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[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / gen_maxwell_velocities.cpp

diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
index dee74291c0827e0214df50dbc41b4341ff3eb1a1..fbcd56eeb4dca313c17ba18a999440d242c5eeae 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
@@ -50,38 +50,37 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-static void low_mspeed(real tempi,
-                       gmx_mtop_t *mtop, rvec v[], gmx::ThreeFry2x64<> * rng)
+static void low_mspeed(real tempi, gmx_mtop_t* mtop, rvec v[], gmx::ThreeFry2x64<>* rng)
 {
-    int                                     nrdf;
-    real                                    boltz;
-    real                                    ekin, temp;
-    gmx::TabulatedNormalDistribution<real>  normalDist;
+    int                                    nrdf;
+    real                                   boltz;
+    real                                   ekin, temp;
+    gmx::TabulatedNormalDistribution<real> normalDist;
 
-    boltz = BOLTZ*tempi;
+    boltz = BOLTZ * tempi;
     ekin  = 0.0;
     nrdf  = 0;
     for (const AtomProxy atomP : AtomRange(*mtop))
     {
-        const t_atom &local = atomP.atom();
+        const t_atom& local = atomP.atom();
         int           i     = atomP.globalAtomNumber();
         real          mass  = local.m;
         if (mass > 0)
         {
             rng->restart(i, 0);
-            real sd = std::sqrt(boltz/mass);
+            real sd = std::sqrt(boltz / mass);
             for (int m = 0; (m < DIM); m++)
             {
-                v[i][m] = sd*normalDist(*rng);
-                ekin   += 0.5*mass*v[i][m]*v[i][m];
+                v[i][m] = sd * normalDist(*rng);
+                ekin += 0.5 * mass * v[i][m] * v[i][m];
             }
             nrdf += DIM;
         }
     }
-    temp = (2.0*ekin)/(nrdf*BOLTZ);
+    temp = (2.0 * ekin) / (nrdf * BOLTZ);
     if (temp > 0)
     {
-        real scal = std::sqrt(tempi/temp);
+        real scal = std::sqrt(tempi / temp);
         for (int i = 0; (i < mtop->natoms); i++)
         {
             for (int m = 0; (m < DIM); m++)
@@ -90,8 +89,7 @@ static void low_mspeed(real tempi,
             }
         }
     }
-    fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n",
-            tempi);
+    fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n", tempi);
     if (debug)
     {
         fprintf(debug,
@@ -101,7 +99,7 @@ static void low_mspeed(real tempi,
     }
 }
 
-void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t *mtop, rvec v[])
+void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t* mtop, rvec v[])
 {
 
     if (seed == 0)
@@ -109,13 +107,12 @@ void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t *mtop, rvec v[])
         seed = static_cast<int>(gmx::makeRandomSeed());
         fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
     }
-    gmx::ThreeFry2x64<>  rng(seed, gmx::RandomDomain::MaxwellVelocities);
+    gmx::ThreeFry2x64<> rng(seed, gmx::RandomDomain::MaxwellVelocities);
 
     low_mspeed(tempi, mtop, v, &rng);
 }
 
-static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[],
-                    rvec xcm, rvec vcm, rvec acm, matrix L)
+static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[], rvec xcm, rvec vcm, rvec acm, matrix L)
 {
     rvec dx, a0;
     real tm, m0;
@@ -127,14 +124,14 @@ static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[],
     tm = 0.0;
     for (i = 0; (i < natoms); i++)
     {
-        m0  = mass[i];
+        m0 = mass[i];
         tm += m0;
         cprod(x[i], v[i], a0);
         for (m = 0; (m < DIM); m++)
         {
-            xcm[m] += m0*x[i][m]; /* c.o.m. position */
-            vcm[m] += m0*v[i][m]; /* c.o.m. velocity */
-            acm[m] += m0*a0[m];   /* rotational velocity around c.o.m. */
+            xcm[m] += m0 * x[i][m]; /* c.o.m. position */
+            vcm[m] += m0 * v[i][m]; /* c.o.m. velocity */
+            acm[m] += m0 * a0[m];   /* rotational velocity around c.o.m. */
         }
     }
     cprod(xcm, vcm, a0);
@@ -142,12 +139,11 @@ static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[],
     {
         xcm[m] /= tm;
         vcm[m] /= tm;
-        acm[m] -= a0[m]/tm;
+        acm[m] -= a0[m] / tm;
     }
 
-#define PVEC(str, v) fprintf(log, \
-                             "%s[X]: %10.5e  %s[Y]: %10.5e  %s[Z]: %10.5e\n", \
-                             str, (v)[0], str, (v)[1], str, (v)[2])
+#define PVEC(str, v) \
+    fprintf(log, "%s[X]: %10.5e  %s[Y]: %10.5e  %s[Z]: %10.5e\n", str, (v)[0], str, (v)[1], str, (v)[2])
 #ifdef DEBUG
     PVEC("xcm", xcm);
     PVEC("acm", acm);
@@ -160,14 +156,14 @@ static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[],
         m0 = mass[i];
         for (m = 0; (m < DIM); m++)
         {
-            dx[m] = x[i][m]-xcm[m];
+            dx[m] = x[i][m] - xcm[m];
         }
-        L[XX][XX] += dx[XX]*dx[XX]*m0;
-        L[XX][YY] += dx[XX]*dx[YY]*m0;
-        L[XX][ZZ] += dx[XX]*dx[ZZ]*m0;
-        L[YY][YY] += dx[YY]*dx[YY]*m0;
-        L[YY][ZZ] += dx[YY]*dx[ZZ]*m0;
-        L[ZZ][ZZ] += dx[ZZ]*dx[ZZ]*m0;
+        L[XX][XX] += dx[XX] * dx[XX] * m0;
+        L[XX][YY] += dx[XX] * dx[YY] * m0;
+        L[XX][ZZ] += dx[XX] * dx[ZZ] * m0;
+        L[YY][YY] += dx[YY] * dx[YY] * m0;
+        L[YY][ZZ] += dx[YY] * dx[ZZ] * m0;
+        L[ZZ][ZZ] += dx[ZZ] * dx[ZZ] * m0;
     }
 #ifdef DEBUG
     PVEC("L-x", L[XX]);
@@ -178,7 +174,7 @@ static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[],
     return tm;
 }
 
-void stop_cm(FILE gmx_unused *log, int natoms, real mass[], rvec x[], rvec v[])
+void stop_cm(FILE gmx_unused* log, int natoms, real mass[], rvec x[], rvec v[])
 {
     rvec   xcm, vcm, acm;
     tensor L;