From ae3edb194e84ce40d08d2c6b57afbe82639b0dfc Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Wed, 18 Nov 2020 22:40:23 +0100
Subject: [PATCH] multicolvar: removed namespace std

---
 src/multicolvar/AlphaBeta.cpp           |  6 ++----
 src/multicolvar/Angles.cpp              |  2 --
 src/multicolvar/Bridge.cpp              |  2 --
 src/multicolvar/CenterOfMultiColvar.cpp |  2 --
 src/multicolvar/CoordinationNumbers.cpp |  6 ++----
 src/multicolvar/Density.cpp             |  2 --
 src/multicolvar/DihedralCorrelation.cpp |  6 ++----
 src/multicolvar/Distances.cpp           |  2 --
 src/multicolvar/DumpMultiColvar.cpp     |  8 +++-----
 src/multicolvar/InPlaneDistances.cpp    |  4 +---
 src/multicolvar/MultiColvarBase.cpp     |  6 ++----
 src/multicolvar/MultiColvarDensity.cpp  | 11 ++++-------
 src/multicolvar/Torsions.cpp            |  2 --
 src/multicolvar/XAngle.cpp              |  2 --
 src/multicolvar/XDistances.cpp          |  2 --
 src/multicolvar/XYDistances.cpp         |  2 --
 src/multicolvar/XYTorsion.cpp           |  2 --
 17 files changed, 16 insertions(+), 51 deletions(-)

diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index 871205257f..d1b4971f3f 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -27,8 +27,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
@@ -185,8 +183,8 @@ double AlphaBeta::compute( const unsigned& tindex, AtomValuePack& myatoms ) cons
   Vector dd0,dd1,dd2;
   PLMD::Torsion t;
   const double value  = t.compute(d0,d1,d2,dd0,dd1,dd2);
-  const double svalue = -0.5*coefficient[tindex]*sin(value-target[tindex]);
-  const double cvalue = coefficient[tindex]*(1.+cos(value-target[tindex]));
+  const double svalue = -0.5*coefficient[tindex]*std::sin(value-target[tindex]);
+  const double cvalue = coefficient[tindex]*(1.+std::cos(value-target[tindex]));
 
   dd0 *= svalue;
   dd1 *= svalue;
diff --git a/src/multicolvar/Angles.cpp b/src/multicolvar/Angles.cpp
index 839d380547..3560b2a4e0 100644
--- a/src/multicolvar/Angles.cpp
+++ b/src/multicolvar/Angles.cpp
@@ -28,8 +28,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index 480cf38d95..8ac5048913 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -27,8 +27,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index 4943905cc7..30f8e7cb39 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -28,8 +28,6 @@
 #include "BridgedMultiColvarFunction.h"
 #include "vesselbase/StoreDataVessel.h"
 
-using namespace std;
-
 //+PLUMEDOC VATOM CENTER_OF_MULTICOLVAR
 /*
 Calculate a a weighted average position based on the value of some multicolvar.
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index e06ec26009..0e2505d19d 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -28,8 +28,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
@@ -142,7 +140,7 @@ CoordinationNumbers::CoordinationNumbers(const ActionOptions&ao):
   parse("R_POWER", r_power);
   if(r_power > 0) {
     log.printf("  Multiplying switching function by r^%d\n", r_power);
-    double offset = switchingFunction.calculate(rcut*0.9999, rcut2) * pow(rcut*0.9999, r_power);
+    double offset = switchingFunction.calculate(rcut*0.9999, rcut2) * std::pow(rcut*0.9999, r_power);
     log.printf("  You will have a discontinuous jump of %f to 0 near the cutoff of your switching function. "
                "Consider setting D_MAX or reducing R_POWER if this is large\n", offset);
   }
@@ -168,7 +166,7 @@ double CoordinationNumbers::compute( const unsigned& tindex, AtomValuePack& myat
 
       sw = switchingFunction.calculateSqr( d2, dfunc );
       if(r_power > 0) {
-        d = sqrt(d2); raised = pow( d, r_power - 1 );
+        d = std::sqrt(d2); raised = std::pow( d, r_power - 1 );
         accumulateSymmetryFunction( 1, i, sw * raised * d,
                                     (dfunc * d * raised + sw * r_power * raised / d) * distance,
                                     (-dfunc * d * raised - sw * r_power * raised / d) * Tensor(distance, distance),
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index 8ee0053c03..74a6acf00f 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -26,8 +26,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index be36ea894e..4d4a4b14d3 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -27,8 +27,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
@@ -146,9 +144,9 @@ double DihedralCorrelation::compute( const unsigned& tindex, AtomValuePack& myat
 
   // Calculate value
   const double diff = phi2 - phi1;
-  const double value = 0.5*(1.+cos(diff));
+  const double value = 0.5*(1.+std::cos(diff));
   // Derivatives wrt phi1
-  const double dval = 0.5*sin(diff);
+  const double dval = 0.5*std::sin(diff);
   dd10 *= dval;
   dd11 *= dval;
   dd12 *= dval;
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index c8cbd98055..7a3969b410 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -28,8 +28,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 4dafc551fc..8ddfe689b6 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -34,8 +34,6 @@
 #include "vesselbase/ActionWithInputVessel.h"
 #include "vesselbase/StoreDataVessel.h"
 
-using namespace std;
-
 namespace PLMD
 {
 namespace multicolvar {
@@ -113,7 +111,7 @@ DumpMultiColvar::DumpMultiColvar(const ActionOptions&ao):
   if( atom.size()>1 ) error("should only be one atom specified");
   if( atom.size()==1 ) log.printf("  origin is at position of atom : %d\n",atom[0].serial() );
 
-  string file; parse("FILE",file);
+  std::string file; parse("FILE",file);
   if(file.length()==0) error("name out output file was not specified");
   std::string type=Tools::extension(file);
   log<<"  file name "<<file<<"\n";
@@ -121,11 +119,11 @@ DumpMultiColvar::DumpMultiColvar(const ActionOptions&ao):
 
   fmt_xyz="%f";
 
-  string precision; parse("PRECISION",precision);
+  std::string precision; parse("PRECISION",precision);
   if(precision.length()>0) {
     int p; Tools::convert(precision,p);
     log<<"  with precision "<<p<<"\n";
-    string a,b;
+    std::string a,b;
     Tools::convert(p+5,a);
     Tools::convert(p,b);
     fmt_xyz="%"+a+"."+b+"f";
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index 0a7ef6da40..a2389e5862 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -30,8 +30,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
@@ -134,7 +132,7 @@ double InPlaneDistances::compute( const unsigned& tindex, AtomValuePack& myatoms
   Vector normal=getSeparation( myatoms.getPosition(1), myatoms.getPosition(2) );
   Vector dir=getSeparation( myatoms.getPosition(1), myatoms.getPosition(0) );
   PLMD::Angle a; Vector ddij, ddik; double angle=a.compute(normal,dir,ddij,ddik);
-  double sangle=sin(angle), cangle=cos(angle);
+  double sangle=std::sin(angle), cangle=std::cos(angle);
   double dd=dir.modulo(), invdd=1.0/dd, val=dd*sangle;
 
   addAtomDerivatives( 1, 0, dd*cangle*ddik + sangle*invdd*dir, myatoms );
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index 3e177c93bf..7ce2e0d849 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -32,8 +32,6 @@
 #include <string>
 #include <limits>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
@@ -410,11 +408,11 @@ void MultiColvarBase::setupMultiColvarBase( const std::vector<AtomNumber>& atoms
     if( allthirdblockintasks ) {
       decoder.resize(2); plumed_assert( ablocks.size()==3 );
       // Check if number of atoms is too large
-      if( pow( double(nblock), 2.0 )>std::numeric_limits<unsigned>::max() ) error("number of atoms in groups is too big for PLUMED to handle");
+      if( std::pow( double(nblock), 2.0 )>std::numeric_limits<unsigned>::max() ) error("number of atoms in groups is too big for PLUMED to handle");
     } else {
       decoder.resize( ablocks.size() );
       // Check if number of atoms is too large
-      if( pow( double(nblock), double(ablocks.size()) )>std::numeric_limits<unsigned>::max() ) error("number of atoms in groups is too big for PLUMED to handle");
+      if( std::pow( double(nblock), double(ablocks.size()) )>std::numeric_limits<unsigned>::max() ) error("number of atoms in groups is too big for PLUMED to handle");
     }
     unsigned code=1; for(unsigned i=0; i<decoder.size(); ++i) { decoder[decoder.size()-1-i]=code; code *= nblock; }
   } else if( !usespecies ) {
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index 46c9d2532c..c9ddabf78b 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -29,10 +29,7 @@
 #include "MultiColvarBase.h"
 #include "gridtools/ActionWithGrid.h"
 
-using namespace std;
-
-namespace PLMD
-{
+namespace PLMD {
 namespace multicolvar {
 
 //+PLUMEDOC GRIDCALC MULTICOLVARDENS
@@ -186,7 +183,7 @@ MultiColvarDensity::MultiColvarDensity(const ActionOptions&ao):
       if( confined[i] ) {
         cmin[i]=cmax[i]=0.0; parse("XLOWER",cmin[i]); parse("XUPPER",cmax[i]);
         if( fractional ) error("XREDUCED is incompatible with FRACTIONAL");
-        if( fabs(cmin[i]-cmax[i])<epsilon ) error("range set for x axis makes no sense");
+        if( std::abs(cmin[i]-cmax[i])<epsilon ) error("range set for x axis makes no sense");
         log.printf("  confining calculation in x direction to between %f and %f \n",cmin[i],cmax[i]);
       }
     } else if( directions[i]==1 ) {
@@ -194,7 +191,7 @@ MultiColvarDensity::MultiColvarDensity(const ActionOptions&ao):
       if( confined[i] ) {
         cmin[i]=cmax[i]=0.0; parse("YLOWER",cmin[i]); parse("YUPPER",cmax[i]);
         if( fractional ) error("YREDUCED is incompatible with FRACTIONAL");
-        if( fabs(cmin[i]-cmax[i])<epsilon ) error("range set for y axis makes no sense");
+        if( std::abs(cmin[i]-cmax[i])<epsilon ) error("range set for y axis makes no sense");
         log.printf("  confining calculation in y direction to between %f and %f \n",cmin[i],cmax[i]);
       }
     } else if( directions[i]==2 ) {
@@ -202,7 +199,7 @@ MultiColvarDensity::MultiColvarDensity(const ActionOptions&ao):
       if( confined[i] ) {
         cmin[i]=cmax[i]=0.0; parse("ZLOWER",cmin[i]); parse("ZUPPER",cmax[i]);
         if( fractional ) error("ZREDUCED is incompatible with FRACTIONAL");
-        if( fabs(cmin[i]-cmax[i])<epsilon ) error("range set for z axis search makes no sense");
+        if( std::abs(cmin[i]-cmax[i])<epsilon ) error("range set for z axis search makes no sense");
         log.printf("  confining calculation in z direction to between %f and %f \n",cmin[i],cmax[i]);
       }
     }
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 770368aabd..2343e52d11 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -27,8 +27,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/XAngle.cpp b/src/multicolvar/XAngle.cpp
index a26d686751..eec41f8e85 100644
--- a/src/multicolvar/XAngle.cpp
+++ b/src/multicolvar/XAngle.cpp
@@ -28,8 +28,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index a52ad38e21..e05ecc3d43 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -26,8 +26,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index 92e7b068b4..879d91531f 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -26,8 +26,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {
 
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index 3fd8ab8718..f2e672d178 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -28,8 +28,6 @@
 #include <string>
 #include <cmath>
 
-using namespace std;
-
 namespace PLMD {
 namespace multicolvar {