Merge branch 'master' into pygromacs

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_pme_error.cpp

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index b23a4d971fe12606f827eca82562c8559e75ad44..d7589f8b4d288ad9b984920abb43a55dc63daba7 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -36,6 +36,8 @@
 
 #include "config.h"
 
+#include <cmath>
+
 #include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
@@ -211,19 +213,19 @@ static inline real eps_poly1(
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += pow( tmp, -n );
+        nom += std::pow( tmp, -n );
     }
 
     for (i = SUMORDER; i > 0; i--)
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += pow( tmp, -n );
+        nom += std::pow( tmp, -n );
     }
 
     tmp   = m / K;
     tmp  *= 2.0*M_PI;
-    denom = pow( tmp, -n )+nom;
+    denom = std::pow( tmp, -n )+nom;
 
     return -nom/denom;
 
@@ -248,21 +250,21 @@ static inline real eps_poly2(
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += pow( tmp, -2*n );
+        nom += std::pow( tmp, -2*n );
     }
 
     for (i = SUMORDER; i > 0; i--)
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += pow( tmp, -2*n );
+        nom += std::pow( tmp, -2*n );
     }
 
     for (i = -SUMORDER; i < SUMORDER+1; i++)
     {
         tmp    = m / K + i;
         tmp   *= 2.0*M_PI;
-        denom += pow( tmp, -n );
+        denom += std::pow( tmp, -n );
     }
     tmp = eps_poly1(m, K, n);
     return nom / denom / denom + tmp*tmp;
@@ -288,21 +290,21 @@ static inline real eps_poly3(
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += i * pow( tmp, -2*n );
+        nom += i * std::pow( tmp, -2*n );
     }
 
     for (i = SUMORDER; i > 0; i--)
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += i * pow( tmp, -2*n );
+        nom += i * std::pow( tmp, -2*n );
     }
 
     for (i = -SUMORDER; i < SUMORDER+1; i++)
     {
         tmp    = m / K + i;
         tmp   *= 2.0*M_PI;
-        denom += pow( tmp, -n );
+        denom += std::pow( tmp, -n );
     }
 
     return 2.0 * M_PI * nom / denom / denom;
@@ -328,21 +330,21 @@ static inline real eps_poly4(
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += i * i * pow( tmp, -2*n );
+        nom += i * i * std::pow( tmp, -2*n );
     }
 
     for (i = SUMORDER; i > 0; i--)
     {
         tmp  = m / K + i;
         tmp *= 2.0*M_PI;
-        nom += i * i * pow( tmp, -2*n );
+        nom += i * i * std::pow( tmp, -2*n );
     }
 
     for (i = -SUMORDER; i < SUMORDER+1; i++)
     {
         tmp    = m / K + i;
         tmp   *= 2.0*M_PI;
-        denom += pow( tmp, -n );
+        denom += std::pow( tmp, -n );
     }
 
     return 4.0 * M_PI * M_PI * nom / denom / denom;
@@ -375,18 +377,18 @@ static inline real eps_self(
 
     for (i = -SUMORDER; i < 0; i++)
     {
-        tmp    = -sin(2.0 * M_PI * i * K * rcoord);
+        tmp    = -std::sin(2.0 * M_PI * i * K * rcoord);
         tmp1   = 2.0 * M_PI * m / K + 2.0 * M_PI * i;
-        tmp2   = pow(tmp1, -n);
+        tmp2   = std::pow(tmp1, -n);
         nom   += tmp * tmp2 * i;
         denom += tmp2;
     }
 
     for (i = SUMORDER; i > 0; i--)
     {
-        tmp    = -sin(2.0 * M_PI * i * K * rcoord);
+        tmp    = -std::sin(2.0 * M_PI * i * K * rcoord);
         tmp1   = 2.0 * M_PI * m / K + 2.0 * M_PI * i;
-        tmp2   = pow(tmp1, -n);
+        tmp2   = std::pow(tmp1, -n);
         nom   += tmp * tmp2 * i;
         denom += tmp2;
     }
@@ -491,7 +493,7 @@ static real estimate_reciprocal(
     xtot        = stopglobal*2+1;
     if (PAR(cr))
     {
-        x_per_core = static_cast<int>(ceil(static_cast<real>(xtot) / cr->nnodes));
+        x_per_core = static_cast<int>(std::ceil(static_cast<real>(xtot) / cr->nnodes));
         startlocal = startglobal + x_per_core*cr->nodeid;
         stoplocal  = startlocal + x_per_core -1;
         if (stoplocal > stopglobal)
@@ -543,7 +545,7 @@ static real estimate_reciprocal(
                 svmul(nz, info->recipbox[ZZ], tmpvec);
                 rvec_add(gridpxy, tmpvec, gridp);
                 tmp    = norm2(gridp);
-                coeff  = exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
+                coeff  = std::exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
                 coeff /= 2.0 * M_PI * info->volume * tmp;
                 coeff2 = tmp;
 
@@ -637,14 +639,14 @@ static real estimate_reciprocal(
         /* Here xtot is the number of samples taken for the Monte Carlo calculation
          * of the average of term IV of equation 35 in Wang2010. Round up to a
          * number of samples that is divisible by the number of nodes */
-        x_per_core  = static_cast<int>(ceil(info->fracself * nr / cr->nnodes));
+        x_per_core  = static_cast<int>(std::ceil(info->fracself * nr / cr->nnodes));
         xtot        = x_per_core * cr->nnodes;
     }
     else
     {
         /* In this case we use all nr particle positions */
         xtot       = nr;
-        x_per_core = static_cast<int>(ceil(static_cast<real>(xtot) / cr->nnodes));
+        x_per_core = static_cast<int>(std::ceil(static_cast<real>(xtot) / cr->nnodes));
     }
 
     startlocal = x_per_core *  cr->nodeid;
@@ -660,7 +662,7 @@ static real estimate_reciprocal(
         {
             for (i = 0; i < xtot; i++)
             {
-                numbers[i] = static_cast<int>(floor(gmx_rng_uniform_real(rng) * nr));
+                numbers[i] = static_cast<int>(std::floor(gmx_rng_uniform_real(rng) * nr));
             }
         }
         /* Broadcast the random number array to the other nodes */
@@ -720,7 +722,7 @@ static real estimate_reciprocal(
                     svmul(nz, info->recipbox[ZZ], tmpvec);
                     rvec_add(gridpxy, tmpvec, gridp);
                     tmp      = norm2(gridp);
-                    coeff    = exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
+                    coeff    = std::exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
                     coeff   /= tmp;
                     e_rec3x += coeff*eps_self(nx, info->nkx[0], info->recipbox[XX], info->pme_order[0], x[ci]);
                     e_rec3y += coeff*eps_self(ny, info->nky[0], info->recipbox[YY], info->pme_order[0], x[ci]);
@@ -782,7 +784,7 @@ static real estimate_reciprocal(
        e_rec2*=  q2_all / M_PI / M_PI / info->volume / info->volume / nr ;
        e_rec3/= M_PI * M_PI * info->volume * info->volume * nr ;
      */
-    e_rec = sqrt(e_rec1+e_rec2+e_rec3);
+    e_rec = std::sqrt(e_rec1+e_rec2+e_rec3);
 
 
     return ONE_4PI_EPS0 * e_rec;
@@ -1023,7 +1025,7 @@ static void estimate_PME_error(t_inputinfo *info, t_state *state,
         edir = info->e_dir[0];
         erec = info->e_rec[0];
         derr = edir-erec;
-        while (fabs(derr/std::min(erec, edir)) > 1e-4)
+        while (std::abs(derr/std::min(erec, edir)) > 1e-4)
         {
 
             beta                = info->ewald_beta[0];
@@ -1048,7 +1050,7 @@ static void estimate_PME_error(t_inputinfo *info, t_state *state,
             if (MASTER(cr))
             {
                 i++;
-                fprintf(stderr, "difference between real and rec. space error (step %d): %g\n", i, fabs(derr));
+                fprintf(stderr, "difference between real and rec. space error (step %d): %g\n", i, std::abs(derr));
                 fprintf(stderr, "old beta: %f\n", beta0);
                 fprintf(stderr, "new beta: %f\n", beta);
             }