use std:: for some math functions

Diagnostics/DustCollapse/main.cpp

@@ -105,15 +105,15 @@ int main(int argc, char* argv[])
         auto x_maxdist = fmax(fabs(problo[0]), fabs(probhi[0]));
         auto y_maxdist = fmax(fabs(problo[1] - yctr), fabs(probhi[1] - yctr));
 
-        auto max_dist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
+        auto max_dist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
 
         int nbins = int(max_dist / dx_fine);
 #else
-        auto x_maxdist = fmax(fabs(problo[0] - xctr), fabs(probhi[0] - xctr));
-        auto y_maxdist = fmax(fabs(problo[1] - yctr), fabs(probhi[1] - yctr));
-        auto z_maxdist = fmax(fabs(problo[2] - zctr), fabs(probhi[2] - zctr));
+        auto x_maxdist = std::max(std::abs(problo[0] - xctr), std::abs(probhi[0] - xctr));
+        auto y_maxdist = std::max(std::abs(problo[1] - yctr), std::abs(probhi[1] - yctr));
+        auto z_maxdist = std::max(std::abs(problo[2] - zctr), std::abs(probhi[2] - zctr));
 
-        auto max_dist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist +
+        auto max_dist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist +
                              z_maxdist*z_maxdist);
 
         int nbins = int(max_dist / dx_fine);
@@ -147,7 +147,7 @@ int main(int argc, char* argv[])
         // over levels, we will compare to the finest level index space to
         // determine if we've already output here
         int mask_size = domain.length().max();
-        Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+        Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
         // counter
         int cnt = 0;

Diagnostics/Radiation/gaussian_pulse.cpp

@@ -64,9 +64,9 @@ int main(int argc, char* argv[])
 
     // compute the size of the radially-binned array -- we'll do it to
     // the furtherest corner of the domain
-    double x_maxdist = max(fabs(probhi[0] - xctr), fabs(problo[0] - xctr));
-    double y_maxdist = max(fabs(probhi[1] - yctr), fabs(problo[1] - yctr));
-    double maxdist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
+    double x_maxdist = std::max(std::abs(probhi[0] - xctr), std::abs(problo[0] - xctr));
+    double y_maxdist = std::max(std::abs(probhi[1] - yctr), std::abs(problo[1] - yctr));
+    double maxdist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
 
     double dx_fine = *(std::min_element(dx.begin(), dx.end()));
 
@@ -102,7 +102,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // loop over the data, starting at the finest grid, and if we haven't
     // already stored data in that grid location (according to imask),

Diagnostics/Radiation/lgt_frnt1d.cpp

@@ -93,7 +93,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // loop over the data, starting at the finest grid, and if we haven't
     // already stored data in that grid location (according to imask),

Diagnostics/Radiation/rad_shock.cpp

@@ -106,7 +106,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // counter
     auto cnt = 0;
@@ -214,7 +214,7 @@ int main(int argc, char* argv[])
             slicefile << std::setw(w) << vars_bin[isv[i]+((*it)+1)*nbins];
 
         auto it = comps.end()-1;
-        slicefile << std::setw(w) << pow(vars_bin[isv[i]+((*it)+1)*nbins] / arad, 0.25);
+        slicefile << std::setw(w) << std::pow(vars_bin[isv[i]+((*it)+1)*nbins] / arad, 0.25);
 
         slicefile << std::endl;
     }

Diagnostics/Radiation/rad_sphere.cpp

@@ -142,7 +142,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length()[0];
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // counter
     int cnt = 0;

Exec/science/nova/problem_initialize_state_data.H

@@ -121,10 +121,10 @@ void problem_initialize_state_data (int i, int j, int k,
 
         if (problem::num_vortices % 2 == 0){
             temp_pert = delta * (1.0_rt + std::sin(static_cast<Real>(problem::num_vortices)*M_PI*x/problem::L) )*
-                                    delta*exp(-pow(ydist / problem::width, 2));
+                                    delta*std::exp(-pow(ydist / problem::width, 2));
         } else {
             temp_pert = delta * (1.0_rt + std::cos(static_cast<Real>(problem::num_vortices)*M_PI*x/problem::L) )*
-                                     delta*exp(-pow(ydist / problem::width, 2));
+                                     delta*std::exp(-pow(ydist / problem::width, 2));
         }
 
         state(i,j,k,UTEMP)  = state(i,j,k, UTEMP)*(1.0_rt + temp_pert);

Exec/science/planet/HotJupiter.cpp

@@ -19,10 +19,10 @@ long double Temp(long double P1,long double Pc,long double P_char,long double T_
   long double Temp;
 
   if(Pc>P1){
-    Temp = Td * pow(1.0e0 + (Lad / (Lin - Lad))*pow((P1/Pc),exp1),exp2);
+    Temp = Td * std::pow(1.0e0 + (Lad / (Lin - Lad)) * std::pow((P1/Pc),exp1),exp2);
   }
   else{
-    Temp = T_char * pow(P1/P_char,Lad);
+    Temp = T_char * std::pow(P1/P_char,Lad);
   }
   return Temp;
 }
@@ -95,9 +95,9 @@ int main(){
   //Defining the properties of the planet atmosphere
                             // the density limit at the top of the atmosphere
   P_top=den_top*R*Td ;                       // the pressure limit at the density limit
-  Tc = Td * pow(Lin/(Lin-Lad),exp2);                 //the temperature at the radiative-convective boundary (RCB)
-  Pc = P_char * pow(Tc/T_char,1.0/Lad);              //the pressure at the RCB
-  Pd = pow((Lin-Lad)/(2.0*Lin-Lad),1.0/exp1)*Pc;     //the characteristic pressure defining the radiative zone
+  Tc = Td * std::pow(Lin/(Lin-Lad),exp2);                 //the temperature at the radiative-convective boundary (RCB)
+  Pc = P_char * std::pow(Tc/T_char,1.0/Lad);              //the pressure at the RCB
+  Pd = std::pow((Lin-Lad)/(2.0*Lin-Lad),1.0/exp1)*Pc;     //the characteristic pressure defining the radiative zone
 
 
 
@@ -112,7 +112,7 @@ int main(){
   }
 
   buffer_height=z_top*2.25/4.0;               // the height at which the buffer and the top of the atmosphere meet (not continuous at RCB).-> needs sponge
-  optical_depth_buffer=6.35e-3*T_buffer*pow(den_buffer,2.0)*(z_top-buffer_height);// the optical depth in the buffer region [dimensionless]
+  optical_depth_buffer=6.35e-3*T_buffer*std::pow(den_buffer,2.0)*(z_top-buffer_height);// the optical depth in the buffer region [dimensionless]
 
 
 
@@ -157,28 +157,28 @@ int main(){
       den2 = density(P2, T2, R);
       T3 = T1;
       den3 = den1;
-      dz2 = abs ((-P1+P2)* (1.0/grav)/((1.0/2.0)*(den1+den2)));
-      dz3 = abs ((-P1+P3)* (1.0/grav)/((1.0/2.0)*(den1+den3)));
+      dz2 = std::abs ((-P1+P2)* (1.0/grav)/((1.0/2.0)*(den1+den2)));
+      dz3 = std::abs ((-P1+P3)* (1.0/grav)/((1.0/2.0)*(den1+den3)));
 
     a:  if(difference(dz2, delta_z)*difference(dz3, delta_z)<0.0){
         P_sol = (P2+P3)/2.0;
         T_sol = Temp(P_sol, Pc, P_char, T_char, Td, Lin, Lad, exp1, exp2);
         den_sol = density(P_sol,T_sol, R);
-        dz_sol = abs ((-P1+P_sol)* (1.0/grav)/((1.0/2.0)*(den1+den_sol)));
+        dz_sol = std::abs ((-P1+P_sol)* (1.0/grav)/((1.0/2.0)*(den1+den_sol)));
         count2++;
         }
         else{
           if(difference(dz2, delta_z)>0.0){
           P3 = P3 - P3/dP_factor/1.0;
           T3 = Temp(P3, Pc, P_char, T_char, Td, Lin, Lad, exp1, exp2);
           den3 = density(P3, T3, R);
-          dz3 = abs ((-P1+P3)* (1.0/grav)/((1.0/2.0)*(den1+den3)));
+          dz3 = std::abs ((-P1+P3)* (1.0/grav)/((1.0/2.0)*(den1+den3)));
           }
         else if(difference(dz2, delta_z)<0.0){
           P2 = P2 + P2/dP_factor/1.0;
           T2 = Temp(P2, Pc, P_char, T_char, Td, Lin, Lad, exp1, exp2);
           den2 = density(P2,T2,R);
-          dz2 = abs ((-P1+P2)* (1.0/grav)/((1.0/2.0)*(den1+den2)));
+          dz2 = std::abs ((-P1+P2)* (1.0/grav)/((1.0/2.0)*(den1+den2)));
           }
           goto a;
         }
@@ -192,11 +192,11 @@ int main(){
       if(count2>100000){
         goto b;
       }
-      if(abs(difference(dz_sol, delta_z)) >= error_expected){
+      if(std::abs(difference(dz_sol, delta_z)) >= error_expected){
         goto a;
       }
 
-    b:  cout<<count_cell<<' ' <<setprecision(5) << "Final value, "<<' '<<"height[km]="<< ' '<< z/1.e5<<' ' <<"pressure[bar]=" <<' ' << P_sol/1.e6  <<' '<< "error="<<' ' << abs(difference(dz_sol, delta_z))<<' ' << abs ((-P1+P_sol)/dz_sol+ grav*((1.0/2.0)*(den1+den_sol))) << '\n';
+    b:  cout<<count_cell<<' ' <<setprecision(5) << "Final value, "<<' '<<"height[km]="<< ' '<< z/1.e5<<' ' <<"pressure[bar]=" <<' ' << P_sol/1.e6  <<' '<< "error="<<' ' << std::abs(difference(dz_sol, delta_z))<<' ' << std::abs ((-P1+P_sol)/dz_sol+ grav*((1.0/2.0)*(den1+den_sol))) << '\n';
       T[count] = T_sol;
       P[count] = P_sol;
       den[count] = den_sol;
@@ -207,9 +207,9 @@ int main(){
       P1 = P_sol;
       count_cell++;
       if(P_sol < Pc){
-      optical_depth_radiative = optical_depth_radiative+kappa0*pow(den_sol,2.0)*T_sol*delta_z;
+      optical_depth_radiative = optical_depth_radiative+kappa0*std::pow(den_sol,2.0)*T_sol*delta_z;
       }
-      optical_depth_atm = optical_depth_atm+kappa0*pow(den_sol,2.0)*T_sol*delta_z;
+      optical_depth_atm = optical_depth_atm+kappa0*std::pow(den_sol,2.0)*T_sol*delta_z;
       if(optical_depth_atm+optical_depth_buffer>=1.0 && P_at_1opticaldepth==0.0 ){
         P_at_1opticaldepth=P_sol;
         T_at_1opticaldepth=T_sol;

Exec/science/wdmerger/Prob.cpp

@@ -252,7 +252,7 @@ Castro::wd_update (Real time, Real dt)
     bool local_flag = true;
 
     for (int i = 0; i <= 6; ++i) {
-        Castro::volInBoundary(time, vol_P[i], vol_S[i], pow(10.0,i), local_flag);
+        Castro::volInBoundary(time, vol_P[i], vol_S[i], std::pow(10.0,i), local_flag);
     }
 
     // Do all of the reductions.
@@ -355,12 +355,12 @@ Castro::wd_update (Real time, Real dt)
 
     if (mass_P > 0.0 && vol_P[2] > 0.0) {
         rho_avg_P = mass_P / vol_P[2];
-        t_ff_P = sqrt(3.0 * M_PI / (32.0 * C::Gconst * rho_avg_P));
+        t_ff_P = std::sqrt(3.0 * M_PI / (32.0 * C::Gconst * rho_avg_P));
     }
 
     if (mass_S > 0.0 && vol_S[2] > 0.0) {
         rho_avg_S = mass_S / vol_S[2];
-        t_ff_S = sqrt(3.0 * M_PI / (32.0 * C::Gconst * rho_avg_S));
+        t_ff_S = std::sqrt(3.0 * M_PI / (32.0 * C::Gconst * rho_avg_S));
     }
 
     // Compute updated roche Radii

Exec/unit_tests/particles_test/Prob.cpp

@@ -100,7 +100,7 @@ void Castro::problem_post_simulation(Vector<std::unique_ptr<AmrLevel> >& amr_lev
             auto deltax = it->m_pos[0] - p.m_pos[0];
             auto deltay = it->m_pos[1] - p.m_pos[1];
 
-            auto delta = sqrt(deltax*deltax + deltay*deltay);
+            auto delta = std::sqrt(deltax*deltax + deltay*deltay);
 
             // quick nan check here
             if (delta == delta)

Source/driver/Castro.cpp

@@ -4215,12 +4215,12 @@ Castro::get_numpts ()
 #elif (AMREX_SPACEDIM == 2)
      long ny = bx.size()[1];
      Real ndiagsq = Real(nx*nx + ny*ny);
-     numpts_1d = int(sqrt(ndiagsq))+2*NUM_GROW;
+     numpts_1d = int(std::sqrt(ndiagsq))+2*NUM_GROW;
 #elif (AMREX_SPACEDIM == 3)
      long ny = bx.size()[1];
      long nz = bx.size()[2];
      Real ndiagsq = Real(nx*nx + ny*ny + nz*nz);
-     numpts_1d = int(sqrt(ndiagsq))+2*NUM_GROW;
+     numpts_1d = int(std::sqrt(ndiagsq))+2*NUM_GROW;
 #endif
 
      if (verbose && ParallelDescriptor::IOProcessor()) {

Source/radiation/HypreABec.cpp

@@ -1779,7 +1779,7 @@ void HypreABec::solve(MultiFab& dest, int icomp, MultiFab& rhs, BC_Mode inhom)
     Real bnorm;
     bnorm = hypre_StructInnerProd((hypre_StructVector *) b,
                                   (hypre_StructVector *) b);
-    bnorm = sqrt(bnorm);
+    bnorm = std::sqrt(bnorm);
 
     const BoxArray& grids = acoefs->boxArray();
     Real volume = 0.0;
@@ -1788,7 +1788,7 @@ void HypreABec::solve(MultiFab& dest, int icomp, MultiFab& rhs, BC_Mode inhom)
     }
 
     Real reltol_new = (bnorm > 0.0
-                       ? abstol / bnorm * sqrt(volume)
+                       ? abstol / bnorm * std::sqrt(volume)
                        : reltol);
 
     if (reltol_new > reltol) {
@@ -1898,7 +1898,7 @@ Real HypreABec::getAbsoluteResidual()
   Real bnorm;
   bnorm = hypre_StructInnerProd((hypre_StructVector *) b,
                                 (hypre_StructVector *) b);
-  bnorm = sqrt(bnorm);
+  bnorm = std::sqrt(bnorm);
 
   Real res;
   if (solver_flag == 0) {
@@ -1925,5 +1925,5 @@ Real HypreABec::getAbsoluteResidual()
     volume += grids[i].numPts();
   }
 
-  return bnorm * res / sqrt(volume);
+  return bnorm * res / std::sqrt(volume);
 }

Source/radiation/HypreMultiABec.cpp

@@ -3476,7 +3476,7 @@ void HypreMultiABec::solve()
     hypre_SStructInnerProd((hypre_SStructVector *) b,
                            (hypre_SStructVector *) b,
                            &bnorm);
-    bnorm = sqrt(bnorm);
+    bnorm = std::sqrt(bnorm);
 
     Real volume = 0.0;
     for (int level = crse_level; level <= fine_level; level++) {
@@ -3486,7 +3486,7 @@ void HypreMultiABec::solve()
     }
 
     Real reltol_new = (bnorm > 0.0
-                       ? abstol / bnorm * sqrt(volume)
+                       ? abstol / bnorm * std::sqrt(volume)
                        : reltol);
 
     if (reltol_new > reltol) {
@@ -3830,7 +3830,7 @@ Real HypreMultiABec::getAbsoluteResidual()
   hypre_SStructInnerProd((hypre_SStructVector *) b,
                          (hypre_SStructVector *) b,
                          &bnorm);
-  bnorm = sqrt(bnorm);
+  bnorm = std::sqrt(bnorm);
 
   Real res;
   if (solver_flag == 100) {
@@ -3891,7 +3891,7 @@ Real HypreMultiABec::getAbsoluteResidual()
     }
   }
 
-  return bnorm * res / sqrt(volume);
+  return bnorm * res / std::sqrt(volume);
 }
 
 void HypreMultiABec::boundaryFlux(int level,

Source/radiation/RadMultiGroup.cpp

@@ -43,37 +43,37 @@ void Radiation::get_groups(int verbose)
 
       if (lowest == 0.0) {
         nugroup[0] = 0.5*dnugroup[0];
-        dlognugroup[0] = 2.0 * (log(xnu[1]) - log(nugroup[0]));
+        dlognugroup[0] = 2.0 * (std::log(xnu[1]) - std::log(nugroup[0]));
       }
       else {
-        nugroup[0] = sqrt(xnu[0]*xnu[1]);
-        dlognugroup[0] = log(xnu[1]) - log(xnu[0]);
+        nugroup[0] = std::sqrt(xnu[0]*xnu[1]);
+        dlognugroup[0] = std::log(xnu[1]) - std::log(xnu[0]);
       }
 
       for (int i=1; i<nGroups; i++) {
         dnugroup[i] = dnugroup[i-1] * groupGrowFactor;
         xnu[i+1] = xnu[i] + dnugroup[i];
-        nugroup[i] = sqrt(xnu[i]*xnu[i+1]);
-        dlognugroup[i] = log(xnu[i+1]) - log(xnu[i]);
+        nugroup[i] = std::sqrt(xnu[i]*xnu[i+1]);
+        dlognugroup[i] = std::log(xnu[i+1]) - std::log(xnu[i]);
       }
     }
     else {
       Real highest;
       pp.get("highestGroupHz", highest);
 
-      Real loglowest = log10(lowest);
-      Real loghighest = log10(highest);
+      Real loglowest = std::log10(lowest);
+      Real loghighest = std::log10(highest);
       Real dlognu = (loghighest - loglowest) / Real(nGroups);
 
       for (int i=0; i<nGroups; i++) {
-        xnu[i] = pow(10.0, loglowest+i*dlognu);
-        nugroup[i] = pow(10.0, loglowest+(i+0.5)*dlognu);
+        xnu[i] = std::pow(10.0, loglowest+i*dlognu);
+        nugroup[i] = std::pow(10.0, loglowest+(i+0.5)*dlognu);
       }
       xnu[nGroups] = highest;
 
       for (int i=0; i<nGroups; i++) {
         dnugroup[i] = xnu[i+1] - xnu[i];
-        dlognugroup[i] = log(xnu[i+1]) - log(xnu[i]);
+        dlognugroup[i] = std::log(xnu[i+1]) - std::log(xnu[i]);
       }
     }
 

Source/radiation/_interpbndry/RadInterpBndryData.cpp

@@ -106,7 +106,7 @@ RadInterpBndryData::setBndryValues(BndryRegister& crse, int c_start,
         auto cblo = crse_bx.loVect3d();
         auto cbhi = crse_bx.hiVect3d();
         int mxlen = crse_bx.longside() + 2;
-        if (pow(mxlen,(float)AMREX_SPACEDIM-1) > tmplen) {
+        if (std::pow(mxlen,(float)AMREX_SPACEDIM-1) > tmplen) {
             delete [] derives;
 #if (AMREX_SPACEDIM == 1)
             derives = new Real[1];

Source/scf/scf_relax.cpp

@@ -338,7 +338,7 @@ Castro::do_hscf_solve()
                 amrex::Error();
             }
 
-            Real omega = sqrt(omegasq);
+            Real omega = std::sqrt(omegasq);
 
             // Rotational period is 2 pi / omega.
             // Let's also be sure not to let the period