*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016,2019, 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.
/* The source code in this file should be thread-safe.
Please keep it that way. */
-static void gen_waterhydrogen(int nh, rvec xa[], rvec xh[], int *l)
+static void gen_waterhydrogen(int nh, rvec xa[], rvec xh[], int* l)
{
#define AA 0.081649
#define BB 0.0
#define CC 0.0577350
- const dvec matrix1[6] = {
- { AA, BB, CC },
- { AA, BB, CC },
- { AA, BB, CC },
- { -AA, BB, CC },
- { -AA, BB, CC },
- { BB, AA, -CC }
- };
- const dvec matrix2[6] = {
- { -AA, BB, CC },
- { BB, AA, -CC },
- { BB, -AA, -CC },
- { BB, AA, -CC },
- { BB, -AA, -CC },
- { BB, -AA, -CC }
- };
+ const dvec matrix1[6] = { { AA, BB, CC }, { AA, BB, CC }, { AA, BB, CC },
+ { -AA, BB, CC }, { -AA, BB, CC }, { BB, AA, -CC } };
+ const dvec matrix2[6] = { { -AA, BB, CC }, { BB, AA, -CC }, { BB, -AA, -CC },
+ { BB, AA, -CC }, { BB, -AA, -CC }, { BB, -AA, -CC } };
#undef AA
#undef BB
#undef CC
- int m;
+ int m;
/* This was copied from Gromos */
for (m = 0; (m < DIM); m++)
{
- xH1[m] = xAI[m]+matrix1[*l][m];
- xH2[m] = xAI[m]+matrix2[*l][m];
+ xH1[m] = xAI[m] + matrix1[*l][m];
+ xH2[m] = xAI[m] + matrix2[*l][m];
}
if (nh > 2)
{
copy_rvec(xAI, xH4);
}
- *l = (*l+1) % 6;
+ *l = (*l + 1) % 6;
}
-void calc_h_pos(int nht, rvec xa[], rvec xh[], int *l)
+void calc_h_pos(int nht, rvec xa[], rvec xh[], int* l)
{
-#define alfaH (acos(-1/3.0)) /* 109.47 degrees */
-#define alfaHpl (2*M_PI/3) /* 120 degrees */
-#define distH 0.1
+#define alfaH (acos(-1 / 3.0)) /* 109.47 degrees */
+#define alfaHpl (2 * M_PI / 3) /* 120 degrees */
+#define distH 0.1
-#define alfaCOM (DEG2RAD*117)
-#define alfaCO (DEG2RAD*121)
-#define alfaCOA (DEG2RAD*115)
+#define alfaCOM (DEG2RAD * 117)
+#define alfaCO (DEG2RAD * 121)
+#define alfaCOA (DEG2RAD * 115)
-#define distO 0.123
-#define distOA 0.125
-#define distOM 0.136
+#define distO 0.123
+#define distOA 0.125
+#define distOM 0.136
rvec sa, sb, sij;
real s6, rij, ra, rb, xd;
int d;
- s6 = 0.5*std::sqrt(3.e0);
+ s6 = 0.5 * std::sqrt(3.e0);
/* common work for constructing one, two or three dihedral hydrogens */
switch (nht)
for (d = 0; (d < DIM); d++)
{
xd = xAJ[d];
- sij[d] = xAI[d]-xd;
- sb[d] = xd-xAK[d];
- rij += gmx::square(sij[d]);
+ sij[d] = xAI[d] - xd;
+ sb[d] = xd - xAK[d];
+ rij += gmx::square(sij[d]);
}
rij = std::sqrt(rij);
- sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
- sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
- sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
+ sa[XX] = sij[YY] * sb[ZZ] - sij[ZZ] * sb[YY];
+ sa[YY] = sij[ZZ] * sb[XX] - sij[XX] * sb[ZZ];
+ sa[ZZ] = sij[XX] * sb[YY] - sij[YY] * sb[XX];
ra = 0.e0;
for (d = 0; (d < DIM); d++)
{
- sij[d] = sij[d]/rij;
- ra += gmx::square(sa[d]);
+ sij[d] = sij[d] / rij;
+ ra += gmx::square(sa[d]);
}
ra = std::sqrt(ra);
for (d = 0; (d < DIM); d++)
{
- sa[d] = sa[d]/ra;
+ sa[d] = sa[d] / ra;
}
- sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
- sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
- sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
+ sb[XX] = sa[YY] * sij[ZZ] - sa[ZZ] * sij[YY];
+ sb[YY] = sa[ZZ] * sij[XX] - sa[XX] * sij[ZZ];
+ sb[ZZ] = sa[XX] * sij[YY] - sa[YY] * sij[XX];
break;
} /* end switch */
rb = 0.e0;
for (d = 0; (d < DIM); d++)
{
- sij[d] = xAI[d]-xAJ[d];
- sb[d] = xAI[d]-xAK[d];
- rij += gmx::square(sij[d]);
- rb += gmx::square(sb[d]);
+ sij[d] = xAI[d] - xAJ[d];
+ sb[d] = xAI[d] - xAK[d];
+ rij += gmx::square(sij[d]);
+ rb += gmx::square(sb[d]);
}
rij = std::sqrt(rij);
rb = std::sqrt(rb);
ra = 0.e0;
for (d = 0; (d < DIM); d++)
{
- sa[d] = sij[d]/rij+sb[d]/rb;
- ra += gmx::square(sa[d]);
+ sa[d] = sij[d] / rij + sb[d] / rb;
+ ra += gmx::square(sa[d]);
}
ra = std::sqrt(ra);
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]+distH*sa[d]/ra;
+ xH1[d] = xAI[d] + distH * sa[d] / ra;
}
break;
case 2: /* one single hydrogen, e.g. hydroxyl */
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
+ xH1[d] = xAI[d] + distH * sin(alfaH) * sb[d] - distH * cos(alfaH) * sij[d];
}
break;
case 3: /* two planar hydrogens, e.g. -NH2 */
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]-distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
- xH2[d] = xAI[d]+distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
+ xH1[d] = xAI[d] - distH * sin(alfaHpl) * sb[d] - distH * cos(alfaHpl) * sij[d];
+ xH2[d] = xAI[d] + distH * sin(alfaHpl) * sb[d] - distH * cos(alfaHpl) * sij[d];
}
break;
case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
- xH2[d] = ( xAI[d]
- - distH*sin(alfaH)*0.5*sb[d]
- + distH*sin(alfaH)*s6*sa[d]
- - distH*cos(alfaH)*sij[d] );
+ xH1[d] = xAI[d] + distH * sin(alfaH) * sb[d] - distH * cos(alfaH) * sij[d];
+ xH2[d] = (xAI[d] - distH * sin(alfaH) * 0.5 * sb[d]
+ + distH * sin(alfaH) * s6 * sa[d] - distH * cos(alfaH) * sij[d]);
if (xH3[XX] != NOTSET && xH3[YY] != NOTSET && xH3[ZZ] != NOTSET)
{
- xH3[d] = ( xAI[d]
- - distH*sin(alfaH)*0.5*sb[d]
- - distH*sin(alfaH)*s6*sa[d]
- - distH*cos(alfaH)*sij[d] );
+ xH3[d] = (xAI[d] - distH * sin(alfaH) * 0.5 * sb[d]
+ - distH * sin(alfaH) * s6 * sa[d] - distH * cos(alfaH) * sij[d]);
}
}
break;
for (d = 0; (d < DIM); d++)
{
- center = (xAJ[d]+xAK[d]+xAL[d])/3.0;
- dxc[d] = xAI[d]-center;
+ center = (xAJ[d] + xAK[d] + xAL[d]) / 3.0;
+ dxc[d] = xAI[d] - center;
}
center = norm(dxc);
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]+dxc[d]*distH/center;
+ xH1[d] = xAI[d] + dxc[d] * distH / center;
}
break;
}
for (d = 0; (d < DIM); d++)
{
- rBB[d] = xAI[d]-0.5*(xAJ[d]+xAK[d]);
+ rBB[d] = xAI[d] - 0.5 * (xAJ[d] + xAK[d]);
}
bb = norm(rBB);
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
- sin(alfaH/2.0)*rNN[d]/nn);
- xH2[d] = xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
- sin(alfaH/2.0)*rNN[d]/nn);
+ xH1[d] = xAI[d] + distH * (cos(alfaH / 2.0) * rBB[d] / bb + sin(alfaH / 2.0) * rNN[d] / nn);
+ xH2[d] = xAI[d] + distH * (cos(alfaH / 2.0) * rBB[d] / bb - sin(alfaH / 2.0) * rNN[d] / nn);
}
break;
}
- case 7: /* two water hydrogens */
- gen_waterhydrogen(2, xa, xh, l);
- break;
- case 10: /* three water hydrogens */
- gen_waterhydrogen(3, xa, xh, l);
- break;
- case 11: /* four water hydrogens */
- gen_waterhydrogen(4, xa, xh, l);
- break;
+ case 7: /* two water hydrogens */ gen_waterhydrogen(2, xa, xh, l); break;
+ case 10: /* three water hydrogens */ gen_waterhydrogen(3, xa, xh, l); break;
+ case 11: /* four water hydrogens */ gen_waterhydrogen(4, xa, xh, l); break;
case 8: /* two carboxyl oxygens, -COO- */
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
- xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
+ xH1[d] = xAI[d] - distOM * sin(alfaCOM) * sb[d] - distOM * cos(alfaCOM) * sij[d];
+ xH2[d] = xAI[d] + distOM * sin(alfaCOM) * sb[d] - distOM * cos(alfaCOM) * sij[d];
}
break;
- case 9: /* carboxyl oxygens and hydrogen, -COOH */
+ case 9: /* carboxyl oxygens and hydrogen, -COOH */
{
rvec xa2[4]; /* i,j,k,l */
/* first add two oxygens */
for (d = 0; (d < DIM); d++)
{
- xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
- xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
+ xH1[d] = xAI[d] - distO * sin(alfaCO) * sb[d] - distO * cos(alfaCO) * sij[d];
+ xH2[d] = xAI[d] + distOA * sin(alfaCOA) * sb[d] - distOA * cos(alfaCOA) * sij[d];
}
/* now use rule 2 to add hydrogen to 2nd oxygen */
copy_rvec(xAI, xa2[1]); /* new j = i */
copy_rvec(xAJ, xa2[2]); /* new k = j */
copy_rvec(xAK, xa2[3]); /* new l = k, not used */
- calc_h_pos(2, xa2, (xh+2), l);
+ calc_h_pos(2, xa2, (xh + 2), l);
break;
}
- default:
- gmx_fatal(FARGS, "Invalid argument (%d) for nht in routine genh\n", nht);
+ default: gmx_fatal(FARGS, "Invalid argument (%d) for nht in routine genh\n", nht);
} /* end switch */
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff