Moved tools files to C++

Added extern-c declarations to gmxcpp.h for calling
from the new C++ source.

Change-Id: I7b21398808a1d58849bff44690ece4d1f4e9db04

diff --git a/src/gromacs/gmxpreprocess/gmxcpp.h b/src/gromacs/gmxpreprocess/gmxcpp.h
index 5488a220cf2c13cf285715fa173e4ac3b0ae800c..035fdc56e9ac943c6a86c05ee1f156090ef01207 100644 (file)
--- a/src/gromacs/gmxpreprocess/gmxcpp.h
+++ b/src/gromacs/gmxpreprocess/gmxcpp.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015, 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.
@@ -37,6 +37,11 @@
 
 #ifndef GMX_GMXPREPROCESS_GMXCPP_H
 #define GMX_GMXPREPROCESS_GMXCPP_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef struct gmx_cpp *gmx_cpp_t;
 
 /* The possible return codes for these functions */
@@ -93,4 +98,9 @@ void cpp_done();
    NOT THREAD SAFE
  */
 char *cpp_error(gmx_cpp_t *handlep, int status);
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

diff --git a/src/gromacs/tools/CMakeLists.txt b/src/gromacs/tools/CMakeLists.txt
index ceec518fe6a0b676c3bdbaae0d708bbe3c511021..061fcf2168067e3762951214c67d1e13c90dc179 100644 (file)
--- a/src/gromacs/tools/CMakeLists.txt
+++ b/src/gromacs/tools/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 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.
@@ -32,7 +32,7 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
-file(GLOB TOOLS_SOURCES *.cpp *.c)
+file(GLOB TOOLS_SOURCES *.cpp)
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOOLS_SOURCES} PARENT_SCOPE)
 
 if (BUILD_TESTING)

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.cpp
similarity index 97%
rename from src/gromacs/tools/check.c
rename to src/gromacs/tools/check.cpp
index d54b84ce1408df1de6d8933bd9a2eacfc6d598f6..cc19905b072b0d06a8d053070335c61e36d3908d 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.cpp
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
@@ -85,7 +85,7 @@ typedef struct {
 
 static void tpx2system(FILE *fp, gmx_mtop_t *mtop)
 {
-    int                       i, nmol, nvsite = 0;
+    int                       nmol, nvsite = 0;
     gmx_mtop_atomloop_block_t aloop;
     t_atom                   *atom;
 
@@ -144,7 +144,6 @@ static void tpx2params(FILE *fp, t_inputrec *ir)
 static void tpx2methods(const char *tpx, const char *tex)
 {
     FILE         *fp;
-    t_tpxheader   sh;
     t_inputrec    ir;
     t_state       state;
     gmx_mtop_t    mtop;
@@ -223,12 +222,11 @@ static void chk_forces(int frame, int natoms, rvec *f)
 
 static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol)
 {
-    int   ftype, i, k, ai, aj, type;
-    real  b0, blen, deviation, devtot;
+    int   ftype, k, ai, aj, type;
+    real  b0, blen, deviation;
     t_pbc pbc;
     rvec  dx;
 
-    devtot = 0;
     set_pbc(&pbc, ePBC, box);
     for (ftype = 0; (ftype < F_NRE); ftype++)
     {
@@ -246,7 +244,7 @@ static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol)
                         b0 = idef->iparams[type].harmonic.rA;
                         break;
                     case F_G96BONDS:
-                        b0 = sqrt(idef->iparams[type].harmonic.rA);
+                        b0 = std::sqrt(idef->iparams[type].harmonic.rA);
                         break;
                     case F_MORSE:
                         b0 = idef->iparams[type].morse.b0A;
@@ -265,7 +263,7 @@ static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol)
                     pbc_dx(&pbc, x[ai], x[aj], dx);
                     blen      = norm(dx);
                     deviation = sqr(blen-b0);
-                    if (sqrt(deviation/sqr(b0) > tol))
+                    if (std::sqrt(deviation/sqr(b0)) > tol)
                     {
                         fprintf(stderr, "Distance between atoms %d and %d is %.3f, should be %.3f\n", ai+1, aj+1, blen, b0);
                     }
@@ -281,8 +279,8 @@ void chk_trj(const output_env_t oenv, const char *fn, const char *tpr, real tol)
     t_count          count;
     t_fr_time        first, last;
     int              j = -1, new_natoms, natoms;
-    real             rdum, tt, old_t1, old_t2, prec;
-    gmx_bool         bShowTimestep = TRUE, bOK, newline = FALSE;
+    real             old_t1, old_t2;
+    gmx_bool         bShowTimestep = TRUE, newline = FALSE;
     t_trxstatus     *status;
     gmx_mtop_t       mtop;
     gmx_localtop_t  *top = NULL;
@@ -549,7 +547,7 @@ void chk_tps(const char *fn, real vdw_fac, real bon_lo, real bon_hi)
                             *(atoms->resinfo[atoms->atom[j].resind].name),
                             atoms->resinfo[atoms->atom[j].resind].nr,
                             atom_vdw[j],
-                            sqrt(r2) );
+                            std::sqrt(r2) );
                 }
             }
         }
@@ -616,7 +614,7 @@ void chk_ndx(const char *fn)
 {
     t_blocka *grps;
     char    **grpname;
-    int       i, j;
+    int       i;
 
     grps = init_index(fn, &grpname);
     if (debug)
@@ -646,7 +644,7 @@ void chk_ndx(const char *fn)
 
 void chk_enx(const char *fn)
 {
-    int            nre, fnr, ndr;
+    int            nre, fnr;
     ener_file_t    in;
     gmx_enxnm_t   *enm = NULL;
     t_enxframe    *fr;

diff --git a/src/gromacs/tools/check.h b/src/gromacs/tools/check.h
index 3eb6acd56f68f3112be85e6e1a6269a7ac4a00d5..435cd0d88ad0cd918827208e96a2ad6efb88109f 100644 (file)
--- a/src/gromacs/tools/check.h
+++ b/src/gromacs/tools/check.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -35,13 +35,6 @@
 #ifndef GMX_TOOLS_CHECK_H
 #define GMX_TOOLS_CHECK_H
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
 /*! \brief Implements gmx check
  *
  * \param[in] argc  argc value passed to main().
@@ -49,8 +42,4 @@ extern "C" {
  */
 int gmx_check(int argc, char *argv[]);
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.cpp
similarity index 96%
rename from src/gromacs/tools/compare.c
rename to src/gromacs/tools/compare.cpp
index 975b62f53697e3e5335b22f24e159683cef54754..bdbd351d3157bcb5d12b36c49ba5e89678386014 100644 (file)
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.cpp
@@ -35,11 +35,14 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 /* This file is completely threadsafe - keep it that way! */
+
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
@@ -73,9 +76,9 @@ static void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2)
     if (i1 != i2)
     {
         fprintf(fp, "%s (", s);
-        fprintf(fp, "%"GMX_PRId64, i1);
+        fprintf(fp, "%" GMX_PRId64, i1);
         fprintf(fp, " - ");
-        fprintf(fp, "%"GMX_PRId64, i2);
+        fprintf(fp, "%" GMX_PRId64, i2);
         fprintf(fp, ")\n");
     }
 }
@@ -147,7 +150,7 @@ static gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bo
 static void cmp_str(FILE *fp, const char *s, int index,
                     const char *s1, const char *s2)
 {
-    if (strcmp(s1, s2) != 0)
+    if (std::strcmp(s1, s2) != 0)
     {
         if (index != -1)
         {
@@ -347,7 +350,7 @@ static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol)
     {
         cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes);
         cmp_int(fp, "idef->atnr",  -1, id1->atnr, id2->atnr);
-        for (i = 0; (i < min(id1->ntypes, id2->ntypes)); i++)
+        for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++)
         {
             sprintf(buf1, "idef->functype[%d]", i);
             sprintf(buf2, "idef->iparam[%d]", i);
@@ -372,7 +375,6 @@ static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol)
 
 static void cmp_block(FILE *fp, t_block *b1, t_block *b2, const char *s)
 {
-    int  i, j, k;
     char buf[32];
 
     fprintf(fp, "comparing block %s\n", s);
@@ -382,7 +384,6 @@ static void cmp_block(FILE *fp, t_block *b1, t_block *b2, const char *s)
 
 static void cmp_blocka(FILE *fp, t_blocka *b1, t_blocka *b2, const char *s)
 {
-    int  i, j, k;
     char buf[32];
 
     fprintf(fp, "comparing blocka %s\n", s);
@@ -394,9 +395,6 @@ static void cmp_blocka(FILE *fp, t_blocka *b1, t_blocka *b2, const char *s)
 
 static void cmp_atom(FILE *fp, int index, t_atom *a1, t_atom *a2, real ftol, real abstol)
 {
-    int  i;
-    char buf[256];
-
     if (a2)
     {
         cmp_us(fp, "atom.type", index, a1->type, a2->type);
@@ -442,8 +440,6 @@ static void cmp_atoms(FILE *fp, t_atoms *a1, t_atoms *a2, real ftol, real abstol
 
 static void cmp_top(FILE *fp, t_topology *t1, t_topology *t2, real ftol, real abstol)
 {
-    int i;
-
     fprintf(fp, "comparing top\n");
     if (t2)
     {
@@ -464,7 +460,7 @@ static void cmp_top(FILE *fp, t_topology *t1, t_topology *t2, real ftol, real ab
 static void cmp_groups(FILE *fp, gmx_groups_t *g0, gmx_groups_t *g1,
                        int natoms0, int natoms1)
 {
-    int  i, j, ndiff;
+    int  i, j;
     char buf[32];
 
     fprintf(fp, "comparing groups\n");
@@ -515,7 +511,7 @@ static void cmp_rvecs(FILE *fp, const char *title, int n, rvec x1[], rvec x2[],
                 ssd += d*d;
             }
         }
-        fprintf(fp, "%s RMSD %g\n", title, sqrt(ssd/n));
+        fprintf(fp, "%s RMSD %g\n", title, std::sqrt(ssd/n));
     }
     else
     {
@@ -562,7 +558,7 @@ static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, rvec x1[], rvec
             rms_x1 += d*d;
         }
     }
-    rms_x1 = sqrt(rms_x1/(DIM*n));
+    rms_x1 = std::sqrt(rms_x1/(DIM*n));
     /* And now do the actual comparision with a hopefully realistic abstol. */
     for (i = 0; (i < n); i++)
     {
@@ -579,7 +575,7 @@ static void cmp_grpopts(FILE *fp, t_grpopts *opt1, t_grpopts *opt2, real ftol, r
     cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
     cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
     cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
-    for (i = 0; (i < min(opt1->ngtc, opt2->ngtc)); i++)
+    for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
     {
         cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
         cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
@@ -611,11 +607,11 @@ static void cmp_grpopts(FILE *fp, t_grpopts *opt1, t_grpopts *opt2, real ftol, r
             }
         }
     }
-    for (i = 0; (i < min(opt1->ngacc, opt2->ngacc)); i++)
+    for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
     {
         cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
     }
-    for (i = 0; (i < min(opt1->ngfrz, opt2->ngfrz)); i++)
+    for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
     {
         cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
     }
@@ -630,7 +626,7 @@ static void cmp_cosines(FILE *fp, const char *s, t_cosines c1[DIM], t_cosines c2
     {
         sprintf(buf, "inputrec->%s[%d]", s, m);
         cmp_int(fp, buf, 0, c1->n, c2->n);
-        for (i = 0; (i < min(c1->n, c2->n)); i++)
+        for (i = 0; (i < std::min(c1->n, c2->n)); i++)
         {
             cmp_real(fp, buf, i, c1->a[i], c2->a[i], ftol, abstol);
             cmp_real(fp, buf, i, c1->phi[i], c2->phi[i], ftol, abstol);
@@ -712,7 +708,7 @@ static void cmp_fepvals(FILE *fp, t_lambda *fep1, t_lambda *fep2, real ftol, rea
     cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
     for (i = 0; i < efptNR; i++)
     {
-        for (j = 0; j < min(fep1->n_lambda, fep2->n_lambda); j++)
+        for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
         {
             cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol);
         }
@@ -822,12 +818,12 @@ static void cmp_inputrec(FILE *fp, t_inputrec *ir1, t_inputrec *ir2, real ftol,
     cmp_int(fp, "inputrec->bSimTemp", -1, ir1->bSimTemp, ir2->bSimTemp);
     if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
     {
-        cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+        cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
     }
     cmp_int(fp, "inputrec->bExpanded", -1, ir1->bExpanded, ir2->bExpanded);
     if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
     {
-        cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+        cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
     }
     cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
     cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
@@ -976,7 +972,6 @@ void comp_tpx(const char *fn1, const char *fn2,
               gmx_bool bRMSD, real ftol, real abstol)
 {
     const char  *ff[2];
-    t_tpxheader  sh[2];
     t_inputrec   ir[2];
     t_state      state[2];
     gmx_mtop_t   mtop[2];
@@ -1060,21 +1055,21 @@ void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
     }
     if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX))
     {
-        cmp_rvecs(fp, "x", min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol);
+        cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol);
     }
     if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV))
     {
-        cmp_rvecs(fp, "v", min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol);
+        cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol);
     }
     if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF))
     {
         if (bRMSD)
         {
-            cmp_rvecs(fp, "f", min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol);
+            cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol);
         }
         else
         {
-            cmp_rvecs_rmstol(fp, "f", min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, ftol, abstol);
+            cmp_rvecs_rmstol(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, ftol, abstol);
         }
     }
     if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox))
@@ -1133,25 +1128,25 @@ static real ener_tensor_diag(int n, int *ind1, int *ind2,
                              int *tensi, int i,
                              t_energy e1[], t_energy e2[])
 {
-    int  d1, d2;
-    int  len;
-    int  j;
-    real prod1, prod2;
-    int  nfound;
+    int    d1, d2;
+    int    j;
+    real   prod1, prod2;
+    int    nfound;
+    size_t len;
 
     d1 = tensi[i]/DIM;
     d2 = tensi[i] - d1*DIM;
 
     /* Find the diagonal elements d1 and d2 */
-    len    = strlen(enm1[ind1[i]].name);
+    len    = std::strlen(enm1[ind1[i]].name);
     prod1  = 1;
     prod2  = 1;
     nfound = 0;
     for (j = 0; j < n; j++)
     {
         if (tensi[j] >= 0 &&
-            strlen(enm1[ind1[j]].name) == len &&
-            strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 &&
+            std::strlen(enm1[ind1[j]].name) == len &&
+            std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 &&
             (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2))
         {
             prod1 *= fabs(e1[ind1[j]].e);
@@ -1162,7 +1157,7 @@ static real ener_tensor_diag(int n, int *ind1, int *ind2,
 
     if (nfound == 2)
     {
-        return 0.5*(sqrt(prod1) + sqrt(prod2));
+        return 0.5*(std::sqrt(prod1) + std::sqrt(prod2));
     }
     else
     {
@@ -1174,15 +1169,15 @@ static gmx_bool enernm_equal(const char *nm1, const char *nm2)
 {
     int len1, len2;
 
-    len1 = strlen(nm1);
-    len2 = strlen(nm2);
+    len1 = std::strlen(nm1);
+    len2 = std::strlen(nm2);
 
     /* Remove " (bar)" at the end of a name */
-    if (len1 > 6 && strcmp(nm1+len1-6, " (bar)") == 0)
+    if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0)
     {
         len1 -= 6;
     }
-    if (len2 > 6 && strcmp(nm2+len2-6, " (bar)") == 0)
+    if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0)
     {
         len2 -= 6;
     }
@@ -1206,7 +1201,7 @@ static void cmp_energies(FILE *fp, int step1, int step2,
     {
         ii       = ind1[i];
         tensi[i] = -1;
-        len      = strlen(enm1[ii].name);
+        len      = std::strlen(enm1[ii].name);
         if (len > 3 && enm1[ii].name[len-3] == '-')
         {
             d1 = enm1[ii].name[len-2] - 'X';
@@ -1238,7 +1233,7 @@ static void cmp_energies(FILE *fp, int step1, int step2,
             if (abstol_i > 0)
             {
                 /* We found a diagonal, we need to check with the minimum tolerance */
-                abstol_i = min(abstol_i, abstol);
+                abstol_i = std::min(abstol_i, abstol);
             }
             else
             {
@@ -1374,10 +1369,9 @@ static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol
 
 void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener)
 {
-    int            nre, nre1, nre2, block;
+    int            nre, nre1, nre2;
     ener_file_t    in1, in2;
     int            i, j, maxener, *ind1, *ind2, *have;
-    char           buf[256];
     gmx_enxnm_t   *enm1 = NULL, *enm2 = NULL;
     t_enxframe    *fr1, *fr2;
     gmx_bool       b1, b2;
@@ -1431,7 +1425,7 @@ void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const ch
     maxener = nre;
     for (i = 0; i < nre; i++)
     {
-        if ((lastener != NULL) && (strstr(enm1[i].name, lastener) != NULL))
+        if ((lastener != NULL) && (std::strstr(enm1[i].name, lastener) != NULL))
         {
             maxener = i+1;
             break;

diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.cpp
similarity index 98%
rename from src/gromacs/tools/convert_tpr.c
rename to src/gromacs/tools/convert_tpr.cpp
index ff2fd1044719719d083a14534f8da82df4c32f86..696f61c20289b3a56dcf575a392e33062d06cbbd 100644 (file)
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
+#include <cmath>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/enxio.h"
@@ -360,8 +360,7 @@ int gmx_convert_tpr(int argc, char *argv[])
     gmx_bool          bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
     gmx_mtop_t        mtop;
     t_atoms           atoms;
-    t_inputrec       *ir, *irnew = NULL;
-    t_gromppopts     *gopts;
+    t_inputrec       *ir;
     t_state           state;
     rvec             *newx = NULL, *newv = NULL, *tmpx, *tmpv;
     matrix            newbox;
@@ -405,7 +404,6 @@ int gmx_convert_tpr(int argc, char *argv[])
         { "-init_fep_state", FALSE, etINT, {&init_fep_state},
           "fep state to initialize from" },
     };
-    int             nerror = 0;
 
     /* Parse the command line */
     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
@@ -467,9 +465,9 @@ int gmx_convert_tpr(int argc, char *argv[])
 
         if (EI_SD(ir->eI) || ir->eI == eiBD)
         {
-            fprintf(stderr, "\nChanging ld-seed from %"GMX_PRId64 " ", ir->ld_seed);
+            fprintf(stderr, "\nChanging ld-seed from %" GMX_PRId64 " ", ir->ld_seed);
             ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
-            fprintf(stderr, "to %"GMX_PRId64 "\n\n", ir->ld_seed);
+            fprintf(stderr, "to %" GMX_PRId64 "\n\n", ir->ld_seed);
         }
 
         frame_fn = ftp2fn(efTRN, NFILE, fnm);

diff --git a/src/gromacs/tools/convert_tpr.h b/src/gromacs/tools/convert_tpr.h
index bb7fc46c445bb55f2f4219956b5eea05451a3ece..23c52ffa7e3ceff1cf8163e6fc502e05b99968fa 100644 (file)
--- a/src/gromacs/tools/convert_tpr.h
+++ b/src/gromacs/tools/convert_tpr.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -35,13 +35,6 @@
 #ifndef GMX_TOOLS_CONVERT_TPR_H
 #define GMX_TOOLS_CONVERT_TPR_H
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
 /*! \brief Implements gmx convert-tpr
  *
  * \param[in] argc  argc value passed to main().
@@ -49,8 +42,4 @@ extern "C" {
  */
 int gmx_convert_tpr(int argc, char *argv[]);
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.cpp
similarity index 98%
rename from src/gromacs/tools/dump.c
rename to src/gromacs/tools/dump.cpp
index 76dd6f7df7dac4bd19899a80646ec63caa663166..d9b20863d961305c046d3dc13fb2d1adca760c2c 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.cpp
@@ -38,10 +38,10 @@
 
 #include "config.h"
 
-#include <assert.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cassert>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/enxio.h"
@@ -67,7 +67,7 @@ static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
                      gmx_bool bSysTop)
 {
     FILE         *gp;
-    int           fp, indent, i, j, **gcount, atot;
+    int           indent, i, j, **gcount, atot;
     t_state       state;
     rvec         *f = NULL;
     t_inputrec    ir;
@@ -100,10 +100,9 @@ static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
         if (available(stdout, &tpx, 0, fn))
         {
             indent = 0;
-            indent = pr_title(stdout, indent, fn);
+            pr_title(stdout, indent, fn);
             pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL, FALSE);
 
-            indent = 0;
             pr_header(stdout, indent, "header", &(tpx));
 
             if (!bSysTop)
@@ -419,13 +418,11 @@ void list_trx(const char *fn)
 
 void list_ene(const char *fn)
 {
-    int            ndr;
     ener_file_t    in;
     gmx_bool       bCont;
     gmx_enxnm_t   *enm = NULL;
     t_enxframe    *fr;
     int            i, j, nre, b;
-    real           rav, minthird;
     char           buf[22];
 
     printf("gmx dump: %s\n", fn);
@@ -439,7 +436,6 @@ void list_ene(const char *fn)
         printf("%5d  %-24s (%s)\n", i, enm[i].name, enm[i].unit);
     }
 
-    minthird = -1.0/3.0;
     snew(fr, 1);
     do
     {

diff --git a/src/gromacs/tools/dump.h b/src/gromacs/tools/dump.h
index cf0195e1e3f3379586942d8bfa602983a0a0e100..c1457d097e506da4862c8f283d4ae45cb334b8ef 100644 (file)
--- a/src/gromacs/tools/dump.h
+++ b/src/gromacs/tools/dump.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -35,13 +35,6 @@
 #ifndef GMX_TOOLS_DUMP_H
 #define GMX_TOOLS_DUMP_H
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
 /*! \brief Implements gmx dump
  *
  * \param[in] argc  argc value passed to main().
@@ -49,8 +42,4 @@ extern "C" {
  */
 int gmx_dump(int argc, char *argv[]);
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif