#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-static int count_hydrogens (char ***atomname, int nra, gmx::ArrayRef<const int> a)
+static int count_hydrogens(char*** atomname, int nra, gmx::ArrayRef<const int> a)
{
- int nh;
+ int nh;
if (!atomname)
{
- gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
- __FILE__, __LINE__);
+ gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)", __FILE__, __LINE__);
}
nh = 0;
return nh;
}
-void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms *atoms, int nshake)
+void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms* atoms, int nshake)
{
- char ***info = atoms->atomname;
- real b_ij, b_jk;
+ char*** info = atoms->atomname;
+ real b_ij, b_jk;
if (nshake != eshNONE)
{
switch (nshake)
{
- case eshHBONDS:
- printf("turning H bonds into constraints...\n");
- break;
- case eshALLBONDS:
- printf("turning all bonds into constraints...\n");
- break;
- case eshHANGLES:
- printf("turning all bonds and H angles into constraints...\n");
- break;
- case eshALLANGLES:
- printf("turning all bonds and angles into constraints...\n");
- break;
- default:
- gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
+ case eshHBONDS: printf("turning H bonds into constraints...\n"); break;
+ case eshALLBONDS: printf("turning all bonds into constraints...\n"); break;
+ case eshHANGLES: printf("turning all bonds and H angles into constraints...\n"); break;
+ case eshALLANGLES: printf("turning all bonds and angles into constraints...\n"); break;
+ default: gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
}
if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
{
if (interaction_function[ftype].flags & IF_CHEMBOND)
{
- InteractionsOfType *bonds = &(plist[ftype]);
+ InteractionsOfType* bonds = &(plist[ftype]);
for (int ftype_a = 0; (gmx::ssize(*bonds) > 0 && ftype_a < F_NRE); ftype_a++)
{
if (interaction_function[ftype_a].flags & IF_ATYPE)
{
- InteractionsOfType *pr = &(plist[ftype_a]);
+ InteractionsOfType* pr = &(plist[ftype_a]);
- for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end(); )
+ for (auto parm = pr->interactionTypes.begin();
+ parm != pr->interactionTypes.end();)
{
- const InteractionOfType *ang = &(*parm);
+ const InteractionOfType* ang = &(*parm);
#ifdef DEBUG
printf("Angle: %d-%d-%d\n", ang->ai(), ang->aj(), ang->ak());
#endif
int numhydrogens = count_hydrogens(info, 3, ang->atoms());
- if ((nshake == eshALLANGLES) ||
- (numhydrogens > 1) ||
- (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
+ if ((nshake == eshALLANGLES) || (numhydrogens > 1)
+ || (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
{
/* Can only add hydrogen angle shake, if the two bonds
* are constrained.
* append this angle to the shake list
*/
- std::vector<int> atomNumbers = {ang->ai(), ang->ak()};
+ std::vector<int> atomNumbers = { ang->ai(), ang->ak() };
/* Calculate length of constraint */
bool bFound = false;
- b_ij = b_jk = 0.0;
- for (const auto &bond : bonds->interactionTypes)
+ b_ij = b_jk = 0.0;
+ for (const auto& bond : bonds->interactionTypes)
{
- if (((bond.ai() == ang->ai()) &&
- (bond.aj() == ang->aj())) ||
- ((bond.ai() == ang->aj()) &&
- (bond.aj() == ang->ai())))
+ if (((bond.ai() == ang->ai()) && (bond.aj() == ang->aj()))
+ || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ai())))
{
b_ij = bond.c0();
}
- if (((bond.ai() == ang->ak()) &&
- (bond.aj() == ang->aj())) ||
- ((bond.ai() == ang->aj()) &&
- (bond.aj() == ang->ak())))
+ if (((bond.ai() == ang->ak()) && (bond.aj() == ang->aj()))
+ || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ak())))
{
b_jk = bond.c0();
}
}
if (bFound)
{
- real param = std::sqrt( b_ij*b_ij + b_jk*b_jk -
- 2.0*b_ij*b_jk*cos(DEG2RAD*ang->c0()));
- std::vector<real> forceParm = {param, param};
- if (ftype == F_CONNBONDS ||
- ftype_a == F_CONNBONDS)
+ real param = std::sqrt(b_ij * b_ij + b_jk * b_jk
+ - 2.0 * b_ij * b_jk
+ * cos(DEG2RAD * ang->c0()));
+ std::vector<real> forceParm = { param, param };
+ if (ftype == F_CONNBONDS || ftype_a == F_CONNBONDS)
{
- gmx_fatal(FARGS, "Can not constrain all angles when they involved bonds of type %s",
+ gmx_fatal(FARGS,
+ "Can not constrain all angles when they "
+ "involved bonds of type %s",
interaction_function[F_CONNBONDS].longname);
}
/* apply law of cosines */
printf("p: %d, q: %d, dist: %12.5e\n", atomNumbers[0],
atomNumbers[1], forceParm[0]);
#endif
- add_param_to_list (&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
+ add_param_to_list(&(plist[F_CONSTR]),
+ InteractionOfType(atomNumbers, forceParm));
/* move the last bond to this position */
*parm = *(pr->interactionTypes.end() - 1);
pr->interactionTypes.erase(pr->interactionTypes.end() - 1);
{
if (interaction_function[ftype].flags & IF_BTYPE)
{
- InteractionsOfType *pr = &(plist[ftype]);
- for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end(); )
+ InteractionsOfType* pr = &(plist[ftype]);
+ for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end();)
{
- if ( (nshake != eshHBONDS) ||
- (count_hydrogens (info, 2, parm->atoms()) > 0) )
+ if ((nshake != eshHBONDS) || (count_hydrogens(info, 2, parm->atoms()) > 0))
{
/* append this bond to the shake list */
- std::vector<int> atomNumbers = {parm->ai(), parm->aj()};
- std::vector<real> forceParm = { parm->c0(), parm->c2()};
- add_param_to_list (&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
+ std::vector<int> atomNumbers = { parm->ai(), parm->aj() };
+ std::vector<real> forceParm = { parm->c0(), parm->c2() };
+ add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
parm = pr->interactionTypes.erase(parm);
}
else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff