Merge release-4-6 into release-5-0

Conflicts:
CMakeLists.txt (applied to cmake/gmxManageSharedLibraries.cmake)

Replaced gmx_llabs by llabs as mentioned in TODO.

Change-Id: I37e8cf5d6725cc9836e6dc29ca44e7ef915417c4

diff --git a/cmake/gmxManageSharedLibraries.cmake b/cmake/gmxManageSharedLibraries.cmake
index cc73de31b447636ff325072a75fc7a9daabf4116..fced521e952c7c254a6ae553b181c617a8385992 100644 (file)
--- a/cmake/gmxManageSharedLibraries.cmake
+++ b/cmake/gmxManageSharedLibraries.cmake
@@ -39,7 +39,7 @@
 ########################################################################
 # Determine the defaults (this block has no effect if the variables have
 # already been set)
-if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD") AND NOT GMX_BUILD_MDRUN_ONLY)
+if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU") AND NOT GMX_BUILD_MDRUN_ONLY)
     # Maybe Solaris should be here? Patch this if you know!
     SET(SHARED_LIBS_DEFAULT ON)
 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")

diff --git a/src/gromacs/fileio/libxdrf.c b/src/gromacs/fileio/libxdrf.c
index 219e64ead90b2e339e186640d2250d39b820eaa5..14c750190067f0181998b79d4d972f06d210c32a 100644 (file)
--- a/src/gromacs/fileio/libxdrf.c
+++ b/src/gromacs/fileio/libxdrf.c
@@ -1345,7 +1345,6 @@ xdr_xtc_estimate_dt(FILE *fp, XDR *xdrs, int natoms, gmx_bool * bOK)
     return res;
 }
 
-
 int
 xdr_xtc_seek_frame(int frame, FILE *fp, XDR *xdrs, int natoms)
 {
@@ -1383,7 +1382,7 @@ xdr_xtc_seek_frame(int frame, FILE *fp, XDR *xdrs, int natoms)
         {
             return -1;
         }
-        if (fr != frame && abs(low-high) > header_size)
+        if (fr != frame && llabs(low-high) > header_size)
         {
             if (fr < frame)
             {
@@ -1517,10 +1516,9 @@ int xdr_xtc_seek_time(real time, FILE *fp, XDR *xdrs, int natoms, gmx_bool bSeek
            the current time and the target time is bigger than dt and above all the distance between high
            and low is bigger than 1 frame, then do another step of binary search. Otherwise stop and check
            if we reached the solution */
-        if ((((t < time && dt_sign >= 0) || (t > time && dt_sign == -1)) || ((t
-                                                                              - time) >= dt && dt_sign >= 0)
-             || ((time - t) >= -dt && dt_sign < 0)) && (abs(low - high)
-                                                        > header_size))
+        if ((((t < time && dt_sign >= 0) || (t > time && dt_sign == -1)) ||
+             ((t - time) >= dt && dt_sign >= 0) || ((time - t) >= -dt && dt_sign < 0)) &&
+            (llabs(low - high) > header_size))
         {
             if (dt >= 0 && dt_sign != -1)
             {
@@ -1558,7 +1556,7 @@ int xdr_xtc_seek_time(real time, FILE *fp, XDR *xdrs, int natoms, gmx_bool bSeek
         }
         else
         {
-            if (abs(low - high) <= header_size)
+            if (llabs(low - high) <= header_size)
             {
                 break;
             }

diff --git a/src/gromacs/gmxana/geminate.c b/src/gromacs/gmxana/geminate.c
index 79dc949fd34513b316c3684b7de219dde6fb8751..a9ee8113de24ba2119bab8c271d90ef89d61d8a7 100644 (file)
--- a/src/gromacs/gmxana/geminate.c
+++ b/src/gromacs/gmxana/geminate.c
@@ -716,10 +716,10 @@ extern void fixGemACF(double *ct, int len)
     bBad = FALSE;
 
     /* An acf of binary data must be one at t=0. */
-    if (abs(ct[0]-1.0) > 1e-6)
+    if (fabs(ct[0]-1.0) > 1e-6)
     {
         ct[0] = 1.0;
-        fprintf(stderr, "|ct[0]-1.0| = %1.6d. Setting ct[0] to 1.0.\n", abs(ct[0]-1.0));
+        fprintf(stderr, "|ct[0]-1.0| = %1.6f. Setting ct[0] to 1.0.\n", fabs(ct[0]-1.0));
     }
 
     for (i = 0; i < len; i++)

diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index f59b1130d807e8be4ecea627030dfd60ed670c1a..053e9c585ffde54f6ed2589769737327db30d6b2 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -257,7 +257,7 @@ static void write_xvgr_graphs(const char *file, int ngraphs, int nsetspergraph,
         {
             for (i = 0; i < n; i++)
             {
-                if (bSplit && i > 0 && abs(x[i]) < 1e-5)
+                if (bSplit && i > 0 && fabs(x[i]) < 1e-5)
                 {
                     if (output_env_get_print_xvgr_codes(oenv))
                     {
@@ -670,7 +670,7 @@ static void project(const char *trajfile, t_topology *top, int ePBC, matrix topb
                            oenv);
         for (i = 0; i < nframes; i++)
         {
-            if (bSplit && i > 0 && abs(inprod[noutvec][i]) < 1e-5)
+            if (bSplit && i > 0 && fabs(inprod[noutvec][i]) < 1e-5)
             {
                 fprintf(xvgrout, "&\n");
             }
@@ -758,7 +758,7 @@ static void project(const char *trajfile, t_topology *top, int ePBC, matrix topb
             j = 0;
             for (i = 0; i < atoms.nr; i++)
             {
-                if (j > 0 && bSplit && abs(inprod[noutvec][i]) < 1e-5)
+                if (j > 0 && bSplit && fabs(inprod[noutvec][i]) < 1e-5)
                 {
                     fprintf(out, "TER\n");
                     j = 0;

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index c706b40be5b1c35159b77c012b2c4ca38f57ba81..ec1a988f5d85c8713b2ca3580f575d0be8be1b03 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -138,7 +138,7 @@ static gmx_bool precalc(t_topology top, real mass2[], real qmol[])
         }
     }
 
-    if (abs(qall) > 0.01)
+    if (fabs(qall) > 0.01)
     {
         printf("\n\nSystem not neutral (q=%f) will not calculate translational part of the dipole moment.\n", qall);
         bNEU = FALSE;

diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 2ec58643ef35908043df659bd21c36d58905c1b3..311e3d687365422e2222e2d0eb08d85e9339cef3 100644 (file)
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -170,7 +170,7 @@ static void periodic_mindist_plot(const char *trxfn, const char *outfn,
             ind_mini = ind_min[0];
             ind_minj = ind_min[1];
         }
-        if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
+        if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
         {
             fprintf(out, "&\n");
         }
@@ -421,7 +421,7 @@ void dist_plot(const char *fn, const char *afile, const char *dfile,
     bFirst = TRUE;
     do
     {
-        if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
+        if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
         {
             fprintf(dist, "&\n");
             if (num)

diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 13aeb6c807a88773a68b382568b3ee7dbaf598c3..3962646be66226b11eadeef7d569ae65025032c9 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -1135,7 +1135,7 @@ int gmx_rms(int argc, char *argv[])
     for (i = 0; (i < teller); i++)
     {
         if (bSplit && i > 0 &&
-            abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
+            fabs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
         {
             fprintf(fp, "&\n");
         }
@@ -1177,7 +1177,7 @@ int gmx_rms(int argc, char *argv[])
         }
         for (i = 0; (i < teller); i++)
         {
-            if (bSplit && i > 0 && abs(time[i]) < 1e-5)
+            if (bSplit && i > 0 && fabs(time[i]) < 1e-5)
             {
                 fprintf(fp, "&\n");
             }

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
index 064e667c3c4806806378c1011f6440aae18874f3..d8c5ebe56de890b9be68e5172beb32129307dc0a 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.c
+++ b/src/gromacs/gmxana/gmx_xpm2ps.c
@@ -523,8 +523,8 @@ static void draw_zerolines(t_psdata out, real x0, real y0, real w,
                 xx = xx00+(x+0.7)*psr->xboxsize;
                 /* draw lines whenever tick label almost zero (e.g. next trajectory) */
                 if (x != 0 && x < mat[i].nx-1 &&
-                    abs(mat[i].axis_x[x]) <
-                    0.1*abs(mat[i].axis_x[x+1]-mat[i].axis_x[x]) )
+                    fabs(mat[i].axis_x[x]) <
+                    0.1*fabs(mat[i].axis_x[x+1]-mat[i].axis_x[x]) )
                 {
                     ps_line (out, xx, yy00, xx, yy00+dy+2);
                 }
@@ -538,8 +538,8 @@ static void draw_zerolines(t_psdata out, real x0, real y0, real w,
                 yy = yy00+(y+0.7)*psr->yboxsize;
                 /* draw lines whenever tick label almost zero (e.g. next trajectory) */
                 if (y != 0 && y < mat[i].ny-1 &&
-                    abs(mat[i].axis_y[y]) <
-                    0.1*abs(mat[i].axis_y[y+1]-mat[i].axis_y[y]) )
+                    fabs(mat[i].axis_y[y]) <
+                    0.1*fabs(mat[i].axis_y[y+1]-mat[i].axis_y[y]) )
                 {
                     ps_line (out, xx00, yy, xx00+w+2, yy);
                 }
@@ -1135,7 +1135,7 @@ void zero_lines(int nmat, t_matrix *mat, t_matrix *mat2)
             }
             for (x = 0; x < mats[i].nx-1; x++)
             {
-                if (abs(mats[i].axis_x[x+1]) < 1e-5)
+                if (fabs(mats[i].axis_x[x+1]) < 1e-5)
                 {
                     for (y = 0; y < mats[i].ny; y++)
                     {
@@ -1145,7 +1145,7 @@ void zero_lines(int nmat, t_matrix *mat, t_matrix *mat2)
             }
             for (y = 0; y < mats[i].ny-1; y++)
             {
-                if (abs(mats[i].axis_y[y+1]) < 1e-5)
+                if (fabs(mats[i].axis_y[y+1]) < 1e-5)
                 {
                     for (x = 0; x < mats[i].nx; x++)
                     {