From 7afcfccf48fb06deccf9d185cabc377a5124d437 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 24 Jun 2019 13:51:41 -0400
Subject: [PATCH 1/2] follow convention to list all commands in a  file as
 header

---
 doc/src/kim_commands.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt
index f039202e4e..2aa705b483 100644
--- a/doc/src/kim_commands.txt
+++ b/doc/src/kim_commands.txt
@@ -6,7 +6,9 @@
 
 :line
 
-kim_commands :h3
+kim_init command :h3
+kim_interactions command :h3
+kim_query command :h3
 
 [Syntax:]
 

From f2380a24ef90945f421a90e5d482c58e0bef49b5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 24 Jun 2019 14:27:05 -0400
Subject: [PATCH 2/2] fix parallel processing input include bug

---
 src/input.cpp | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/src/input.cpp b/src/input.cpp
index 268be5b774..2f617d2cd0 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -239,8 +239,8 @@ void Input::file()
 }
 
 /* ----------------------------------------------------------------------
-   process all input from filename
-   called from library interface
+   process all input from file at filename
+   mostly called from library interface
 ------------------------------------------------------------------------- */
 
 void Input::file(const char *filename)
@@ -250,21 +250,30 @@ void Input::file(const char *filename)
   // call to file() will close filename and decrement nfile
 
   if (me == 0) {
-    if (nfile > 1)
-      error->one(FLERR,"Invalid use of library file() function");
+    if (nfile == maxfile) {
+      maxfile++;
+      infiles = (FILE **)
+        memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles");
+    }
 
-    if (infile && infile != stdin) fclose(infile);
     infile = fopen(filename,"r");
     if (infile == NULL) {
       char str[128];
       snprintf(str,128,"Cannot open input script %s",filename);
       error->one(FLERR,str);
     }
-    infiles[0] = infile;
-    nfile = 1;
+    infiles[nfile++] = infile;
   }
 
+  // process contents of file
+
   file();
+
+  if (me == 0) {
+    fclose(infile);
+    nfile--;
+    infile = infiles[nfile-1];
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -1041,7 +1050,13 @@ void Input::include()
       error->one(FLERR,str);
     }
     infiles[nfile++] = infile;
-    file();
+  }
+
+  // process contents of file
+
+  file();
+
+  if (me == 0) {
     fclose(infile);
     nfile--;
     infile = infiles[nfile-1];