@ class PairPACE : public Pair {
 
  protected:
   struct ACEImpl *aceimpl;
-  int nmax_corerep = 0;
+  int nmax_corerep;
 
   virtual void allocate();
   double *corerep_factor;                    //per-atom core-rep factor (= 1 - fcut)

src/ML-PACE/pair_pace_extrapolation.h

@@ -46,15 +46,15 @@ class PairPACEExtrapolation : public Pair {
 
  protected:
   struct ACEALImpl *aceimpl;
-  int nmax = 0, nmax_corerep = 0;
+  int nmax, nmax_corerep;
 
   virtual void allocate();
   std::vector<std::string> element_names;    // list of elements (used by dump pace/extrapolation)
-  double *extrapolation_grade_gamma = nullptr;         //per-atom gamma value
-  double *corerep_factor = nullptr;                    //per-atom core-rep factor (= 1 - fcut)
+  double *extrapolation_grade_gamma;         //per-atom gamma value
+  double *corerep_factor;                    //per-atom core-rep factor (= 1 - fcut)
 
-  int flag_compute_extrapolation_grade = 0;
-  int flag_corerep_factor = 0;
+  int flag_compute_extrapolation_grade;
+  int flag_corerep_factor;
 
   double **scale;
 

src/replicate.cpp

@@ -26,29 +26,34 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
+#include "label_map.h"
 #include "memory.h"
 #include "special.h"
-#include "label_map.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
 static constexpr double LB_FACTOR = 1.1;
-static constexpr double EPSILON =   1.0e-6;
+static constexpr double EPSILON = 1.0e-6;
 
 /* ---------------------------------------------------------------------- */
 
-Replicate::Replicate(LAMMPS *lmp) : Command(lmp) {}
+Replicate::Replicate(LAMMPS *lmp) : Command(lmp), old(nullptr), old_x(nullptr), old_tag(nullptr)
+{
+  bbox_flag = 0;
+  bond_flag = 0;
+}
 
 /* ---------------------------------------------------------------------- */
 
 void Replicate::command(int narg, char **arg)
 {
-  int i,j,m,n;
+  int i,n;
 
   if (domain->box_exist == 0)
     error->all(FLERR,"Replicate command before simulation box is defined");
+
   if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
 
   int me = comm->me;
@@ -78,9 +83,6 @@ void Replicate::command(int narg, char **arg)
 
   // optional keywords
 
-  bbox_flag = 0;
-  bond_flag = 0;
-
   int iarg = 3;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"bbox") == 0) {

tools/lammps-gui/CMakeLists.txt

@@ -250,7 +250,9 @@ if(APPLE)
 elseif(MSVC)
   install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES $<TARGET_RUNTIME_DLLS:lammps-gui> TYPE BIN)
-  install(FILES $<TARGET_RUNTIME_DLLS:lammps> TYPE BIN)
+  if(BUILD_SHARED_LIBS)
+    install(FILES $<TARGET_RUNTIME_DLLS:lammps> TYPE BIN)
+  endif()
   install(FILES $<TARGET_RUNTIME_DLLS:lmp> TYPE BIN)
   # find path to VC++ init batch file
   get_filename_component(VC_COMPILER_DIR "${CMAKE_CXX_COMPILER}" DIRECTORY)
@@ -262,7 +264,9 @@ elseif(MSVC)
 elseif((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
   install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES $<TARGET_RUNTIME_DLLS:lammps-gui> TYPE BIN)
-  install(FILES $<TARGET_RUNTIME_DLLS:lammps> TYPE BIN)
+  if(BUILD_SHARED_LIBS)
+    install(FILES $<TARGET_RUNTIME_DLLS:lammps> TYPE BIN)
+  endif()
   install(FILES $<TARGET_RUNTIME_DLLS:lmp> TYPE BIN)
   add_custom_target(zip
     COMMAND sh -vx ${LAMMPS_DIR}/cmake/packaging/build_windows_cross_zip.sh ${CMAKE_INSTALL_PREFIX}