From: Erik Lindahl <erik@kth.se>
Date: Sat, 11 Jul 2015 20:51:14 +0000 (+0200)
Subject: Move fileio sources to C++
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=a772ad17234cccd6ec9572f9904a03266bfbd129

Move fileio sources to C++

String functions have been moved into std namespace,
unused variables removed. The internal XDR implementation has
been modified to work in C++, and while doing so it has been
renamed to gmx_internal_xdr.cpp to avoid confusion with the
external system implementations.

Change-Id: Iadaf812da88ba24530b637b8e3259fd3cac417e0
---

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.cpp
similarity index 96%
rename from src/gromacs/fileio/confio.c
rename to src/gromacs/fileio/confio.cpp
index c8a35d79cf..e7fbebf333 100644
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.cpp
@@ -38,9 +38,13 @@
 
 #include "confio.h"
 
-#include <errno.h>
-#include <math.h>
-#include <stdio.h>
+#include <cerrno>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
@@ -96,7 +100,7 @@ static int read_g96_pos(char line[], t_symtab *symtab,
         bEnd    = FALSE;
         while (!bEnd && fgets2(line, STRLEN, fp))
         {
-            bEnd = (strncmp(line, "END", 3) == 0);
+            bEnd = (std::strncmp(line, "END", 3) == 0);
             if (!bEnd  && (line[0] != '#'))
             {
                 if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
@@ -250,7 +254,7 @@ int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
     {
         while (!fr->bTitle && fgets2(line, STRLEN, fp))
         {
-            fr->bTitle = (strcmp(line, "TITLE") == 0);
+            fr->bTitle = (std::strcmp(line, "TITLE") == 0);
         }
         if (fr->title == NULL)
         {
@@ -260,7 +264,7 @@ int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
         bEnd = FALSE;
         while (!bEnd && fgets2(line, STRLEN, fp))
         {
-            bEnd = (strcmp(line, "END") == 0);
+            bEnd = (std::strcmp(line, "END") == 0);
         }
         fgets2(line, STRLEN, fp);
     }
@@ -272,11 +276,11 @@ int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
     bFinished = FALSE;
     do
     {
-        bTime  = (strcmp(line, "TIMESTEP") == 0);
-        bAtoms = (strcmp(line, "POSITION") == 0);
+        bTime  = (std::strcmp(line, "TIMESTEP") == 0);
+        bAtoms = (std::strcmp(line, "POSITION") == 0);
         bPos   = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
-        bVel   = (strncmp(line, "VELOCITY", 8) == 0);
-        bBox   = (strcmp(line, "BOX") == 0);
+        bVel   = (std::strncmp(line, "VELOCITY", 8) == 0);
+        bBox   = (std::strcmp(line, "BOX") == 0);
         if (bTime)
         {
             if (!fr->bTime && !fr->bX)
@@ -601,7 +605,7 @@ static void read_espresso_conf(const char *infile,
     t_symtab *symtab = NULL;
     FILE     *fp;
     char      word[STRLEN], buf[STRLEN];
-    int       natoms, level, npar, r, nprop, p, i, m, molnr;
+    int       level, r, nprop, p, i, m, molnr;
     int       prop[32];
     double    d;
     gmx_bool  bFoundParticles, bFoundProp, bFoundVariable, bMol;
@@ -622,7 +626,7 @@ static void read_espresso_conf(const char *infile,
     level           = 0;
     while ((r = get_espresso_word(fp, word)))
     {
-        if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
+        if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
         {
             bFoundParticles = TRUE;
             level          += check_open_parenthesis(fp, r, infile, "particles");
@@ -684,7 +688,7 @@ static void read_espresso_conf(const char *infile,
                                 break;
                             case espTYPE:
                                 r                   = get_espresso_word(fp, word);
-                                atoms->atom[i].type = strtol(word, NULL, 10);
+                                atoms->atom[i].type = std::strtol(word, NULL, 10);
                                 break;
                             case espQ:
                                 r = get_espresso_word(fp, word);
@@ -708,7 +712,7 @@ static void read_espresso_conf(const char *infile,
                                 break;
                             case espMOLECULE:
                                 r     = get_espresso_word(fp, word);
-                                molnr = strtol(word, NULL, 10);
+                                molnr = std::strtol(word, NULL, 10);
                                 if (i == 0 ||
                                     atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
                                 {
@@ -768,13 +772,13 @@ static void read_espresso_conf(const char *infile,
                 gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
             }
         }
-        else if (level == 1 && strcmp(word, "variable") == 0 && !bFoundVariable)
+        else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
         {
             bFoundVariable = TRUE;
             level         += check_open_parenthesis(fp, r, infile, "variable");
             while (level == 2 && (r = get_espresso_word(fp, word)))
             {
-                if (level == 2 && strcmp(word, "box_l") == 0)
+                if (level == 2 && std::strcmp(word, "box_l") == 0)
                 {
                     for (m = 0; m < 3; m++)
                     {
@@ -1024,11 +1028,11 @@ static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
         }
 
         /* atomname */
-        memcpy(name, line+10, 5);
+        std::memcpy(name, line+10, 5);
         atoms->atomname[i] = put_symtab(symtab, name);
 
         /* Copy resname to oldresname after we are done with the sanity check above */
-        strncpy(oldresname, resname, sizeof(oldresname));
+        std::strncpy(oldresname, resname, sizeof(oldresname));
 
         /* eventueel controle atomnumber met i+1 */
 
@@ -1094,8 +1098,8 @@ static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
         {
             for (m = 0; (m < DIM); m++)
             {
-                xmin[m] = min(xmin[m], x[i][m]);
-                xmax[m] = max(xmax[m], x[i][m]);
+                xmin[m] = std::min(xmin[m], x[i][m]);
+                xmax[m] = std::max(xmax[m], x[i][m]);
             }
         }
         for (i = 0; i < DIM; i++)
@@ -1325,25 +1329,25 @@ void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
         ai = index[i];
 
         resind = atoms->atom[ai].resind;
-        strncpy(resnm, " ??? ", sizeof(resnm)-1);
+        std::strncpy(resnm, " ??? ", sizeof(resnm)-1);
         if (resind < atoms->nres)
         {
-            strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
+            std::strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
             resnr = atoms->resinfo[resind].nr;
         }
         else
         {
-            strncpy(resnm, " ??? ", sizeof(resnm)-1);
+            std::strncpy(resnm, " ??? ", sizeof(resnm)-1);
             resnr = resind + 1;
         }
 
         if (atoms->atom)
         {
-            strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
+            std::strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
         }
         else
         {
-            strncpy(nm, " ??? ", sizeof(nm)-1);
+            std::strncpy(nm, " ??? ", sizeof(nm)-1);
         }
 
         fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000);
@@ -1632,12 +1636,10 @@ void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
                    rvec x[], rvec *v, int *ePBC, matrix box)
 {
     FILE       *in;
-    char        buf[256];
     gmx_mtop_t *mtop;
     t_topology  top;
     t_trxframe  fr;
     int         i, ftp, natoms;
-    real        d;
     char        g96_line[STRLEN+1];
 
     if (atoms->nr == 0)
@@ -1671,7 +1673,7 @@ void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
             read_g96_conf(in, infile, &fr, g96_line);
             gmx_fio_fclose(in);
             copy_mat(fr.box, box);
-            strncpy(title, fr.title, STRLEN);
+            std::strncpy(title, fr.title, STRLEN);
             break;
         case efPDB:
         case efBRK:
diff --git a/src/gromacs/fileio/enxio.c b/src/gromacs/fileio/enxio.cpp
similarity index 97%
rename from src/gromacs/fileio/enxio.c
rename to src/gromacs/fileio/enxio.cpp
index 892ef18119..ece8f4eea4 100644
--- a/src/gromacs/fileio/enxio.c
+++ b/src/gromacs/fileio/enxio.cpp
@@ -38,8 +38,10 @@
 
 #include "enxio.h"
 
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/gmxfio-xdr.h"
@@ -50,6 +52,7 @@
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 /* The source code in this file should be thread-safe.
@@ -386,7 +389,6 @@ void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **nms)
     XDR     *xdr;
     gmx_bool bRead = gmx_fio_getread(ef->fio);
     int      file_version;
-    int      i;
 
     xdr = gmx_fio_getxdr(ef->fio);
 
@@ -438,9 +440,8 @@ static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
 {
     int          magic = -7777777;
     real         first_real_to_check;
-    int          b, i, zero = 0, dum = 0;
+    int          b, zero = 0, dum = 0;
     gmx_bool     bRead      = gmx_fio_getread(ef->fio);
-    int          tempfix_nr = 0;
     int          ndisre     = 0;
     int          startb     = 0;
 #ifndef GMX_DOUBLE
@@ -536,7 +537,7 @@ static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
         }
         else
         {
-            fr->nsteps = max(1, fr->nsum);
+            fr->nsteps = std::max(1, fr->nsum);
         }
         if (*file_version >= 5)
         {
@@ -596,7 +597,10 @@ static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
         ((fr->nre > 0 && fr->nre != nre_test) ||
          fr->nre < 0 || ndisre < 0 || fr->nblock < 0))
     {
-        *bWrongPrecision = TRUE;
+        if (bWrongPrecision)
+        {
+            *bWrongPrecision = TRUE;
+        }
         return *bOK;
     }
 
@@ -746,7 +750,17 @@ void close_enx(ener_file_t ef)
     }
 }
 
-static gmx_bool empty_file(const char *fn)
+/*!\brief Return TRUE if a file exists but is empty, otherwise FALSE.
+ *
+ * If the file exists but has length larger than zero, if it does not exist, or
+ * if there is a file system error, FALSE will be returned instead.
+ *
+ * \param fn  File name to test
+ *
+ * \return TRUE if file could be open but is empty, otherwise FALSE.
+ */
+static gmx_bool
+empty_file(const char *fn)
 {
     FILE    *fp;
     char     dum;
@@ -758,13 +772,15 @@ static gmx_bool empty_file(const char *fn)
     bEmpty = feof(fp);
     gmx_fio_fclose(fp);
 
-    return bEmpty;
+    // bEmpty==TRUE but ret!=0 would likely be some strange I/O error, but at
+    // least it's not a normal empty file, so we return FALSE in that case.
+    return (bEmpty && ret == 0);
 }
 
 
 ener_file_t open_enx(const char *fn, const char *mode)
 {
-    int               nre, i;
+    int               nre;
     gmx_enxnm_t      *nms          = NULL;
     int               file_version = -1;
     t_enxframe       *fr;
@@ -970,7 +986,7 @@ gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
     {
         fprintf(stderr, "\nWARNING: there may be something wrong with energy file %s\n",
                 gmx_fio_getname(ef->fio));
-        fprintf(stderr, "Found: step=%"GMX_PRId64 ", nre=%d, nblock=%d, time=%g.\n"
+        fprintf(stderr, "Found: step=%" GMX_PRId64 ", nre=%d, nblock=%d, time=%g.\n"
                 "Trying to skip frame expect a crash though\n",
                 fr->step, fr->nre, fr->nblock, fr->t);
     }
@@ -1045,7 +1061,6 @@ gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
             }
 
             /* read/write data */
-            bOK1 = TRUE;
             switch (sub->type)
             {
                 case xdr_datatype_float:
@@ -1107,7 +1122,7 @@ static real find_energy(const char *name, int nre, gmx_enxnm_t *enm,
 
     for (i = 0; i < nre; i++)
     {
-        if (strcmp(enm[i].name, name) == 0)
+        if (std::strcmp(enm[i].name, name) == 0)
         {
             return fr->ener[i].e;
         }
@@ -1128,10 +1143,6 @@ void get_enx_state(const char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
         "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
     };
 
-    static const char *pcouplmu_nm[] = {
-        "Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
-        "Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
-    };
     static const char *baro_nm[] = {
         "Barostat"
     };
diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.cpp
similarity index 97%
rename from src/gromacs/fileio/filenm.c
rename to src/gromacs/fileio/filenm.cpp
index 1333091c11..ca750d2200 100644
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.cpp
@@ -38,8 +38,8 @@
 
 #include "filenm.h"
 
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
 
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -169,10 +169,6 @@ static const t_deffile
     { eftASC, "", "rundir", NULL, "Run directory" }
 };
 
-#define NZEXT 2
-static const char *z_ext[NZEXT] =
-{ ".gz", ".Z" };
-
 const char *ftp2ext(int ftp)
 {
     if ((0 <= ftp) && (ftp < efNR))
@@ -312,7 +308,7 @@ int fn2ftp(const char *fn)
         return efNR;
     }
 
-    len = strlen(fn);
+    len = std::strlen(fn);
     if ((len >= 4) && (fn[len - 4] == '.'))
     {
         feptr = &(fn[len - 4]);
@@ -342,7 +338,7 @@ const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
 
     for (i = 0; (i < nfile); i++)
     {
-        if (strcmp(opt, fnm[i].opt) == 0)
+        if (std::strcmp(opt, fnm[i].opt) == 0)
         {
             return fnm[i].fns[0];
         }
@@ -432,7 +428,7 @@ gmx_bool opt2bSet(const char *opt, int nfile, const t_filenm fnm[])
 
     for (i = 0; (i < nfile); i++)
     {
-        if (strcmp(opt, fnm[i].opt) == 0)
+        if (std::strcmp(opt, fnm[i].opt) == 0)
         {
             return (gmx_bool) IS_SET(fnm[i]);
         }
@@ -449,7 +445,7 @@ const char *opt2fn_null(const char *opt, int nfile, const t_filenm fnm[])
 
     for (i = 0; (i < nfile); i++)
     {
-        if (strcmp(opt, fnm[i].opt) == 0)
+        if (std::strcmp(opt, fnm[i].opt) == 0)
         {
             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
             {
@@ -504,7 +500,7 @@ gmx_bool is_set(const t_filenm *fnm)
 
 int add_suffix_to_output_names(t_filenm *fnm, int nfile, const char *suffix)
 {
-    int   i, j, pos;
+    int   i, j;
     char  buf[STRLEN], newname[STRLEN];
     char *extpos;
 
@@ -516,7 +512,7 @@ int add_suffix_to_output_names(t_filenm *fnm, int nfile, const char *suffix)
                for it, just in case... */
             for (j = 0; j < fnm[i].nfiles; j++)
             {
-                strncpy(buf, fnm[i].fns[j], STRLEN - 1);
+                std::strncpy(buf, fnm[i].fns[j], STRLEN - 1);
                 extpos  = strrchr(buf, '.');
                 *extpos = '\0';
                 sprintf(newname, "%s%s.%s", buf, suffix, extpos + 1);
diff --git a/src/gromacs/fileio/gmx_system_xdr.c b/src/gromacs/fileio/gmx_internal_xdr.cpp
similarity index 86%
rename from src/gromacs/fileio/gmx_system_xdr.c
rename to src/gromacs/fileio/gmx_internal_xdr.cpp
index 3a01286733..d711909f3a 100644
--- a/src/gromacs/fileio/gmx_system_xdr.c
+++ b/src/gromacs/fileio/gmx_internal_xdr.cpp
@@ -41,11 +41,10 @@
 #if GMX_INTERNAL_XDR
 
 
-#include "gmx_system_xdr.h"
+#include "gmx_internal_xdr.h"
 
-#include <limits.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
 
 
 /* NB - THIS FILE IS ONLY USED ON MICROSOFT WINDOWS, since that
@@ -103,8 +102,8 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x)
 {
     xdr_uint32_t y;
     int          i;
-    char        *px = (char *)&x;
-    char        *py = (char *)&y;
+    char        *px = reinterpret_cast<char *>(&x);
+    char        *py = reinterpret_cast<char *>(&y);
 
     for (i = 0; i < 4; i++)
     {
@@ -117,7 +116,7 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x)
 static xdr_uint32_t xdr_htonl(xdr_uint32_t x)
 {
     short s = 0x0F00;
-    if (*((char *)&s) == (char)0x0F)
+    if (*(reinterpret_cast<char *>(&s)) == static_cast<char>(0x0F))
     {
         /* bigendian, do nothing */
         return x;
@@ -132,7 +131,7 @@ static xdr_uint32_t xdr_htonl(xdr_uint32_t x)
 static xdr_uint32_t xdr_ntohl(xdr_uint32_t x)
 {
     short s = 0x0F00;
-    if (*((char *)&s) == (char)0x0F)
+    if (*(reinterpret_cast<char *>(&s)) == static_cast<char>(0x0F))
     {
         /* bigendian, do nothing */
         return x;
@@ -178,7 +177,7 @@ xdr_int (XDR *xdrs, int *ip)
     switch (xdrs->x_op)
     {
         case XDR_ENCODE:
-            l = (xdr_int32_t) (*ip);
+            l = static_cast<xdr_int32_t>(*ip);
             return xdr_putint32 (xdrs, &l);
 
         case XDR_DECODE:
@@ -186,7 +185,7 @@ xdr_int (XDR *xdrs, int *ip)
             {
                 return FALSE;
             }
-            *ip = (int) l;
+            *ip = static_cast<int>(l);
 
         case XDR_FREE:
             return TRUE;
@@ -206,7 +205,7 @@ xdr_u_int (XDR *xdrs, unsigned int *up)
     switch (xdrs->x_op)
     {
         case XDR_ENCODE:
-            l = (xdr_uint32_t) (*up);
+            l = static_cast<xdr_uint32_t>(*up);
             return xdr_putuint32 (xdrs, &l);
 
         case XDR_DECODE:
@@ -214,7 +213,7 @@ xdr_u_int (XDR *xdrs, unsigned int *up)
             {
                 return FALSE;
             }
-            *up = (unsigned int) l;
+            *up = static_cast<unsigned int>(l);
 
         case XDR_FREE:
             return TRUE;
@@ -236,7 +235,7 @@ xdr_short (XDR *xdrs, short *sp)
     switch (xdrs->x_op)
     {
         case XDR_ENCODE:
-            l = (xdr_int32_t) *sp;
+            l = static_cast<xdr_int32_t>(*sp);
             return xdr_putint32 (xdrs, &l);
 
         case XDR_DECODE:
@@ -244,7 +243,7 @@ xdr_short (XDR *xdrs, short *sp)
             {
                 return FALSE;
             }
-            *sp = (short) l;
+            *sp = static_cast<short>(l);
             return TRUE;
 
         case XDR_FREE:
@@ -265,7 +264,7 @@ xdr_u_short (XDR *xdrs, unsigned short *usp)
     switch (xdrs->x_op)
     {
         case XDR_ENCODE:
-            l = (xdr_uint32_t) *usp;
+            l = static_cast<xdr_uint32_t>(*usp);
             return xdr_putuint32 (xdrs, &l);
 
         case XDR_DECODE:
@@ -273,7 +272,7 @@ xdr_u_short (XDR *xdrs, unsigned short *usp)
             {
                 return FALSE;
             }
-            *usp = (unsigned short) l;
+            *usp = static_cast<unsigned short>(l);
             return TRUE;
 
         case XDR_FREE:
@@ -391,7 +390,7 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
             {
                 return TRUE;
             }
-            return xdr_getbytes (xdrs, (char *)crud, rndup);
+            return xdr_getbytes (xdrs, crud, rndup);
 
         case XDR_ENCODE:
             if (!xdr_putbytes (xdrs, cp, cnt))
@@ -419,11 +418,7 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
  * storage is allocated.  The last parameter is the max allowed length
  * of the string as specified by a protocol.
  */
-bool_t
-xdr_string (xdrs, cpp, maxsize)
-XDR *xdrs;
-char       **cpp;
-unsigned int maxsize;
+bool_t xdr_string (XDR *xdrs, char ** cpp, unsigned int maxsize)
 {
     char        *sp       = *cpp; /* sp is the actual string pointer */
     unsigned int size     = 0;
@@ -445,7 +440,7 @@ unsigned int maxsize;
             {
                 return FALSE;
             }
-            size = strlen (sp);
+            size = std::strlen (sp);
             break;
         case XDR_DECODE:
             break;
@@ -473,7 +468,7 @@ unsigned int maxsize;
             }
             if (sp == NULL)
             {
-                *cpp = sp = (char *) malloc (nodesize);
+                *cpp = sp = static_cast<char *>(std::malloc (nodesize));
             }
             if (sp == NULL)
             {
@@ -498,10 +493,7 @@ unsigned int maxsize;
 
 /* Floating-point stuff */
 
-bool_t
-xdr_float(xdrs, fp)
-XDR *xdrs;
-float *fp;
+bool_t xdr_float(XDR * xdrs, float * fp)
 {
     xdr_int32_t tmp;
 
@@ -509,7 +501,7 @@ float *fp;
     {
 
         case XDR_ENCODE:
-            tmp = *(xdr_int32_t *)fp;
+            tmp = *(reinterpret_cast<xdr_int32_t *>(fp));
             return (xdr_putint32(xdrs, &tmp));
 
             break;
@@ -517,7 +509,7 @@ float *fp;
         case XDR_DECODE:
             if (xdr_getint32(xdrs, &tmp))
             {
-                *(xdr_int32_t *)fp = tmp;
+                *(reinterpret_cast<xdr_int32_t *>(fp)) = tmp;
                 return (TRUE);
             }
 
@@ -530,10 +522,7 @@ float *fp;
 }
 
 
-bool_t
-xdr_double(xdrs, dp)
-XDR *xdrs;
-double *dp;
+bool_t xdr_double(XDR * xdrs, double * dp)
 {
 
     /* Windows and some other systems dont define double-precision
@@ -564,7 +553,7 @@ double *dp;
          *     B           B       3f ef 9a dd 3c 0e 56 b8
          */
 
-        unsigned char ix = *((char *)&x);
+        unsigned char ix = *(reinterpret_cast<char *>(&x));
 
         if (ix == 0xdd || ix == 0x3f)
         {
@@ -588,7 +577,7 @@ double *dp;
     {
 
         case XDR_ENCODE:
-            ip     = (int *)dp;
+            ip     = reinterpret_cast<int *>(dp);
             tmp[0] = ip[!LSW];
             tmp[1] = ip[LSW];
             return (xdr_putint32(xdrs, tmp) &&
@@ -597,7 +586,7 @@ double *dp;
             break;
 
         case XDR_DECODE:
-            ip = (int *)dp;
+            ip = reinterpret_cast<int *>(dp);
             if (xdr_getint32(xdrs, tmp+!LSW) &&
                 xdr_getint32(xdrs, tmp+LSW))
             {
@@ -627,13 +616,8 @@ double *dp;
  * > elemsize: size of each element
  * > xdr_elem: routine to XDR each element
  */
-bool_t
-xdr_vector (xdrs, basep, nelem, elemsize, xdr_elem)
-XDR *xdrs;
-char        *basep;
-unsigned int nelem;
-unsigned int elemsize;
-xdrproc_t    xdr_elem;
+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;
@@ -665,40 +649,6 @@ 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 *);
 
-/*
- * Ops vector for stdio type XDR
- */
-static const struct 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;
-    /* We have to add the const since the `struct xdr_ops' in `struct XDR'
-       is not `const'.  */
-    xdrs->x_ops     = (struct xdr_ops *) &xdrstdio_ops;
-    xdrs->x_private = (char *) file;
-    xdrs->x_handy   = 0;
-    xdrs->x_base    = 0;
-}
-
 /*
  * Destroy a stdio xdr stream.
  * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create.
@@ -706,7 +656,7 @@ xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)
 static void
 xdrstdio_destroy (XDR *xdrs)
 {
-    (void) fflush ((FILE *) xdrs->x_private);
+    fflush (reinterpret_cast<FILE *>(xdrs->x_private));
     /* xx should we close the file ?? */
 }
 
@@ -714,8 +664,8 @@ xdrstdio_destroy (XDR *xdrs)
 static bool_t
 xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
 {
-    if ((len != 0) && (fread (addr, (int) len, 1,
-                              (FILE *) xdrs->x_private) != 1))
+    if ((len != 0) && (fread (addr, static_cast<int>(len), 1,
+                              reinterpret_cast<FILE *>(xdrs->x_private)) != 1))
     {
         return FALSE;
     }
@@ -725,8 +675,8 @@ xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
 static bool_t
 xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
 {
-    if ((len != 0) && (fwrite (addr, (int) len, 1,
-                               (FILE *) xdrs->x_private) != 1))
+    if ((len != 0) && (fwrite (addr, static_cast<int>(len), 1,
+                               reinterpret_cast<FILE *>(xdrs->x_private)) != 1))
     {
         return FALSE;
     }
@@ -736,13 +686,13 @@ xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
 static unsigned int
 xdrstdio_getpos (XDR *xdrs)
 {
-    return (unsigned int) ftell ((FILE *) xdrs->x_private);
+    return static_cast<int>(ftell (reinterpret_cast<FILE *>(xdrs->x_private)));
 }
 
 static bool_t
 xdrstdio_setpos (XDR *xdrs, unsigned int pos)
 {
-    return fseek ((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE;
+    return fseek (reinterpret_cast<FILE *>(xdrs->x_private), static_cast<xdr_int32_t>(pos), 0) < 0 ? FALSE : TRUE;
 }
 
 static xdr_int32_t *
@@ -767,7 +717,7 @@ xdrstdio_getint32 (XDR *xdrs, xdr_int32_t *ip)
 {
     xdr_int32_t mycopy;
 
-    if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
+    if (fread (&mycopy, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
     {
         return FALSE;
     }
@@ -781,7 +731,7 @@ xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip)
     xdr_int32_t mycopy = xdr_htonl (*ip);
 
     ip = &mycopy;
-    if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
+    if (fwrite (ip, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
     {
         return FALSE;
     }
@@ -793,7 +743,7 @@ xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip)
 {
     xdr_uint32_t mycopy;
 
-    if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
+    if (fread (&mycopy, 4, 1, reinterpret_cast<FILE *>(xdrs->x_private)) != 1)
     {
         return FALSE;
     }
@@ -807,14 +757,45 @@ xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip)
     xdr_uint32_t mycopy = xdr_htonl (*ip);
 
     ip = &mycopy;
-    if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
+    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_system_xdr_empty;
-#endif /* GMX_SYSTEM_XDR */
+int gmx_internal_xdr_empty;
+#endif /* GMX_INTERNAL_XDR */
diff --git a/src/gromacs/fileio/gmx_system_xdr.h b/src/gromacs/fileio/gmx_internal_xdr.h
similarity index 98%
rename from src/gromacs/fileio/gmx_system_xdr.h
rename to src/gromacs/fileio/gmx_internal_xdr.h
index 23e156bec7..bc38df8afd 100644
--- a/src/gromacs/fileio/gmx_system_xdr.h
+++ b/src/gromacs/fileio/gmx_internal_xdr.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2015, 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.
@@ -38,10 +38,9 @@
 #ifndef GMX_FILEIO_GMX_SYSTEM_XDR_H
 #define GMX_FILEIO_GMX_SYSTEM_XDR_H
 
-#include <limits.h>
-#include <stdio.h>
-#include <stdlib.h>
-
+#include <climits>
+#include <cstdio>
+#include <cstdlib>
 
 /*
  * This header file is ONLY used on windows systems, since these do
diff --git a/src/gromacs/fileio/gmxfio-xdr.cpp b/src/gromacs/fileio/gmxfio-xdr.cpp
index b2876d0566..0d3b70bb25 100644
--- a/src/gromacs/fileio/gmxfio-xdr.cpp
+++ b/src/gromacs/fileio/gmxfio-xdr.cpp
@@ -38,13 +38,13 @@
 
 #include "gmxfio-xdr.h"
 
-#include <assert.h>
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "gmxfio-impl.h"
@@ -73,7 +73,7 @@ XDR *gmx_fio_getxdr(t_fileio *fio)
 {
     XDR *ret = NULL;
     gmx_fio_lock(fio);
-    assert(fio->xdr != NULL);
+    GMX_RELEASE_ASSERT( fio->xdr != NULL, "Implementation error: NULL XDR pointers");
     ret = fio->xdr;
     gmx_fio_unlock(fio);
     return ret;
@@ -95,7 +95,6 @@ static void gmx_fio_check_nitem(int eio, int nitem, const char *file, int line)
 static void gmx_fio_fe(t_fileio *fio, int eio, const char *desc,
                        const char *srcfile, int line)
 {
-
     gmx_fatal(FARGS, "Trying to %s %s type %d (%s), src %s, line %d",
               fio->bRead ? "read" : "write", desc, eio,
               ((eio >= 0) && (eio < eioNR)) ? eioNames[eio] : "unknown",
@@ -118,7 +117,7 @@ static gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
     double          d = 0;
     float           f = 0;
 
-    assert(fio->xdr != NULL);
+    GMX_RELEASE_ASSERT( fio->xdr != NULL, "Implementation error: NULL XDR pointers");
     gmx_fio_check_nitem(eio, nitem, srcfile, line);
     switch (eio)
     {
@@ -233,7 +232,7 @@ static gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
                     }
                 }
                 res = xdr_vector(fio->xdr, (char *) dvec, DIM,
-                                 (unsigned int) sizeof(double),
+                                 static_cast<unsigned int>(sizeof(double)),
                                  (xdrproc_t) xdr_double);
                 if (item)
                 {
@@ -253,7 +252,7 @@ static gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
                     }
                 }
                 res = xdr_vector(fio->xdr, (char *) fvec, DIM,
-                                 (unsigned int) sizeof(float),
+                                 static_cast<unsigned int>(sizeof(float)),
                                  (xdrproc_t) xdr_float);
                 if (item)
                 {
diff --git a/src/gromacs/fileio/gmxfio.cpp b/src/gromacs/fileio/gmxfio.cpp
index a094435c73..e08f55a1e3 100644
--- a/src/gromacs/fileio/gmxfio.cpp
+++ b/src/gromacs/fileio/gmxfio.cpp
@@ -40,9 +40,9 @@
 
 #include "config.h"
 
-#include <errno.h>
-#include <stdio.h>
-#include <string.h>
+#include <cerrno>
+#include <cstdio>
+#include <cstring>
 
 #ifdef HAVE_IO_H
 #include <io.h>
@@ -273,29 +273,29 @@ t_fileio *gmx_fio_open(const char *fn, const char *mode)
     gmx_bool  bRead, bReadWrite;
 
     /* sanitize the mode string */
-    if (strncmp(mode, "r+", 2) == 0)
+    if (std::strncmp(mode, "r+", 2) == 0)
     {
-        strcpy(newmode, "r+");
+        std::strcpy(newmode, "r+");
     }
     else if (mode[0] == 'r')
     {
-        strcpy(newmode, "r");
+        std::strcpy(newmode, "r");
     }
     else if (strncmp(mode, "w+", 2) == 0)
     {
-        strcpy(newmode, "w+");
+        std::strcpy(newmode, "w+");
     }
     else if (mode[0] == 'w')
     {
-        strcpy(newmode, "w");
+        std::strcpy(newmode, "w");
     }
     else if (strncmp(mode, "a+", 2) == 0)
     {
-        strcpy(newmode, "a+");
+        std::strcpy(newmode, "a+");
     }
     else if (mode[0] == 'a')
     {
-        strcpy(newmode, "a");
+        std::strcpy(newmode, "a");
     }
     else
     {
@@ -347,6 +347,11 @@ t_fileio *gmx_fio_open(const char *fn, const char *mode)
             gmx_fseek(fio->fp, 0, SEEK_END);
         }
     }
+    else
+    {
+        gmx_fatal(FARGS, "Cannot open file with NULL filename string");
+    }
+
     fio->bRead             = bRead;
     fio->bReadWrite        = bReadWrite;
     fio->bDouble           = (sizeof(real) == sizeof(double));
@@ -606,7 +611,7 @@ int gmx_fio_get_output_file_positions(gmx_file_position_t **p_outputfiles,
                 srenew(outputfiles, nalloc);
             }
 
-            strncpy(outputfiles[nfiles].filename, cur->fn, STRLEN - 1);
+            std::strncpy(outputfiles[nfiles].filename, cur->fn, STRLEN - 1);
 
             /* Get the file position */
             gmx_fio_int_get_file_position(cur, &outputfiles[nfiles].offset);
@@ -688,7 +693,6 @@ static int gmx_fio_int_fsync(t_fileio *fio)
     {
         rc = gmx_fsync(fio->fp);
     }
-
     return rc;
 }
 
diff --git a/src/gromacs/fileio/libxdrf.c b/src/gromacs/fileio/libxdrf.cpp
similarity index 93%
rename from src/gromacs/fileio/libxdrf.c
rename to src/gromacs/fileio/libxdrf.cpp
index 401cfa8883..8f6aecf9b8 100644
--- a/src/gromacs/fileio/libxdrf.c
+++ b/src/gromacs/fileio/libxdrf.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -36,11 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include <limits.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <climits>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/fileio/xdr_datatype.h"
 #include "gromacs/fileio/xdrf.h"
@@ -69,12 +71,6 @@ const char *xdr_datatype_names[] =
  */
 #define MAXABS INT_MAX-2
 
-#ifndef MIN
-#define MIN(x, y) ((x) < (y) ? (x) : (y))
-#endif
-#ifndef MAX
-#define MAX(x, y) ((x) > (y) ? (x) : (y))
-#endif
 #ifndef SQR
 #define SQR(x) ((x)*(x))
 #endif
@@ -91,7 +87,7 @@ static const int magicints[] = {
 
 #define FIRSTIDX 9
 /* note that magicints[FIRSTIDX-1] == 0 */
-#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
+#define LASTIDX static_cast<int>((sizeof(magicints) / sizeof(*magicints)))
 
 
 /*____________________________________________________________________________
@@ -112,10 +108,10 @@ static void sendbits(int buf[], int num_of_bits, int num)
     int             lastbits;
     unsigned char * cbuf;
 
-    cbuf     = ((unsigned char *)buf) + 3 * sizeof(*buf);
-    cnt      = (unsigned int) buf[0];
+    cbuf     = (reinterpret_cast<unsigned char *>(buf)) + 3 * sizeof(*buf);
+    cnt      = static_cast<unsigned int>(buf[0]);
     lastbits = buf[1];
-    lastbyte = (unsigned int) buf[2];
+    lastbyte = static_cast<unsigned int>(buf[2]);
     while (num_of_bits >= 8)
     {
         lastbyte     = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
@@ -299,10 +295,10 @@ static int receivebits(int buf[], int num_of_bits)
     unsigned char * cbuf;
     int             mask = (1 << num_of_bits) -1;
 
-    cbuf     = ((unsigned char *)buf) + 3 * sizeof(*buf);
+    cbuf     = reinterpret_cast<unsigned char *>(buf) + 3 * sizeof(*buf);
     cnt      = buf[0];
-    lastbits = (unsigned int) buf[1];
-    lastbyte = (unsigned int) buf[2];
+    lastbits = static_cast<unsigned int>(buf[1]);
+    lastbyte = static_cast<unsigned int>(buf[2]);
 
     num = 0;
     while (num_of_bits >= 8)
@@ -420,7 +416,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
     int          tmp, *thiscoord,  prevcoord[3];
     unsigned int tmpcoord[30];
 
-    int          bufsize, xdrid, lsize;
+    int          bufsize, lsize;
     unsigned int bitsize;
     float        inv_precision;
     int          errval = 1;
@@ -430,6 +426,14 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
     bitsizeint[0] = bitsizeint[1] = bitsizeint[2] = 0;
     prevcoord[0]  = prevcoord[1]  = prevcoord[2]  = 0;
 
+    // The static analyzer warns about garbage values for thiscoord[] further
+    // down. It might be thrown off by all the reinterpret_casts, but we might
+    // as well make sure the small preallocated buffer is zero-initialized.
+    for (i = 0; i < static_cast<int>(prealloc_size); i++)
+    {
+        prealloc_ip[i] = 0;
+    }
+
     if (!bRead)
     {
         /* xdrs is open for writing */
@@ -444,8 +448,8 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
          */
         if (*size <= 9)
         {
-            return (xdr_vector(xdrs, (char *) fp, (unsigned int)size3,
-                               (unsigned int)sizeof(*fp), (xdrproc_t)xdr_float));
+            return (xdr_vector(xdrs, reinterpret_cast<char *>(fp), static_cast<unsigned int>(size3),
+                               static_cast<unsigned int>(sizeof(*fp)), (xdrproc_t)xdr_float));
         }
 
         if (xdr_float(xdrs, precision) == 0)
@@ -461,9 +465,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         else
         {
             we_should_free = 1;
-            bufsize        = size3 * 1.2;
-            ip             = (int *)malloc((size_t)(size3 * sizeof(*ip)));
-            buf            = (int *)malloc((size_t)(bufsize * sizeof(*buf)));
+            bufsize        = static_cast<int>(size3 * 1.2);
+            ip             = reinterpret_cast<int *>(malloc(size3 * sizeof(*ip)));
+            buf            = reinterpret_cast<int *>(malloc(bufsize * sizeof(*buf)));
             if (ip == NULL || buf == NULL)
             {
                 fprintf(stderr, "malloc failed\n");
@@ -495,7 +499,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
                 /* scaling would cause overflow */
                 errval = 0;
             }
-            lint1 = lf;
+            lint1 = static_cast<int>(lf);
             if (lint1 < minint[0])
             {
                 minint[0] = lint1;
@@ -519,7 +523,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
                 /* scaling would cause overflow */
                 errval = 0;
             }
-            lint2 = lf;
+            lint2 = static_cast<int>(lf);
             if (lint2 < minint[1])
             {
                 minint[1] = lint2;
@@ -538,12 +542,12 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
             {
                 lf = *lfp * *precision - 0.5;
             }
-            if (fabs(lf) > MAXABS)
+            if (std::abs(lf) > MAXABS)
             {
                 /* scaling would cause overflow */
                 errval = 0;
             }
-            lint3 = lf;
+            lint3 = static_cast<int>(lf);
             if (lint3 < minint[2])
             {
                 minint[2] = lint3;
@@ -554,7 +558,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
             }
             *lip++ = lint3;
             lfp++;
-            diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
+            diff = std::abs(oldlint1-lint1)+std::abs(oldlint2-lint2)+std::abs(oldlint3-lint3);
             if (diff < mindiff && lfp > fp + 3)
             {
                 mindiff = diff;
@@ -603,8 +607,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         {
             bitsize = sizeofints(3, sizeint);
         }
-        lip      = ip;
-        luip     = (unsigned int *) ip;
+        luip     = reinterpret_cast<unsigned int *>(ip);
         smallidx = FIRSTIDX;
         while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
         {
@@ -620,9 +623,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
             return 0;
         }
 
-        maxidx       = MIN(LASTIDX, smallidx + 8);
+        maxidx       = std::min(LASTIDX, smallidx + 8);
         minidx       = maxidx - 8; /* often this equal smallidx */
-        smaller      = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+        smaller      = magicints[std::max(FIRSTIDX, smallidx-1)] / 2;
         smallnum     = magicints[smallidx] / 2;
         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
         larger       = magicints[maxidx] / 2;
@@ -630,11 +633,11 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         while (i < *size)
         {
             is_small  = 0;
-            thiscoord = (int *)(luip) + i * 3;
+            thiscoord = reinterpret_cast<int *>(luip) + i * 3;
             if (smallidx < maxidx && i >= 1 &&
-                abs(thiscoord[0] - prevcoord[0]) < larger &&
-                abs(thiscoord[1] - prevcoord[1]) < larger &&
-                abs(thiscoord[2] - prevcoord[2]) < larger)
+                std::abs(thiscoord[0] - prevcoord[0]) < larger &&
+                std::abs(thiscoord[1] - prevcoord[1]) < larger &&
+                std::abs(thiscoord[2] - prevcoord[2]) < larger)
             {
                 is_smaller = 1;
             }
@@ -648,9 +651,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
             }
             if (i + 1 < *size)
             {
-                if (abs(thiscoord[0] - thiscoord[3]) < smallnum &&
-                    abs(thiscoord[1] - thiscoord[4]) < smallnum &&
-                    abs(thiscoord[2] - thiscoord[5]) < smallnum)
+                if (std::abs(thiscoord[0] - thiscoord[3]) < smallnum &&
+                    std::abs(thiscoord[1] - thiscoord[4]) < smallnum &&
+                    std::abs(thiscoord[2] - thiscoord[5]) < smallnum)
                 {
                     /* interchange first with second atom for better
                      * compression of water molecules
@@ -764,7 +767,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         }
 
 
-        rc = errval * (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]));
+        rc = errval * (xdr_opaque(xdrs, reinterpret_cast<char *>(&(buf[3])), static_cast<unsigned int>(buf[0])));
         if (we_should_free)
         {
             free(ip);
@@ -792,8 +795,8 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         if (*size <= 9)
         {
             *precision = -1;
-            return (xdr_vector(xdrs, (char *) fp, (unsigned int)size3,
-                               (unsigned int)sizeof(*fp), (xdrproc_t)xdr_float));
+            return (xdr_vector(xdrs, reinterpret_cast<char *>(fp), static_cast<unsigned int>(size3),
+                               static_cast<unsigned int>(sizeof(*fp)), (xdrproc_t)xdr_float));
         }
         if (xdr_float(xdrs, precision) == 0)
         {
@@ -808,9 +811,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         else
         {
             we_should_free = 1;
-            bufsize        = size3 * 1.2;
-            ip             = (int *)malloc((size_t)(size3 * sizeof(*ip)));
-            buf            = (int *)malloc((size_t)(bufsize * sizeof(*buf)));
+            bufsize        = static_cast<int>(size3 * 1.2);
+            ip             = reinterpret_cast<int *>(malloc(size3 * sizeof(*ip)));
+            buf            = reinterpret_cast<int *>(malloc(bufsize * sizeof(*buf)));
             if (ip == NULL || buf == NULL)
             {
                 fprintf(stderr, "malloc failed\n");
@@ -862,12 +865,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
             return 0;
         }
 
-        maxidx       = MIN(LASTIDX, smallidx + 8);
-        minidx       = maxidx - 8; /* often this equal smallidx */
-        smaller      = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+        smaller      = magicints[std::max(FIRSTIDX, smallidx-1)] / 2;
         smallnum     = magicints[smallidx] / 2;
         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
-        larger       = magicints[maxidx];
 
         /* buf[0] holds the length in bytes */
 
@@ -882,7 +882,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         }
 
 
-        if (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]) == 0)
+        if (xdr_opaque(xdrs, reinterpret_cast<char *>(&(buf[3])), static_cast<unsigned int>(buf[0])) == 0)
         {
             if (we_should_free)
             {
@@ -903,7 +903,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         lip           = ip;
         while (i < lsize)
         {
-            thiscoord = (int *)(lip) + i * 3;
+            thiscoord = reinterpret_cast<int *>(lip) + i * 3;
 
             if (bitsize == 0)
             {
@@ -1272,7 +1272,6 @@ xtc_get_current_frame_number(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
 
 static gmx_off_t xtc_get_next_frame_start(FILE *fp, XDR *xdrs, int natoms)
 {
-    int       inp;
     gmx_off_t res;
     int       ret;
     int       step;
@@ -1431,7 +1430,6 @@ int xdr_xtc_seek_time(real time, FILE *fp, XDR *xdrs, int natoms, gmx_bool bSeek
     gmx_bool  bOK = FALSE;
     gmx_off_t low = 0;
     gmx_off_t high, offset, pos;
-    int       res;
     int       dt_sign = 0;
 
     if (bSeekForwardOnly)
@@ -1592,7 +1590,6 @@ xdr_xtc_get_last_frame_time(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
 {
     float      time;
     gmx_off_t  off;
-    int        res;
     *bOK = 1;
     off  = gmx_ftell(fp);
     if (off < 0)
@@ -1601,7 +1598,7 @@ xdr_xtc_get_last_frame_time(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
         return -1;
     }
 
-    if ( (res = gmx_fseek(fp, -3*XDR_INT_SIZE, SEEK_END)) != 0)
+    if (gmx_fseek(fp, -3*XDR_INT_SIZE, SEEK_END) != 0)
     {
         *bOK = 0;
         return -1;
@@ -1613,7 +1610,7 @@ xdr_xtc_get_last_frame_time(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
         return -1;
     }
 
-    if ( (res = gmx_fseek(fp, off, SEEK_SET)) != 0)
+    if (gmx_fseek(fp, off, SEEK_SET) != 0)
     {
         *bOK = 0;
         return -1;
@@ -1627,7 +1624,6 @@ xdr_xtc_get_last_frame_number(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
 {
     int        frame;
     gmx_off_t  off;
-    int        res;
     *bOK = 1;
 
     if ((off = gmx_ftell(fp)) < 0)
diff --git a/src/gromacs/fileio/matio.cpp b/src/gromacs/fileio/matio.cpp
index 6d464f8c91..8b1e7a976a 100644
--- a/src/gromacs/fileio/matio.cpp
+++ b/src/gromacs/fileio/matio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -38,8 +38,9 @@
 
 #include "matio.h"
 
-#include <ctype.h>
-#include <stdio.h>
+#include <cctype>
+#include <cstdio>
+#include <cstring>
 
 #include <algorithm>
 
@@ -294,7 +295,7 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
     llmax = STRLEN;
 
     while ((NULL != fgetline(&line_buf, llmax, &llalloc, in)) &&
-           (strncmp(line_buf, "static", 6) != 0))
+           (std::strncmp(line_buf, "static", 6) != 0))
     {
         line = line_buf;
         parsestring(line, "title", (mm->title));
@@ -361,7 +362,7 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
     m = 0;
     while ((m < mm->nmap) && (NULL != fgetline(&line_buf, llmax, &llalloc, in)))
     {
-        line = strchr(line_buf, '\"');
+        line = std::strchr(line_buf, '\"');
         if  (line)
         {
             line++;
@@ -376,12 +377,12 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
                 map[m].code.c2 = line[1];
             }
             line += nch;
-            str   = strchr(line, '#');
+            str   = std::strchr(line, '#');
             if (str)
             {
                 str++;
                 col_len = 0;
-                while (isxdigit(str[col_len]))
+                while (std::isxdigit(str[col_len]))
                 {
                     col_len++;
                 }
@@ -406,7 +407,7 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
             }
             else
             {
-                str = strchr(line, 'c');
+                str = std::strchr(line, 'c');
                 if (str)
                 {
                     str += 2;
@@ -420,7 +421,7 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
                 map[m].rgb.g = 1;
                 map[m].rgb.b = 1;
             }
-            line = strchr(line, '\"');
+            line = std::strchr(line, '\"');
             line++;
             line2string(&line);
             map[m].desc = gmx_strdup(line);
@@ -446,7 +447,7 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
         bSetLine = TRUE;
         if (strstr(line, "x-axis"))
         {
-            line = strstr(line, "x-axis");
+            line = std::strstr(line, "x-axis");
             skipstr(line);
             if (mm->axis_x == NULL)
             {
@@ -467,9 +468,9 @@ static void read_xpm_entry(FILE *in, t_matrix *mm)
                 skipstr(line);
             }
         }
-        else if (strstr(line, "y-axis"))
+        else if (std::strstr(line, "y-axis"))
         {
-            line = strstr(line, "y-axis");
+            line = std::strstr(line, "y-axis");
             skipstr(line);
             if (mm->axis_y == NULL)
             {
@@ -560,7 +561,7 @@ int read_xpm_matrix(const char *fnm, t_matrix **mat)
     nmat = 0;
     while (NULL != fgetline(&line, STRLEN, &llalloc, in))
     {
-        if (strstr(line, "/* XPM */"))
+        if (std::strstr(line, "/* XPM */"))
         {
             srenew(*mat, nmat+1);
             read_xpm_entry(in, &(*mat)[nmat]);
@@ -705,9 +706,9 @@ static void write_xpm_map3(FILE *out, int n_x, int n_y, int *nlevels,
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
                 mapper[i % NMAP],
                 (*nlevels <= NMAP) ? ' ' : mapper[i/NMAP],
-                (unsigned int)round(255*r),
-                (unsigned int)round(255*g),
-                (unsigned int)round(255*b),
+                static_cast<unsigned int>(round(255*r)),
+                static_cast<unsigned int>(round(255*g)),
+                static_cast<unsigned int>(round(255*b)),
                 ((nmid - i)*lo + i*mid)/clev_lo);
     }
     for (i = 0; (i < (*nlevels-nmid)); i++)
@@ -718,9 +719,9 @@ static void write_xpm_map3(FILE *out, int n_x, int n_y, int *nlevels,
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
                 mapper[(i+nmid) % NMAP],
                 (*nlevels <= NMAP) ? ' ' : mapper[(i+nmid)/NMAP],
-                (unsigned int)round(255*r),
-                (unsigned int)round(255*g),
-                (unsigned int)round(255*b),
+                static_cast<unsigned int>(round(255*r)),
+                static_cast<unsigned int>(round(255*g)),
+                static_cast<unsigned int>(round(255*b)),
                 ((*nlevels - 1 - nmid - i)*mid + i*hi)/clev_hi);
     }
 }
@@ -740,9 +741,9 @@ static void pr_simple_cmap(FILE *out, real lo, real hi, int nlevel, t_rgb rlo,
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
                 mapper[(i+i0) % NMAP],
                 (nlevel <= NMAP) ? ' ' : mapper[(i+i0)/NMAP],
-                (unsigned int)round(255*r),
-                (unsigned int)round(255*g),
-                (unsigned int)round(255*b),
+                static_cast<unsigned int>(round(255*r)),
+                static_cast<unsigned int>(round(255*g)),
+                static_cast<unsigned int>(round(255*b)),
                 lo+fac*(hi-lo));
     }
 }
@@ -777,9 +778,9 @@ static void pr_discrete_cmap(FILE *out, int *nlevel, int i0)
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%3d\" */,\n",
                 mapper[(i+i0) % NMAP],
                 (n <= NMAP) ? ' ' : mapper[(i+i0)/NMAP],
-                (unsigned int)round(255*rgbd[i].r),
-                (unsigned int)round(255*rgbd[i].g),
-                (unsigned int)round(255*rgbd[i].b),
+                static_cast<unsigned int>(round(255*rgbd[i].r)),
+                static_cast<unsigned int>(round(255*rgbd[i].g)),
+                static_cast<unsigned int>(round(255*rgbd[i].b)),
                 i);
     }
 }
@@ -848,9 +849,9 @@ static void write_xpm_map(FILE *out, int n_x, int n_y, int *nlevels,
         b   = (nlo*rlo.b+i*rhi.b)*invlevel;
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
                 mapper[i % NMAP], (*nlevels <= NMAP) ? ' ' : mapper[i/NMAP],
-                (unsigned int)round(255*r),
-                (unsigned int)round(255*g),
-                (unsigned int)round(255*b),
+                static_cast<unsigned int>(round(255*r)),
+                static_cast<unsigned int>(round(255*g)),
+                static_cast<unsigned int>(round(255*b)),
                 (nlo*lo+i*hi)*invlevel);
     }
 }
@@ -1054,9 +1055,9 @@ void write_xpm_m(FILE *out, t_matrix m)
         fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%s\" */,\n",
                 m.map[i].code.c1,
                 bOneChar ? ' ' : m.map[i].code.c2,
-                (unsigned int)round(m.map[i].rgb.r*255),
-                (unsigned int)round(m.map[i].rgb.g*255),
-                (unsigned int)round(m.map[i].rgb.b*255), m.map[i].desc);
+                static_cast<unsigned int>(round(m.map[i].rgb.r*255)),
+                static_cast<unsigned int>(round(m.map[i].rgb.g*255)),
+                static_cast<unsigned int>(round(m.map[i].rgb.b*255)), m.map[i].desc);
     }
     write_xpm_axis(out, "x", m.flags & MAT_SPATIAL_X, m.nx, m.axis_x);
     write_xpm_axis(out, "y", m.flags & MAT_SPATIAL_Y, m.ny, m.axis_y);
diff --git a/src/gromacs/fileio/md5.c b/src/gromacs/fileio/md5.cpp
similarity index 97%
rename from src/gromacs/fileio/md5.c
rename to src/gromacs/fileio/md5.cpp
index 521f37c090..bacff2887d 100644
--- a/src/gromacs/fileio/md5.c
+++ b/src/gromacs/fileio/md5.cpp
@@ -40,6 +40,8 @@
 
 #include "config.h"
 
+#include <cstring>
+
 #if GMX_INTEGER_BIG_ENDIAN
 #define ARCH_IS_BIG_ENDIAN 1
 #else
@@ -100,8 +102,6 @@
 
 #include "md5.h"
 
-#include <string.h>
-
 #undef BYTE_ORDER   /* 1 = big-endian, -1 = little-endian, 0 = unknown */
 #ifdef ARCH_IS_BIG_ENDIAN
 #  define BYTE_ORDER (ARCH_IS_BIG_ENDIAN ? 1 : -1)
@@ -201,15 +201,15 @@ md5_process(md5_state_t *pms, const md5_byte_t *data /*[64]*/)
          */
         static const int w = 1;
 
-        if (*((const md5_byte_t *)&w)) /* dynamic little-endian */
+        if (*(reinterpret_cast<const md5_byte_t *>(&w))) /* dynamic little-endian */
 #endif
-#if BYTE_ORDER <= 0                    /* little-endian */
+#if BYTE_ORDER <= 0                                      /* little-endian */
         {
             /*
              * On little-endian machines, we can process properly aligned
              * data without copying it.
              */
-            if (!((data - (const md5_byte_t *)0) & 3))
+            if (!((data - reinterpret_cast<const md5_byte_t *>(0)) & 3))
             {
                 /* data are properly aligned */
                 X = (const md5_word_t *)data;
@@ -217,7 +217,7 @@ md5_process(md5_state_t *pms, const md5_byte_t *data /*[64]*/)
             else
             {
                 /* not aligned */
-                memcpy(xbuf, data, 64);
+                std::memcpy(xbuf, data, 64);
                 X = xbuf;
             }
         }
@@ -398,7 +398,7 @@ gmx_md5_append(md5_state_t *pms, const md5_byte_t *data, int nbytes)
     {
         int copy = (offset + nbytes > 64 ? 64 - offset : nbytes);
 
-        memcpy(pms->buf + offset, p, copy);
+        std::memcpy(pms->buf + offset, p, copy);
         if (offset + copy < 64)
         {
             return;
diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.cpp
similarity index 96%
rename from src/gromacs/fileio/mdoutf.c
rename to src/gromacs/fileio/mdoutf.cpp
index 5cab6d917a..db89c8ea6a 100644
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.cpp
@@ -98,7 +98,7 @@ gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
     of->bExpanded               = ir->bExpanded;
     of->elamstats               = ir->expandedvals->elamstats;
     of->simulation_part         = ir->simulation_part;
-    of->x_compression_precision = ir->x_compression_precision;
+    of->x_compression_precision = static_cast<int>(ir->x_compression_precision);
     of->wcycle                  = wcycle;
 
     if (MASTER(cr))
@@ -327,11 +327,11 @@ void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
             }
 
             gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
-                           (const rvec *) state_local->box,
+                           state_local->box,
                            top_global->natoms,
-                           (mdof_flags & MDOF_X) ? (const rvec *) state_global->x : NULL,
-                           (mdof_flags & MDOF_V) ? (const rvec *) global_v : NULL,
-                           (mdof_flags & MDOF_F) ? (const rvec *) f_global : NULL);
+                           (mdof_flags & MDOF_X) ? state_global->x : NULL,
+                           (mdof_flags & MDOF_V) ? global_v : NULL,
+                           (mdof_flags & MDOF_F) ? f_global : NULL);
         }
         if (mdof_flags & MDOF_X_COMPRESSED)
         {
@@ -369,9 +369,9 @@ void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
                            step,
                            t,
                            state_local->lambda[efptFEP],
-                           (const rvec *) state_local->box,
+                           state_local->box,
                            of->natoms_x_compressed,
-                           (const rvec *) xxtc,
+                           xxtc,
                            NULL,
                            NULL);
             if (of->natoms_x_compressed != of->natoms_global)
diff --git a/src/gromacs/fileio/mtxio.c b/src/gromacs/fileio/mtxio.cpp
similarity index 94%
rename from src/gromacs/fileio/mtxio.c
rename to src/gromacs/fileio/mtxio.cpp
index ae9b15d9e8..827452131c 100644
--- a/src/gromacs/fileio/mtxio.c
+++ b/src/gromacs/fileio/mtxio.cpp
@@ -87,8 +87,6 @@ void gmx_mtxio_write(const char *             filename,
 {
     t_fileio   *fio;
     int         i, j, prec;
-    gmx_bool    bDum  = TRUE;
-    gmx_bool    bRead = FALSE;
     size_t      sz;
 
     if (full_matrix != NULL && sparse_matrix != NULL)
@@ -125,7 +123,7 @@ void gmx_mtxio_write(const char *             filename,
         i = GMX_MTXIO_FULL_MATRIX;
         gmx_fio_do_int(fio, i);
         sz   = nrow*ncol;
-        bDum = gmx_fio_ndo_real(fio, full_matrix, sz);
+        gmx_fio_ndo_real(fio, full_matrix, sz);
     }
     else
     {
@@ -139,7 +137,7 @@ void gmx_mtxio_write(const char *             filename,
         {
             gmx_fatal(FARGS, "Internal inconsistency in sparse matrix.\n");
         }
-        bDum = gmx_fio_ndo_int(fio, sparse_matrix->ndata, sparse_matrix->nrow);
+        gmx_fio_ndo_int(fio, sparse_matrix->ndata, sparse_matrix->nrow);
         for (i = 0; i < sparse_matrix->nrow; i++)
         {
             for (j = 0; j < sparse_matrix->ndata[i]; j++)
@@ -162,8 +160,6 @@ gmx_mtxio_read (const char *            filename,
 {
     t_fileio   *fio;
     int         i, j, prec;
-    gmx_bool    bDum  = TRUE;
-    gmx_bool    bRead = TRUE;
     char        gmxver[256];
     size_t      sz;
 
@@ -210,7 +206,7 @@ gmx_mtxio_read (const char *            filename,
 
         sz = (*nrow) * (*ncol);
         snew((*full_matrix), sz);
-        bDum = gmx_fio_ndo_real(fio, (*full_matrix), sz);
+        gmx_fio_ndo_real(fio, (*full_matrix), sz);
     }
     else if (NULL != sparse_matrix)
     {
@@ -227,8 +223,8 @@ gmx_mtxio_read (const char *            filename,
         snew((*sparse_matrix)->ndata, (*sparse_matrix)->nrow);
         snew((*sparse_matrix)->nalloc, (*sparse_matrix)->nrow);
         snew((*sparse_matrix)->data, (*sparse_matrix)->nrow);
-        bDum = gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,
-                               (*sparse_matrix)->nrow);
+        gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,
+                        (*sparse_matrix)->nrow);
 
         for (i = 0; i < (*sparse_matrix)->nrow; i++)
         {
diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.cpp
similarity index 90%
rename from src/gromacs/fileio/pdbio.c
rename to src/gromacs/fileio/pdbio.cpp
index 20bd556dae..572b3f94b5 100644
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -38,9 +38,10 @@
 
 #include "pdbio.h"
 
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
@@ -82,8 +83,8 @@ static void xlate_atomname_pdb2gmx(char *name)
     int  i, length;
     char temp;
 
-    length = strlen(name);
-    if (length > 3 && isdigit(name[0]))
+    length = std::strlen(name);
+    if (length > 3 && std::isdigit(name[0]))
     {
         temp = name[0];
         for (i = 1; i < length; i++)
@@ -99,8 +100,8 @@ static void xlate_atomname_gmx2pdb(char *name)
     int  i, length;
     char temp;
 
-    length = strlen(name);
-    if (length > 3 && isdigit(name[length-1]))
+    length = std::strlen(name);
+    if (length > 3 && std::isdigit(name[length-1]))
     {
         temp = name[length-1];
         for (i = length-1; i > 0; --i)
@@ -128,7 +129,7 @@ void gmx_write_pdb_box(FILE *out, int ePBC, matrix box)
 
     if (norm2(box[YY])*norm2(box[ZZ]) != 0)
     {
-        alpha = RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ]));
+        alpha = RAD2DEG*std::acos(cos_angle_no_table(box[YY], box[ZZ]));
     }
     else
     {
@@ -136,7 +137,7 @@ void gmx_write_pdb_box(FILE *out, int ePBC, matrix box)
     }
     if (norm2(box[XX])*norm2(box[ZZ]) != 0)
     {
-        beta  = RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ]));
+        beta  = RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[ZZ]));
     }
     else
     {
@@ -144,7 +145,7 @@ void gmx_write_pdb_box(FILE *out, int ePBC, matrix box)
     }
     if (norm2(box[XX])*norm2(box[YY]) != 0)
     {
-        gamma = RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY]));
+        gamma = RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[YY]));
     }
     else
     {
@@ -217,7 +218,7 @@ static void read_cryst1(char *line, int *ePBC, matrix box)
         {
             if (alpha != 90.0)
             {
-                cosa = cos(alpha*DEG2RAD);
+                cosa = std::cos(alpha*DEG2RAD);
             }
             else
             {
@@ -225,7 +226,7 @@ static void read_cryst1(char *line, int *ePBC, matrix box)
             }
             if (beta != 90.0)
             {
-                cosb = cos(beta*DEG2RAD);
+                cosb = std::cos(beta*DEG2RAD);
             }
             else
             {
@@ -233,8 +234,8 @@ static void read_cryst1(char *line, int *ePBC, matrix box)
             }
             if (gamma != 90.0)
             {
-                cosg = cos(gamma*DEG2RAD);
-                sing = sin(gamma*DEG2RAD);
+                cosg = std::cos(gamma*DEG2RAD);
+                sing = std::sin(gamma*DEG2RAD);
             }
             else
             {
@@ -245,8 +246,8 @@ static void read_cryst1(char *line, int *ePBC, matrix box)
             box[YY][YY] = fb*sing;
             box[ZZ][XX] = fc*cosb;
             box[ZZ][YY] = fc*(cosa - cosb*cosg)/sing;
-            box[ZZ][ZZ] = sqrt(fc*fc
-                               - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
+            box[ZZ][ZZ] = std::sqrt(fc*fc
+                                    - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
         }
         else
         {
@@ -271,9 +272,7 @@ void write_pdbfile_indexed(FILE *out, const char *title,
     char              altloc;
     real              occup, bfac;
     gmx_bool          bOccup;
-    int               nlongname = 0;
     int               chainnum, lastchainnum;
-    int               lastresind, lastchainresind;
     gmx_residuetype_t*rt;
     const char       *p_restype;
     const char       *p_lastrestype;
@@ -305,15 +304,12 @@ void write_pdbfile_indexed(FILE *out, const char *title,
 
     fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
 
-    lastchainresind   = -1;
     lastchainnum      = -1;
-    resind            = -1;
     p_restype         = NULL;
 
     for (ii = 0; ii < nindex; ii++)
     {
         i             = index[ii];
-        lastresind    = resind;
         resind        = atoms->atom[i].resind;
         chainnum      = atoms->resinfo[resind].chainnum;
         p_lastrestype = p_restype;
@@ -328,7 +324,6 @@ void write_pdbfile_indexed(FILE *out, const char *title,
                 fprintf(out, "TER\n");
             }
             lastchainnum    = chainnum;
-            lastchainresind = lastresind;
         }
 
         strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
@@ -359,7 +354,7 @@ void write_pdbfile_indexed(FILE *out, const char *title,
         }
         if (atoms->pdbinfo)
         {
-            type   = (enum PDB_record)(atoms->pdbinfo[i].type);
+            type   = static_cast<enum PDB_record>(atoms->pdbinfo[i].type);
             altloc = atoms->pdbinfo[i].altloc;
             if (!isalnum(altloc))
             {
@@ -444,7 +439,7 @@ int line2type(char *line)
 
     for (k = 0; (k < epdbNR); k++)
     {
-        if (strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
+        if (std::strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
         {
             break;
         }
@@ -478,10 +473,10 @@ static void read_anisou(char line[], int natom, t_atoms *atoms)
     trim(anm);
 
     /* Search backwards for number and name only */
-    atomnr = strtol(anr, NULL, 10);
+    atomnr = std::strtol(anr, NULL, 10);
     for (i = natom-1; (i >= 0); i--)
     {
-        if ((strcmp(anm, *(atoms->atomname[i])) == 0) &&
+        if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) &&
             (atomnr == atoms->pdbinfo[i].atomnr))
         {
             break;
@@ -524,11 +519,11 @@ void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps)
     }
     for (i = 0; (i < atoms->nr); i++)
     {
-        strcpy(anm, atoms->pdbinfo[i].atomnm);
-        strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
+        std::strcpy(anm, atoms->pdbinfo[i].atomnm);
+        std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
         len        = strlen(anm);
         atomnumber = NOTSET;
-        if ((anm[0] != ' ') && ((len <= 2) || ((len > 2) && !isdigit(anm[2]))))
+        if ((anm[0] != ' ') && ((len <= 2) || ((len > 2) && !std::isdigit(anm[2]))))
         {
             anm_copy[2] = nc;
             if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
@@ -547,7 +542,7 @@ void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps)
         if (atomnumber == NOTSET)
         {
             k = 0;
-            while ((k < strlen(anm)) && (isspace(anm[k]) || isdigit(anm[k])))
+            while ((k < std::strlen(anm)) && (std::isspace(anm[k]) || std::isdigit(anm[k])))
             {
                 k++;
             }
@@ -560,7 +555,7 @@ void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps)
         }
         atoms->atom[i].atomnumber = atomnumber;
         ptr = gmx_atomprop_element(aps, atomnumber);
-        strncpy(atoms->atom[i].elem, ptr == NULL ? "" : ptr, 4);
+        std::strncpy(atoms->atom[i].elem, ptr == NULL ? "" : ptr, 4);
         if (debug)
         {
             fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
@@ -601,7 +596,7 @@ static int read_atom(t_symtab *symtab,
         anm[k] = line[j];
     }
     anm[k] = nc;
-    strcpy(anm_copy, anm);
+    std::strcpy(anm_copy, anm);
     rtrim(anm_copy);
     atomnumber = NOTSET;
     trim(anm);
@@ -623,7 +618,7 @@ static int read_atom(t_symtab *symtab,
     }
     rnr[k] = nc;
     trim(rnr);
-    resnr = strtol(rnr, NULL, 10);
+    resnr = std::strtol(rnr, NULL, 10);
     resic = line[j];
     j    += 4;
 
@@ -723,14 +718,14 @@ gmx_bool is_hydrogen(const char *nm)
 {
     char buf[30];
 
-    strcpy(buf, nm);
+    std::strcpy(buf, nm);
     trim(buf);
 
     if (buf[0] == 'H')
     {
         return TRUE;
     }
-    else if ((isdigit(buf[0])) && (buf[1] == 'H'))
+    else if ((std::isdigit(buf[0])) && (buf[1] == 'H'))
     {
         return TRUE;
     }
@@ -741,10 +736,10 @@ gmx_bool is_dummymass(const char *nm)
 {
     char buf[30];
 
-    strcpy(buf, nm);
+    std::strcpy(buf, nm);
     trim(buf);
 
-    if ((buf[0] == 'M') && isdigit(buf[strlen(buf)-1]))
+    if ((buf[0] == 'M') && std::isdigit(buf[strlen(buf)-1]))
     {
         return TRUE;
     }
@@ -763,7 +758,7 @@ static void gmx_conect_addline(gmx_conect_t *con, char *line)
     {
         do
         {
-            strcat(form2, "%*s");
+            std::strcat(form2, "%*s");
             sprintf(format, "%s%%d", form2);
             n = sscanf(line, format, &aj);
             if (n == 1)
@@ -795,19 +790,19 @@ gmx_conect gmx_conect_init()
 
     snew(gc, 1);
 
-    return (gmx_conect) gc;
+    return gc;
 }
 
 void gmx_conect_done(gmx_conect conect)
 {
-    gmx_conect_t *gc = (gmx_conect_t *)conect;
+    gmx_conect_t *gc = conect;
 
     sfree(gc->conect);
 }
 
 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
 {
-    gmx_conect_t *gc = (gmx_conect_t *)conect;
+    gmx_conect_t *gc = conect;
     int           i;
 
     /* if (!gc->bSorted)
@@ -829,7 +824,6 @@ gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
 void gmx_conect_add(gmx_conect conect, int ai, int aj)
 {
     gmx_conect_t *gc = (gmx_conect_t *)conect;
-    int           i;
 
     /* if (!gc->bSorted)
        sort_conect(gc);*/
@@ -846,15 +840,14 @@ int read_pdbfile(FILE *in, char *title, int *model_nr,
                  t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
                  gmx_conect conect)
 {
-    gmx_conect_t *gc = (gmx_conect_t *)conect;
+    gmx_conect_t *gc = conect;
     t_symtab      symtab;
     gmx_bool      bCOMPND;
     gmx_bool      bConnWarn = FALSE;
     char          line[STRLEN+1];
     int           line_type;
     char         *c, *d;
-    int           natom, chainnum, nres_ter_prev = 0;
-    char          chidmax = ' ';
+    int           natom, chainnum;
     gmx_bool      bStop   = FALSE;
 
     if (ePBC)
@@ -897,7 +890,7 @@ int read_pdbfile(FILE *in, char *title, int *model_nr,
 
             case epdbTITLE:
             case epdbHEADER:
-                if (strlen(line) > 6)
+                if (std::strlen(line) > 6)
                 {
                     c = line+6;
                     /* skip HEADER or TITLE and spaces */
@@ -910,22 +903,22 @@ int read_pdbfile(FILE *in, char *title, int *model_nr,
                         c++;
                     }
                     /* truncate after title */
-                    d = strstr(c, "      ");
+                    d = std::strstr(c, "      ");
                     if (d)
                     {
                         d[0] = '\0';
                     }
-                    if (strlen(c) > 0)
+                    if (std::strlen(c) > 0)
                     {
-                        strcpy(title, c);
+                        std::strcpy(title, c);
                     }
                 }
                 break;
 
             case epdbCOMPND:
-                if ((!strstr(line, ": ")) || (strstr(line+6, "MOLECULE:")))
+                if ((!std::strstr(line, ": ")) || (std::strstr(line+6, "MOLECULE:")))
                 {
-                    if (!(c = strstr(line+6, "MOLECULE:")) )
+                    if (!(c = std::strstr(line+6, "MOLECULE:")) )
                     {
                         c = line;
                     }
@@ -952,12 +945,12 @@ int read_pdbfile(FILE *in, char *title, int *model_nr,
                     {
                         if (bCOMPND)
                         {
-                            strcat(title, "; ");
-                            strcat(title, c);
+                            std::strcat(title, "; ");
+                            std::strcat(title, c);
                         }
                         else
                         {
-                            strcpy(title, c);
+                            std::strcpy(title, c);
                         }
                     }
                     bCOMPND = TRUE;
@@ -1006,11 +999,11 @@ void get_pdb_coordnum(FILE *in, int *natoms)
     *natoms = 0;
     while (fgets2(line, STRLEN, in))
     {
-        if (strncmp(line, "ENDMDL", 6) == 0)
+        if (std::strncmp(line, "ENDMDL", 6) == 0)
         {
             break;
         }
-        if ((strncmp(line, "ATOM  ", 6) == 0) || (strncmp(line, "HETATM", 6) == 0))
+        if ((std::strncmp(line, "ATOM  ", 6) == 0) || (std::strncmp(line, "HETATM", 6) == 0))
         {
             (*natoms)++;
         }
@@ -1082,16 +1075,16 @@ gmx_fprintf_pdb_atomline(FILE *            fp,
         /* If the atom name is an element name with two chars, it should start already in column 13.
          * Otherwise it should start in column 14, unless the name length is 4 chars.
          */
-        if ( (element != NULL) && (strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
+        if ( (element != NULL) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
         {
             start_name_in_col13 = TRUE;
         }
         else
         {
-            start_name_in_col13 = (strlen(atom_name) >= 4);
+            start_name_in_col13 = (std::strlen(atom_name) >= 4);
         }
         sprintf(tmp_atomname, start_name_in_col13 ? "" : " ");
-        strncat(tmp_atomname, atom_name, 4);
+        std::strncat(tmp_atomname, atom_name, 4);
         tmp_atomname[5] = '\0';
     }
     else
@@ -1100,14 +1093,14 @@ gmx_fprintf_pdb_atomline(FILE *            fp,
     }
 
     /* Format residue name */
-    strncpy(tmp_resname, (res_name != NULL) ? res_name : "", 4);
+    std::strncpy(tmp_resname, (res_name != NULL) ? res_name : "", 4);
     /* Make sure the string is terminated if strlen was > 4 */
     tmp_resname[4] = '\0';
     /* String is properly terminated, so now we can use strcat. By adding a
      * space we can write it right-justified, and if the original name was
      * three characters or less there will be a space added on the right side.
      */
-    strcat(tmp_resname, " ");
+    std::strcat(tmp_resname, " ");
 
     /* Truncate integers so they fit */
     atom_seq_number = atom_seq_number % 100000;
diff --git a/src/gromacs/fileio/strdb.c b/src/gromacs/fileio/strdb.cpp
similarity index 94%
rename from src/gromacs/fileio/strdb.c
rename to src/gromacs/fileio/strdb.cpp
index a0fc276d8f..937256031b 100644
--- a/src/gromacs/fileio/strdb.c
+++ b/src/gromacs/fileio/strdb.cpp
@@ -38,9 +38,9 @@
 
 #include "strdb.h"
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
@@ -61,12 +61,12 @@ gmx_bool get_a_line(FILE *fp, char line[], int n)
             sfree(line0);
             return FALSE;
         }
-        dum = strchr(line0, '\n');
+        dum = std::strchr(line0, '\n');
         if (dum)
         {
             dum[0] = '\0';
         }
-        else if (strlen(line0) == n)
+        else if (static_cast<int>(std::strlen(line0)) == n)
         {
             fprintf(stderr, "Warning: line length exceeds buffer length (%d), data might be corrupted\n", n);
             line0[n-1] = '\0';
@@ -76,12 +76,12 @@ gmx_bool get_a_line(FILE *fp, char line[], int n)
             fprintf(stderr, "Warning: file does not end with a newline, last line:\n%s\n",
                     line0);
         }
-        dum = strchr(line0, ';');
+        dum = std::strchr(line0, ';');
         if (dum)
         {
             dum[0] = '\0';
         }
-        strncpy(line, line0, n);
+        std::strncpy(line, line0, n);
         dum = line0;
         ltrim(dum);
     }
@@ -95,14 +95,14 @@ gmx_bool get_header(char line[], char *header)
 {
     char temp[STRLEN], *dum;
 
-    strcpy(temp, line);
-    dum = strchr(temp, '[');
+    std::strcpy(temp, line);
+    dum = std::strchr(temp, '[');
     if (dum == NULL)
     {
         return FALSE;
     }
     dum[0] = ' ';
-    dum    = strchr(temp, ']');
+    dum    = std::strchr(temp, ']');
     if (dum == NULL)
     {
         gmx_fatal(FARGS, "header is not terminated on line:\n'%s'\n", line);
diff --git a/src/gromacs/fileio/timecontrol.c b/src/gromacs/fileio/timecontrol.cpp
similarity index 97%
rename from src/gromacs/fileio/timecontrol.c
rename to src/gromacs/fileio/timecontrol.cpp
index 735d649423..06c211e5da 100644
--- a/src/gromacs/fileio/timecontrol.c
+++ b/src/gromacs/fileio/timecontrol.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index 15a92c1398..b006a042f1 100644
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -38,7 +38,7 @@
 
 #include "config.h"
 
-#include <math.h>
+#include <cmath>
 
 #ifdef GMX_USE_TNG
 #include "tng/tng_io.h"
@@ -205,11 +205,11 @@ void gmx_write_tng_from_trxframe(tng_trajectory_t        output,
                    frame->step,
                    frame->time,
                    0,
-                   (const rvec *) frame->box,
+                   frame->box,
                    natoms,
-                   (const rvec *) frame->x,
-                   (const rvec *) frame->v,
-                   (const rvec *) frame->f);
+                   frame->x,
+                   frame->v,
+                   frame->f);
 #else
     GMX_UNUSED_VALUE(output);
     GMX_UNUSED_VALUE(frame);
@@ -243,7 +243,7 @@ convert_array_to_real_array(void       *from,
                     {
                         for (j = 0; j < nValues; j++)
                         {
-                            to[i*nValues+j] = (real)((float *)from)[i*nValues+j] * fact;
+                            to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
                         }
                     }
                 }
@@ -254,7 +254,7 @@ convert_array_to_real_array(void       *from,
                 {
                     for (j = 0; j < nValues; j++)
                     {
-                        to[i*nValues+j] = (real)((float *)from)[i*nValues+j] * fact;
+                        to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
                     }
                 }
             }
@@ -264,7 +264,7 @@ convert_array_to_real_array(void       *from,
             {
                 for (j = 0; j < nValues; j++)
                 {
-                    to[i*nValues+j] = (real)((gmx_int64_t *)from)[i*nValues+j] * fact;
+                    to[i*nValues+j] = reinterpret_cast<gmx_int64_t *>(from)[i*nValues+j] * fact;
                 }
             }
             break;
@@ -281,7 +281,7 @@ convert_array_to_real_array(void       *from,
                     {
                         for (j = 0; j < nValues; j++)
                         {
-                            to[i*nValues+j] = (real)((double *)from)[i*nValues+j] * fact;
+                            to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
                         }
                     }
                 }
@@ -292,7 +292,7 @@ convert_array_to_real_array(void       *from,
                 {
                     for (j = 0; j < nValues; j++)
                     {
-                        to[i*nValues+j] = (real)((double *)from)[i*nValues+j] * fact;
+                        to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
                     }
                 }
             }
@@ -541,8 +541,8 @@ gmx_bool gmx_read_next_tng_frame(tng_trajectory_t            input,
                 }
                 for (int i = 0; i < DIM; i++)
                 {
-                    convert_array_to_real_array((char *)(values) + size * i * DIM,
-                                                (real *) fr->box[i],
+                    convert_array_to_real_array(reinterpret_cast<char *>(values) + size * i * DIM,
+                                                reinterpret_cast<real *>(fr->box[i]),
                                                 getDistanceScaleFactor(input),
                                                 1,
                                                 DIM,
@@ -553,7 +553,7 @@ gmx_bool gmx_read_next_tng_frame(tng_trajectory_t            input,
             case TNG_TRAJ_POSITIONS:
                 srenew(fr->x, fr->natoms);
                 convert_array_to_real_array(values,
-                                            (real *) fr->x,
+                                            reinterpret_cast<real *>(fr->x),
                                             getDistanceScaleFactor(input),
                                             fr->natoms,
                                             DIM,
@@ -587,7 +587,7 @@ gmx_bool gmx_read_next_tng_frame(tng_trajectory_t            input,
             case TNG_TRAJ_FORCES:
                 srenew(fr->f, fr->natoms);
                 convert_array_to_real_array(values,
-                                            (real *) fr->f,
+                                            reinterpret_cast<real *>(fr->f),
                                             getDistanceScaleFactor(input),
                                             fr->natoms,
                                             DIM,
@@ -598,10 +598,10 @@ gmx_bool gmx_read_next_tng_frame(tng_trajectory_t            input,
                 switch (datatype)
                 {
                     case TNG_FLOAT_DATA:
-                        fr->lambda = (*(float *)values);
+                        fr->lambda = *(reinterpret_cast<float *>(values));
                         break;
                     case TNG_DOUBLE_DATA:
-                        fr->lambda = (*(double *)values);
+                        fr->lambda = *(reinterpret_cast<double *>(values));
                         break;
                     default:
                         gmx_incons("Illegal datatype lambda value!");
@@ -615,7 +615,7 @@ gmx_bool gmx_read_next_tng_frame(tng_trajectory_t            input,
          * be reallocated if it is not NULL. */
     }
 
-    fr->step  = (int) frameNumber;
+    fr->step  = static_cast<int>(frameNumber);
     fr->bStep = TRUE;
     // Convert the time to ps
     fr->time  = frameTime / PICO;
diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.cpp
similarity index 99%
rename from src/gromacs/fileio/tpxio.c
rename to src/gromacs/fileio/tpxio.cpp
index 509aa4a15d..8aa9492c46 100644
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.cpp
@@ -40,8 +40,10 @@
 
 #include "tpxio.h"
 
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
@@ -240,7 +242,6 @@ static void do_pullgrp_tpx_pre95(t_fileio     *fio,
                                  gmx_bool      bRead,
                                  int           file_version)
 {
-    int  i;
     rvec tmp;
 
     gmx_fio_do_int(fio, pgrp->nat);
@@ -274,8 +275,6 @@ static void do_pullgrp_tpx_pre95(t_fileio     *fio,
 
 static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
 {
-    int      i;
-
     gmx_fio_do_int(fio, pgrp->nat);
     if (bRead)
     {
@@ -294,8 +293,6 @@ static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
 static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd, int file_version,
                           int ePullOld, int eGeomOld, ivec dimOld)
 {
-    int      i;
-
     gmx_fio_do_int(fio, pcrd->group[0]);
     gmx_fio_do_int(fio, pcrd->group[1]);
     if (file_version >= tpxv_PullCoordTypeGeom)
@@ -334,10 +331,6 @@ static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd, int file_version,
 
 static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
 {
-    /* i is used in the ndo_double macro*/
-    int      i;
-    real     fv;
-    real     rdum;
     int      n_lambda = fepvals->n_lambda;
 
     /* reset the lambda calculation window */
@@ -412,8 +405,7 @@ static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
 static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
 {
     /* i is defined in the ndo_double macro; use g to iterate. */
-    int      i, g;
-    real     fv;
+    int      g;
     real     rdum;
 
     /* free energy values */
@@ -637,7 +629,7 @@ static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int fil
 static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
                     int file_version, int ePullOld)
 {
-    int  eGeomOld;
+    int  eGeomOld = -1;
     ivec dimOld;
     int  g;
 
@@ -700,7 +692,7 @@ static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
         for (g = 0; g < pull->ngroup; g++)
         {
             /* We read and ignore a pull coordinate for group 0 */
-            do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[max(g-1, 0)],
+            do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[std::max(g-1, 0)],
                                  bRead, file_version);
             if (g > 0)
             {
@@ -728,8 +720,6 @@ static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
 
 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
 {
-    int      i;
-
     gmx_fio_do_int(fio, rotg->eType);
     gmx_fio_do_int(fio, rotg->bMassW);
     gmx_fio_do_int(fio, rotg->nat);
@@ -775,8 +765,7 @@ static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
 
 static void do_swapcoords(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead)
 {
-    int i, j;
-
+    int j;
 
     gmx_fio_do_int(fio, swap->nat);
     gmx_fio_do_int(fio, swap->nat_sol);
@@ -2161,7 +2150,7 @@ void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
 
 static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version)
 {
-    int      i, k, idum;
+    int      i, idum;
 
     if (file_version < 44)
     {
@@ -2181,7 +2170,7 @@ static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_ver
 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
                         gmx_bool bRead, int file_version)
 {
-    int          idum, i, j;
+    int          idum, i;
     unsigned int k;
 
     gmx_fio_do_int(fio, ffparams->atnr);
@@ -2276,7 +2265,7 @@ static void add_settle_atoms(t_ilist *ilist)
 static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
                       int file_version)
 {
-    int          i, j, renum[F_NRE];
+    int          j;
     gmx_bool     bClear;
     unsigned int k;
 
@@ -2432,7 +2421,6 @@ static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
                     int file_version, gmx_groups_t *groups, int atnr)
 {
     int    i, myngrp;
-    char * p_elem;
 
     gmx_fio_do_real(fio, atom->m);
     gmx_fio_do_real(fio, atom->q);
@@ -2450,7 +2438,7 @@ static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
             /* Set element string from atomic number if present.
              * This routine returns an empty string if the name is not found.
              */
-            strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
+            std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
             /* avoid warnings about potentially unterminated string */
             atom->elem[3] = '\0';
         }
@@ -2491,7 +2479,7 @@ static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
 static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
                     int file_version)
 {
-    int      i, j, myngrp;
+    int      j, myngrp;
 
     if (file_version < 23)
     {
@@ -2635,7 +2623,7 @@ static void do_groups(t_fileio *fio, gmx_groups_t *groups,
                       gmx_bool bRead, t_symtab *symtab,
                       int file_version)
 {
-    int      g, n, i;
+    int      g;
 
     do_grps(fio, egcNR, groups->grps, bRead, file_version);
     gmx_fio_do_int(fio, groups->ngrpname);
@@ -2668,7 +2656,7 @@ static void do_groups(t_fileio *fio, gmx_groups_t *groups,
 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
                          int file_version)
 {
-    int      i, j;
+    int      j;
 
     if (file_version > 25)
     {
@@ -2832,8 +2820,6 @@ static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
                        t_symtab *symtab, int file_version,
                        gmx_groups_t *groups)
 {
-    int i;
-
     if (file_version >= 57)
     {
         do_symstr(fio, &(molt->name), bRead, symtab);
@@ -2863,8 +2849,6 @@ static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
 
 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead)
 {
-    int i;
-
     gmx_fio_do_int(fio, molb->type);
     gmx_fio_do_int(fio, molb->nmol);
     gmx_fio_do_int(fio, molb->natoms_mol);
@@ -2941,7 +2925,7 @@ static void add_posres_molblock(gmx_mtop_t *mtop)
     for (i = 0; i < il->nr; i += 2)
     {
         ip = &mtop->ffparams.iparams[il->iatoms[i]];
-        am = max(am, il->iatoms[i+1]);
+        am = std::max(am, il->iatoms[i+1]);
         if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
             ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
             ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ])
@@ -2956,8 +2940,7 @@ static void add_posres_molblock(gmx_mtop_t *mtop)
     {
         for (i = 0; i < ilfb->nr; i += 2)
         {
-            ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
-            am = max(am, ilfb->iatoms[i+1]);
+            am = std::max(am, ilfb->iatoms[i+1]);
         }
     }
     /* Make the posres coordinate block end at a molecule end */
@@ -3042,7 +3025,7 @@ static void set_disres_npair(gmx_mtop_t *mtop)
 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
                     int file_version)
 {
-    int            mt, mb, i;
+    int            mt, mb;
     t_blocka       dumb;
 
     if (bRead)
@@ -3227,7 +3210,7 @@ static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
     if (bRead)
     {
         gmx_fio_do_string(fio, buf);
-        if (strncmp(buf, "VERSION", 7))
+        if (std::strncmp(buf, "VERSION", 7))
         {
             gmx_fatal(FARGS, "Can not read file %s,\n"
                       "             this file is from a GROMACS version which is older than 2.0\n"
@@ -3291,7 +3274,7 @@ static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
             sprintf(file_tag, "%s", TPX_TAG_RELEASE);
         }
 
-        if (strcmp(file_tag, tpx_tag) != 0)
+        if (std::strcmp(file_tag, tpx_tag) != 0)
         {
             fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
                     file_tag, tpx_tag);
@@ -3299,7 +3282,7 @@ static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
             /* We only support reading tpx files with the same tag as the code
              * or tpx files with the release tag and with lower version number.
              */
-            if (strcmp(file_tag, TPX_TAG_RELEASE) != 0 && fver < tpx_version)
+            if (std::strcmp(file_tag, TPX_TAG_RELEASE) != 0 && fver < tpx_version)
             {
                 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
                           gmx_fio_getname(fio), fver, file_tag,
@@ -3374,7 +3357,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     gmx_mtop_t      dum_top;
     gmx_bool        TopOnlyOK;
     int             file_version, file_generation;
-    int             i;
     rvec           *xptr, *vptr;
     int             ePBC;
     gmx_bool        bPeriodicMols;
@@ -3714,7 +3696,6 @@ int read_tpx_top(const char *fn,
                  rvec *x, rvec *v, rvec *f, t_topology *top)
 {
     gmx_mtop_t  mtop;
-    t_topology *ltop;
     int         ePBC;
 
     ePBC = read_tpx(fn, ir, box, natoms, x, v, f, &mtop);
@@ -3757,7 +3738,6 @@ gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *eP
     int              natoms, i, version, generation;
     gmx_bool         bTop, bXNULL = FALSE;
     gmx_mtop_t      *mtop;
-    t_topology      *topconv;
     gmx_atomprop_t   aps;
 
     bTop  = fn2bTPX(infile);
@@ -3780,7 +3760,7 @@ gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *eP
         /* In this case we need to throw away the group data too */
         done_gmx_groups_t(&mtop->groups);
         sfree(mtop);
-        strcpy(title, *top->name);
+        std::strcpy(title, *top->name);
         tpx_make_chain_identifiers(&top->atoms, &top->mols);
     }
     else
diff --git a/src/gromacs/fileio/trajectory_writing.c b/src/gromacs/fileio/trajectory_writing.cpp
similarity index 100%
rename from src/gromacs/fileio/trajectory_writing.c
rename to src/gromacs/fileio/trajectory_writing.cpp
diff --git a/src/gromacs/fileio/trnio.c b/src/gromacs/fileio/trnio.cpp
similarity index 99%
rename from src/gromacs/fileio/trnio.c
rename to src/gromacs/fileio/trnio.cpp
index 5afef1afa2..b843db3317 100644
--- a/src/gromacs/fileio/trnio.c
+++ b/src/gromacs/fileio/trnio.cpp
@@ -38,7 +38,7 @@
 
 #include "trnio.h"
 
-#include <string.h>
+#include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/gmxfio-xdr.h"
diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.cpp
similarity index 99%
rename from src/gromacs/fileio/trxio.c
rename to src/gromacs/fileio/trxio.cpp
index 8c296dcee5..86b52201af 100644
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.cpp
@@ -40,8 +40,8 @@
 
 #include "config.h"
 
-#include <assert.h>
-#include <math.h>
+#include <cassert>
+#include <cmath>
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
@@ -61,6 +61,7 @@
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_USE_PLUGINS
@@ -784,7 +785,6 @@ gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxfram
     real     pt;
     int      ct;
     gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
-    int      dummy = 0;
     int      ftp;
 
     bRet = FALSE;
@@ -914,9 +914,7 @@ int read_first_frame(const output_env_t oenv, t_trxstatus **status,
 {
     t_fileio      *fio;
     gmx_bool       bFirst, bOK;
-    int            dummy = 0;
     int            ftp   = fn2ftp(fn);
-    gmx_int64_t   *tng_ids;
 
     clear_trxframe(fr, TRUE);
     fr->flags = flags;
@@ -964,13 +962,13 @@ int read_first_frame(const output_env_t oenv, t_trxstatus **status,
             {
                 snew(fr->v, fr->natoms);
             }
-            fio = (*status)->fio = gmx_fio_open(fn, "r");
+            (*status)->fio = gmx_fio_open(fn, "r");
             break;
         case efXTC:
             if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
                                &fr->prec, &bOK) == 0)
             {
-                assert(!bOK);
+                GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
                 fr->not_ok = DATA_NOT_OK;
             }
             if (fr->not_ok)
diff --git a/src/gromacs/fileio/vmdio.c b/src/gromacs/fileio/vmdio.cpp
similarity index 98%
rename from src/gromacs/fileio/vmdio.c
rename to src/gromacs/fileio/vmdio.cpp
index 8533c243f6..84e6878716 100644
--- a/src/gromacs/fileio/vmdio.c
+++ b/src/gromacs/fileio/vmdio.cpp
@@ -262,10 +262,9 @@ gmx_bool read_next_vmd_frame(t_trxframe *fr)
 
 static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
 {
-    char            pathname[GMX_PATH_MAX], filename[GMX_PATH_MAX];
+    char            pathname[GMX_PATH_MAX];
     const char     *pathenv;
     const char     *err;
-    int             i;
     int             ret = 0;
     char            pathenv_buffer[GMX_PATH_MAX];
 #ifndef GMX_NATIVE_WINDOWS
@@ -328,7 +327,7 @@ static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
                "The architecture (e.g. 32bit versus 64bit) of GROMACS and VMD has to match.\n");
         return 0;
     }
-    for (i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
+    for (size_t i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
     {
         /* FIXME: Undefined which plugin is chosen if more than one plugin
            can read a certain file ending. Requires some additional command
@@ -348,6 +347,7 @@ static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
     }
     do
     {
+        char filename[GMX_PATH_MAX];
         sprintf(filename, "%s\\%s", pathenv, ffd.cFileName);
         ret |= load_sharedlibrary_plugins(filename, vmdplugin);
     }
diff --git a/src/gromacs/fileio/writeps.c b/src/gromacs/fileio/writeps.cpp
similarity index 99%
rename from src/gromacs/fileio/writeps.c
rename to src/gromacs/fileio/writeps.cpp
index a0ae4e15cb..7f9f6229f5 100644
--- a/src/gromacs/fileio/writeps.c
+++ b/src/gromacs/fileio/writeps.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -38,7 +38,7 @@
 
 #include "writeps.h"
 
-#include <stdio.h>
+#include <cstdio>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/fileio/xdrd.c b/src/gromacs/fileio/xdrd.cpp
similarity index 89%
rename from src/gromacs/fileio/xdrd.c
rename to src/gromacs/fileio/xdrd.cpp
index 5af573e7b3..5556316ae1 100644
--- a/src/gromacs/fileio/xdrd.c
+++ b/src/gromacs/fileio/xdrd.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -88,7 +88,7 @@ int xdr3drcoord(XDR *xdrs, real *fp, int *size, real *precision)
     sfree(ffp);
     return ret;
 #else
-    return xdr3dfcoord(xdrs, (float *)fp, size, (float *)precision);
+    return xdr3dfcoord(xdrs, reinterpret_cast<float *>(fp), size, reinterpret_cast<float *>(precision));
 #endif
 }
 
@@ -104,12 +104,12 @@ int xdr_int64(XDR *xdrs, gmx_int64_t *i)
 
     imaj64 = ((*i)>>32) & two_p32_m1;
     imin64 = (*i) & two_p32_m1;
-    imaj   = (int)imaj64;
-    imin   = (int)imin64;
+    imaj   = static_cast<int>(imaj64);
+    imin   = static_cast<int>(imin64);
     ret    = xdr_int(xdrs, &imaj);
     ret   |= xdr_int(xdrs, &imin);
 
-    *i = (((gmx_int64_t)imaj << 32) | ((gmx_int64_t)imin & two_p32_m1));
+    *i = ((static_cast<gmx_int64_t>(imaj) << 32) | (static_cast<gmx_int64_t>(imin) & two_p32_m1));
 
     return ret;
 }
diff --git a/src/gromacs/fileio/xdrf.h b/src/gromacs/fileio/xdrf.h
index 258a19b71c..72a67afb66 100644
--- a/src/gromacs/fileio/xdrf.h
+++ b/src/gromacs/fileio/xdrf.h
@@ -49,7 +49,7 @@
 #include "config.h"
 
 #if GMX_INTERNAL_XDR
-#include "gromacs/fileio/gmx_system_xdr.h"
+#include "gromacs/fileio/gmx_internal_xdr.h"
 #else
 #include <rpc/rpc.h>
 #include <rpc/xdr.h>
diff --git a/src/gromacs/fileio/xtcio.c b/src/gromacs/fileio/xtcio.cpp
similarity index 99%
rename from src/gromacs/fileio/xtcio.c
rename to src/gromacs/fileio/xtcio.cpp
index a477f568d5..cf4bfd4573 100644
--- a/src/gromacs/fileio/xtcio.c
+++ b/src/gromacs/fileio/xtcio.cpp
@@ -38,7 +38,7 @@
 
 #include "xtcio.h"
 
-#include <string.h>
+#include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/gmxfio-xdr.h"
diff --git a/src/gromacs/fileio/xvgr.cpp b/src/gromacs/fileio/xvgr.cpp
index f38f950b8c..1b5a47909a 100644
--- a/src/gromacs/fileio/xvgr.cpp
+++ b/src/gromacs/fileio/xvgr.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
@@ -38,8 +38,8 @@
 
 #include "xvgr.h"
 
-#include <ctype.h>
-#include <string.h>
+#include <cctype>
+#include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
@@ -166,23 +166,23 @@ static char *xvgrstr(const char *gmx, const output_env_t oenv,
                         break;
                 }
                 g++;
-                b = strlen(buf);
+                b = std::strlen(buf);
             }
             else
             {
                 /* Check for special symbol */
                 i = 0;
                 while (sym[i] != NULL &&
-                       gmx_strncasecmp(sym[i], gmx+g, strlen(sym[i])) != 0)
+                       gmx_strncasecmp(sym[i], gmx+g, std::strlen(sym[i])) != 0)
                 {
                     i++;
                 }
                 if (sym[i] != NULL)
                 {
                     c = symc[i];
-                    if (isupper(gmx[g]))
+                    if (std::isupper(gmx[g]))
                     {
-                        c = toupper(c);
+                        c = std::toupper(c);
                     }
                     switch (xvgf)
                     {
@@ -193,17 +193,17 @@ static char *xvgrstr(const char *gmx, const output_env_t oenv,
                             sprintf(buf+b, "%s%c%s", "\\8", c, "\\4");
                             break;
                         default:
-                            strncat(buf+b, gmx+g, strlen(sym[i]));
-                            b += strlen(sym[i]);
-                            if (gmx[g+strlen(sym[i])] != ' ')
+                            std::strncat(buf+b, gmx+g, std::strlen(sym[i]));
+                            b += std::strlen(sym[i]);
+                            if (gmx[g+std::strlen(sym[i])] != ' ')
                             {
                                 buf[b++] = ' ';
                             }
                             buf[b] = '\0';
                             break;
                     }
-                    g += strlen(sym[i]);
-                    b  = strlen(buf);
+                    g += std::strlen(sym[i]);
+                    b  = std::strlen(buf);
                 }
                 else
                 {
@@ -467,7 +467,7 @@ static char *fgets3(FILE *fp, char **ptr, int *len, int maxlen)
         curp         += len_remaining-1; /* overwrite the nul char in next iteration */
         len_remaining = 1;
     }
-    while ((strchr(*ptr, '\n') == NULL) && (!feof(fp)));
+    while ((std::strchr(*ptr, '\n') == NULL) && (!feof(fp)));
 
     if (*len + STRLEN >= maxlen)
     {
@@ -481,7 +481,7 @@ static char *fgets3(FILE *fp, char **ptr, int *len, int maxlen)
     }
     {
         /* now remove newline */
-        int slen = strlen(*ptr);
+        int slen = std::strlen(*ptr);
         if ((*ptr)[slen-1] == '\n')
         {
             (*ptr)[slen-1] = '\0';
@@ -501,7 +501,7 @@ static int wordcount(char *ptr)
     {
         for (i = 0; (ptr[i] != '\0'); i++)
         {
-            is[cur] = isspace(ptr[i]);
+            is[cur] = std::isspace(ptr[i]);
             if ((0 == i) && !is[cur])
             {
                 n++;
@@ -521,11 +521,11 @@ static char *read_xvgr_string(const char *line)
     const char *ptr0, *ptr1;
     char       *str;
 
-    ptr0 = strchr(line, '"');
+    ptr0 = std::strchr(line, '"');
     if (ptr0 != NULL)
     {
         ptr0++;
-        ptr1 = strchr(ptr0, '"');
+        ptr1 = std::strchr(ptr0, '"');
         if (ptr1 != NULL)
         {
             str            = gmx_strdup(ptr0);
@@ -584,7 +584,7 @@ int read_xvg_legend(const char *fn, double ***y, int *ny,
                 ptr++;
                 trim(ptr);
                 set = -1;
-                if (strncmp(ptr, "subtitle", 8) == 0)
+                if (std::strncmp(ptr, "subtitle", 8) == 0)
                 {
                     ptr += 8;
                     if (subtitle != NULL)
@@ -592,7 +592,7 @@ int read_xvg_legend(const char *fn, double ***y, int *ny,
                         *subtitle = read_xvgr_string(ptr);
                     }
                 }
-                else if (strncmp(ptr, "legend string", 13) == 0)
+                else if (std::strncmp(ptr, "legend string", 13) == 0)
                 {
                     ptr += 13;
                     sscanf(ptr, "%d%n", &set, &nchar);
@@ -604,7 +604,7 @@ int read_xvg_legend(const char *fn, double ***y, int *ny,
                     sscanf(ptr, "%d%n", &set, &nchar);
                     ptr += nchar;
                     trim(ptr);
-                    if (strncmp(ptr, "legend", 6) == 0)
+                    if (std::strncmp(ptr, "legend", 6) == 0)
                     {
                         ptr += 6;
                     }
@@ -654,8 +654,8 @@ int read_xvg_legend(const char *fn, double ***y, int *ny,
             /* fprintf(stderr,"ptr='%s'\n",ptr);*/
             for (k = 0; (k < nny); k++)
             {
-                strcpy(fmt, base);
-                strcat(fmt, "%lf");
+                std::strcpy(fmt, base);
+                std::strcat(fmt, "%lf");
                 rval = sscanf(ptr, fmt, &lf);
                 /* fprintf(stderr,"rval = %d\n",rval);*/
                 if ((rval == EOF) || (rval == 0))
@@ -665,7 +665,7 @@ int read_xvg_legend(const char *fn, double ***y, int *ny,
                 yy[k][nx] = lf;
                 srenew(fmt, 3*(nny+1)+1);
                 srenew(base, 3*nny+1);
-                strcat(base, "%*s");
+                std::strcat(base, "%*s");
             }
             if (k != nny)
             {