}
static void mk_bonds(int nnm, t_nm2type nmt[],
- t_atoms *atoms, const rvec x[], t_params *bond, int nbond[],
+ t_atoms *atoms, const rvec x[], InteractionTypeParameters *bond, int nbond[],
bool bPBC, matrix box)
{
t_param b;
return cgnr;
}
-static gpp_atomtype *set_atom_type(t_symtab *tab, t_atoms *atoms, t_params *bonds,
+static gpp_atomtype *set_atom_type(t_symtab *tab, t_atoms *atoms, InteractionTypeParameters *bonds,
int *nbonds, int nnm, t_nm2type nm2t[])
{
gpp_atomtype *atype;
return atype;
}
-static void lo_set_force_const(t_params *plist, real c[], int nrfp, bool bRound,
+static void lo_set_force_const(InteractionTypeParameters *plist, real c[], int nrfp, bool bRound,
bool bDih, bool bParam)
{
- int i, j;
double cc;
char buf[32];
- for (i = 0; (i < plist->nr); i++)
+ for (int i = 0; (i < plist->nr); i++)
{
if (!bParam)
{
- for (j = 0; j < nrfp; j++)
+ for (int j = 0; j < nrfp; j++)
{
c[j] = NOTSET;
}
}
}
GMX_ASSERT(nrfp <= MAXFORCEPARAM/2, "Only 6 parameters may be used for an interaction");
- for (j = 0; (j < nrfp); j++)
+ for (int j = 0; (j < nrfp); j++)
{
plist->param[i].c[j] = c[j];
plist->param[i].c[nrfp+j] = c[j];
}
}
-static void set_force_const(t_params plist[], real kb, real kt, real kp, bool bRound,
+static void set_force_const(gmx::ArrayRef<InteractionTypeParameters> plist, real kb, real kt, real kp, bool bRound,
bool bParam)
{
real c[MAXFORCEPARAM];
lo_set_force_const(&plist[F_PDIHS], c, 3, bRound, TRUE, bParam);
}
-static void calc_angles_dihs(t_params *ang, t_params *dih, const rvec x[], bool bPBC,
+static void calc_angles_dihs(InteractionTypeParameters *ang, InteractionTypeParameters *dih, const rvec x[], bool bPBC,
matrix box)
{
- int i, ai, aj, ak, al, t1, t2, t3;
+ int t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
- real th, costh, ph;
+ real costh;
t_pbc pbc;
if (bPBC)
{
set_pbc(&pbc, epbcXYZ, box);
}
- for (i = 0; (i < ang->nr); i++)
+ for (int i = 0; (i < ang->nr); i++)
{
- ai = ang->param[i].ai();
- aj = ang->param[i].aj();
- ak = ang->param[i].ak();
- th = RAD2DEG*bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : nullptr,
- r_ij, r_kj, &costh, &t1, &t2);
+ int ai = ang->param[i].ai();
+ int aj = ang->param[i].aj();
+ int ak = ang->param[i].ak();
+ real th = RAD2DEG*bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : nullptr,
+ r_ij, r_kj, &costh, &t1, &t2);
ang->param[i].c0() = th;
}
- for (i = 0; (i < dih->nr); i++)
+ for (int i = 0; (i < dih->nr); i++)
{
- ai = dih->param[i].ai();
- aj = dih->param[i].aj();
- ak = dih->param[i].ak();
- al = dih->param[i].al();
- ph = RAD2DEG*dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : nullptr,
- r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
+ int ai = dih->param[i].ai();
+ int aj = dih->param[i].aj();
+ int ak = dih->param[i].ak();
+ int al = dih->param[i].al();
+ real ph = RAD2DEG*dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : nullptr,
+ r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
dih->param[i].c0() = ph;
}
}
}
}
-static void print_pl(FILE *fp, t_params plist[], int ftp, const char *name,
+static void print_pl(FILE *fp, gmx::ArrayRef<const InteractionTypeParameters> plist, int ftp, const char *name,
char ***atomname)
{
- int i, j, nral, nrfp;
-
if (plist[ftp].nr > 0)
{
fprintf(fp, "\n");
fprintf(fp, "[ %s ]\n", name);
- nral = interaction_function[ftp].nratoms;
- nrfp = interaction_function[ftp].nrfpA;
- for (i = 0; (i < plist[ftp].nr); i++)
+ int nral = interaction_function[ftp].nratoms;
+ int nrfp = interaction_function[ftp].nrfpA;
+ for (int i = 0; (i < plist[ftp].nr); i++)
{
- for (j = 0; (j < nral); j++)
+ for (int j = 0; (j < nral); j++)
{
fprintf(fp, " %5s", *atomname[plist[ftp].param[i].a[j]]);
}
- for (j = 0; (j < nrfp); j++)
+ for (int j = 0; (j < nrfp); j++)
{
if (plist[ftp].param[i].c[j] != NOTSET)
{
}
static void print_rtp(const char *filenm, const char *title, t_atoms *atoms,
- t_params plist[], gpp_atomtype *atype, int cgnr[])
+ gmx::ArrayRef<const InteractionTypeParameters> plist, gpp_atomtype *atype, int cgnr[])
{
FILE *fp;
int i, tp;
int gmx_x2top(int argc, char *argv[])
{
- const char *desc[] = {
+ const char *desc[] = {
"[THISMODULE] generates a primitive topology from a coordinate file.",
"The program assumes all hydrogens are present when defining",
"the hybridization from the atom name and the number of bonds.",
"one of the short names above on the command line instead. In that",
"case [THISMODULE] just looks for the corresponding file.[PAR]",
};
- const char *bugs[] = {
+ const char *bugs[] = {
"The atom type selection is primitive. Virtually no chemical knowledge is used",
"Periodic boundary conditions screw up the bonding",
"No improper dihedrals are generated",
"The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in the data directory). Please extend it and send the results back to the GROMACS crew."
};
- FILE *fp;
- t_params plist[F_NRE];
- t_excls *excls;
- gpp_atomtype *atype;
- t_nextnb nnb;
- t_nm2type *nm2t;
- t_mols mymol;
- int nnm;
- char forcefield[32], ffdir[STRLEN];
- rvec *x; /* coordinates? */
- int *nbonds, *cgnr;
- int bts[] = { 1, 1, 1, 2 };
- matrix box; /* box length matrix */
- int natoms; /* number of atoms in one molecule */
- int epbc;
- bool bRTP, bTOP, bOPLS;
- t_symtab symtab;
- real qtot, mtot;
- char n2t[STRLEN];
- gmx_output_env_t *oenv;
-
- t_filenm fnm[] = {
+ FILE *fp;
+ std::array<InteractionTypeParameters, F_NRE> plist;
+ t_excls *excls;
+ gpp_atomtype *atype;
+ t_nextnb nnb;
+ t_nm2type *nm2t;
+ t_mols mymol;
+ int nnm;
+ char forcefield[32], ffdir[STRLEN];
+ rvec *x; /* coordinates? */
+ int *nbonds, *cgnr;
+ int bts[] = { 1, 1, 1, 2 };
+ matrix box; /* box length matrix */
+ int natoms; /* number of atoms in one molecule */
+ int epbc;
+ bool bRTP, bTOP, bOPLS;
+ t_symtab symtab;
+ real qtot, mtot;
+ char n2t[STRLEN];
+ gmx_output_env_t *oenv;
+
+ t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efTOP, "-o", "out", ffOPTWR },
{ efRTP, "-r", "out", ffOPTWR }
};
#define NFILE asize(fnm)
- real kb = 4e5, kt = 400, kp = 5;
- PreprocessResidue rtp_header_settings;
- bool bRemoveDihedralIfWithImproper = FALSE;
- bool bGenerateHH14Interactions = TRUE;
- bool bKeepAllGeneratedDihedrals = FALSE;
- int nrexcl = 3;
- bool bParam = TRUE, bRound = TRUE;
- bool bPairs = TRUE, bPBC = TRUE;
- bool bUsePDBcharge = FALSE, bVerbose = FALSE;
- const char *molnm = "ICE";
- const char *ff = "oplsaa";
- t_pargs pa[] = {
+ real kb = 4e5, kt = 400, kp = 5;
+ PreprocessResidue rtp_header_settings;
+ bool bRemoveDihedralIfWithImproper = FALSE;
+ bool bGenerateHH14Interactions = TRUE;
+ bool bKeepAllGeneratedDihedrals = FALSE;
+ int nrexcl = 3;
+ bool bParam = TRUE, bRound = TRUE;
+ bool bPairs = TRUE, bPBC = TRUE;
+ bool bUsePDBcharge = FALSE, bVerbose = FALSE;
+ const char *molnm = "ICE";
+ const char *ff = "oplsaa";
+ t_pargs pa[] = {
{ "-ff", FALSE, etSTR, {&ff},
"Force field for your simulation. Type \"select\" for interactive selection." },
{ "-v", FALSE, etBOOL, {&bVerbose},
mymol.name = gmx_strdup(molnm);
mymol.nr = 1;
- /* Init parameter lists */
- init_plist(plist);
-
/* Read coordinates */
t_topology *top;
snew(top, 1);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff