Merge branch 'master' into pygromacs

[alexxy/gromacs.git] / src / gromacs / mdlib / adress.cpp

diff --git a/src/gromacs/mdlib/adress.c b/src/gromacs/mdlib/adress.cpp
similarity index 94%
rename from src/gromacs/mdlib/adress.c
rename to src/gromacs/mdlib/adress.cpp
index 9e9db2908984f30cd6a842a4780d2979b194382e..4f5fb2a471dc8ee3d3af2e82491b337b40b63f4e 100644 (file)
--- a/src/gromacs/mdlib/adress.c
+++ b/src/gromacs/mdlib/adress.cpp
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,6 +38,8 @@
 
 #include "adress.h"
 
+#include <cmath>
+
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/utilities.h"
@@ -95,7 +97,7 @@ adress_weight(rvec                 x,
             return 1;
     }
 
-    dl = sqrt(sqr_dl);
+    dl = std::sqrt(sqr_dl);
 
     /* molecule is coarse grained */
     if (dl > l2)
@@ -110,7 +112,7 @@ adress_weight(rvec                 x,
     /* hybrid region */
     else
     {
-        tmp = cos((dl-adressr)*M_PI/2/adressw);
+        tmp = std::cos((dl-adressr)*M_PI/2/adressw);
         return tmp*tmp;
     }
 }
@@ -261,14 +263,11 @@ void update_adress_weights_atom_per_atom(
         t_mdatoms *          mdatoms,
         t_pbc *              pbc)
 {
-    int            icg, k, k0, k1, d;
-    real           nrcg, inv_ncg, mtot, inv_mtot;
+    int            icg, k, k0, k1;
     atom_id *      cgindex;
-    rvec           ix;
     int            adresstype;
     real           adressr, adressw;
     rvec *         ref;
-    real *         massT;
     real *         wf;
 
 
@@ -281,7 +280,6 @@ void update_adress_weights_atom_per_atom(
     adresstype         = fr->adress_type;
     adressr            = fr->adress_ex_width;
     adressw            = fr->adress_hy_width;
-    massT              = mdatoms->massT;
     wf                 = mdatoms->wf;
     ref                = &(fr->adress_refs);
 
@@ -296,7 +294,6 @@ void update_adress_weights_atom_per_atom(
     {
         k0   = cgindex[icg];
         k1   = cgindex[icg + 1];
-        nrcg = k1 - k0;
 
         for (k = (k0); (k < k1); k++)
         {
@@ -326,7 +323,7 @@ update_adress_weights_cog(t_iparams            ip[],
                           t_mdatoms *          mdatoms,
                           t_pbc *              pbc)
 {
-    int            i, j, k, nr, nra, inc;
+    int            i, j, nr, nra, inc;
     int            ftype, adresstype;
     t_iatom        avsite, ai, aj, ak, al;
     t_iatom *      ia;
@@ -464,13 +461,11 @@ update_adress_weights_atom(int                  cg0,
     int            adresstype;
     real           adressr, adressw;
     rvec *         ref;
-    real *         massT;
     real *         wf;
 
     adresstype         = fr->adress_type;
     adressr            = fr->adress_ex_width;
     adressw            = fr->adress_hy_width;
-    massT              = mdatoms->massT;
     wf                 = mdatoms->wf;
     ref                = &(fr->adress_refs);
     cgindex            = cgs->index;
@@ -497,33 +492,25 @@ update_adress_weights_atom(int                  cg0,
 void
 adress_thermo_force(int                  start,
                     int                  homenr,
-                    t_block *            cgs,
                     rvec                 x[],
                     rvec                 f[],
                     t_forcerec *         fr,
                     t_mdatoms *          mdatoms,
                     t_pbc *              pbc)
 {
-    int              iatom, n0, nnn, nrcg, i;
+    int              iatom, n0, nnn, i;
     int              adresstype;
-    real             adressw, adressr;
-    atom_id *        cgindex;
     unsigned short * ptype;
     rvec *           ref;
-    real *           wf;
     real             tabscale;
     real *           ATFtab;
     rvec             dr;
-    real             w, wsq, wmin1, wmin1sq, wp, wt, rinv, sqr_dl, dl;
-    real             eps, eps2, F, Geps, Heps2, Fp, dmu_dwp, dwp_dr, fscal;
+    real             wt, rinv, sqr_dl, dl;
+    real             eps, eps2, F, Geps, Heps2, Fp, fscal;
 
     adresstype        = fr->adress_type;
-    adressw           = fr->adress_hy_width;
-    adressr           = fr->adress_ex_width;
-    cgindex           = cgs->index;
     ptype             = mdatoms->ptype;
     ref               = &(fr->adress_refs);
-    wf                = mdatoms->wf;
 
     for (iatom = start; (iatom < start+homenr); iatom++)
     {
@@ -531,7 +518,6 @@ adress_thermo_force(int                  start,
         {
             if (ptype[iatom] == eptVSite)
             {
-                w    = wf[iatom];
                 /* is it hybrid or apply the thermodynamics force everywhere?*/
                 if (mdatoms->tf_table_index[iatom] != NO_TF_TABLE)
                 {
@@ -548,7 +534,6 @@ adress_thermo_force(int                  start,
                         tabscale = fr->atf_tabs[DEFAULT_TF_TABLE].scale;
                     }
 
-                    fscal            = 0;
                     if (pbc)
                     {
                         pbc_dx(pbc, (*ref), x[iatom], dr);
@@ -583,10 +568,10 @@ adress_thermo_force(int                  start,
                             rinv = 0.0;
                     }
 
-                    dl = sqrt(sqr_dl);
+                    dl = std::sqrt(sqr_dl);
                     /* table origin is adress center */
                     wt               = dl*tabscale;
-                    n0               = wt;
+                    n0               = static_cast<int>(wt);
                     eps              = wt-n0;
                     eps2             = eps*eps;
                     nnn              = 4*n0;