avoid segfaults if a dump is created and followed by run pre no

src/MPIIO/dump_atom_mpiio.cpp

@@ -283,6 +283,8 @@ void DumpAtomMPIIO::init_style()
 
 void DumpAtomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 

src/MPIIO/dump_custom_mpiio.cpp

@@ -309,6 +309,8 @@ void DumpCustomMPIIO::init_style()
 
 void DumpCustomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 

src/dump.cpp

@@ -1,4 +1,4 @@
-// clang-format off
+  // clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -41,14 +41,20 @@ Dump *Dump::dumpptr;
 #define BIG 1.0e20
 #define EPSILON 1.0e-6
 
-enum{ASCEND,DESCEND};
+enum { ASCEND, DESCEND };
 
 /* ---------------------------------------------------------------------- */
 
-Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
+Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
+    Pointers(lmp), multiname(nullptr), refresh(nullptr), skipvar(nullptr), format(nullptr),
+    format_default(nullptr), format_line_user(nullptr), format_float_user(nullptr),
+    format_int_user(nullptr), format_bigint_user(nullptr), format_column_user(nullptr), fp(nullptr),
+    nameslist(nullptr), buf(nullptr), sbuf(nullptr), ids(nullptr), bufsort(nullptr),
+    idsort(nullptr), index(nullptr), proclist(nullptr), xpbc(nullptr), vpbc(nullptr),
+    imagepbc(nullptr), irregular(nullptr)
 {
-  MPI_Comm_rank(world,&me);
+  MPI_Comm_rank(world, &me);
-  MPI_Comm_size(world,&nprocs);
+  MPI_Comm_size(world, &nprocs);
 
   id = utils::strdup(arg[0]);
 
@@ -64,17 +70,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   first_flag = 0;
   flush_flag = 1;
 
-  format = nullptr;
-  format_default = nullptr;
-
-  format_line_user = nullptr;
-  format_float_user = nullptr;
-  format_int_user = nullptr;
-  format_bigint_user = nullptr;
-  format_column_user = nullptr;
-
   refreshflag = 0;
-  refresh = nullptr;
 
   clearstep = 0;
   sort_flag = 0;
@@ -92,25 +88,15 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   has_id = 1;
 
   skipflag = 0;
-  skipvar = nullptr;
 
   maxfiles = -1;
   numfiles = 0;
   fileidx = 0;
-  nameslist = nullptr;
 
   maxbuf = maxids = maxsort = maxproc = 0;
-  buf = bufsort = nullptr;
-  ids = idsort = nullptr;
-  index = proclist = nullptr;
-  irregular = nullptr;
-
   maxsbuf = 0;
-  sbuf = nullptr;
 
   maxpbc = -1;
-  xpbc = vpbc = nullptr;
-  imagepbc = nullptr;
 
   // parse filename for special syntax
   // if contains '%', write one file per proc and replace % with proc-ID
@@ -120,18 +106,17 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   //   else if ends in .gz or other known extensions -> compressed text file
   //   else ASCII text file
 
-  fp = nullptr;
   singlefile_opened = 0;
   compressed = 0;
   binary = 0;
   multifile = 0;
+  size_one = 0;
 
   multiproc = 0;
   nclusterprocs = nprocs;
   filewriter = 0;
   if (me == 0) filewriter = 1;
   fileproc = 0;
-  multiname = nullptr;
 
   char *ptr;
   if ((ptr = strchr(filename,'%'))) {

src/dump_atom.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -29,8 +28,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
+DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) :
+  Dump(lmp, narg, arg), header_choice(nullptr), pack_choice(nullptr)
 {
+  // clang-format off
   if (narg != 5) error->all(FLERR,"Illegal dump atom command");
 
   scale_flag = 1;
@@ -146,6 +147,8 @@ int DumpAtom::modify_param(int narg, char **arg)
 
 void DumpAtom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
@@ -154,6 +157,8 @@ void DumpAtom::write_header(bigint ndump)
 
 void DumpAtom::pack(tagint *ids)
 {
+  if (!pack_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*pack_choice)(ids);
 }
 

src/dump_custom.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -53,13 +52,14 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
 /* ---------------------------------------------------------------------- */
 
 DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
-  Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
+    Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
-  thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
+    thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
-  thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
+    thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
-  columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
+    columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
-  field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
+    field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
-  fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
+    fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
-  custom(nullptr), custom_flag(nullptr), typenames(nullptr), pack_choice(nullptr)
+    custom(nullptr), custom_flag(nullptr), typenames(nullptr), header_choice(nullptr),
+    pack_choice(nullptr)
 {
   if (narg == 5) error->all(FLERR,"No dump {} arguments specified", style);
 
@@ -352,6 +352,8 @@ void DumpCustom::init_style()
 
 void DumpCustom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }

src/dump_grid.cpp

@@ -311,6 +311,8 @@ void DumpGrid::init_style()
 
 void DumpGrid::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }

src/dump_xyz.cpp

@@ -130,6 +130,8 @@ int DumpXYZ::modify_param(int narg, char **arg)
 void DumpXYZ::write_header(bigint n)
 {
   if (me == 0) {
+    if (!fp) error->one(FLERR, "Must not use 'run pre no' after creating a new dump");
+
     auto header = fmt::format("{}\n Atoms. Timestep: {}", n, update->ntimestep);
     if (time_flag) header += fmt::format(" Time: {:.6f}", compute_time());
     header += "\n";
@@ -177,9 +179,8 @@ int DumpXYZ::convert_string(int n, double *mybuf)
       memory->grow(sbuf,maxsbuf,"dump:sbuf");
     }
 
-    offset += sprintf(&sbuf[offset],format,
+    offset += sprintf(&sbuf[offset], format, typenames[static_cast<int> (mybuf[m+1])],
-                      typenames[static_cast<int> (mybuf[m+1])],
+                      mybuf[m+2], mybuf[m+3], mybuf[m+4]);
-                      mybuf[m+2],mybuf[m+3],mybuf[m+4]);
     m += size_one;
   }