git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15084 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/COUPLE/fortran2/makefile

@@ -13,7 +13,7 @@ CXX = mpicxx   # replace with your C++ compiler
 # Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
 FFLAGS = -O2 -fPIC
 CXXFLAGS = -O2 -fPIC
-CPPFLAGS =
+CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
 
 all : liblammps_fortran.a liblammps_fortran.so
 

examples/COUPLE/library/Makefile.g++

@@ -4,10 +4,10 @@ SHELL = /bin/sh
 
 # System-specific settings
 
-CC =		g++
-CCFLAGS =	-g -O -DMPICH_IGNORE_CXX_SEEK
+CC =		mpicxx
+CCFLAGS =	-g -O -DMPICH_IGNORE_CXX_SEEK  -DOMPI_SKIP_MPICXX=1 
 DEPFLAGS =	-M
-LINK =		g++
+LINK =		mpicxx
 LINKFLAGS =	-g -O
 ARCHIVE =	ar
 ARFLAGS =	-rc

examples/COUPLE/library/error.cpp

@@ -1,6 +1,6 @@
-#include "mpi.h"
-#include "stdlib.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
 #include "error.h"
 
 /* ---------------------------------------------------------------------- */

examples/COUPLE/library/error.h

@@ -1,7 +1,7 @@
 #ifndef ERROR_H
 #define ERROR_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Error {
  public:

examples/COUPLE/library/files.cpp

@@ -1,5 +1,5 @@
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
 #include "files.h"
 
 #define MAXLINE 256

examples/COUPLE/library/files.h

@@ -1,2 +1,5 @@
+#ifndef FILES_H
+#define FILES_H
 void replace(char *, char *, int, char **);
 char **extract(char *, char *, int, char **);
+#endif

examples/COUPLE/library/irregular.h

@@ -1,7 +1,7 @@
 #ifndef IRREGULAR_H
 #define IRREGULAR_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Irregular {
  public:

examples/COUPLE/library/lammps_data_write.cpp

@@ -1,5 +1,6 @@
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
 #include "lammps_data_write.h"
 #include "memory.h"
 #include "error.h"

examples/COUPLE/library/lammps_data_write.h

@@ -1,8 +1,8 @@
 #ifndef LAMMPS_DATA_WRITE_H
 #define LAMMPS_DATA_WRITE_H
 
+#include <stdio.h>
 #include "send2one.h"
-#include "stdio.h"
 
 class LAMMPSDataWrite : public Send2One {
  public:

examples/COUPLE/library/many2many.cpp

@@ -1,4 +1,6 @@
-#include "mpi.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "many2many.h"
 #include "irregular.h"
 #include "memory.h"

examples/COUPLE/library/many2many.h

@@ -1,7 +1,7 @@
 #ifndef MANY2MANY_H
 #define MANY2MANY_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Many2Many {
  public:

examples/COUPLE/library/many2one.h

@@ -1,7 +1,7 @@
 #ifndef MANY2ONE_H
 #define MANY2ONE_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Many2One {
  public:

examples/COUPLE/library/memory.cpp

@@ -1,6 +1,6 @@
-#include "mpi.h"
-#include "stdlib.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "memory.h"
 #include "error.h"
 

examples/COUPLE/library/memory.h

@@ -1,7 +1,7 @@
 #ifndef MEMORY_H
 #define MEMORY_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Memory {
  public:

examples/COUPLE/library/one2many.cpp

@@ -1,4 +1,5 @@
-#include "mpi.h"
+#include <mpi.h>
+#include <stdlib.h>
 #include "one2many.h"
 #include "memory.h"
 

examples/COUPLE/library/one2many.h

@@ -1,7 +1,7 @@
 #ifndef ONE2MANY_H
 #define ONE2MANY_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 #include <map>
 

examples/COUPLE/library/send2one.h

@@ -1,7 +1,7 @@
 #ifndef SEND2ONE_H
 #define SEND2ONE_H
 
-#include "mpi.h"
+#include <mpi.h>
 
 class Send2One {
  public:

examples/KAPPA/in.heat

@@ -59,15 +59,15 @@ fix             cold all heat 1 -100.0 region cold
 
 thermo_style    custom step temp c_Thot c_Tcold
 thermo	        1000
-run             10000 
+run             10000
 
 # thermal conductivity calculation
 
 compute		ke all ke/atom
 variable	temp atom c_ke/1.5
 
-fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
-		  file profile.heat units reduced
+compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
 
 variable        tdiff equal f_2[11][3]-f_2[1][3]
 fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000