From f2bb49ba68c5edfb215cf732c27d4497ccdab007 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Wed, 26 Jun 2024 17:57:56 -0400
Subject: [PATCH 01/11] Create objects.mk and dependency.mk using only sh
 script and add windows compatibility files

---
 ED/build/shell/build_objects.sh |   36 +
 ED/src/include/dirent_win.h     | 1239 +++++++++++++++++++++++++++++++
 ED/src/utils/utils_c.c          |    6 +-
 Makefile.am                     |   32 +
 4 files changed, 1312 insertions(+), 1 deletion(-)
 create mode 100644 ED/build/shell/build_objects.sh
 create mode 100644 ED/src/include/dirent_win.h
 create mode 100644 Makefile.am

diff --git a/ED/build/shell/build_objects.sh b/ED/build/shell/build_objects.sh
new file mode 100644
index 000000000..62a29634a
--- /dev/null
+++ b/ED/build/shell/build_objects.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Add your build commands here
+SOURCES=$( (cd ../../.. && find ED/src -name "*.[Ff]90" -and -not -path "ED/src/preproc/*"))
+
+# Remove ED/src/driver/edmain.F90 from OBJECTS
+SOURCES=$(echo $SOURCES | sed 's/ED\/src\/driver\/edmain.F90//')
+
+echo SOURCES = $SOURCES ED/src/utils/utils_c.c > sources.mk
+
+rm -f dependency.mk
+
+# Build dependency rules for object files
+for src in $SOURCES; do
+  # Mod depends on the source file building
+  SRC_MOD_NAME=$(echo $(basename "${src%.[Ff]90}.mod"))
+  echo $SRC_MOD_NAME: ${src%.[Ff]90}.o >> dependency.mk
+
+  # Find modules used in the source file and add as dependency for the object file
+  MODS_USED=$(cd ../../.. && grep -i '^\s*use\s\+' $src | awk '{print $2}' | sed 's/,.*//' | sort | uniq)
+
+  # Update MODS_USED to include only modules that has a corresponding
+  # source file with the pattern ED/src/*/$mod.[Ff]90
+  MODS_USED=$(for mod in $MODS_USED; do
+    if [ -f ../../../ED/src/*/$mod.F90 -o -f ../../../ED/src/*/$mod.f90 ]; then
+      echo $mod
+    fi
+  done)
+
+  MODS_USED_MOD=$(for line in $MODS_USED; do echo -n "$line.mod "; done)
+
+  length=$(echo $MODS_USED_MOD | wc -w)
+  if [ $length -gt 0 ]; then
+    echo ${src%.[Ff]90}.o: $MODS_USED_MOD >> dependency.mk
+  fi;
+done
diff --git a/ED/src/include/dirent_win.h b/ED/src/include/dirent_win.h
new file mode 100644
index 000000000..56ab58fd4
--- /dev/null
+++ b/ED/src/include/dirent_win.h
@@ -0,0 +1,1239 @@
+/*
+ * Dirent interface for Microsoft Visual Studio
+ *
+ * Copyright (C) 1998-2019 Toni Ronkko
+ * This file is part of dirent.  Dirent may be freely distributed
+ * under the MIT license.  For all details and documentation, see
+ * https://github.com/tronkko/dirent
+ */
+#ifndef DIRENT_H
+#define DIRENT_H
+
+/* Hide warnings about unreferenced local functions */
+#if defined(__clang__)
+#	pragma clang diagnostic ignored "-Wunused-function"
+#elif defined(_MSC_VER)
+#	pragma warning(disable:4505)
+#elif defined(__GNUC__)
+#	pragma GCC diagnostic ignored "-Wunused-function"
+#endif
+
+/*
+ * Include windows.h without Windows Sockets 1.1 to prevent conflicts with
+ * Windows Sockets 2.0.
+ */
+#ifndef WIN32_LEAN_AND_MEAN
+#	define WIN32_LEAN_AND_MEAN
+#endif
+#include <windows.h>
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <wchar.h>
+#include <string.h>
+#include <stdlib.h>
+#include <malloc.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <ctype.h>
+
+/* Indicates that d_type field is available in dirent structure */
+#define _DIRENT_HAVE_D_TYPE
+
+/* Indicates that d_namlen field is available in dirent structure */
+#define _DIRENT_HAVE_D_NAMLEN
+
+/* Entries missing from MSVC 6.0 */
+#if !defined(FILE_ATTRIBUTE_DEVICE)
+#	define FILE_ATTRIBUTE_DEVICE 0x40
+#endif
+
+/* File type and permission flags for stat(), general mask */
+#if !defined(S_IFMT)
+#	define S_IFMT _S_IFMT
+#endif
+
+/* Directory bit */
+#if !defined(S_IFDIR)
+#	define S_IFDIR _S_IFDIR
+#endif
+
+/* Character device bit */
+#if !defined(S_IFCHR)
+#	define S_IFCHR _S_IFCHR
+#endif
+
+/* Pipe bit */
+#if !defined(S_IFFIFO)
+#	define S_IFFIFO _S_IFFIFO
+#endif
+
+/* Regular file bit */
+#if !defined(S_IFREG)
+#	define S_IFREG _S_IFREG
+#endif
+
+/* Read permission */
+#if !defined(S_IREAD)
+#	define S_IREAD _S_IREAD
+#endif
+
+/* Write permission */
+#if !defined(S_IWRITE)
+#	define S_IWRITE _S_IWRITE
+#endif
+
+/* Execute permission */
+#if !defined(S_IEXEC)
+#	define S_IEXEC _S_IEXEC
+#endif
+
+/* Pipe */
+#if !defined(S_IFIFO)
+#	define S_IFIFO _S_IFIFO
+#endif
+
+/* Block device */
+#if !defined(S_IFBLK)
+#	define S_IFBLK 0
+#endif
+
+/*
+ * Symbolic link.  Be ware that S_IFLNK value and S_ISLNK() macro are only
+ * usable with dirent - they do not work with stat() function call!
+ */
+#if !defined(S_IFLNK)
+#	define S_IFLNK (_S_IFDIR | _S_IFREG)
+#endif
+
+/* Socket */
+#if !defined(S_IFSOCK)
+#	define S_IFSOCK 0
+#endif
+
+/* Read user permission */
+#if !defined(S_IRUSR)
+#	define S_IRUSR S_IREAD
+#endif
+
+/* Write user permission */
+#if !defined(S_IWUSR)
+#	define S_IWUSR S_IWRITE
+#endif
+
+/* Execute user permission */
+#if !defined(S_IXUSR)
+#	define S_IXUSR 0
+#endif
+
+/* User full permissions */
+#if !defined(S_IRWXU)
+#	define S_IRWXU (S_IRUSR | S_IWUSR | S_IXUSR)
+#endif
+
+/* Read group permission */
+#if !defined(S_IRGRP)
+#	define S_IRGRP 0
+#endif
+
+/* Write group permission */
+#if !defined(S_IWGRP)
+#	define S_IWGRP 0
+#endif
+
+/* Execute group permission */
+#if !defined(S_IXGRP)
+#	define S_IXGRP 0
+#endif
+
+/* Group full permissions */
+#if !defined(S_IRWXG)
+#	define S_IRWXG (S_IRGRP | S_IWGRP | S_IXGRP)
+#endif
+
+/* Read others permission */
+#if !defined(S_IROTH)
+#	define S_IROTH 0
+#endif
+
+/* Write others permission */
+#if !defined(S_IWOTH)
+#	define S_IWOTH 0
+#endif
+
+/* Execute others permission */
+#if !defined(S_IXOTH)
+#	define S_IXOTH 0
+#endif
+
+/* Other full permissions */
+#if !defined(S_IRWXO)
+#	define S_IRWXO (S_IROTH | S_IWOTH | S_IXOTH)
+#endif
+
+/* Maximum length of file name */
+#if !defined(PATH_MAX)
+#	define PATH_MAX MAX_PATH
+#endif
+#if !defined(FILENAME_MAX)
+#	define FILENAME_MAX MAX_PATH
+#endif
+#if !defined(NAME_MAX)
+#	define NAME_MAX FILENAME_MAX
+#endif
+
+/* File type flags for d_type */
+#define DT_UNKNOWN 0
+#define DT_REG S_IFREG
+#define DT_DIR S_IFDIR
+#define DT_FIFO S_IFIFO
+#define DT_SOCK S_IFSOCK
+#define DT_CHR S_IFCHR
+#define DT_BLK S_IFBLK
+#define DT_LNK S_IFLNK
+
+/* Macros for converting between st_mode and d_type */
+#define IFTODT(mode) ((mode) & S_IFMT)
+#define DTTOIF(type) (type)
+
+/*
+ * File type macros.  Note that block devices and sockets cannot be
+ * distinguished on Windows, and the macros S_ISBLK and S_ISSOCK are only
+ * defined for compatibility.  These macros should always return false on
+ * Windows.
+ */
+#if !defined(S_ISFIFO)
+#	define S_ISFIFO(mode) (((mode) & S_IFMT) == S_IFIFO)
+#endif
+#if !defined(S_ISDIR)
+#	define S_ISDIR(mode) (((mode) & S_IFMT) == S_IFDIR)
+#endif
+#if !defined(S_ISREG)
+#	define S_ISREG(mode) (((mode) & S_IFMT) == S_IFREG)
+#endif
+#if !defined(S_ISLNK)
+#	define S_ISLNK(mode) (((mode) & S_IFMT) == S_IFLNK)
+#endif
+#if !defined(S_ISSOCK)
+#	define S_ISSOCK(mode) (((mode) & S_IFMT) == S_IFSOCK)
+#endif
+#if !defined(S_ISCHR)
+#	define S_ISCHR(mode) (((mode) & S_IFMT) == S_IFCHR)
+#endif
+#if !defined(S_ISBLK)
+#	define S_ISBLK(mode) (((mode) & S_IFMT) == S_IFBLK)
+#endif
+
+/* Return the exact length of the file name without zero terminator */
+#define _D_EXACT_NAMLEN(p) ((p)->d_namlen)
+
+/* Return the maximum size of a file name */
+#define _D_ALLOC_NAMLEN(p) ((PATH_MAX)+1)
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/* Wide-character version */
+struct _wdirent {
+	/* Always zero */
+	long d_ino;
+
+	/* Position of next file in a directory stream */
+	long d_off;
+
+	/* Structure size */
+	unsigned short d_reclen;
+
+	/* Length of name without \0 */
+	size_t d_namlen;
+
+	/* File type */
+	int d_type;
+
+	/* File name */
+	wchar_t d_name[PATH_MAX+1];
+};
+typedef struct _wdirent _wdirent;
+
+struct _WDIR {
+	/* Current directory entry */
+	struct _wdirent ent;
+
+	/* Private file data */
+	WIN32_FIND_DATAW data;
+
+	/* True if data is valid */
+	int cached;
+
+	/* True if next entry is invalid */
+	int invalid;
+
+	/* Win32 search handle */
+	HANDLE handle;
+
+	/* Initial directory name */
+	wchar_t *patt;
+};
+typedef struct _WDIR _WDIR;
+
+/* Multi-byte character version */
+struct dirent {
+	/* Always zero */
+	long d_ino;
+
+	/* Position of next file in a directory stream */
+	long d_off;
+
+	/* Structure size */
+	unsigned short d_reclen;
+
+	/* Length of name without \0 */
+	size_t d_namlen;
+
+	/* File type */
+	int d_type;
+
+	/* File name */
+	char d_name[PATH_MAX+1];
+};
+typedef struct dirent dirent;
+
+struct DIR {
+	struct dirent ent;
+	struct _WDIR *wdirp;
+};
+typedef struct DIR DIR;
+
+
+/* Dirent functions */
+static DIR *opendir(const char *dirname);
+static _WDIR *_wopendir(const wchar_t *dirname);
+
+static struct dirent *readdir(DIR *dirp);
+static struct _wdirent *_wreaddir(_WDIR *dirp);
+
+static int readdir_r(
+	DIR *dirp, struct dirent *entry, struct dirent **result);
+static int _wreaddir_r(
+	_WDIR *dirp, struct _wdirent *entry, struct _wdirent **result);
+
+static int closedir(DIR *dirp);
+static int _wclosedir(_WDIR *dirp);
+
+static void rewinddir(DIR *dirp);
+static void _wrewinddir(_WDIR *dirp);
+
+static long telldir(DIR *dirp);
+static long _wtelldir(_WDIR *dirp);
+
+static void seekdir(DIR *dirp, long loc);
+static void _wseekdir(_WDIR *dirp, long loc);
+
+static int scandir(const char *dirname, struct dirent ***namelist,
+	int (*filter)(const struct dirent*),
+	int (*compare)(const struct dirent**, const struct dirent**));
+
+static int alphasort(const struct dirent **a, const struct dirent **b);
+
+static int versionsort(const struct dirent **a, const struct dirent **b);
+
+static int strverscmp(const char *a, const char *b);
+
+/* For compatibility with Symbian */
+#define wdirent _wdirent
+#define WDIR _WDIR
+#define wopendir _wopendir
+#define wreaddir _wreaddir
+#define wclosedir _wclosedir
+#define wrewinddir _wrewinddir
+#define wtelldir _wtelldir
+#define wseekdir _wseekdir
+
+/* Compatibility with older Microsoft compilers and non-Microsoft compilers */
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+#	define wcstombs_s dirent_wcstombs_s
+#	define mbstowcs_s dirent_mbstowcs_s
+#endif
+
+/* Optimize dirent_set_errno() away on modern Microsoft compilers */
+#if defined(_MSC_VER) && _MSC_VER >= 1400
+#	define dirent_set_errno _set_errno
+#endif
+
+
+/* Internal utility functions */
+static WIN32_FIND_DATAW *dirent_first(_WDIR *dirp);
+static WIN32_FIND_DATAW *dirent_next(_WDIR *dirp);
+static long dirent_hash(WIN32_FIND_DATAW *datap);
+
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static int dirent_mbstowcs_s(
+	size_t *pReturnValue, wchar_t *wcstr, size_t sizeInWords,
+	const char *mbstr, size_t count);
+#endif
+
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static int dirent_wcstombs_s(
+	size_t *pReturnValue, char *mbstr, size_t sizeInBytes,
+	const wchar_t *wcstr, size_t count);
+#endif
+
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static void dirent_set_errno(int error);
+#endif
+
+
+/*
+ * Open directory stream DIRNAME for read and return a pointer to the
+ * internal working area that is used to retrieve individual directory
+ * entries.
+ */
+static _WDIR *
+_wopendir(const wchar_t *dirname)
+{
+	wchar_t *p;
+
+	/* Must have directory name */
+	if (dirname == NULL || dirname[0] == '\0') {
+		dirent_set_errno(ENOENT);
+		return NULL;
+	}
+
+	/* Allocate new _WDIR structure */
+	_WDIR *dirp = (_WDIR*) malloc(sizeof(struct _WDIR));
+	if (!dirp)
+		return NULL;
+
+	/* Reset _WDIR structure */
+	dirp->handle = INVALID_HANDLE_VALUE;
+	dirp->patt = NULL;
+	dirp->cached = 0;
+	dirp->invalid = 0;
+
+	/*
+	 * Compute the length of full path plus zero terminator
+	 *
+	 * Note that on WinRT there's no way to convert relative paths
+	 * into absolute paths, so just assume it is an absolute path.
+	 */
+#if WINAPI_FAMILY_PARTITION(WINAPI_PARTITION_DESKTOP)
+	/* Desktop */
+	DWORD n = GetFullPathNameW(dirname, 0, NULL, NULL);
+#else
+	/* WinRT */
+	size_t n = wcslen(dirname);
+#endif
+
+	/* Allocate room for absolute directory name and search pattern */
+	dirp->patt = (wchar_t*) malloc(sizeof(wchar_t) * n + 16);
+	if (dirp->patt == NULL)
+		goto exit_closedir;
+
+	/*
+	 * Convert relative directory name to an absolute one.  This
+	 * allows rewinddir() to function correctly even when current
+	 * working directory is changed between opendir() and rewinddir().
+	 *
+	 * Note that on WinRT there's no way to convert relative paths
+	 * into absolute paths, so just assume it is an absolute path.
+	 */
+#if WINAPI_FAMILY_PARTITION(WINAPI_PARTITION_DESKTOP)
+	/* Desktop */
+	n = GetFullPathNameW(dirname, n, dirp->patt, NULL);
+	if (n <= 0)
+		goto exit_closedir;
+#else
+	/* WinRT */
+	wcsncpy_s(dirp->patt, n+1, dirname, n);
+#endif
+
+	/* Append search pattern \* to the directory name */
+	p = dirp->patt + n;
+	switch (p[-1]) {
+	case '\\':
+	case '/':
+	case ':':
+		/* Directory ends in path separator, e.g. c:\temp\ */
+		/*NOP*/;
+		break;
+
+	default:
+		/* Directory name doesn't end in path separator */
+		*p++ = '\\';
+	}
+	*p++ = '*';
+	*p = '\0';
+
+	/* Open directory stream and retrieve the first entry */
+	if (!dirent_first(dirp))
+		goto exit_closedir;
+
+	/* Success */
+	return dirp;
+
+	/* Failure */
+exit_closedir:
+	_wclosedir(dirp);
+	return NULL;
+}
+
+/*
+ * Read next directory entry.
+ *
+ * Returns pointer to static directory entry which may be overwritten by
+ * subsequent calls to _wreaddir().
+ */
+static struct _wdirent *
+_wreaddir(_WDIR *dirp)
+{
+	/*
+	 * Read directory entry to buffer.  We can safely ignore the return
+	 * value as entry will be set to NULL in case of error.
+	 */
+	struct _wdirent *entry;
+	(void) _wreaddir_r(dirp, &dirp->ent, &entry);
+
+	/* Return pointer to statically allocated directory entry */
+	return entry;
+}
+
+/*
+ * Read next directory entry.
+ *
+ * Returns zero on success.  If end of directory stream is reached, then sets
+ * result to NULL and returns zero.
+ */
+static int
+_wreaddir_r(
+	_WDIR *dirp, struct _wdirent *entry, struct _wdirent **result)
+{
+	/* Validate directory handle */
+	if (!dirp || dirp->handle == INVALID_HANDLE_VALUE || !dirp->patt) {
+		dirent_set_errno(EBADF);
+		*result = NULL;
+		return -1;
+	}
+
+	/* Read next directory entry */
+	WIN32_FIND_DATAW *datap = dirent_next(dirp);
+	if (!datap) {
+		/* Return NULL to indicate end of directory */
+		*result = NULL;
+		return /*OK*/0;
+	}
+
+	/*
+	 * Copy file name as wide-character string.  If the file name is too
+	 * long to fit in to the destination buffer, then truncate file name
+	 * to PATH_MAX characters and zero-terminate the buffer.
+	 */
+	size_t i = 0;
+	while (i < PATH_MAX && datap->cFileName[i] != 0) {
+		entry->d_name[i] = datap->cFileName[i];
+		i++;
+	}
+	entry->d_name[i] = 0;
+
+	/* Length of file name excluding zero terminator */
+	entry->d_namlen = i;
+
+	/* Determine file type */
+	DWORD attr = datap->dwFileAttributes;
+	if ((attr & FILE_ATTRIBUTE_DEVICE) != 0)
+		entry->d_type = DT_CHR;
+	else if ((attr & FILE_ATTRIBUTE_REPARSE_POINT) != 0)
+		entry->d_type = DT_LNK;
+	else if ((attr & FILE_ATTRIBUTE_DIRECTORY) != 0)
+		entry->d_type = DT_DIR;
+	else
+		entry->d_type = DT_REG;
+
+	/* Read the next directory entry to cache */
+	datap = dirent_next(dirp);
+	if (datap) {
+		/* Compute 31-bit hash of the next directory entry */
+		entry->d_off = dirent_hash(datap);
+
+		/* Push the next directory entry back to cache */
+		dirp->cached = 1;
+	} else {
+		/* End of directory stream */
+		entry->d_off = (long) ((~0UL) >> 1);
+	}
+
+	/* Reset other fields */
+	entry->d_ino = 0;
+	entry->d_reclen = sizeof(struct _wdirent);
+
+	/* Set result address */
+	*result = entry;
+	return /*OK*/0;
+}
+
+/*
+ * Close directory stream opened by opendir() function.  This invalidates the
+ * DIR structure as well as any directory entry read previously by
+ * _wreaddir().
+ */
+static int
+_wclosedir(_WDIR *dirp)
+{
+	if (!dirp) {
+		dirent_set_errno(EBADF);
+		return /*failure*/-1;
+	}
+
+	/*
+	 * Release search handle if we have one.  Being able to handle
+	 * partially initialized _WDIR structure allows us to use this
+	 * function to handle errors occuring within _wopendir.
+	 */
+	if (dirp->handle != INVALID_HANDLE_VALUE) {
+		FindClose(dirp->handle);
+	}
+
+	/*
+	 * Release search pattern.  Note that we don't need to care if
+	 * dirp->patt is NULL or not: function free is guaranteed to act
+	 * appropriately.
+	 */
+	free(dirp->patt);
+
+	/* Release directory structure */
+	free(dirp);
+	return /*success*/0;
+}
+
+/*
+ * Rewind directory stream such that _wreaddir() returns the very first
+ * file name again.
+ */
+static void _wrewinddir(_WDIR* dirp)
+{
+	/* Check directory pointer */
+	if (!dirp || dirp->handle == INVALID_HANDLE_VALUE || !dirp->patt)
+		return;
+
+	/* Release existing search handle */
+	FindClose(dirp->handle);
+
+	/* Open new search handle */
+	dirent_first(dirp);
+}
+
+/* Get first directory entry */
+static WIN32_FIND_DATAW *
+dirent_first(_WDIR *dirp)
+{
+	/* Open directory and retrieve the first entry */
+	dirp->handle = FindFirstFileExW(
+		dirp->patt, FindExInfoStandard, &dirp->data,
+		FindExSearchNameMatch, NULL, 0);
+	if (dirp->handle == INVALID_HANDLE_VALUE)
+		goto error;
+
+	/* A directory entry is now waiting in memory */
+	dirp->cached = 1;
+	return &dirp->data;
+
+error:
+	/* Failed to open directory: no directory entry in memory */
+	dirp->cached = 0;
+	dirp->invalid = 1;
+
+	/* Set error code */
+	DWORD errorcode = GetLastError();
+	switch (errorcode) {
+	case ERROR_ACCESS_DENIED:
+		/* No read access to directory */
+		dirent_set_errno(EACCES);
+		break;
+
+	case ERROR_DIRECTORY:
+		/* Directory name is invalid */
+		dirent_set_errno(ENOTDIR);
+		break;
+
+	case ERROR_PATH_NOT_FOUND:
+	default:
+		/* Cannot find the file */
+		dirent_set_errno(ENOENT);
+	}
+	return NULL;
+}
+
+/* Get next directory entry */
+static WIN32_FIND_DATAW *
+dirent_next(_WDIR *dirp)
+{
+	/* Return NULL if seek position was invalid */
+	if (dirp->invalid)
+		return NULL;
+
+	/* Is the next directory entry already in cache? */
+	if (dirp->cached) {
+		/* Yes, a valid directory entry found in memory */
+		dirp->cached = 0;
+		return &dirp->data;
+	}
+
+	/* Read the next directory entry from stream */
+	if (FindNextFileW(dirp->handle, &dirp->data) == FALSE) {
+		/* End of directory stream */
+		return NULL;
+	}
+
+	/* Success */
+	return &dirp->data;
+}
+
+/*
+ * Compute 31-bit hash of file name.
+ *
+ * See djb2 at http://www.cse.yorku.ca/~oz/hash.html
+ */
+static long
+dirent_hash(WIN32_FIND_DATAW *datap)
+{
+	unsigned long hash = 5381;
+	unsigned long c;
+	const wchar_t *p = datap->cFileName;
+	const wchar_t *e = p + MAX_PATH;
+	while (p != e && (c = *p++) != 0) {
+		hash = (hash << 5) + hash + c;
+	}
+
+	return (long) (hash & ((~0UL) >> 1));
+}
+
+/* Open directory stream using plain old C-string */
+static DIR *opendir(const char *dirname)
+{
+	/* Must have directory name */
+	if (dirname == NULL || dirname[0] == '\0') {
+		dirent_set_errno(ENOENT);
+		return NULL;
+	}
+
+	/* Allocate memory for DIR structure */
+	struct DIR *dirp = (DIR*) malloc(sizeof(struct DIR));
+	if (!dirp)
+		return NULL;
+
+	/* Convert directory name to wide-character string */
+	wchar_t wname[PATH_MAX + 1];
+	size_t n;
+	int error = mbstowcs_s(&n, wname, PATH_MAX + 1, dirname, PATH_MAX+1);
+	if (error)
+		goto exit_failure;
+
+	/* Open directory stream using wide-character name */
+	dirp->wdirp = _wopendir(wname);
+	if (!dirp->wdirp)
+		goto exit_failure;
+
+	/* Success */
+	return dirp;
+
+	/* Failure */
+exit_failure:
+	free(dirp);
+	return NULL;
+}
+
+/* Read next directory entry */
+static struct dirent *
+readdir(DIR *dirp)
+{
+	/*
+	 * Read directory entry to buffer.  We can safely ignore the return
+	 * value as entry will be set to NULL in case of error.
+	 */
+	struct dirent *entry;
+	(void) readdir_r(dirp, &dirp->ent, &entry);
+
+	/* Return pointer to statically allocated directory entry */
+	return entry;
+}
+
+/*
+ * Read next directory entry into called-allocated buffer.
+ *
+ * Returns zero on success.  If the end of directory stream is reached, then
+ * sets result to NULL and returns zero.
+ */
+static int
+readdir_r(
+	DIR *dirp, struct dirent *entry, struct dirent **result)
+{
+	/* Read next directory entry */
+	WIN32_FIND_DATAW *datap = dirent_next(dirp->wdirp);
+	if (!datap) {
+		/* No more directory entries */
+		*result = NULL;
+		return /*OK*/0;
+	}
+
+	/* Attempt to convert file name to multi-byte string */
+	size_t n;
+	int error = wcstombs_s(
+		&n, entry->d_name, PATH_MAX + 1,
+		datap->cFileName, PATH_MAX + 1);
+
+	/*
+	 * If the file name cannot be represented by a multi-byte string, then
+	 * attempt to use old 8+3 file name.  This allows the program to
+	 * access files although file names may seem unfamiliar to the user.
+	 *
+	 * Be ware that the code below cannot come up with a short file name
+	 * unless the file system provides one.  At least VirtualBox shared
+	 * folders fail to do this.
+	 */
+	if (error && datap->cAlternateFileName[0] != '\0') {
+		error = wcstombs_s(
+			&n, entry->d_name, PATH_MAX + 1,
+			datap->cAlternateFileName, PATH_MAX + 1);
+	}
+
+	if (!error) {
+		/* Length of file name excluding zero terminator */
+		entry->d_namlen = n - 1;
+
+		/* Determine file type */
+		DWORD attr = datap->dwFileAttributes;
+		if ((attr & FILE_ATTRIBUTE_DEVICE) != 0)
+			entry->d_type = DT_CHR;
+		else if ((attr & FILE_ATTRIBUTE_REPARSE_POINT) != 0)
+			entry->d_type = DT_LNK;
+		else if ((attr & FILE_ATTRIBUTE_DIRECTORY) != 0)
+			entry->d_type = DT_DIR;
+		else
+			entry->d_type = DT_REG;
+
+		/* Get offset of next file */
+		datap = dirent_next(dirp->wdirp);
+		if (datap) {
+			/* Compute 31-bit hash of the next directory entry */
+			entry->d_off = dirent_hash(datap);
+
+			/* Push the next directory entry back to cache */
+			dirp->wdirp->cached = 1;
+		} else {
+			/* End of directory stream */
+			entry->d_off = (long) ((~0UL) >> 1);
+		}
+
+		/* Reset fields */
+		entry->d_ino = 0;
+		entry->d_reclen = sizeof(struct dirent);
+	} else {
+		/*
+		 * Cannot convert file name to multi-byte string so construct
+		 * an erroneous directory entry and return that.  Note that
+		 * we cannot return NULL as that would stop the processing
+		 * of directory entries completely.
+		 */
+		entry->d_name[0] = '?';
+		entry->d_name[1] = '\0';
+		entry->d_namlen = 1;
+		entry->d_type = DT_UNKNOWN;
+		entry->d_ino = 0;
+		entry->d_off = -1;
+		entry->d_reclen = 0;
+	}
+
+	/* Return pointer to directory entry */
+	*result = entry;
+	return /*OK*/0;
+}
+
+/* Close directory stream */
+static int
+closedir(DIR *dirp)
+{
+	int ok;
+
+	if (!dirp)
+		goto exit_failure;
+
+	/* Close wide-character directory stream */
+	ok = _wclosedir(dirp->wdirp);
+	dirp->wdirp = NULL;
+
+	/* Release multi-byte character version */
+	free(dirp);
+	return ok;
+
+exit_failure:
+	/* Invalid directory stream */
+	dirent_set_errno(EBADF);
+	return /*failure*/-1;
+}
+
+/* Rewind directory stream to beginning */
+static void
+rewinddir(DIR *dirp)
+{
+	if (!dirp)
+		return;
+
+	/* Rewind wide-character string directory stream */
+	_wrewinddir(dirp->wdirp);
+}
+
+/* Get position of directory stream */
+static long
+_wtelldir(_WDIR *dirp)
+{
+	if (!dirp || dirp->handle == INVALID_HANDLE_VALUE) {
+		dirent_set_errno(EBADF);
+		return /*failure*/-1;
+	}
+
+	/* Read next file entry */
+	WIN32_FIND_DATAW *datap = dirent_next(dirp);
+	if (!datap) {
+		/* End of directory stream */
+		return (long) ((~0UL) >> 1);
+	}
+
+	/* Store file entry to cache for readdir() */
+	dirp->cached = 1;
+
+	/* Return the 31-bit hash code to be used as stream position */
+	return dirent_hash(datap);
+}
+
+/* Get position of directory stream */
+static long
+telldir(DIR *dirp)
+{
+	if (!dirp) {
+		dirent_set_errno(EBADF);
+		return -1;
+	}
+
+	return _wtelldir(dirp->wdirp);
+}
+
+/* Seek directory stream to offset */
+static void
+_wseekdir(_WDIR *dirp, long loc)
+{
+	if (!dirp)
+		return;
+	
+	/* Directory must be open */
+	if (dirp->handle == INVALID_HANDLE_VALUE)
+		goto exit_failure;
+
+	/* Ensure that seek position is valid */
+	if (loc < 0)
+		goto exit_failure;
+
+	/* Restart directory stream from the beginning */
+	FindClose(dirp->handle);
+	if (!dirent_first(dirp))
+		goto exit_failure;
+
+	/* Reset invalid flag so that we can read from the stream again */
+	dirp->invalid = 0;
+
+	/*
+	 * Read directory entries from the beginning until the hash matches a
+	 * file name.  Be ware that hash code is only 31 bits longs and
+	 * duplicates are possible: the hash code cannot return the position
+	 * with 100.00% accuracy! Moreover, the method is slow for large
+	 * directories.
+	 */
+	long hash;
+	do {
+		/* Read next directory entry */
+		WIN32_FIND_DATAW *datap = dirent_next(dirp);
+		if (!datap) {
+			/*
+			 * End of directory stream was reached before finding
+			 * the requested location.  Perhaps the file in
+			 * question was deleted or moved out of the directory.
+			 */
+			goto exit_failure;
+		}
+
+		/* Does the file name match the hash? */
+		hash = dirent_hash(datap);
+	} while (hash != loc);
+
+	/*
+	 * File name matches the hash!  Push the directory entry back to cache
+	 * from where next readdir() will return it.
+	 */
+	dirp->cached = 1;
+	dirp->invalid = 0;
+	return;
+
+exit_failure:
+	/* Ensure that readdir will return NULL */
+	dirp->invalid = 1;
+}
+
+/* Seek directory stream to offset */
+static void
+seekdir(DIR *dirp, long loc)
+{
+	if (!dirp)
+		return;
+
+	_wseekdir(dirp->wdirp, loc);
+}
+
+/* Scan directory for entries */
+static int
+scandir(
+	const char *dirname, struct dirent ***namelist,
+	int (*filter)(const struct dirent*),
+	int (*compare)(const struct dirent**, const struct dirent**))
+{
+	int result;
+
+	/* Open directory stream */
+	DIR *dir = opendir(dirname);
+	if (!dir) {
+		/* Cannot open directory */
+		return /*Error*/ -1;
+	}
+
+	/* Read directory entries to memory */
+	struct dirent *tmp = NULL;
+	struct dirent **files = NULL;
+	size_t size = 0;
+	size_t allocated = 0;
+	while (1) {
+		/* Allocate room for a temporary directory entry */
+		if (!tmp) {
+			tmp = (struct dirent*) malloc(sizeof(struct dirent));
+			if (!tmp)
+				goto exit_failure;
+		}
+
+		/* Read directory entry to temporary area */
+		struct dirent *entry;
+		if (readdir_r(dir, tmp, &entry) != /*OK*/0)
+			goto exit_failure;
+
+		/* Stop if we already read the last directory entry */
+		if (entry == NULL)
+			goto exit_success;
+
+		/* Determine whether to include the entry in results */
+		if (filter && !filter(tmp))
+			continue;
+
+		/* Enlarge pointer table to make room for another pointer */
+		if (size >= allocated) {
+			/* Compute number of entries in the new table */
+			size_t num_entries = size * 2 + 16;
+
+			/* Allocate new pointer table or enlarge existing */
+			void *p = realloc(files, sizeof(void*) * num_entries);
+			if (!p)
+				goto exit_failure;
+
+			/* Got the memory */
+			files = (dirent**) p;
+			allocated = num_entries;
+		}
+
+		/* Store the temporary entry to ptr table */
+		files[size++] = tmp;
+		tmp = NULL;
+	}
+
+exit_failure:
+	/* Release allocated entries */
+	for (size_t i = 0; i < size; i++) {
+		free(files[i]);
+	}
+
+	/* Release the pointer table */
+	free(files);
+	files = NULL;
+
+	/* Exit with error code */
+	result = /*error*/ -1;
+	goto exit_status;
+
+exit_success:
+	/* Sort directory entries */
+	if (size > 1 && compare) {
+		qsort(files, size, sizeof(void*),
+			(int (*) (const void*, const void*)) compare);
+	}
+
+	/* Pass pointer table to caller */
+	if (namelist)
+		*namelist = files;
+
+	/* Return the number of directory entries read */
+	result = (int) size;
+
+exit_status:
+	/* Release temporary directory entry, if we had one */
+	free(tmp);
+
+	/* Close directory stream */
+	closedir(dir);
+	return result;
+}
+
+/* Alphabetical sorting */
+static int
+alphasort(const struct dirent **a, const struct dirent **b)
+{
+	return strcoll((*a)->d_name, (*b)->d_name);
+}
+
+/* Sort versions */
+static int
+versionsort(const struct dirent **a, const struct dirent **b)
+{
+	return strverscmp((*a)->d_name, (*b)->d_name);
+}
+
+/* Compare strings */
+static int
+strverscmp(const char *a, const char *b)
+{
+	size_t i = 0;
+	size_t j;
+
+	/* Find first difference */
+	while (a[i] == b[i]) {
+		if (a[i] == '\0') {
+			/* No difference */
+			return 0;
+		}
+		++i;
+	}
+
+	/* Count backwards and find the leftmost digit */
+	j = i;
+	while (j > 0 && isdigit(a[j-1])) {
+		--j;
+	}
+
+	/* Determine mode of comparison */
+	if (a[j] == '0' || b[j] == '0') {
+		/* Find the next non-zero digit */
+		while (a[j] == '0' && a[j] == b[j]) {
+			j++;
+		}
+
+		/* String with more digits is smaller, e.g 002 < 01 */
+		if (isdigit(a[j])) {
+			if (!isdigit(b[j])) {
+				return -1;
+			}
+		} else if (isdigit(b[j])) {
+			return 1;
+		}
+	} else if (isdigit(a[j]) && isdigit(b[j])) {
+		/* Numeric comparison */
+		size_t k1 = j;
+		size_t k2 = j;
+
+		/* Compute number of digits in each string */
+		while (isdigit(a[k1])) {
+			k1++;
+		}
+		while (isdigit(b[k2])) {
+			k2++;
+		}
+
+		/* Number with more digits is bigger, e.g 999 < 1000 */
+		if (k1 < k2)
+			return -1;
+		else if (k1 > k2)
+			return 1;
+	}
+
+	/* Alphabetical comparison */
+	return (int) ((unsigned char) a[i]) - ((unsigned char) b[i]);
+}
+
+/* Convert multi-byte string to wide character string */
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static int
+dirent_mbstowcs_s(
+	size_t *pReturnValue, wchar_t *wcstr,
+	size_t sizeInWords, const char *mbstr, size_t count)
+{
+	/* Older Visual Studio or non-Microsoft compiler */
+	size_t n = mbstowcs(wcstr, mbstr, sizeInWords);
+	if (wcstr && n >= count)
+		return /*error*/ 1;
+
+	/* Zero-terminate output buffer */
+	if (wcstr && sizeInWords) {
+		if (n >= sizeInWords)
+			n = sizeInWords - 1;
+		wcstr[n] = 0;
+	}
+
+	/* Length of multi-byte string with zero terminator */
+	if (pReturnValue) {
+		*pReturnValue = n + 1;
+	}
+
+	/* Success */
+	return 0;
+}
+#endif
+
+/* Convert wide-character string to multi-byte string */
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static int
+dirent_wcstombs_s(
+	size_t *pReturnValue, char *mbstr,
+	size_t sizeInBytes, const wchar_t *wcstr, size_t count)
+{
+	/* Older Visual Studio or non-Microsoft compiler */
+	size_t n = wcstombs(mbstr, wcstr, sizeInBytes);
+	if (mbstr && n >= count)
+		return /*error*/1;
+
+	/* Zero-terminate output buffer */
+	if (mbstr && sizeInBytes) {
+		if (n >= sizeInBytes) {
+			n = sizeInBytes - 1;
+		}
+		mbstr[n] = '\0';
+	}
+
+	/* Length of resulting multi-bytes string WITH zero-terminator */
+	if (pReturnValue) {
+		*pReturnValue = n + 1;
+	}
+
+	/* Success */
+	return 0;
+}
+#endif
+
+/* Set errno variable */
+#if !defined(_MSC_VER) || _MSC_VER < 1400
+static void
+dirent_set_errno(int error)
+{
+	/* Non-Microsoft compiler or older Microsoft compiler */
+	errno = error;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+#endif /*DIRENT_H*/
\ No newline at end of file
diff --git a/ED/src/utils/utils_c.c b/ED/src/utils/utils_c.c
index ac26b5727..7bc79f1f3 100644
--- a/ED/src/utils/utils_c.c
+++ b/ED/src/utils/utils_c.c
@@ -314,7 +314,11 @@ int vfscale(float *a,int n,double *min,double *max )
 }
 
 /************************************************************************/
+#ifdef _WIN32
+#include <dirent_win.h>
+#else
 #include <dirent.h>
+#endif
 #include <string.h>
 
 void filelist_c_( int *inum, int *indices, char *prefix, char *chario){
@@ -535,7 +539,7 @@ void filelist_c_( int *inum, int *indices, char *prefix, char *chario){
 
 /* This is for the omp thread/processor pinning check. */
 /* MLO.  This didn't work in the SUNHPC cluster, disabling it for now */
-#if defined(SUNHPC) || defined(__APPLE__)
+#if defined(SUNHPC) || defined(__APPLE__) || defined(_WIN32)
 int findmycpu_ ()
 {
 	int cpu;
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 000000000..1aa1a8e81
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,32 @@
+# Include the objects.mk file first to define $(SRC_MAIN) and $(OBJ_MODEL)
+include ED/build/shell/sources.mk
+
+SRC_MAIN = ED/src/driver/edmain.F90
+
+AUTOMAKE_OPTIONS = subdir-objects
+
+# Define the main program and static library variables
+MAIN = ed2
+STATICLIB = libed2.a
+
+# Define the programs and libraries
+bin_PROGRAMS = $(MAIN)
+lib_LIBRARIES = $(STATICLIB)
+
+# Compiler and linker flags
+AM_CFLAGS = @CFLAGS@
+AM_FCFLAGS = @CFLAGS@
+AM_LDFLAGS = @LIBS@
+
+# Define source files for the main program
+ed2_SOURCES = $(SRC_MAIN)
+ed2_LDADD = $(STATICLIB)
+
+# Define source files for the static library
+libed2_a_SOURCES = $(SOURCES)
+
+# Additional Fortran clean files
+CLEANFILES = *.mod
+
+# Include the dependency makefile
+include ED/build/shell/dependency.mk

From 851d1a7a8aad033b3d84988053e93fed1d2246d4 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Wed, 26 Jun 2024 15:42:47 -0400
Subject: [PATCH 02/11] Add necessary files for automake to work (should be
 filled afterwards)

---
 .gitignore |  31 +++++
 AUTHORS    |   0
 COPYING    |   0
 ChangeLog  |   0
 INSTALL    | 368 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 NEWS       |   0
 6 files changed, 399 insertions(+)
 create mode 100644 AUTHORS
 create mode 100644 COPYING
 create mode 100644 ChangeLog
 create mode 100644 INSTALL
 create mode 100644 NEWS

diff --git a/.gitignore b/.gitignore
index 72c31d845..393393b34 100644
--- a/.gitignore
+++ b/.gitignore
@@ -166,3 +166,34 @@ R-utils/read.q.quick.r
 #Xiangtao Ignores
 ED/build/ed2_gfortran
 ED/build/ed2_ifort
+
+
+# http://www.gnu.org/software/automake
+Makefile.in
+/ar-lib
+/mdate-sh
+/py-compile
+/test-driver
+/ylwrap
+.deps/
+.dirstamp
+
+# http://www.gnu.org/software/autoconf
+autom4te.cache
+/autoscan.log
+/autoscan-*.log
+/aclocal.m4
+/compile
+/config.cache
+/config.guess
+/config.h.in
+/config.log
+/config.status
+/config.sub
+/configure
+/configure.scan
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+/Makefile
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 000000000..e69de29bb
diff --git a/COPYING b/COPYING
new file mode 100644
index 000000000..e69de29bb
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 000000000..e69de29bb
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 000000000..e82fd21de
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,368 @@
+Installation Instructions
+*************************
+
+   Copyright (C) 1994-1996, 1999-2002, 2004-2017, 2020-2021 Free
+Software Foundation, Inc.
+
+   Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved.  This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+   Briefly, the shell command './configure && make && make install'
+should configure, build, and install this package.  The following
+more-detailed instructions are generic; see the 'README' file for
+instructions specific to this package.  Some packages provide this
+'INSTALL' file but do not implement all of the features documented
+below.  The lack of an optional feature in a given package is not
+necessarily a bug.  More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+   The 'configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a 'Makefile' in each directory of the package.
+It may also create one or more '.h' files containing system-dependent
+definitions.  Finally, it creates a shell script 'config.status' that
+you can run in the future to recreate the current configuration, and a
+file 'config.log' containing compiler output (useful mainly for
+debugging 'configure').
+
+   It can also use an optional file (typically called 'config.cache' and
+enabled with '--cache-file=config.cache' or simply '-C') that saves the
+results of its tests to speed up reconfiguring.  Caching is disabled by
+default to prevent problems with accidental use of stale cache files.
+
+   If you need to do unusual things to compile the package, please try
+to figure out how 'configure' could check whether to do them, and mail
+diffs or instructions to the address given in the 'README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point 'config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+   The file 'configure.ac' (or 'configure.in') is used to create
+'configure' by a program called 'autoconf'.  You need 'configure.ac' if
+you want to change it or regenerate 'configure' using a newer version of
+'autoconf'.
+
+   The simplest way to compile this package is:
+
+  1. 'cd' to the directory containing the package's source code and type
+     './configure' to configure the package for your system.
+
+     Running 'configure' might take a while.  While running, it prints
+     some messages telling which features it is checking for.
+
+  2. Type 'make' to compile the package.
+
+  3. Optionally, type 'make check' to run any self-tests that come with
+     the package, generally using the just-built uninstalled binaries.
+
+  4. Type 'make install' to install the programs and any data files and
+     documentation.  When installing into a prefix owned by root, it is
+     recommended that the package be configured and built as a regular
+     user, and only the 'make install' phase executed with root
+     privileges.
+
+  5. Optionally, type 'make installcheck' to repeat any self-tests, but
+     this time using the binaries in their final installed location.
+     This target does not install anything.  Running this target as a
+     regular user, particularly if the prior 'make install' required
+     root privileges, verifies that the installation completed
+     correctly.
+
+  6. You can remove the program binaries and object files from the
+     source code directory by typing 'make clean'.  To also remove the
+     files that 'configure' created (so you can compile the package for
+     a different kind of computer), type 'make distclean'.  There is
+     also a 'make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+  7. Often, you can also type 'make uninstall' to remove the installed
+     files again.  In practice, not all packages have tested that
+     uninstallation works correctly, even though it is required by the
+     GNU Coding Standards.
+
+  8. Some packages, particularly those that use Automake, provide 'make
+     distcheck', which can by used by developers to test that all other
+     targets like 'make install' and 'make uninstall' work correctly.
+     This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+   Some systems require unusual options for compilation or linking that
+the 'configure' script does not know about.  Run './configure --help'
+for details on some of the pertinent environment variables.
+
+   You can give 'configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here is
+an example:
+
+     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you can use GNU 'make'.  'cd' to the
+directory where you want the object files and executables to go and run
+the 'configure' script.  'configure' automatically checks for the source
+code in the directory that 'configure' is in and in '..'.  This is known
+as a "VPATH" build.
+
+   With a non-GNU 'make', it is safer to compile the package for one
+architecture at a time in the source code directory.  After you have
+installed the package for one architecture, use 'make distclean' before
+reconfiguring for another architecture.
+
+   On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple '-arch' options to the
+compiler but only a single '-arch' option to the preprocessor.  Like
+this:
+
+     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CPP="gcc -E" CXXCPP="g++ -E"
+
+   This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the 'lipo' tool if you have problems.
+
+Installation Names
+==================
+
+   By default, 'make install' installs the package's commands under
+'/usr/local/bin', include files under '/usr/local/include', etc.  You
+can specify an installation prefix other than '/usr/local' by giving
+'configure' the option '--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+pass the option '--exec-prefix=PREFIX' to 'configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like '--bindir=DIR' to specify different values for particular
+kinds of files.  Run 'configure --help' for a list of the directories
+you can set and what kinds of files go in them.  In general, the default
+for these options is expressed in terms of '${prefix}', so that
+specifying just '--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+   The most portable way to affect installation locations is to pass the
+correct locations to 'configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+'make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+   The first method involves providing an override variable for each
+affected directory.  For example, 'make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+'${prefix}'.  Any directories that were specified during 'configure',
+but not in terms of '${prefix}', must each be overridden at install time
+for the entire installation to be relocated.  The approach of makefile
+variable overrides for each directory variable is required by the GNU
+Coding Standards, and ideally causes no recompilation.  However, some
+platforms have known limitations with the semantics of shared libraries
+that end up requiring recompilation when using this method, particularly
+noticeable in packages that use GNU Libtool.
+
+   The second method involves providing the 'DESTDIR' variable.  For
+example, 'make install DESTDIR=/alternate/directory' will prepend
+'/alternate/directory' before all installation names.  The approach of
+'DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters.  On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of '${prefix}'
+at 'configure' time.
+
+Optional Features
+=================
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving 'configure' the
+option '--program-prefix=PREFIX' or '--program-suffix=SUFFIX'.
+
+   Some packages pay attention to '--enable-FEATURE' options to
+'configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to '--with-PACKAGE' options, where PACKAGE
+is something like 'gnu-as' or 'x' (for the X Window System).  The
+'README' should mention any '--enable-' and '--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, 'configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the 'configure' options '--x-includes=DIR' and
+'--x-libraries=DIR' to specify their locations.
+
+   Some packages offer the ability to configure how verbose the
+execution of 'make' will be.  For these packages, running './configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with 'make V=1'; while running './configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with 'make V=0'.
+
+Particular systems
+==================
+
+   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU CC
+is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+   HP-UX 'make' updates targets which have the same timestamps as their
+prerequisites, which makes it generally unusable when shipped generated
+files such as 'configure' are involved.  Use GNU 'make' instead.
+
+   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its '<wchar.h>' header file.  The option '-nodtk' can be used as a
+workaround.  If GNU CC is not installed, it is therefore recommended to
+try
+
+     ./configure CC="cc"
+
+and if that doesn't work, try
+
+     ./configure CC="cc -nodtk"
+
+   On Solaris, don't put '/usr/ucb' early in your 'PATH'.  This
+directory contains several dysfunctional programs; working variants of
+these programs are available in '/usr/bin'.  So, if you need '/usr/ucb'
+in your 'PATH', put it _after_ '/usr/bin'.
+
+   On Haiku, software installed for all users goes in '/boot/common',
+not '/usr/local'.  It is recommended to use the following options:
+
+     ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+   There may be some features 'configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, 'configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+'--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as 'sun4', or a canonical name which has the form:
+
+     CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+     OS
+     KERNEL-OS
+
+   See the file 'config.sub' for the possible values of each field.  If
+'config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+   If you are _building_ compiler tools for cross-compiling, you should
+use the option '--target=TYPE' to select the type of system they will
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with '--host=TYPE'.
+
+Sharing Defaults
+================
+
+   If you want to set default values for 'configure' scripts to share,
+you can create a site shell script called 'config.site' that gives
+default values for variables like 'CC', 'cache_file', and 'prefix'.
+'configure' looks for 'PREFIX/share/config.site' if it exists, then
+'PREFIX/etc/config.site' if it exists.  Or, you can set the
+'CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all 'configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+   Variables not defined in a site shell script can be set in the
+environment passed to 'configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the 'configure' command line, using 'VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+causes the specified 'gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for 'CONFIG_SHELL' due to an
+Autoconf limitation.  Until the limitation is lifted, you can use this
+workaround:
+
+     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+'configure' Invocation
+======================
+
+   'configure' recognizes the following options to control how it
+operates.
+
+'--help'
+'-h'
+     Print a summary of all of the options to 'configure', and exit.
+
+'--help=short'
+'--help=recursive'
+     Print a summary of the options unique to this package's
+     'configure', and exit.  The 'short' variant lists options used only
+     in the top level, while the 'recursive' variant lists options also
+     present in any nested packages.
+
+'--version'
+'-V'
+     Print the version of Autoconf used to generate the 'configure'
+     script, and exit.
+
+'--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally 'config.cache'.  FILE defaults to '/dev/null' to
+     disable caching.
+
+'--config-cache'
+'-C'
+     Alias for '--cache-file=config.cache'.
+
+'--quiet'
+'--silent'
+'-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to '/dev/null' (any error
+     messages will still be shown).
+
+'--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     'configure' can determine that directory automatically.
+
+'--prefix=DIR'
+     Use DIR as the installation prefix.  *note Installation Names:: for
+     more details, including other options available for fine-tuning the
+     installation locations.
+
+'--no-create'
+'-n'
+     Run the configure checks, but stop before creating any output
+     files.
+
+'configure' also accepts some other, not widely useful, options.  Run
+'configure --help' for more details.
diff --git a/NEWS b/NEWS
new file mode 100644
index 000000000..e69de29bb

From a108c800e5379332c95dd2138b4242ab4d06b658 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Wed, 26 Jun 2024 15:59:25 -0400
Subject: [PATCH 03/11] Use autotools to automatically find the libraries and
 define the compilation rules

---
 configure.ac | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 configure.ac

diff --git a/configure.ac b/configure.ac
new file mode 100644
index 000000000..422406a1c
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,79 @@
+AC_INIT([ED2],[m4_esyscmd_s([sed -n 's/.*ED_VERSION=\(.*\)/\1/p' ED/build/make/paths.mk])])
+AM_INIT_AUTOMAKE
+
+MAIN="ed-${PACKAGE_VERSION}"
+os_name=$(uname | sed "s/-.*//")
+SHLIB="rED2.so"
+
+CFLAGS="${CFLAGS} -I\"ED/src/include\""
+
+PKG_PROG_PKG_CONFIG()
+AS_IF([test "x$os_name" != "xDarwin" -a "x$os_name" != "xLinux"],
+  [
+    AC_DEFINE_UNQUOTED([PKG_CONFIG_SYSTEM_INCLUDE_PATH], ["$PKG_CONFIG_SYSTEM_INCLUDE_PATH"], [MINGW defined pkg-config default system path])
+    CFLAGS="${CFLAGS} -I\"${PKG_CONFIG_SYSTEM_INCLUDE_PATH}\" ${FFLAGS} -D_WIN32"
+    CPPFLAGS="${CFLAGS} ${FFLAGS} -D_WIN32"
+    MAIN="${MAIN}.exe"
+    SHLIB="rED2.dll"
+  ]
+)
+
+
+AC_PROG_FC([ifx ifort mpif90 gfortran])
+AC_PROG_CC
+AC_PROG_RANLIB
+AC_LANG([Fortran])
+
+
+PKG_CHECK_MODULES([HDF5], [hdf5_fortran], [have_hdf5=yes], [have_hdf5=no])
+
+AS_IF([test "x$FC" = "xmpif90"],
+  [
+    AS_IF([test "x$os_name" = "xMSYS_NT"],
+      [
+        PKG_CHECK_MODULES([MPI], [msmpi], [have_mpi=yes], [have_mpi=no])
+      ],
+      [
+        PKG_CHECK_MODULES([MPI], [mpi-fort mpich], [have_mpi=yes], [have_mpi=no])
+      ]
+    )
+
+    AS_IF([test "x$have_mpi" = "xyes"],
+      [
+        CFLAGS="${CFLAGS} ${MPI_CFLAGS}"
+        LIBS="${LIBS} ${MPI_LIBS}"
+      ],
+      [
+        AC_PROG_FC([gfortran])
+      ]
+    )
+  ]
+)
+
+
+AS_IF([test "x$have_hdf5" = "xyes"],
+  [
+    LIBS="${LIBS} ${HDF5_LIBS} ${MPILIBS}"
+    CFLAGS="${CFLAGS} ${HDF5_CFLAGS}"
+  ],
+  [
+    AC_MSG_ERROR([HDF5 library not found!
+    Please install HDF5 library and try again:
+    
+      Debian: sudo apt-get install libhdf5-dev
+      Fedora: sudo dnf install hdf5-devel
+      CentOS: sudo yum install hdf5-devel
+      MacOS: brew install hdf5
+      Windows MinGW: pacman -S mingw-w64-x86_64-hdf5
+    ])
+  ]
+)
+
+AC_SUBST([CC])
+AC_SUBST([FC])
+AC_SUBST([SHLIB])
+AC_SUBST([MAIN])
+AC_SUBST([LIBS])
+AC_SUBST([CFLAGS])
+AC_CONFIG_FILES([Makefile])
+AC_OUTPUT
\ No newline at end of file

From 52aa1a6de9b279170a27965306cfdf2e4dc99456 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Wed, 26 Jun 2024 16:23:05 -0400
Subject: [PATCH 04/11] First attempt to compile with MPI

---
 configure.ac | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configure.ac b/configure.ac
index 422406a1c..6400a13f7 100644
--- a/configure.ac
+++ b/configure.ac
@@ -29,7 +29,7 @@ PKG_CHECK_MODULES([HDF5], [hdf5_fortran], [have_hdf5=yes], [have_hdf5=no])
 
 AS_IF([test "x$FC" = "xmpif90"],
   [
-    AS_IF([test "x$os_name" = "xMSYS_NT"],
+    AS_IF([test "x$os_name" != "xDarwin" -a "x$os_name" != "xLinux"],
       [
         PKG_CHECK_MODULES([MPI], [msmpi], [have_mpi=yes], [have_mpi=no])
       ],
@@ -40,7 +40,7 @@ AS_IF([test "x$FC" = "xmpif90"],
 
     AS_IF([test "x$have_mpi" = "xyes"],
       [
-        CFLAGS="${CFLAGS} ${MPI_CFLAGS}"
+        CFLAGS="${CFLAGS} ${MPI_CFLAGS} -DRAMS_MPI -fallow-invalid-boz -fallow-argument-mismatch"
         LIBS="${LIBS} ${MPI_LIBS}"
       ],
       [

From ee984bf46c25fefe101d8dfcbd5b1e9ba2889a06 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Wed, 26 Jun 2024 16:48:33 -0400
Subject: [PATCH 05/11] Update configure.ac: try to link to hdf5_fortran even
 without hdf5_fortran.pc

---
 configure.ac | 58 +++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 44 insertions(+), 14 deletions(-)

diff --git a/configure.ac b/configure.ac
index 6400a13f7..203c16033 100644
--- a/configure.ac
+++ b/configure.ac
@@ -11,8 +11,8 @@ PKG_PROG_PKG_CONFIG()
 AS_IF([test "x$os_name" != "xDarwin" -a "x$os_name" != "xLinux"],
   [
     AC_DEFINE_UNQUOTED([PKG_CONFIG_SYSTEM_INCLUDE_PATH], ["$PKG_CONFIG_SYSTEM_INCLUDE_PATH"], [MINGW defined pkg-config default system path])
-    CFLAGS="${CFLAGS} -I\"${PKG_CONFIG_SYSTEM_INCLUDE_PATH}\" ${FFLAGS} -D_WIN32"
-    CPPFLAGS="${CFLAGS} ${FFLAGS} -D_WIN32"
+    CFLAGS="${CFLAGS} -I\"${PKG_CONFIG_SYSTEM_INCLUDE_PATH}\" ${FCFLAGS} -D_WIN32"
+    CPPFLAGS="${CFLAGS} ${FCFLAGS} -D_WIN32"
     MAIN="${MAIN}.exe"
     SHLIB="rED2.dll"
   ]
@@ -25,7 +25,7 @@ AC_PROG_RANLIB
 AC_LANG([Fortran])
 
 
-PKG_CHECK_MODULES([HDF5], [hdf5_fortran], [have_hdf5=yes], [have_hdf5=no])
+PKG_CHECK_MODULES([hdf5_fortran], [hdf5_fortran], [have_hdf5=yes], [have_hdf5=no])
 
 AS_IF([test "x$FC" = "xmpif90"],
   [
@@ -34,7 +34,7 @@ AS_IF([test "x$FC" = "xmpif90"],
         PKG_CHECK_MODULES([MPI], [msmpi], [have_mpi=yes], [have_mpi=no])
       ],
       [
-        PKG_CHECK_MODULES([MPI], [mpi-fort mpich], [have_mpi=yes], [have_mpi=no])
+        PKG_CHECK_MODULES([MPI], [mpi-fort], [have_mpi=yes], [have_mpi=no])
       ]
     )
 
@@ -53,22 +53,52 @@ AS_IF([test "x$FC" = "xmpif90"],
 
 AS_IF([test "x$have_hdf5" = "xyes"],
   [
-    LIBS="${LIBS} ${HDF5_LIBS} ${MPILIBS}"
-    CFLAGS="${CFLAGS} ${HDF5_CFLAGS}"
+    LIBS="${LIBS} ${hdf5_fortran_LIBS} ${MPILIBS}"
+    CFLAGS="${CFLAGS} ${hdf5_fortran_CFLAGS}"
   ],
   [
-    AC_MSG_ERROR([HDF5 library not found!
-    Please install HDF5 library and try again:
+    PKG_CHECK_MODULES([HDF5], [hdf5], [have_hdf5=yes], [have_hdf5=no])
     
-      Debian: sudo apt-get install libhdf5-dev
-      Fedora: sudo dnf install hdf5-devel
-      CentOS: sudo yum install hdf5-devel
-      MacOS: brew install hdf5
-      Windows MinGW: pacman -S mingw-w64-x86_64-hdf5
-    ])
+    AS_IF([test "x$have_hdf5" = "xyes"],
+      [
+        LIBS="${LIBS} ${HDF5_LIBS} -lhdf5 -lhdf5_fortran"
+        FCFLAGS="${CFLAGS} ${HDF5_CFLAGS}"
+
+        AC_MSG_CHECKING([for HDF5 support in Fortran])
+        AC_LANG_PUSH([Fortran])
+
+        AC_LINK_IFELSE([AC_LANG_PROGRAM([], [[
+              use hdf5
+              integer :: hdferr
+              call h5open_f(hdferr)
+              call h5close_f(hdferr)
+        ]])],
+        [AC_MSG_RESULT([yes])
+        HDF5_OK=yes],
+        [AC_MSG_RESULT([no])
+        HDF5_OK=no])
+
+        AC_LANG_POP([Fortran])
+      ],
+      [have_hdf5=no])
   ]
 )
 
+AS_IF([test "x$have_hdf5" = "xno"],[
+      AC_MSG_ERROR([
+HDF5 library not found!
+
+Please install HDF5 library and try again:
+
+    Debian: sudo apt-get install libhdf5-dev
+    Fedora: sudo dnf install hdf5-devel
+    CentOS: sudo yum install hdf5-devel
+    MacOS: brew install hdf5
+    Windows MinGW: pacman -S mingw-w64-x86_64-hdf5
+      ])
+])
+
+
 AC_SUBST([CC])
 AC_SUBST([FC])
 AC_SUBST([SHLIB])

From a6ac5ab6abe7ca08545ed6a52278b30d5e8be63d Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Thu, 27 Jun 2024 16:07:48 -0400
Subject: [PATCH 06/11] Change CI installation instructions

---
 .github/workflows/ci.yml | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b3381f063..98af3a864 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,6 @@
 name: CI
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   build:
@@ -11,13 +11,20 @@ jobs:
       run: sudo apt-get install -y --no-install-recommends gfortran libhdf5-openmpi-dev libopenmpi-dev
     - name: Install ED2
       run: |
-        cd ED/build
-        ./install.sh -g -p travisci -k A
+        pushd ED/build/shell
+        bash build_objects.sh
+        popd
+        aclocal
+        automake --add-missing
+        autoconf
+        ./configure
+        make
+        sudo make install
     - name: Upload compiled ED2 binary
       uses: actions/upload-artifact@v1
       with:
         name: ed2-binary
-        path: ED/build/ed_2.2-dbg
+        path: ed2
 
   test-umbs-bg:
     needs: build
@@ -33,8 +40,8 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh umbs.bg "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh umbs.bg "$GITHUB_WORKSPACE/ed2-binary/ed2"
 
   test-tonzi:
     needs: build
@@ -50,8 +57,8 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh tonzi "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh tonzi "$GITHUB_WORKSPACE/ed2-binary/ed2"
 
   test-tonzi-harvest:
     needs: build
@@ -67,5 +74,5 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh tonzi.harvest "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh tonzi.harvest "$GITHUB_WORKSPACE/ed2-binary/ed2"

From 063e63e300492df91e0d0c9b753aa1d32189d221 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Fri, 28 Jun 2024 16:22:50 -0400
Subject: [PATCH 07/11] configure.ac: more robust configuration setting test to
 f90

---
 configure.ac | 151 +++++++++++++++++++++++++++++++--------------------
 1 file changed, 92 insertions(+), 59 deletions(-)

diff --git a/configure.ac b/configure.ac
index 203c16033..69df7b639 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5,100 +5,133 @@ MAIN="ed-${PACKAGE_VERSION}"
 os_name=$(uname | sed "s/-.*//")
 SHLIB="rED2.so"
 
-CFLAGS="${CFLAGS} -I\"ED/src/include\""
+CFLAGS="${CFLAGS} -IED/src/include"
 
 PKG_PROG_PKG_CONFIG()
 AS_IF([test "x$os_name" != "xDarwin" -a "x$os_name" != "xLinux"],
   [
     AC_DEFINE_UNQUOTED([PKG_CONFIG_SYSTEM_INCLUDE_PATH], ["$PKG_CONFIG_SYSTEM_INCLUDE_PATH"], [MINGW defined pkg-config default system path])
-    CFLAGS="${CFLAGS} -I\"${PKG_CONFIG_SYSTEM_INCLUDE_PATH}\" ${FCFLAGS} -D_WIN32"
-    CPPFLAGS="${CFLAGS} ${FCFLAGS} -D_WIN32"
+    AS_IF([test "x$PKG_CONFIG_SYSTEM_INCLUDE_PATH" != "x"],
+    [
+      CFLAGS="${CFLAGS} -I\"${PKG_CONFIG_SYSTEM_INCLUDE_PATH}\" ${FCFLAGS} -D_WIN32"
+    ])
     MAIN="${MAIN}.exe"
     SHLIB="rED2.dll"
   ]
 )
 
 
+
 AC_PROG_FC([ifx ifort mpif90 gfortran])
 AC_PROG_CC
 AC_PROG_RANLIB
 AC_LANG([Fortran])
 
+# Check for hdf5_fortran
+PKG_CHECK_MODULES([hdf5_fortran], [hdf5_fortran], [
+    LIBS="${LIBS} ${hdf5_fortran_LIBS}"
+    CFLAGS="${CFLAGS} ${hdf5_fortran_CFLAGS}"
+  ], [
+    # If hdf5_fortran is not found, check for hdf5
+    PKG_CHECK_MODULES([hdf5], [hdf5], [
+      # Add hdf5 flags
+      LIBS="${LIBS} ${hdf5_LIBS} -lhdf5_fortran"
+      CFLAGS="${CFLAGS} ${hdf5_CFLAGS}"
+    ], [
+      # Try to link directly
+      LIBS="${LIBS} -lhdf5_fortran -lhdf5"
+    ])
+])
+
+# Link check for HDF5 support in Fortran
+FCFLAGS="${CFLAGS}"
+FFLAGS="${CFLAGS}"
+AC_FC_SRCEXT(f90)
+
+AC_MSG_CHECKING([if HDF5 library can link with Fortran code])
+AC_LINK_IFELSE([AC_LANG_PROGRAM(, [[
+  use hdf5
+  integer :: hdferr
+    call h5open_f(hdferr)
+    call h5close_f(hdferr)
+  ]])], [
+    AC_MSG_RESULT([yes])
+    have_hdf5=yes
+  ], [
+    AC_MSG_RESULT([no])
+    have_hdf5=no
+  ]
+)
+
+# Case where HDF5 library is not found    
+AS_IF([test "x$have_hdf5" = "xno"],[
+      AC_MSG_ERROR([
+HDF5 library not found!
+
+Please install HDF5 library and try again:
 
-PKG_CHECK_MODULES([hdf5_fortran], [hdf5_fortran], [have_hdf5=yes], [have_hdf5=no])
+    Debian: sudo apt-get install libhdf5-dev
+    Fedora: sudo dnf install hdf5-devel
+    CentOS: sudo yum install hdf5-devel
+    MacOS: brew install hdf5
+    Windows MinGW: pacman -S mingw-w64-ucrt-x86_64-hdf5
+      ])
+])
 
+# Check for MPI library if mpif90 was found
 AS_IF([test "x$FC" = "xmpif90"],
   [
+    ORIGINAL_CFLAGS="${CFLAGS}"
+    ORIGINAL_LIBS="${LIBS}"
+    
     AS_IF([test "x$os_name" != "xDarwin" -a "x$os_name" != "xLinux"],
       [
-        PKG_CHECK_MODULES([MPI], [msmpi], [have_mpi=yes], [have_mpi=no])
+        PKG_CHECK_MODULES([MPI], [msmpi], [have_mpi=yes], [
+          LIBS="${LIBS} -lmsmpi"
+        ])
       ],
       [
-        PKG_CHECK_MODULES([MPI], [mpi-fort], [have_mpi=yes], [have_mpi=no])
+        PKG_CHECK_MODULES([MPI], [mpi-fort], [have_mpi=yes], [
+          LIBS="${LIBS} -lmpi_usempif08 -lmpi_mpifh -lmpi"
+        ])
       ]
     )
 
-    AS_IF([test "x$have_mpi" = "xyes"],
-      [
+    AS_IF([test "x$have_mpi" = "xyes"], [
         CFLAGS="${CFLAGS} ${MPI_CFLAGS} -DRAMS_MPI -fallow-invalid-boz -fallow-argument-mismatch"
         LIBS="${LIBS} ${MPI_LIBS}"
-      ],
-      [
-        AC_PROG_FC([gfortran])
+      ], [
+        # If pkg-config is not found try to link directly
+        CFLAGS="${CFLAGS} -DRAMS_MPI -fallow-invalid-boz -fallow-argument-mismatch"
+
       ]
     )
-  ]
-)
-
 
-AS_IF([test "x$have_hdf5" = "xyes"],
-  [
-    LIBS="${LIBS} ${hdf5_fortran_LIBS} ${MPILIBS}"
-    CFLAGS="${CFLAGS} ${hdf5_fortran_CFLAGS}"
-  ],
-  [
-    PKG_CHECK_MODULES([HDF5], [hdf5], [have_hdf5=yes], [have_hdf5=no])
-    
-    AS_IF([test "x$have_hdf5" = "xyes"],
-      [
-        LIBS="${LIBS} ${HDF5_LIBS} -lhdf5 -lhdf5_fortran"
-        FCFLAGS="${CFLAGS} ${HDF5_CFLAGS}"
-
-        AC_MSG_CHECKING([for HDF5 support in Fortran])
-        AC_LANG_PUSH([Fortran])
-
-        AC_LINK_IFELSE([AC_LANG_PROGRAM([], [[
-              use hdf5
-              integer :: hdferr
-              call h5open_f(hdferr)
-              call h5close_f(hdferr)
-        ]])],
-        [AC_MSG_RESULT([yes])
-        HDF5_OK=yes],
-        [AC_MSG_RESULT([no])
-        HDF5_OK=no])
-
-        AC_LANG_POP([Fortran])
-      ],
-      [have_hdf5=no])
+    FCFLAGS="${CFLAGS}"
+
+    AC_MSG_CHECKING([for MPI can link in Fortran])
+    AC_LINK_IFELSE([
+      AC_LANG_PROGRAM([], [[
+        program test_mpi
+            use mpi
+            integer :: ierr, rank
+            call MPI_Init(ierr)
+            call MPI_Comm_rank(MPI_COMM_WORLD, rank, ierr)
+            call MPI_Finalize(ierr)
+        end program test_mpi
+        ]], [[]]
+      )], [
+          AC_MSG_RESULT([yes])
+      ], [
+          AC_MSG_RESULT([no])
+          CFLAGS="${ORIGINAL_CFLAGS}"
+          LIBS="${ORIGINAL_LIBS}"
+          AC_PROG_FC([gfortran])
+      ]
+    )
   ]
 )
 
-AS_IF([test "x$have_hdf5" = "xno"],[
-      AC_MSG_ERROR([
-HDF5 library not found!
-
-Please install HDF5 library and try again:
-
-    Debian: sudo apt-get install libhdf5-dev
-    Fedora: sudo dnf install hdf5-devel
-    CentOS: sudo yum install hdf5-devel
-    MacOS: brew install hdf5
-    Windows MinGW: pacman -S mingw-w64-x86_64-hdf5
-      ])
-])
-
-
 AC_SUBST([CC])
 AC_SUBST([FC])
 AC_SUBST([SHLIB])

From c189e3317ad8213d5f3b8638b5ffd453cf0cc856 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Mon, 1 Jul 2024 11:10:12 -0400
Subject: [PATCH 08/11] Add includde EDR EDTS and R-utils to EXTRA_DIST

---
 Makefile.am | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Makefile.am b/Makefile.am
index 1aa1a8e81..ee2422127 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -28,5 +28,8 @@ libed2_a_SOURCES = $(SOURCES)
 # Additional Fortran clean files
 CLEANFILES = *.mod
 
+# Additional files for distribution
+EXTRA_DIST = ED/src/include EDR EDTS R-utils
+
 # Include the dependency makefile
 include ED/build/shell/dependency.mk

From 9df6749f06b322f1712c205fd2d5bc10db6ff16c Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Mon, 1 Jul 2024 12:11:43 -0400
Subject: [PATCH 09/11] Change include mpi.h to use mpi

---
 ED/build/shell/dependency.mk    | 208 ++++++++++++++++++++++++++++++++
 ED/build/shell/sources.mk       |   1 +
 ED/src/driver/ed_1st.F90        |  10 +-
 ED/src/driver/ed_driver.F90     |   7 +-
 ED/src/driver/ed_model.F90      |   5 +-
 ED/src/driver/edmain.F90        |  10 +-
 ED/src/init/ed_init.F90         |   4 +-
 ED/src/init/ed_init_atm.F90     |   5 +-
 ED/src/io/ed_print.F90          |   5 +-
 ED/src/io/h5_output.F90         |   8 +-
 ED/src/memory/ed_state_vars.F90 |   4 +-
 ED/src/mpi/ed_mpass_init.F90    |  53 +++++---
 ED/src/utils/fatal_error.F90    |   8 +-
 13 files changed, 279 insertions(+), 49 deletions(-)
 create mode 100644 ED/build/shell/dependency.mk
 create mode 100644 ED/build/shell/sources.mk

diff --git a/ED/build/shell/dependency.mk b/ED/build/shell/dependency.mk
new file mode 100644
index 000000000..da5060653
--- /dev/null
+++ b/ED/build/shell/dependency.mk
@@ -0,0 +1,208 @@
+ed_1st.mod: ED/src/driver/ed_1st.o
+ED/src/driver/ed_1st.o: ed_mem_alloc.mod ed_met_driver.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod
+ed_driver.mod: ED/src/driver/ed_driver.o
+ED/src/driver/ed_driver.o: canopy_radiation_coms.mod consts_coms.mod detailed_coms.mod ed_init.mod ed_init_history.mod ed_met_driver.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod fuse_fiss_utils.mod grid_coms.mod hrzshade_utils.mod lsm_hyd.mod phenology_aux.mod random_utils.mod soil_coms.mod update_derived_utils.mod
+ed_met_driver.mod: ED/src/driver/ed_met_driver.o
+ED/src/driver/ed_met_driver.o: canopy_air_coms.mod canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod grid_coms.mod hdf5_utils.mod lapse.mod met_driver_coms.mod pft_coms.mod radiate_utils.mod random_utils.mod therm_lib.mod update_derived_utils.mod
+ed_model.mod: ED/src/driver/ed_model.o
+ED/src/driver/ed_model.o: average_utils.mod budget_utils.mod consts_coms.mod ed_init.mod ed_met_driver.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod ed_type_init.mod edio.mod euler_driver.mod grid_coms.mod heun_driver.mod hybrid_driver.mod lsm_hyd.mod mem_polygons.mod radiate_driver.mod rk4_coms.mod rk4_driver.mod rk4_integ_utils.mod soil_respiration.mod stable_cohorts.mod update_derived_utils.mod vegetation_dynamics.mod
+bdf2_solver.mod: ED/src/dynamics/bdf2_solver.o
+ED/src/dynamics/bdf2_solver.o: consts_coms.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod rk4_coms.mod soil_coms.mod therm_lib8.mod
+canopy_struct_dynamics.mod: ED/src/dynamics/canopy_struct_dynamics.o
+ED/src/dynamics/canopy_struct_dynamics.o: allometry.mod canopy_air_coms.mod canopy_layer_coms.mod consts_coms.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+disturbance.mod: ED/src/dynamics/disturbance.o
+ED/src/dynamics/disturbance.o: allometry.mod consts_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod ed_type_init.mod forestry.mod fuse_fiss_utils.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod mortality.mod pft_coms.mod phenology_aux.mod plant_hydro.mod stable_cohorts.mod therm_lib.mod update_derived_utils.mod
+euler_driver.mod: ED/src/dynamics/euler_driver.o
+ED/src/dynamics/euler_driver.o: budget_utils.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod photosyn_driv.mod plant_hydro.mod rk4_coms.mod rk4_copy_patch.mod rk4_derivs.mod rk4_integ_utils.mod rk4_misc.mod soil_coms.mod soil_respiration.mod stem_resp_driv.mod therm_lib.mod therm_lib8.mod update_derived_utils.mod
+events.mod: ED/src/dynamics/events.o
+ED/src/dynamics/events.o: allometry.mod consts_coms.mod disturbance.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod ed_type_init.mod fuse_fiss_utils.mod grid_coms.mod met_driver_coms.mod pft_coms.mod plant_hydro.mod rk4_integ_utils.mod stable_cohorts.mod therm_lib.mod update_derived_utils.mod
+farq_katul.mod: ED/src/dynamics/farq_katul.o
+ED/src/dynamics/farq_katul.o: c34constants.mod consts_coms.mod ed_misc_coms.mod farq_leuning.mod pft_coms.mod physiology_coms.mod rk4_coms.mod
+farq_leuning.mod: ED/src/dynamics/farq_leuning.o
+ED/src/dynamics/farq_leuning.o: c34constants.mod consts_coms.mod pft_coms.mod physiology_coms.mod rk4_coms.mod therm_lib8.mod
+fire.mod: ED/src/dynamics/fire.o
+ED/src/dynamics/fire.o: consts_coms.mod disturb_coms.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod pft_coms.mod soil_coms.mod
+forestry.mod: ED/src/dynamics/forestry.o
+ED/src/dynamics/forestry.o: consts_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_state_vars.mod fuse_fiss_utils.mod
+growth_balive.mod: ED/src/dynamics/growth_balive.o
+ED/src/dynamics/growth_balive.o: allometry.mod budget_utils.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod fuse_fiss_utils.mod met_driver_coms.mod mortality.mod pft_coms.mod physiology_coms.mod plant_hydro.mod stable_cohorts.mod update_derived_utils.mod
+heun_driver.mod: ED/src/dynamics/heun_driver.o
+ED/src/dynamics/heun_driver.o: budget_utils.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod photosyn_driv.mod plant_hydro.mod rk4_coms.mod rk4_copy_patch.mod rk4_derivs.mod rk4_integ_utils.mod rk4_misc.mod soil_coms.mod soil_respiration.mod stem_resp_driv.mod therm_lib.mod therm_lib8.mod update_derived_utils.mod
+hybrid_driver.mod: ED/src/dynamics/hybrid_driver.o
+ED/src/dynamics/hybrid_driver.o: bdf2_solver.mod budget_utils.mod consts_coms.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod photosyn_driv.mod plant_hydro.mod rk4_coms.mod rk4_copy_patch.mod rk4_derivs.mod rk4_integ_utils.mod rk4_misc.mod soil_coms.mod soil_respiration.mod stem_resp_driv.mod therm_lib.mod therm_lib8.mod update_derived_utils.mod
+lsm_hyd.mod: ED/src/dynamics/lsm_hyd.o
+ED/src/dynamics/lsm_hyd.o: consts_coms.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod grid_coms.mod hydrology_coms.mod hydrology_constants.mod pft_coms.mod soil_coms.mod therm_lib.mod
+mortality.mod: ED/src/dynamics/mortality.o
+ED/src/dynamics/mortality.o: consts_coms.mod disturb_coms.mod ed_max_dims.mod ed_state_vars.mod pft_coms.mod physiology_coms.mod
+multiple_scatter.mod: ED/src/dynamics/multiple_scatter.o
+ED/src/dynamics/multiple_scatter.o: canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod rk4_coms.mod
+old_twostream_rad.mod: ED/src/dynamics/old_twostream_rad.o
+ED/src/dynamics/old_twostream_rad.o: canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod rk4_coms.mod
+phenology_aux.mod: ED/src/dynamics/phenology_aux.o
+ED/src/dynamics/phenology_aux.o: allometry.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod plant_hydro.mod soil_coms.mod stable_cohorts.mod therm_lib.mod
+phenology_driv.mod: ED/src/dynamics/phenology_driv.o
+ED/src/dynamics/phenology_driv.o: allometry.mod budget_utils.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod pft_coms.mod phenology_aux.mod phenology_coms.mod plant_hydro.mod stable_cohorts.mod therm_lib.mod
+photosyn_driv.mod: ED/src/dynamics/photosyn_driv.o
+ED/src/dynamics/photosyn_driv.o: allometry.mod canopy_air_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod farq_katul.mod farq_leuning.mod met_driver_coms.mod pft_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod therm_lib.mod
+plant_hydro.mod: ED/src/dynamics/plant_hydro.o
+ED/src/dynamics/plant_hydro.o: allometry.mod consts_coms.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod pft_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+radiate_driver.mod: ED/src/dynamics/radiate_driver.o
+ED/src/dynamics/radiate_driver.o: allometry.mod canopy_layer_coms.mod canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod multiple_scatter.mod old_twostream_rad.mod radiate_utils.mod rk4_coms.mod soil_coms.mod twostream_rad.mod
+reproduction.mod: ED/src/dynamics/reproduction.o
+ED/src/dynamics/reproduction.o: allometry.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod ed_type_init.mod fuse_fiss_utils.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod pft_coms.mod phenology_aux.mod phenology_coms.mod physiology_coms.mod plant_hydro.mod stable_cohorts.mod update_derived_utils.mod
+rk4_copy_patch.mod: ED/src/dynamics/rk4_copy_patch.o
+ED/src/dynamics/rk4_copy_patch.o: allometry.mod budget_utils.mod canopy_air_coms.mod canopy_struct_dynamics.mod consts_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod phenology_coms.mod physiology_coms.mod plant_hydro.mod rk4_coms.mod rk4_misc.mod soil_coms.mod therm_lib.mod therm_lib8.mod
+rk4_derivs.mod: ED/src/dynamics/rk4_derivs.o
+ED/src/dynamics/rk4_derivs.o: budget_utils.mod canopy_struct_dynamics.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod therm_lib8.mod
+rk4_driver.mod: ED/src/dynamics/rk4_driver.o
+ED/src/dynamics/rk4_driver.o: budget_utils.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod photosyn_driv.mod plant_hydro.mod rk4_coms.mod rk4_copy_patch.mod rk4_integ_utils.mod rk4_misc.mod soil_respiration.mod stem_resp_driv.mod therm_lib.mod update_derived_utils.mod
+rk4_integ_utils.mod: ED/src/dynamics/rk4_integ_utils.o
+ED/src/dynamics/rk4_integ_utils.o: c34constants.mod canopy_air_coms.mod canopy_layer_coms.mod canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod ed_state_vars.mod grid_coms.mod hydrology_coms.mod physiology_coms.mod rk4_coms.mod rk4_copy_patch.mod rk4_derivs.mod rk4_misc.mod soil_coms.mod therm_lib8.mod
+rk4_misc.mod: ED/src/dynamics/rk4_misc.o
+ED/src/dynamics/rk4_misc.o: budget_utils.mod canopy_struct_dynamics.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod pft_coms.mod physiology_coms.mod plant_hydro.mod rk4_coms.mod soil_coms.mod therm_lib.mod therm_lib8.mod
+soil_respiration.mod: ED/src/dynamics/soil_respiration.o
+ED/src/dynamics/soil_respiration.o: budget_utils.mod consts_coms.mod decomp_coms.mod ed_misc_coms.mod ed_state_vars.mod farq_leuning.mod grid_coms.mod pft_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod therm_lib.mod
+stem_resp_driv.mod: ED/src/dynamics/stem_resp_driv.o
+ED/src/dynamics/stem_resp_driv.o: consts_coms.mod ed_misc_coms.mod ed_state_vars.mod farq_leuning.mod pft_coms.mod physiology_coms.mod rk4_coms.mod
+structural_growth.mod: ED/src/dynamics/structural_growth.o
+ED/src/dynamics/structural_growth.o: allometry.mod budget_utils.mod consts_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod fuse_fiss_utils.mod pft_coms.mod physiology_coms.mod plant_hydro.mod stable_cohorts.mod update_derived_utils.mod
+twostream_rad.mod: ED/src/dynamics/twostream_rad.o
+ED/src/dynamics/twostream_rad.o: canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod rk4_coms.mod
+vegetation_dynamics.mod: ED/src/dynamics/vegetation_dynamics.o
+ED/src/dynamics/vegetation_dynamics.o: average_utils.mod budget_utils.mod canopy_radiation_coms.mod consts_coms.mod disturbance.mod ed_cn_utils.mod ed_misc_coms.mod ed_state_vars.mod fire.mod fuse_fiss_utils.mod fusion_fission_coms.mod grid_coms.mod growth_balive.mod hrzshade_utils.mod mem_polygons.mod phenology_driv.mod reproduction.mod soil_respiration.mod structural_growth.mod update_derived_utils.mod
+ed_bigleaf_init.mod: ED/src/init/ed_bigleaf_init.o
+ED/src/init/ed_bigleaf_init.o: allometry.mod consts_coms.mod ed_max_dims.mod ed_node_coms.mod ed_state_vars.mod ed_type_init.mod fuse_fiss_utils.mod grid_coms.mod pft_coms.mod physiology_coms.mod
+ed_init.mod: ED/src/init/ed_init.o
+ED/src/init/ed_init.o: consts_coms.mod ed_bigleaf_init.mod ed_max_dims.mod ed_misc_coms.mod ed_nbg_init.mod ed_node_coms.mod ed_state_vars.mod ed_work_vars.mod grid_coms.mod landuse_init.mod mem_polygons.mod phenology_startup.mod rk4_coms.mod soil_coms.mod
+ed_init_atm.mod: ED/src/init/ed_init_atm.o
+ED/src/init/ed_init_atm.o: canopy_layer_coms.mod canopy_radiation_coms.mod canopy_struct_dynamics.mod consts_coms.mod ed_misc_coms.mod ed_node_coms.mod ed_para_coms.mod ed_state_vars.mod ed_therm_lib.mod fuse_fiss_utils.mod fusion_fission_coms.mod grid_coms.mod hrzshade_utils.mod met_driver_coms.mod soil_coms.mod stable_cohorts.mod therm_lib.mod update_derived_utils.mod
+ed_nbg_init.mod: ED/src/init/ed_nbg_init.o
+ED/src/init/ed_nbg_init.o: allometry.mod consts_coms.mod decomp_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_type_init.mod fuse_fiss_utils.mod grid_coms.mod pft_coms.mod physiology_coms.mod
+ed_params.mod: ED/src/init/ed_params.o
+ED/src/init/ed_params.o: allometry.mod budget_utils.mod canopy_air_coms.mod canopy_layer_coms.mod canopy_radiation_coms.mod consts_coms.mod decomp_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_therm_lib.mod farq_leuning.mod fusion_fission_coms.mod grid_coms.mod hydrology_coms.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod plant_hydro.mod rk4_coms.mod soil_coms.mod
+ed_type_init.mod: ED/src/init/ed_type_init.o
+ED/src/init/ed_type_init.o: allometry.mod canopy_air_coms.mod consts_coms.mod ed_cn_utils.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod grid_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod plant_hydro.mod rk4_coms.mod soil_coms.mod therm_lib.mod
+landuse_init.mod: ED/src/init/landuse_init.o
+ED/src/init/landuse_init.o: consts_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod
+phenology_startup.mod: ED/src/init/phenology_startup.o
+ED/src/init/phenology_startup.o: ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod phenology_aux.mod phenology_coms.mod
+average_utils.mod: ED/src/io/average_utils.o
+ED/src/io/average_utils.o: consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod met_driver_coms.mod physiology_coms.mod soil_coms.mod therm_lib.mod
+edio.mod: ED/src/io/edio.o
+ED/src/io/edio.o: average_utils.mod ed_misc_coms.mod ed_print.mod ed_state_vars.mod grid_coms.mod
+ed_init_history.mod: ED/src/io/ed_init_history.o
+ED/src/io/ed_init_history.o: ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod fusion_fission_coms.mod grid_coms.mod hdf5_coms.mod landuse_init.mod phenology_startup.mod soil_coms.mod
+ed_load_namelist.mod: ED/src/io/ed_load_namelist.o
+ED/src/io/ed_load_namelist.o: canopy_air_coms.mod canopy_layer_coms.mod canopy_radiation_coms.mod consts_coms.mod decomp_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod ename_coms.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+ed_opspec.mod: ED/src/io/ed_opspec.o
+ED/src/io/ed_opspec.o: canopy_air_coms.mod canopy_layer_coms.mod canopy_radiation_coms.mod consts_coms.mod decomp_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_para_coms.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+ed_print.mod: ED/src/io/ed_print.o
+ED/src/io/ed_print.o: ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod ed_var_tables.mod
+ed_read_ed10_20_history.mod: ED/src/io/ed_read_ed10_20_history.o
+ED/src/io/ed_read_ed10_20_history.o: allometry.mod consts_coms.mod decomp_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_type_init.mod fuse_fiss_utils.mod grid_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod update_derived_utils.mod
+ed_read_ed21_history.mod: ED/src/io/ed_read_ed21_history.o
+ED/src/io/ed_read_ed21_history.o: allometry.mod consts_coms.mod decomp_coms.mod disturb_coms.mod ed_init.mod ed_init_history.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_type_init.mod fuse_fiss_utils.mod grid_coms.mod hdf5_coms.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod soil_coms.mod update_derived_utils.mod
+ed_xml_config.mod: ED/src/io/ed_xml_config.o
+ED/src/io/ed_xml_config.o: budget_utils.mod canopy_air_coms.mod canopy_radiation_coms.mod decomp_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod fusion_fission_coms.mod grid_coms.mod hydrology_coms.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+h5_output.mod: ED/src/io/h5_output.o
+ED/src/io/h5_output.o: ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod ed_var_tables.mod fusion_fission_coms.mod grid_coms.mod hdf5_coms.mod
+leaf_database.mod: ED/src/io/leaf_database.o
+ED/src/io/leaf_database.o: grid_coms.mod hdf5_utils.mod soil_coms.mod
+c34constants.mod: ED/src/memory/c34constants.o
+canopy_air_coms.mod: ED/src/memory/canopy_air_coms.o
+ED/src/memory/canopy_air_coms.o: consts_coms.mod therm_lib8.mod
+canopy_layer_coms.mod: ED/src/memory/canopy_layer_coms.o
+canopy_radiation_coms.mod: ED/src/memory/canopy_radiation_coms.o
+ED/src/memory/canopy_radiation_coms.o: ed_max_dims.mod
+consts_coms.mod: ED/src/memory/consts_coms.o
+decomp_coms.mod: ED/src/memory/decomp_coms.o
+detailed_coms.mod: ED/src/memory/detailed_coms.o
+disturb_coms.mod: ED/src/memory/disturb_coms.o
+ED/src/memory/disturb_coms.o: ed_max_dims.mod
+ed_max_dims.mod: ED/src/memory/ed_max_dims.o
+ed_mem_alloc.mod: ED/src/memory/ed_mem_alloc.o
+ED/src/memory/ed_mem_alloc.o: ed_max_dims.mod ed_node_coms.mod ed_state_vars.mod ed_work_vars.mod grid_coms.mod mem_polygons.mod
+ed_misc_coms.mod: ED/src/memory/ed_misc_coms.o
+ED/src/memory/ed_misc_coms.o: ed_max_dims.mod
+ed_state_vars.mod: ED/src/memory/ed_state_vars.o
+ED/src/memory/ed_state_vars.o: disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_var_tables.mod fusion_fission_coms.mod grid_coms.mod met_driver_coms.mod phenology_coms.mod soil_coms.mod
+ed_var_tables.mod: ED/src/memory/ed_var_tables.o
+ED/src/memory/ed_var_tables.o: ed_max_dims.mod
+ed_work_vars.mod: ED/src/memory/ed_work_vars.o
+ED/src/memory/ed_work_vars.o: ed_max_dims.mod
+ename_coms.mod: ED/src/memory/ename_coms.o
+ED/src/memory/ename_coms.o: ed_max_dims.mod
+fusion_fission_coms.mod: ED/src/memory/fusion_fission_coms.o
+ED/src/memory/fusion_fission_coms.o: ed_max_dims.mod
+grid_coms.mod: ED/src/memory/grid_coms.o
+ED/src/memory/grid_coms.o: ed_max_dims.mod
+hdf5_coms.mod: ED/src/memory/hdf5_coms.o
+hydrology_coms.mod: ED/src/memory/hydrology_coms.o
+hydrology_constants.mod: ED/src/memory/hydrology_constants.o
+mem_polygons.mod: ED/src/memory/mem_polygons.o
+ED/src/memory/mem_polygons.o: ed_max_dims.mod
+met_driver_coms.mod: ED/src/memory/met_driver_coms.o
+ED/src/memory/met_driver_coms.o: ed_max_dims.mod
+pft_coms.mod: ED/src/memory/pft_coms.o
+ED/src/memory/pft_coms.o: ed_max_dims.mod
+phenology_coms.mod: ED/src/memory/phenology_coms.o
+ED/src/memory/phenology_coms.o: ed_max_dims.mod
+physiology_coms.mod: ED/src/memory/physiology_coms.o
+ED/src/memory/physiology_coms.o: ed_max_dims.mod
+rk4_coms.mod: ED/src/memory/rk4_coms.o
+ED/src/memory/rk4_coms.o: ed_max_dims.mod grid_coms.mod
+soil_coms.mod: ED/src/memory/soil_coms.o
+ED/src/memory/soil_coms.o: consts_coms.mod ed_max_dims.mod grid_coms.mod
+ed_mpass_init.mod: ED/src/mpi/ed_mpass_init.o
+ED/src/mpi/ed_mpass_init.o: canopy_air_coms.mod canopy_layer_coms.mod canopy_radiation_coms.mod decomp_coms.mod detailed_coms.mod disturb_coms.mod ed_max_dims.mod ed_mem_alloc.mod ed_misc_coms.mod ed_node_coms.mod ed_para_coms.mod ed_state_vars.mod ed_work_vars.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod rk4_coms.mod soil_coms.mod
+ed_node_coms.mod: ED/src/mpi/ed_node_coms.o
+ED/src/mpi/ed_node_coms.o: ed_max_dims.mod
+ed_para_coms.mod: ED/src/mpi/ed_para_coms.o
+ED/src/mpi/ed_para_coms.o: ed_max_dims.mod
+ed_para_init.mod: ED/src/mpi/ed_para_init.o
+ED/src/mpi/ed_para_init.o: ed_init_history.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_para_coms.mod ed_work_vars.mod grid_coms.mod hdf5_coms.mod mem_polygons.mod soil_coms.mod
+allometry.mod: ED/src/utils/allometry.o
+ED/src/utils/allometry.o: consts_coms.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod pft_coms.mod rk4_coms.mod soil_coms.mod therm_lib.mod
+budget_utils.mod: ED/src/utils/budget_utils.o
+ED/src/utils/budget_utils.o: consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod rk4_coms.mod soil_coms.mod therm_lib.mod
+charutils.mod: ED/src/utils/charutils.o
+dateutils.mod: ED/src/utils/dateutils.o
+ED/src/utils/dateutils.o: consts_coms.mod
+ed_cn_utils.mod: ED/src/utils/ed_cn_utils.o
+ED/src/utils/ed_cn_utils.o: ed_max_dims.mod ed_state_vars.mod pft_coms.mod
+ed_filelist.mod: ED/src/utils/ed_filelist.o
+ED/src/utils/ed_filelist.o: ed_max_dims.mod
+ed_grid.mod: ED/src/utils/ed_grid.o
+ED/src/utils/ed_grid.o: consts_coms.mod ed_max_dims.mod ed_node_coms.mod grid_coms.mod
+ed_therm_lib.mod: ED/src/utils/ed_therm_lib.o
+ED/src/utils/ed_therm_lib.o: canopy_air_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod grid_coms.mod pft_coms.mod rk4_coms.mod soil_coms.mod therm_lib.mod therm_lib8.mod
+fatal_error.mod: ED/src/utils/fatal_error.o
+ED/src/utils/fatal_error.o: ed_node_coms.mod
+fuse_fiss_utils.mod: ED/src/utils/fuse_fiss_utils.o
+ED/src/utils/fuse_fiss_utils.o: allometry.mod budget_utils.mod consts_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod ed_therm_lib.mod ed_type_init.mod fusion_fission_coms.mod grid_coms.mod mem_polygons.mod met_driver_coms.mod pft_coms.mod plant_hydro.mod rk4_coms.mod soil_coms.mod stable_cohorts.mod therm_lib.mod update_derived_utils.mod
+great_circle.mod: ED/src/utils/great_circle.o
+ED/src/utils/great_circle.o: consts_coms.mod
+hdf5_utils.mod: ED/src/utils/hdf5_utils.o
+ED/src/utils/hdf5_utils.o: hdf5_coms.mod
+hrzshade_utils.mod: ED/src/utils/hrzshade_utils.o
+ED/src/utils/hrzshade_utils.o: allometry.mod canopy_radiation_coms.mod consts_coms.mod disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod pft_coms.mod random_utils.mod rk4_coms.mod
+invmondays.mod: ED/src/utils/invmondays.o
+ED/src/utils/invmondays.o: ed_misc_coms.mod
+lapse.mod: ED/src/utils/lapse.o
+ED/src/utils/lapse.o: consts_coms.mod ed_misc_coms.mod ed_state_vars.mod met_driver_coms.mod
+libxml2f90.f90_pp.mod: ED/src/utils/libxml2f90.f90_pp.o
+numutils.mod: ED/src/utils/numutils.o
+ED/src/utils/numutils.o: consts_coms.mod
+radiate_utils.mod: ED/src/utils/radiate_utils.o
+ED/src/utils/radiate_utils.o: canopy_radiation_coms.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod met_driver_coms.mod phenology_coms.mod update_derived_utils.mod
+random_utils.mod: ED/src/utils/random_utils.o
+rsys.mod: ED/src/utils/rsys.o
+stable_cohorts.mod: ED/src/utils/stable_cohorts.o
+ED/src/utils/stable_cohorts.o: allometry.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod pft_coms.mod physiology_coms.mod plant_hydro.mod
+therm_lib.mod: ED/src/utils/therm_lib.o
+ED/src/utils/therm_lib.o: consts_coms.mod
+therm_lib8.mod: ED/src/utils/therm_lib8.o
+ED/src/utils/therm_lib8.o: consts_coms.mod therm_lib.mod
+update_derived_utils.mod: ED/src/utils/update_derived_utils.o
+ED/src/utils/update_derived_utils.o: allometry.mod canopy_air_coms.mod canopy_radiation_coms.mod consts_coms.mod detailed_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod ed_therm_lib.mod fusion_fission_coms.mod grid_coms.mod pft_coms.mod phenology_coms.mod physiology_coms.mod soil_coms.mod therm_lib.mod
+utils_f.mod: ED/src/utils/utils_f.o
diff --git a/ED/build/shell/sources.mk b/ED/build/shell/sources.mk
new file mode 100644
index 000000000..e1d63ed08
--- /dev/null
+++ b/ED/build/shell/sources.mk
@@ -0,0 +1 @@
+SOURCES = ED/src/driver/ed_1st.F90 ED/src/driver/ed_driver.F90 ED/src/driver/ed_met_driver.f90 ED/src/driver/ed_model.F90 ED/src/dynamics/bdf2_solver.f90 ED/src/dynamics/canopy_struct_dynamics.f90 ED/src/dynamics/disturbance.f90 ED/src/dynamics/euler_driver.f90 ED/src/dynamics/events.f90 ED/src/dynamics/farq_katul.f90 ED/src/dynamics/farq_leuning.f90 ED/src/dynamics/fire.f90 ED/src/dynamics/forestry.f90 ED/src/dynamics/growth_balive.f90 ED/src/dynamics/heun_driver.f90 ED/src/dynamics/hybrid_driver.f90 ED/src/dynamics/lsm_hyd.f90 ED/src/dynamics/mortality.f90 ED/src/dynamics/multiple_scatter.f90 ED/src/dynamics/old_twostream_rad.f90 ED/src/dynamics/phenology_aux.f90 ED/src/dynamics/phenology_driv.f90 ED/src/dynamics/photosyn_driv.f90 ED/src/dynamics/plant_hydro.f90 ED/src/dynamics/radiate_driver.f90 ED/src/dynamics/reproduction.f90 ED/src/dynamics/rk4_copy_patch.f90 ED/src/dynamics/rk4_derivs.f90 ED/src/dynamics/rk4_driver.F90 ED/src/dynamics/rk4_integ_utils.f90 ED/src/dynamics/rk4_misc.f90 ED/src/dynamics/soil_respiration.f90 ED/src/dynamics/stem_resp_driv.f90 ED/src/dynamics/structural_growth.f90 ED/src/dynamics/twostream_rad.f90 ED/src/dynamics/vegetation_dynamics.f90 ED/src/init/ed_bigleaf_init.f90 ED/src/init/ed_init.F90 ED/src/init/ed_init_atm.F90 ED/src/init/ed_nbg_init.f90 ED/src/init/ed_params.f90 ED/src/init/ed_type_init.f90 ED/src/init/landuse_init.f90 ED/src/init/phenology_startup.f90 ED/src/io/average_utils.f90 ED/src/io/edio.f90 ED/src/io/ed_init_history.f90 ED/src/io/ed_load_namelist.f90 ED/src/io/ed_opspec.F90 ED/src/io/ed_print.F90 ED/src/io/ed_read_ed10_20_history.f90 ED/src/io/ed_read_ed21_history.f90 ED/src/io/ed_xml_config.f90 ED/src/io/h5_output.F90 ED/src/io/leaf_database.f90 ED/src/memory/c34constants.f90 ED/src/memory/canopy_air_coms.f90 ED/src/memory/canopy_layer_coms.f90 ED/src/memory/canopy_radiation_coms.f90 ED/src/memory/consts_coms.F90 ED/src/memory/decomp_coms.f90 ED/src/memory/detailed_coms.f90 ED/src/memory/disturb_coms.f90 ED/src/memory/ed_max_dims.F90 ED/src/memory/ed_mem_alloc.f90 ED/src/memory/ed_misc_coms.f90 ED/src/memory/ed_state_vars.F90 ED/src/memory/ed_var_tables.f90 ED/src/memory/ed_work_vars.f90 ED/src/memory/ename_coms.f90 ED/src/memory/fusion_fission_coms.f90 ED/src/memory/grid_coms.f90 ED/src/memory/hdf5_coms.f90 ED/src/memory/hydrology_coms.f90 ED/src/memory/hydrology_constants.f90 ED/src/memory/mem_polygons.f90 ED/src/memory/met_driver_coms.f90 ED/src/memory/pft_coms.f90 ED/src/memory/phenology_coms.f90 ED/src/memory/physiology_coms.f90 ED/src/memory/rk4_coms.f90 ED/src/memory/soil_coms.F90 ED/src/mpi/ed_mpass_init.F90 ED/src/mpi/ed_node_coms.f90 ED/src/mpi/ed_para_coms.f90 ED/src/mpi/ed_para_init.f90 ED/src/utils/allometry.f90 ED/src/utils/budget_utils.f90 ED/src/utils/charutils.f90 ED/src/utils/dateutils.f90 ED/src/utils/ed_cn_utils.f90 ED/src/utils/ed_filelist.F90 ED/src/utils/ed_grid.f90 ED/src/utils/ed_therm_lib.f90 ED/src/utils/fatal_error.F90 ED/src/utils/fuse_fiss_utils.f90 ED/src/utils/great_circle.f90 ED/src/utils/hdf5_utils.f90 ED/src/utils/hrzshade_utils.f90 ED/src/utils/invmondays.f90 ED/src/utils/lapse.f90 ED/src/utils/libxml2f90.f90_pp.f90 ED/src/utils/numutils.f90 ED/src/utils/radiate_utils.f90 ED/src/utils/random_utils.F90 ED/src/utils/rsys.F90 ED/src/utils/stable_cohorts.f90 ED/src/utils/therm_lib.f90 ED/src/utils/therm_lib8.f90 ED/src/utils/update_derived_utils.f90 ED/src/utils/utils_f.f90 ED/src/utils/utils_c.c
diff --git a/ED/src/driver/ed_1st.F90 b/ED/src/driver/ed_1st.F90
index e2d3acd3b..5490bf5f1 100644
--- a/ED/src/driver/ed_1st.F90
+++ b/ED/src/driver/ed_1st.F90
@@ -23,12 +23,12 @@ subroutine ed_1st_master (ipara, nnodestotal,nslaves, headnode_num, max_threads,
    use ed_state_vars, only : allocate_edglobals   & ! subroutine
                            , filltab_alltypes     ! ! subroutine
 
+#if defined(RAMS_MPI)
+  use mpi
+#endif
    implicit none
 
    !----- Pre-compiled variables from MPI. ------------------------------------------------!
-#if defined(RAMS_MPI)
-   include 'mpif.h'
-#endif
    !----- Arguments. ----------------------------------------------------------------------!
    integer         , intent(in) :: ipara        ! 0 if sequential run; 1 if parallel run
    integer         , intent(in) :: nnodestotal  ! total number of nodes on any run
@@ -176,10 +176,12 @@ end subroutine ed_1st_master
 !------------------------------------------------------------------------------------------!
 subroutine ed_1st_node()
    use ed_mem_alloc, only : ed_memory_allocation ! ! subroutine
+#if defined(RAMS_MPI)
+     use mpi
+#endif
    implicit none
    !----- Pre-compiled variables from MPI. ------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
    !----- Local variable (MPI only). ------------------------------------------------------!
    integer             :: ierr
 #endif
diff --git a/ED/src/driver/ed_driver.F90 b/ED/src/driver/ed_driver.F90
index 1c7ff8724..81b3f7cc4 100644
--- a/ED/src/driver/ed_driver.F90
+++ b/ED/src/driver/ed_driver.F90
@@ -36,11 +36,12 @@ subroutine ed_driver()
    use hrzshade_utils       , only : init_cci_variables            ! ! subroutine
    use canopy_radiation_coms, only : ihrzrad                       ! ! intent(in)
    use random_utils         , only : init_random_seed              ! ! subroutine
-   implicit none
-   !----- Included variables. -------------------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h' ! MPI commons
+  use mpi ! MPI commons
 #endif
+   implicit none
+
+   !----- Included variables. -------------------------------------------------------------!
    !----- Local variables. ----------------------------------------------------------------!
    character(len=12)           :: c0
    character(len=12)           :: c1
diff --git a/ED/src/driver/ed_model.F90 b/ED/src/driver/ed_model.F90
index 77cc8f9d0..49bcb72a7 100644
--- a/ED/src/driver/ed_model.F90
+++ b/ED/src/driver/ed_model.F90
@@ -94,11 +94,10 @@ subroutine ed_model()
    use vegetation_dynamics , only : veg_dynamics_driver         ! ! sub-routine
    use ed_type_init        , only : ed_init_viable              ! ! sub-routine
    use soil_respiration    , only : zero_litter_inputs          ! ! sub-routine
-   implicit none
-   !----- Common blocks. ------------------------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
+   use mpi
 #endif
+   implicit none
    !----- Local variables. ----------------------------------------------------------------!
    type(simtime)      :: daybefore
    character(len=28)  :: fmthead
diff --git a/ED/src/driver/edmain.F90 b/ED/src/driver/edmain.F90
index 53995bf4a..e74dad025 100644
--- a/ED/src/driver/edmain.F90
+++ b/ED/src/driver/edmain.F90
@@ -14,7 +14,10 @@
 !------------------------------------------------------------------------------------------!
 program main
    !$ use omp_lib
-   implicit none
+#if defined(RAMS_MPI)
+  use mpi
+#endif
+  implicit none
 
    !---------------------------------------------------------------------------------------!
    !      Local constants.                                                                 !
@@ -49,10 +52,7 @@ program main
    integer, dimension(64)                :: thread_use
    integer, dimension(64)                :: cpu_use
    integer, external                     :: findmycpu
-   !------ MPI interface. -----------------------------------------------------------------!
-#if defined(RAMS_MPI)
-   include 'mpif.h'
-#endif
+
    !---------------------------------------------------------------------------------------!
 
 
diff --git a/ED/src/init/ed_init.F90 b/ED/src/init/ed_init.F90
index b4913d66c..48a149ae4 100644
--- a/ED/src/init/ed_init.F90
+++ b/ED/src/init/ed_init.F90
@@ -319,10 +319,10 @@ subroutine load_ecosystem_state()
       use ed_node_coms      , only : mynum                          ! ! intent(in)
 #endif
 
-      implicit none
 #if defined(RAMS_MPI)
-      include 'mpif.h'
+      use mpi
 #endif
+      implicit none
       !----- Local variables --------------------------------------------------------------!
       integer                :: igr
       integer                :: ping 
diff --git a/ED/src/init/ed_init_atm.F90 b/ED/src/init/ed_init_atm.F90
index 65cf07ee4..041ab13d0 100644
--- a/ED/src/init/ed_init_atm.F90
+++ b/ED/src/init/ed_init_atm.F90
@@ -33,6 +33,7 @@ subroutine ed_init_atm()
                                     , terminate_cohorts            & ! subroutine
                                     , split_cohorts                ! ! subroutine
 #if defined(RAMS_MPI)
+   use mpi
    use ed_node_coms          , only : nnodetot                     & ! intent(in)
                                     , mynum                        & ! intent(in)
                                     , sendnum                      & ! intent(in)
@@ -95,10 +96,6 @@ subroutine ed_init_atm()
    !----- Local variables (MPI only). -----------------------------------------------------!
 #if defined(RAMS_MPI)
    integer                        :: ierr
-#endif
-   !----- Add the MPI common block. -------------------------------------------------------!
-#if defined(RAMS_MPI)
-   include 'mpif.h'
 #endif
    !---------------------------------------------------------------------------------------!
 
diff --git a/ED/src/io/ed_print.F90 b/ED/src/io/ed_print.F90
index aeb2115b8..badb0e998 100644
--- a/ED/src/io/ed_print.F90
+++ b/ED/src/io/ed_print.F90
@@ -48,11 +48,12 @@ subroutine print_fields(ifm,cgrid)
       use ed_var_tables, only : vt_info       & ! intent(in)
                               , num_var       ! ! intent(in)
       use ed_max_dims  , only : str_len_short ! ! intent(in)
-      implicit none
+      
       !----- Standard common blocks. ------------------------------------------------------!
 #if defined(RAMS_MPI)
-      include 'mpif.h'
+      use mpi
 #endif
+      implicit none
       !----- Arguments. -------------------------------------------------------------------!
       integer                            , intent(in) :: ifm
       type(edtype)                       , target     :: cgrid
diff --git a/ED/src/io/h5_output.F90 b/ED/src/io/h5_output.F90
index 209b184aa..943e3b1ce 100644
--- a/ED/src/io/h5_output.F90
+++ b/ED/src/io/h5_output.F90
@@ -48,12 +48,12 @@ subroutine h5_output(vtype)
                            , sitetype              & ! structure
                            , patchtype             & ! structure
                            , gdpy                  ! ! intent(in)
-   implicit none
-
-   !------ Include standard common blocks. ------------------------------------------------!
+                           
+                           !------ Include standard common blocks. ------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
+    use mpi
 #endif
+  implicit none
    !------ Arguments. ---------------------------------------------------------------------!
    character(len=*)                                 , intent(in) :: vtype
    !------ Local variables. ---------------------------------------------------------------!
diff --git a/ED/src/memory/ed_state_vars.F90 b/ED/src/memory/ed_state_vars.F90
index d27c9f9b2..dad2957f2 100644
--- a/ED/src/memory/ed_state_vars.F90
+++ b/ED/src/memory/ed_state_vars.F90
@@ -12774,11 +12774,11 @@ subroutine filltab_alltypes
 #endif
       use ed_max_dims  , only : maxgrds                  & ! intent(in)
                               , maxmach                  ! ! intent(in)
-      implicit none
 
 #if defined(RAMS_MPI)
-      include 'mpif.h'
+  use mpi
 #endif
+implicit none
       !----- Local variables. -------------------------------------------------------------!
       type(edtype)                                 , pointer   :: cgrid
       type(polygontype)                            , pointer   :: cpoly
diff --git a/ED/src/mpi/ed_mpass_init.F90 b/ED/src/mpi/ed_mpass_init.F90
index 2aebbf93b..ceca96909 100644
--- a/ED/src/mpi/ed_mpass_init.F90
+++ b/ED/src/mpi/ed_mpass_init.F90
@@ -28,7 +28,9 @@ subroutine ed_masterput_processid(nproc,headnode_num,masterworks,par_run)
                           , master_num  & ! intent(out)
                           , machs       ! ! intent(out)
 #endif
-
+#if defined(RAMS_MPI)
+   use mpi
+#endif
    implicit none
    !----- Arguments. ----------------------------------------------------------------------!
    integer, intent(in) :: headnode_num
@@ -38,7 +40,6 @@ subroutine ed_masterput_processid(nproc,headnode_num,masterworks,par_run)
    integer :: nm
 #if defined(RAMS_MPI)
    integer :: ierr
-   include 'mpif.h'
    !---------------------------------------------------------------------------------------!
 #endif
 
@@ -359,6 +360,9 @@ subroutine ed_masterput_nl(par_run)
                                    , idetailed                 & ! intent(in)
                                    , patch_keep                ! ! intent(in)
    use fusion_fission_coms  , only : ifusion                   ! ! intent(in)
+#endif
+#if defined(RAMS_MPI)
+      use mpi
 #endif
    implicit none
 
@@ -369,7 +373,6 @@ subroutine ed_masterput_nl(par_run)
    integer             :: ierr
    integer             :: n
    !------ Pre-compiled options. ----------------------------------------------------------!
-   include 'mpif.h'
 #endif
    !---------------------------------------------------------------------------------------!
 
@@ -727,6 +730,9 @@ subroutine ed_masterput_met_header(par_run)
                              , metvars_len       ! ! intent(in)
 #endif
 
+#if defined(RAMS_MPI)
+     use mpi
+#endif
    implicit none
    !------ Arguments. ---------------------------------------------------------------------!
    integer                      , intent(in)   :: par_run
@@ -737,7 +743,6 @@ subroutine ed_masterput_met_header(par_run)
    integer                                     :: f
    integer                                     :: v
    !------ Pre-compiled options. ----------------------------------------------------------!
-   include 'mpif.h'
    !---------------------------------------------------------------------------------------!
 #endif
 
@@ -813,6 +818,10 @@ subroutine ed_masterput_poly_dims(par_run,masterworks)
                             , npolys_run   ! ! intent(in)
    use mem_polygons  , only : n_ed_region  & ! intent(in)
                             , n_poi        ! ! intent(in)
+   
+#if defined(RAMS_MPI)
+     use mpi
+#endif
    implicit none
    !----- Local constants. ----------------------------------------------------------------!
    integer                     , parameter   :: nmethods = 3
@@ -838,7 +847,6 @@ subroutine ed_masterput_poly_dims(par_run,masterworks)
    real                                      :: totalwork
 #if defined(RAMS_MPI)
    integer                                   :: ierr
-   include 'mpif.h'
 #endif
    !---------------------------------------------------------------------------------------!
 
@@ -1122,6 +1130,9 @@ subroutine ed_masterput_worklist_info(par_run)
                            , py_off                ! ! intent(in)
    use mem_polygons , only : maxsite               ! ! intent(in)
    use ed_mem_alloc , only : ed_memory_allocation  ! ! subroutine
+#if defined(RAMS_MPI)
+     use mpi
+#endif
    implicit none
    !------ Arguments. ---------------------------------------------------------------------!
    integer                      , intent(in)   :: par_run
@@ -1139,8 +1150,6 @@ subroutine ed_masterput_worklist_info(par_run)
    integer                                     :: mpiid
    integer        , dimension(:), allocatable  :: iscratch
    real           , dimension(:), allocatable  :: rscratch
-   !------ Pre-compiled options. ----------------------------------------------------------!
-   include 'mpif.h'
 #endif
    !---------------------------------------------------------------------------------------!
 
@@ -1311,12 +1320,14 @@ subroutine ed_nodeget_processid(init)
    use ed_para_coms, only : nthreads   ! ! intent(out)
 #else
 #endif
+#if defined(RAMS_MPI)
+      use mpi
+#endif   
    implicit none
    !----- Arguments. ----------------------------------------------------------------------!
    integer, intent(in) :: init
    !----- Local variables. ----------------------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
    integer, dimension(MPI_STATUS_SIZE) :: status
 #endif
    integer :: ierr
@@ -1599,6 +1610,7 @@ subroutine ed_nodeget_nl
                                    , time2canopy               & ! intent(out)
                                    , min_patch_area            ! ! intent(out)
    use canopy_layer_coms    , only : crown_mod                 ! ! intent(out)
+   
    use canopy_radiation_coms, only : icanrad                   & ! intent(out)
                                    , ihrzrad                   & ! intent(out)
                                    , ltrans_vis                & ! intent(out)
@@ -1620,9 +1632,12 @@ subroutine ed_nodeget_nl
                                    , patch_keep                ! ! intent(out)
    use fusion_fission_coms  , only : ifusion                   ! ! intent(out)
 #endif
-   implicit none
+
+#if defined(RAMS_MPI)
+  use mpi
+#endif
+implicit none
 #if defined(RAMS_MPI)
-   include 'mpif.h'
    !----- Local variables. ----------------------------------------------------------------!
    integer :: n
 #endif
@@ -1996,9 +2011,11 @@ subroutine ed_nodeget_met_header()
                              , met_land_mask ! ! intent(out)
 #endif
 
-   implicit none
 #if defined(RAMS_MPI)
-   include 'mpif.h'
+    use mpi
+#endif 
+  implicit none
+#if defined(RAMS_MPI)
    !---- Local variables. -----------------------------------------------------------------!
    integer :: ierr
    integer :: nsize
@@ -2084,7 +2101,10 @@ subroutine ed_nodeget_poly_dims
    use grid_coms    , only : ngrids     ! ! intent(in)
 #endif
 
-   implicit none
+#if defined(RAMS_MPI)
+  use mpi
+#endif   
+implicit none
 
 #if defined(RAMS_MPI)
    !----- Local variables. ----------------------------------------------------------------!
@@ -2092,7 +2112,6 @@ subroutine ed_nodeget_poly_dims
    integer :: ifm
    integer :: nm
    !------ Pre-compiled options. ----------------------------------------------------------!
-   include 'mpif.h'
    !---------------------------------------------------------------------------------------!
    do ifm=1,ngrids
       do nm=1,nmachs
@@ -2131,11 +2150,11 @@ subroutine ed_nodeget_worklist_info
    use ed_node_coms , only : master_num          ! ! intent(in)
 #endif
 
-   implicit none
 #if defined(RAMS_MPI)
-   !------ Pre-compiled options. ----------------------------------------------------------!
-   include 'mpif.h'
+!------ Pre-compiled options. ----------------------------------------------------------!
+use mpi
 #endif
+implicit none
    !------ Local variables. ---------------------------------------------------------------!
    integer                             :: npolygons
    integer                             :: ifm
diff --git a/ED/src/utils/fatal_error.F90 b/ED/src/utils/fatal_error.F90
index 18bf18a8c..a4b45aa4d 100644
--- a/ED/src/utils/fatal_error.F90
+++ b/ED/src/utils/fatal_error.F90
@@ -8,6 +8,10 @@
 subroutine fatal_error(reason,subr,file)
    use ed_node_coms   , only : nnodetot       & ! intent(in)
                              , mynum          ! ! intent(in)
+
+#if defined(RAMS_MPI)
+use mpi_f08
+#endif
    implicit none
    !----- Arguments. ----------------------------------------------------------------------!
    character(len=*), intent(in) :: reason
@@ -18,9 +22,7 @@ subroutine fatal_error(reason,subr,file)
    logical                      :: slavenode
    !---------------------------------------------------------------------------------------!
 
-#if defined(RAMS_MPI)
-   include 'mpif.h'
-#endif
+
 
    !---------------------------------------------------------------------------------------!
    !       Check which type of end we should use.  For the main program, this should never !

From 9ecec5248e2de2c10481003beb28653c79f89f5e Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Mon, 1 Jul 2024 13:34:53 -0400
Subject: [PATCH 10/11] Fix token comparison, the result is NULL pointer when
 finished not '\0'

---
 ED/src/utils/utils_c.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/ED/src/utils/utils_c.c b/ED/src/utils/utils_c.c
index 7bc79f1f3..3c5f89ced 100644
--- a/ED/src/utils/utils_c.c
+++ b/ED/src/utils/utils_c.c
@@ -350,7 +350,7 @@ void filelist_c_( int *inum, int *indices, char *prefix, char *chario){
   
   token = strtok (prefix, delim);
   tfound=0;
-  while (token != '\0') {
+  while (token != NULL) {
     tfound += 1;
 
     strcpy(dir,tmpdir);
@@ -381,7 +381,7 @@ void filelist_c_( int *inum, int *indices, char *prefix, char *chario){
     
     /* Try the next token */
     token = strtok(NULL,delim2);
-    if (token != '\0'){
+    if (token != NULL){
       tfound=2;
       strcpy(fpref2,token);
     }
@@ -392,15 +392,15 @@ void filelist_c_( int *inum, int *indices, char *prefix, char *chario){
 
 
     /* Try the first token */
-    token = strtok (fpref0, delim2);
-    if (token != '\0'){
+    token = strtok(fpref0, delim2);
+    if (token != NULL){
       tfound=1;
       strcpy(fpref1,token);
     }
     
     /* Try the next token */
     token = strtok(NULL,delim2);
-    if (token != '\0'){
+    if (token != NULL){
       tfound=2;
       strcpy(fpref2,token);
     }

From dae3ac5f609f0792db873a9658ba9d02ddd82e58 Mon Sep 17 00:00:00 2001
From: caiohamamura <caiohamamura@gmail.com>
Date: Mon, 1 Jul 2024 14:01:01 -0400
Subject: [PATCH 11/11] utils_c: use intptr_t for casting pointer to int

---
 ED/src/utils/utils_c.c | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/ED/src/utils/utils_c.c b/ED/src/utils/utils_c.c
index 3c5f89ced..a17d74581 100644
--- a/ED/src/utils/utils_c.c
+++ b/ED/src/utils/utils_c.c
@@ -8,6 +8,7 @@
 */
 
 #include "utils_sub_names.h"
+#include <stdint.h>
 
 #include <stdio.h>
 #include <math.h>
@@ -58,16 +59,15 @@ int iralloc(int *memtot,int *ia,int *ioff)
 
   iaddr = malloc((*memtot)*sizeof(float));
 
-/* Compute the offset for Fortran */
-
+/* Compute the offset for Fortran */  
 #ifdef CRAY
-  ifaddr = (int)ia;
-  imaddr = (int)iaddr;
-  *ioff=(imaddr-ifaddr);
+    ifaddr = (intptr_t)ia;
+    imaddr = (intptr_t)iaddr;
+    *ioff = (imaddr - ifaddr);
 #else
-  ifaddr = (int )ia;
-  imaddr = (int )iaddr;
-  *ioff = (imaddr-ifaddr)/sizeof(float);
+    ifaddr = (intptr_t)ia;
+    imaddr = (intptr_t)iaddr;
+    *ioff = (imaddr - ifaddr) / sizeof(float);
 #endif
 
 /* Find first empty location in address array */