From 3b091c0bd44c1aa9bede54004e8ec361dee65fa5 Mon Sep 17 00:00:00 2001
From: Jacob Gissinger <jrgiss05@gmail.com>
Date: Tue, 21 May 2024 19:35:04 -0400
Subject: [PATCH] type label support for dump xyz

---
 doc/src/dump.rst        |  5 +++--
 doc/src/dump_modify.rst | 14 +++++++++++---
 src/dump_xyz.cpp        | 27 +++++++++++++++++++++++++++
 src/label_map.h         |  1 +
 4 files changed, 42 insertions(+), 5 deletions(-)

diff --git a/doc/src/dump.rst b/doc/src/dump.rst
index 2e61ad9921..9f2be8c129 100644
--- a/doc/src/dump.rst
+++ b/doc/src/dump.rst
@@ -470,8 +470,9 @@ followed by one line per atom with the atom type and the :math:`x`-,
 :math:`y`-, and :math:`z`-coordinate of that atom.  You can use the
 :doc:`dump_modify element <dump_modify>` option to change the output
 from using the (numerical) atom type to an element name (or some other
-label). This will help many visualization programs to guess bonds and
-colors.
+label). This option will help many visualization programs to guess bonds
+and colors. You can use the :doc:`dump_modify types labels <dump_modify>`
+option to replace numeric atom types with :doc:`type labels <Howto_type_labels>`.
 
 .. versionadded:: 22Dec2022
 
diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst
index a9b71a98e2..79fdf2cc3e 100644
--- a/doc/src/dump_modify.rst
+++ b/doc/src/dump_modify.rst
@@ -17,7 +17,7 @@ Syntax
 * one or more keyword/value pairs may be appended
 
 * these keywords apply to various dump styles
-* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *units* or *unwrap*
+* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *types* or *units* or *unwrap*
 
   .. parsed-literal::
 
@@ -81,6 +81,7 @@ Syntax
          these 3 args can be replaced by the word "none" to turn off thresholding
        *time* arg = *yes* or *no*
        *triclinic/general* arg = *yes* or *no*
+       *types* value = *numeric* or *labels*
        *units* arg = *yes* or *no*
        *unwrap* arg = *yes* or *no*
 
@@ -849,6 +850,13 @@ The default setting is *no*\ .
 
 ----------
 
+The *types* keyword applies only to the dump xyz style. If this keyword is
+used with a value of *numeric*, then numeric atom types are printed in the
+xyz file (default). If the value *labels* is specified, then
+:doc:`type labels <Howto_type_labels>` are printed for atom types.
+
+----------
+
 The *triclinic/general* keyword only applies to the dump *atom* and
 *custom* styles.  It can only be used with a value of *yes* if the
 simulation box was created as a general triclinic box.  See the
@@ -960,11 +968,11 @@ The option defaults are
 * sort = id for dump styles *dcd*, *xtc*, and *xyz*
 * thresh = none
 * time = no
-* triclinic/general no
+* triclinic/general = no
+* types = numeric
 * units = no
 * unwrap = no
 
 * compression_level = 9 (gz variants)
 * compression_level = 0 (zstd variants)
 * checksum = yes (zstd variants)
-
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index f7ab77b2bf..c424a98feb 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -16,6 +16,7 @@
 
 #include "atom.h"
 #include "error.h"
+#include "label_map.h"
 #include "memory.h"
 #include "update.h"
 
@@ -122,6 +123,32 @@ int DumpXYZ::modify_param(int narg, char **arg)
     return ntypes+1;
   }
 
+  if (strcmp(arg[0],"types") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
+    if (strcmp(arg[1],"numeric") == 0) {
+      return 2;
+    } else if (strcmp(arg[1],"labels") == 0) {
+      if (!atom->labelmapflag)
+        error->all(FLERR, "Label map must be defined when using 'types labels'");
+    } else error->all(FLERR, "Illegal option for dump_modify 'types' keyword");
+
+
+    if (typenames) {
+      for (int i = 1; i <= ntypes; i++)
+        delete [] typenames[i];
+
+      delete [] typenames;
+      typenames = nullptr;
+    }
+
+    typenames = new char*[ntypes+1];
+    for (int itype = 1; itype <= ntypes; itype++) {
+      typenames[itype] = utils::strdup(atom->lmap->typelabel[itype-1]);
+    }
+
+    return 2;
+  }
+
   return 0;
 }
 
diff --git a/src/label_map.h b/src/label_map.h
index a96fcc255c..0dfc42c9b5 100644
--- a/src/label_map.h
+++ b/src/label_map.h
@@ -22,6 +22,7 @@ namespace LAMMPS_NS {
 
 class LabelMap : protected Pointers {
   friend class AtomVec;
+  friend class DumpXYZ;
   friend class ReadData;
 
  public: