From 3e053adfbe8ebc441f4c7ff08cbe413bb8563573 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 4 Jan 2023 08:42:43 -0500
Subject: [PATCH] Print warning about unsorted custom dumps without atom IDs.
 Explain in manual.

---
 doc/src/dump.rst    |  8 ++++++++
 src/dump.cpp        | 11 +++++++++--
 src/dump.h          |  1 +
 src/dump_custom.cpp |  3 +++
 4 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/doc/src/dump.rst b/doc/src/dump.rst
index 800542475d..40eafbb427 100644
--- a/doc/src/dump.rst
+++ b/doc/src/dump.rst
@@ -242,6 +242,14 @@ all the processors or multiple smaller files.
    data for a single snapshot is collected from multiple processors,
    each of which owns a subset of the atoms.
 
+.. warning::
+
+   Without either including atom IDs or using the :doc:`dump_modify sort
+   <dump_modify>` option, it is impossible for visualization programs
+   (e.g. OVITO or VMD) or analysis tools to assign data in different
+   frames consistently to the same atom.  This can lead to incorrect
+   visualizations or results.  LAMMPS will print a warning in such cases.
+
 For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting
 is off by default.  For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and
 *molfile* styles, sorting by atom ID or grid ID is on by default. See
diff --git a/src/dump.cpp b/src/dump.cpp
index 82a25c31f2..7c65536df2 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -89,6 +89,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   unit_count = 0;
   delay_flag = 0;
   write_header_flag = 1;
+  has_id = 1;
 
   skipflag = 0;
   skipvar = nullptr;
@@ -231,16 +232,22 @@ void Dump::init()
     ids = idsort = nullptr;
     index = proclist = nullptr;
     irregular = nullptr;
+    if ((has_id == 0) && (me == 0))
+      error->warning(FLERR,"Dump {} is without Atom-IDs and not sorted by id. This may lead to data "
+                     "changing order and prevent tracking individual atoms", id);
   }
 
   if (sort_flag) {
     if (multiproc > 1)
       error->all(FLERR,
-                 "Cannot dump sort when 'nfile' or 'fileper' keywords are set to non-default values");
+                 "Cannot sort dump when 'nfile' or 'fileper' keywords are set to non-default values");
     if (sortcol == 0 && atom->tag_enable == 0)
-      error->all(FLERR,"Cannot dump sort on atom IDs with no atom IDs defined");
+      error->all(FLERR,"Cannot sort dump on atom IDs with no atom IDs defined");
     if (sortcol && sortcol > size_one)
       error->all(FLERR,"Dump sort column is invalid");
+    if ((sortcol != 0) && (has_id == 0) && (me == 0))
+      error->warning(FLERR,"Dump {} is without Atom-IDs and not sorted by id. This may lead to data "
+                     "changing order and prevent tracking individual atoms", id);
     if (nprocs > 1 && irregular == nullptr)
       irregular = new Irregular(lmp);
 
diff --git a/src/dump.h b/src/dump.h
index 4f0019ca2c..bae7dbd8c8 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -90,6 +90,7 @@ class Dump : protected Pointers {
   int unit_count;           // # of times the unit information was written
   int delay_flag;           // 1 if delay output until delaystep
   int write_header_flag;    // 1 if write header, 0 if not
+  int has_id;               // 1 if output contains Atom-IDs
 
   bigint delaystep;
 
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index d2b091eb6d..8d64e532a4 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1245,11 +1245,14 @@ int DumpCustom::parse_fields(int narg, char **arg)
 {
   // customize by adding to if statement
 
+  has_id = 0;
+
   for (int iarg = 0; iarg < narg; iarg++) {
     if (strcmp(arg[iarg],"id") == 0) {
       pack_choice[iarg] = &DumpCustom::pack_id;
       if (sizeof(tagint) == sizeof(smallint)) vtype[iarg] = Dump::INT;
       else vtype[iarg] = Dump::BIGINT;
+      has_id = 1;
     } else if (strcmp(arg[iarg],"mol") == 0) {
       if (!atom->molecule_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");