From ef82677cb25c33c1bfae8198f296585ba5a09938 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 21 Oct 2015 18:51:09 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14129
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/input.cpp  |  2 +-
 src/lammps.cpp | 46 ++++++++++++++++++++++++++++++++++++----------
 src/lammps.h   |  4 +++-
 3 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/input.cpp b/src/input.cpp
index b820607261..5b0c27e603 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -733,7 +733,7 @@ void Input::clear()
   if (narg > 0) error->all(FLERR,"Illegal clear command");
   lmp->destroy();
   lmp->create();
-  lmp->post_create(0,NULL,NULL,NULL);
+  lmp->post_create();
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 49e1311757..4014090aac 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -89,6 +89,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
 
   suffix = suffix2 = NULL;
   suffix_enable = 0;
+  packargs = NULL;
+  num_package = 0;
   char *rfile = NULL;
   char *dfile = NULL;
   int wdfirst,wdlast;
@@ -509,12 +511,25 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
 
   input = new Input(this,narg,arg);
 
+  // copy package cmdline arguments
+  if (npack > 0) {
+    num_package = npack;
+    packargs = new char**[npack];
+    for (int i=0; i < npack; ++i) {
+      int n = plast[i] - pfirst[i];
+      packargs[i] = new char*[n+1];
+      for (int j=0; j < n; ++j)
+        packargs[i][j] = strdup(arg[pfirst[i]+j]);
+      packargs[i][n] = NULL;
+    }
+    memory->destroy(pfirst);
+    memory->destroy(plast);
+  }
+
   // allocate top-level classes
 
   create();
-  post_create(npack,pfirst,plast,arg);
-  memory->destroy(pfirst);
-  memory->destroy(plast);
+  post_create();
 
   // if helpflag set, print help and quit with "success" status
 
@@ -556,6 +571,17 @@ LAMMPS::~LAMMPS()
   destroy();
   delete citeme;
 
+  if (num_package) {
+    for (int i = 0; i < num_package; i++) {
+      for (char **ptr = packargs[i]; *ptr != NULL; ++ptr)
+        free(*ptr);
+      delete[] packargs[i];
+    }
+    delete[] packargs;
+  }
+  num_package = 0;
+  packargs = NULL;
+
   double totalclock = MPI_Wtime() - initclock;
   if ((me == 0) && (screen || logfile)) {
     char outtime[128];
@@ -650,7 +676,7 @@ void LAMMPS::create()
      so that package-specific core classes have been instantiated
 ------------------------------------------------------------------------- */
 
-void LAMMPS::post_create(int npack, int *pfirst, int *plast, char **arg)
+void LAMMPS::post_create()
 {
   // default package commands triggered by "-c on" and "-k on"
 
@@ -687,15 +713,15 @@ void LAMMPS::post_create(int npack, int *pfirst, int *plast, char **arg)
 
   // invoke any command-line package commands
 
-  if (npack) {
-    char str[128];
-    for (int i = 0; i < npack; i++) {
+  if (num_package) {
+    char str[256];
+    for (int i = 0; i < num_package; i++) {
       strcpy(str,"package");
-      for (int j = pfirst[i]; j < plast[i]; j++) {
-        if (strlen(str) + strlen(arg[j]) + 2 > 128)
+      for (char **ptr = packargs[i]; *ptr != NULL; ++ptr) {
+        if (strlen(str) + strlen(*ptr) + 2 > 256)
           error->all(FLERR,"Too many -pk arguments in command line");
         strcat(str," ");
-        strcat(str,arg[j]);
+        strcat(str,*ptr);
       }
       input->one(str);
     }
diff --git a/src/lammps.h b/src/lammps.h
index 51fd2614b1..53848b1010 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -46,6 +46,8 @@ class LAMMPS {
 
   char *suffix,*suffix2;         // suffixes to add to input script style names
   int suffix_enable;             // 1 if suffixes are enabled, 0 if disabled
+  char ***packargs;              // arguments for cmdline package commands
+  int num_package;               // number of cmdline package commands
   int cite_enable;               // 1 if generating log.cite, 0 if disabled
 
   class Cuda *cuda;              // CUDA accelerator class
@@ -57,7 +59,7 @@ class LAMMPS {
   LAMMPS(int, char **, MPI_Comm);
   ~LAMMPS();
   void create();
-  void post_create(int, int *, int *, char **);
+  void post_create();
   void init();
   void destroy();