Refactor SD update

[gromacs.git] / src / gromacs / fileio / gmx_internal_xdr.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#include "gmxpre.h"

#include "config.h"

#if GMX_INTERNAL_XDR


#include "gmx_internal_xdr.h"

#include <cstdlib>
#include <cstring>


/* NB - THIS FILE IS ONLY USED ON MICROSOFT WINDOWS, since that
 * system doesn't provide any standard XDR system libraries. It will
 * most probably work on other platforms too, but make sure you
 * test that the xtc files produced are ok before using it.
 *
 * This header file contains Gromacs versions of the definitions for
 * Sun External Data Representation (XDR) headers and routines.
 *
 * On most UNIX systems this is already present as part of your
 * system libraries, but since we want to make Gromacs portable to
 * platforms like Microsoft Windows we have created a private version
 * of the necessary routines and distribute them with the Gromacs source.
 *
 * Although the rest of Gromacs is LGPL, you can copy and use the XDR
 * routines in any way you want as long as you obey Sun's license:
 *
 * Sun RPC is a product of Sun Microsystems, Inc. and is provided for
 * unrestricted use provided that this legend is included on all tape
 * media and as a part of the software program in whole or part.  Users
 * may copy or modify Sun RPC without charge, but are not authorized
 * to license or distribute it to anyone else except as part of a product or
 * program developed by the user.
 *
 * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
 * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
 * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.
 *
 * Sun RPC is provided with no support and without any obligation on the
 * part of Sun Microsystems, Inc. to assist in its use, correction,
 * modification or enhancement.
 *
 * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
 * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
 * OR ANY PART THEREOF.
 *
 * In no event will Sun Microsystems, Inc. be liable for any lost revenue
 * or profits or other special, indirect and consequential damages, even if
 * Sun has been advised of the possibility of such damages.
 *
 * Sun Microsystems, Inc.
 * 2550 Garcia Avenue
 * Mountain View, California  94043
 */



/*
 * for unit alignment
 */
static char xdr_zero[BYTES_PER_XDR_UNIT] = {0, 0, 0, 0};

static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x)
{
    xdr_uint32_t y;
    int          i;
    char        *px = reinterpret_cast<char *>(&x);
    char        *py = reinterpret_cast<char *>(&y);

    for (i = 0; i < 4; i++)
    {
        py[i] = px[3-i];
    }

    return y;
}

static xdr_uint32_t xdr_htonl(xdr_uint32_t x)
{
    short s = 0x0F00;
    if (*(reinterpret_cast<char *>(&s)) == static_cast<char>(0x0F))
    {
        /* bigendian, do nothing */
        return x;
    }
    else
    {
        /* smallendian,swap bytes */
        return xdr_swapbytes(x);
    }
}

static xdr_uint32_t xdr_ntohl(xdr_uint32_t x)
{
    short s = 0x0F00;
    if (*(reinterpret_cast<char *>(&s)) == static_cast<char>(0x0F))
    {
        /* bigendian, do nothing */
        return x;
    }
    else
    {
        /* smallendian, swap bytes */
        return xdr_swapbytes(x);
    }
}


/*
 * Free a data structure using XDR
 * Not a filter, but a convenient utility nonetheless
 */
void
xdr_free (xdrproc_t proc, char *objp)
{
    XDR x;

    x.x_op = XDR_FREE;
    (*proc) ( &x, objp);
}

/*
 * XDR nothing
 */
bool_t
xdr_void (void)
{
    return TRUE;
}

/*
 * XDR integers
 */
bool_t
xdr_int (XDR *xdrs, int *ip)
{
    xdr_int32_t l;

    switch (xdrs->x_op)
    {
        case XDR_ENCODE:
            l = static_cast<xdr_int32_t>(*ip);
            return xdr_putint32 (xdrs, &l);

        case XDR_DECODE:
            if (!xdr_getint32 (xdrs, &l))
            {
                return FALSE;
            }
            *ip = static_cast<int>(l);

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
}


/*
 * XDR unsigned integers
 */
bool_t
xdr_u_int (XDR *xdrs, unsigned int *up)
{
    xdr_uint32_t l;

    switch (xdrs->x_op)
    {
        case XDR_ENCODE:
            l = static_cast<xdr_uint32_t>(*up);
            return xdr_putuint32 (xdrs, &l);

        case XDR_DECODE:
            if (!xdr_getuint32 (xdrs, &l))
            {
                return FALSE;
            }
            *up = static_cast<unsigned int>(l);

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
}




/*
 * XDR short integers
 */
bool_t
xdr_short (XDR *xdrs, short *sp)
{
    xdr_int32_t l;

    switch (xdrs->x_op)
    {
        case XDR_ENCODE:
            l = static_cast<xdr_int32_t>(*sp);
            return xdr_putint32 (xdrs, &l);

        case XDR_DECODE:
            if (!xdr_getint32 (xdrs, &l))
            {
                return FALSE;
            }
            *sp = static_cast<short>(l);
            return TRUE;

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
}


/*
 * XDR unsigned short integers
 */
bool_t
xdr_u_short (XDR *xdrs, unsigned short *usp)
{
    xdr_uint32_t l;

    switch (xdrs->x_op)
    {
        case XDR_ENCODE:
            l = static_cast<xdr_uint32_t>(*usp);
            return xdr_putuint32 (xdrs, &l);

        case XDR_DECODE:
            if (!xdr_getuint32 (xdrs, &l))
            {
                return FALSE;
            }
            *usp = static_cast<unsigned short>(l);
            return TRUE;

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
}


/*
 * XDR a char
 */
bool_t
xdr_char (XDR *xdrs, char *cp)
{
    int i;

    i = (*cp);
    if (!xdr_int (xdrs, &i))
    {
        return FALSE;
    }
    *cp = i;
    return TRUE;
}

/*
 * XDR an unsigned char
 */
bool_t
xdr_u_char (XDR *xdrs, unsigned char *cp)
{
    unsigned int u;

    u = (*cp);
    if (!xdr_u_int (xdrs, &u))
    {
        return FALSE;
    }
    *cp = u;
    return TRUE;
}

/*
 * XDR booleans
 */
bool_t
xdr_bool (XDR *xdrs, int *bp)
{
#define XDR_FALSE   ((xdr_int32_t) 0)
#define XDR_TRUE    ((xdr_int32_t) 1)

    xdr_int32_t lb;

    switch (xdrs->x_op)
    {
        case XDR_ENCODE:
            lb = *bp ? XDR_TRUE : XDR_FALSE;
            return xdr_putint32 (xdrs, &lb);

        case XDR_DECODE:
            if (!xdr_getint32 (xdrs, &lb))
            {
                return FALSE;
            }
            *bp = (lb == XDR_FALSE) ? FALSE : TRUE;
            return TRUE;

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
#undef XDR_FALSE
#undef XDR_TRUE
}



/*
 * XDR opaque data
 * Allows the specification of a fixed size sequence of opaque bytes.
 * cp points to the opaque object and cnt gives the byte length.
 */
bool_t
xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
{
    unsigned int rndup;
    char         crud[BYTES_PER_XDR_UNIT];

    /*
     * if no data we are done
     */
    if (cnt == 0)
    {
        return TRUE;
    }

    /*
     * round byte count to full xdr units
     */
    rndup = cnt % BYTES_PER_XDR_UNIT;
    if (rndup > 0)
    {
        rndup = BYTES_PER_XDR_UNIT - rndup;
    }

    switch (xdrs->x_op)
    {
        case XDR_DECODE:
            if (!xdr_getbytes (xdrs, cp, cnt))
            {
                return FALSE;
            }
            if (rndup == 0)
            {
                return TRUE;
            }
            return xdr_getbytes (xdrs, crud, rndup);

        case XDR_ENCODE:
            if (!xdr_putbytes (xdrs, cp, cnt))
            {
                return FALSE;
            }
            if (rndup == 0)
            {
                return TRUE;
            }
            return xdr_putbytes (xdrs, xdr_zero, rndup);

        case XDR_FREE:
            return TRUE;
    }
    return FALSE;
}


/*
 * XDR null terminated ASCII strings
 * xdr_string deals with "C strings" - arrays of bytes that are
 * terminated by a NULL character.  The parameter cpp references a
 * pointer to storage; If the pointer is null, then the necessary
 * storage is allocated.  The last parameter is the max allowed length
 * of the string as specified by a protocol.
 */
bool_t xdr_string (XDR *xdrs, char ** cpp, unsigned int maxsize)
{
    char        *sp       = *cpp; /* sp is the actual string pointer */
    unsigned int size     = 0;
    unsigned int nodesize = 0;

    /*
     * first deal with the length since xdr strings are counted-strings
     */
    switch (xdrs->x_op)
    {
        case XDR_FREE:
            if (sp == NULL)
            {
                return TRUE; /* already free */
            }
        /* fall through... */
        case XDR_ENCODE:
            if (sp == NULL)
            {
                return FALSE;
            }
            size = std::strlen (sp);
            break;
        case XDR_DECODE:
            break;
    }

    if (!xdr_u_int (xdrs, &size))
    {
        return FALSE;
    }
    if (size > maxsize)
    {
        return FALSE;
    }
    nodesize = size + 1;

    /*
     * now deal with the actual bytes
     */
    switch (xdrs->x_op)
    {
        case XDR_DECODE:
            if (nodesize == 0)
            {
                return TRUE;
            }
            if (sp == NULL)
            {
                *cpp = sp = static_cast<char *>(std::malloc (nodesize));
            }
            if (sp == NULL)
            {
                (void) fputs ("xdr_string: out of memory\n", stderr);
                return FALSE;
            }
            sp[size] = 0;
        /* fall into ... */

        case XDR_ENCODE:
            return xdr_opaque (xdrs, sp, size);

        case XDR_FREE:
            free (sp);
            *cpp = NULL;
            return TRUE;
    }
    return FALSE;
}



/* Floating-point stuff */

bool_t xdr_float(XDR * xdrs, float * fp)
{
    xdr_int32_t tmp;

    switch (xdrs->x_op)
    {

        case XDR_ENCODE:
            tmp = *(reinterpret_cast<xdr_int32_t *>(fp));
            return (xdr_putint32(xdrs, &tmp));

            break;

        case XDR_DECODE:
            if (xdr_getint32(xdrs, &tmp))
            {
                *(reinterpret_cast<xdr_int32_t *>(fp)) = tmp;
                return (TRUE);
            }

            break;

        case XDR_FREE:
            return (TRUE);
    }
    return (FALSE);
}


bool_t xdr_double(XDR * xdrs, double * dp)
{

    /* Windows and some other systems dont define double-precision
     * word order in the header files, so unfortunately we have
     * to calculate it!
     *
     * For thread safety, we calculate it every time: locking this would
     * be more expensive.
     */
    /*static int LSW=-1;*/ /* Least significant fp word */
    int LSW = -1; /* Least significant fp word */


    int        *ip;
    xdr_int32_t tmp[2];

    if (LSW < 0)
    {
        double x = 0.987654321; /* Just a number */

        /* Possible representations in IEEE double precision:
         * (S=small endian, B=big endian)
         *
         * Byte order, Word order, Hex
         *     S           S       b8 56 0e 3c dd 9a ef 3f
         *     B           S       3c 0e 56 b8 3f ef 9a dd
         *     S           B       dd 9a ef 3f b8 56 0e 3c
         *     B           B       3f ef 9a dd 3c 0e 56 b8
         */

        unsigned char ix = *(reinterpret_cast<char *>(&x));

        if (ix == 0xdd || ix == 0x3f)
        {
            LSW = 1; /* Big endian word order */
        }
        else if (ix == 0xb8 || ix == 0x3c)
        {
            LSW = 0; /* Small endian word order */
        }
        else         /* Catch strange errors */
        {
            printf("Error when detecting floating-point word order.\n"
                   "Do you have a non-IEEE system?\n"
                   "If possible, use the XDR libraries provided with your system,\n"
                   "instead of the GROMACS fallback XDR source.\n");
            exit(0);
        }
    }

    switch (xdrs->x_op)
    {

        case XDR_ENCODE:
            ip     = reinterpret_cast<int *>(dp);
            tmp[0] = ip[!LSW];
            tmp[1] = ip[LSW];
            return (xdr_putint32(xdrs, tmp) &&
                    xdr_putint32(xdrs, tmp+1));

            break;

        case XDR_DECODE:
            ip = reinterpret_cast<int *>(dp);
            if (xdr_getint32(xdrs, tmp+!LSW) &&
                xdr_getint32(xdrs, tmp+LSW))
            {
                ip[0] = tmp[0];
                ip[1] = tmp[1];
                return (TRUE);
            }

            break;

        case XDR_FREE:
            return (TRUE);
    }
    return (FALSE);
}


/* Array routines */

/*
 * xdr_vector():
 *
 * XDR a fixed length array. Unlike variable-length arrays,
 * the storage of fixed length arrays is static and unfreeable.
 * > basep: base of the array
 * > size: size of the array
 * > elemsize: size of each element
 * > xdr_elem: routine to XDR each element
 */
bool_t xdr_vector (XDR * xdrs, char * basep, unsigned int nelem,
                   unsigned int elemsize, xdrproc_t xdr_elem)
{
#define LASTUNSIGNED    ((unsigned int)0-1)
    unsigned int i;
    char        *elptr;

    elptr = basep;
    for (i = 0; i < nelem; i++)
    {
        if (!(*xdr_elem) (xdrs, elptr, LASTUNSIGNED))
        {
            return FALSE;
        }
        elptr += elemsize;
    }
    return TRUE;
#undef LASTUNSIGNED
}



static bool_t xdrstdio_getbytes (XDR *, char *, unsigned int);
static bool_t xdrstdio_putbytes (XDR *, char *, unsigned int);
static unsigned int xdrstdio_getpos (XDR *);
static bool_t xdrstdio_setpos (XDR *, unsigned int);
static xdr_int32_t *xdrstdio_inline (XDR *, int);
static void xdrstdio_destroy (XDR *);
static bool_t xdrstdio_getint32 (XDR *, xdr_int32_t *);
static bool_t xdrstdio_putint32 (XDR *, xdr_int32_t *);
static bool_t xdrstdio_getuint32 (XDR *, xdr_uint32_t *);
static bool_t xdrstdio_putuint32 (XDR *, xdr_uint32_t *);

/*
 * Destroy a stdio xdr stream.
 * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create.
 */
static void
xdrstdio_destroy (XDR *xdrs)
{
    fflush (reinterpret_cast<FILE *>(xdrs->x_private));
    /* xx should we close the file ?? */
}


static bool_t
xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
{
    if ((len != 0) && (fread (addr, static_cast<int>(len), 1,
                              reinterpret_cast<FILE *>(xdrs->x_private)) != 1))
    {
        return FALSE;
    }
    return TRUE;
}

static bool_t
xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
{
    if ((len != 0) && (fwrite (addr, static_cast<int>(len), 1,
                               reinterpret_cast<FILE *>(xdrs->x_private)) != 1))
    {
        return FALSE;
    }
    return TRUE;
}

static unsigned int
xdrstdio_getpos (XDR *xdrs)
{
    return static_cast<int>(ftell (reinterpret_cast<FILE *>(xdrs->x_private)));
}

static bool_t
xdrstdio_setpos (XDR *xdrs, unsigned int pos)
{
    return fseek (reinterpret_cast<FILE *>(xdrs->x_private), static_cast<xdr_int32_t>(pos), 0) < 0 ? FALSE : TRUE;
}

static xdr_int32_t *
xdrstdio_inline (XDR *xdrs, int len)
{
    (void)xdrs;
    (void)len;
    /*
     * Must do some work to implement this: must insure
     * enough data in the underlying stdio buffer,
     * that the buffer is aligned so that we can indirect through a
     * long *, and stuff this pointer in xdrs->x_buf.  Doing
     * a fread or fwrite to a scratch buffer would defeat
     * most of the gains to be had here and require storage
     * management on this buffer, so we don't do this.
     */
    return NULL;
}

static bool_t
xdrstdio_getint32 (XDR *xdrs, xdr_int32_t *ip)
{
    xdr_int32_t mycopy;

    if (fread (&mycopy, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
    {
        return FALSE;
    }
    *ip = xdr_ntohl (mycopy);
    return TRUE;
}

static bool_t
xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip)
{
    xdr_int32_t mycopy = xdr_htonl (*ip);

    ip = &mycopy;
    if (fwrite (ip, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
    {
        return FALSE;
    }
    return TRUE;
}

static bool_t
xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip)
{
    xdr_uint32_t mycopy;

    if (fread (&mycopy, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
    {
        return FALSE;
    }
    *ip = xdr_ntohl (mycopy);
    return TRUE;
}

static bool_t
xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip)
{
    xdr_uint32_t mycopy = xdr_htonl (*ip);

    ip = &mycopy;
    if (fwrite (ip, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
    {
        return FALSE;
    }
    return TRUE;
}

/*
 * Ops vector for stdio type XDR
 */
static struct XDR::xdr_ops xdrstdio_ops =
{
    xdrstdio_getbytes,  /* deserialize counted bytes */
    xdrstdio_putbytes,  /* serialize counted bytes */
    xdrstdio_getpos,    /* get offset in the stream */
    xdrstdio_setpos,    /* set offset in the stream */
    xdrstdio_inline,    /* prime stream for inline macros */
    xdrstdio_destroy,   /* destroy stream */
    xdrstdio_getint32,  /* deserialize a int */
    xdrstdio_putint32,  /* serialize a int */
    xdrstdio_getuint32, /* deserialize a int */
    xdrstdio_putuint32  /* serialize a int */
};

/*
 * Initialize a stdio xdr stream.
 * Sets the xdr stream handle xdrs for use on the stream file.
 * Operation flag is set to op.
 */
void
xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)
{
    xdrs->x_op           = op;
    xdrs->x_ops          = &xdrstdio_ops;
    xdrs->x_private      = reinterpret_cast<char *>(file);
    xdrs->x_handy        = 0;
    xdrs->x_base         = 0;
}

#else
int gmx_internal_xdr_empty;
#endif /* GMX_INTERNAL_XDR */