#include <cstring>
#include <algorithm>
+#include <memory>
#include <unordered_set>
#include <sys/types.h>
}
-static void make_atoms_sys(const std::vector<gmx_molblock_t> &molblock,
- const t_molinfo *molinfo,
- t_atoms *atoms)
+static void make_atoms_sys(gmx::ArrayRef<const gmx_molblock_t> molblock,
+ gmx::ArrayRef<const MoleculeInformation> molinfo,
+ t_atoms *atoms)
{
atoms->nr = 0;
atoms->atom = nullptr;
t_symtab *symtab,
gpp_atomtype *atype,
int *nrmols,
- t_molinfo **molinfo,
- t_molinfo **intermolecular_interactions,
+ std::vector<MoleculeInformation> *molinfo,
+ std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
t_params plist[],
int *combination_rule,
double *reppow,
bool usingFullRangeElectrostatics,
warninp *wi)
{
- FILE *out;
- int i, sl, nb_funct;
- char *pline = nullptr, **title = nullptr;
- char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
- char genpairs[32];
- char *dirstr, *dummy2;
- int nrcopies, nmol, nscan, ncombs, ncopy;
- double fLJ, fQQ, fPOW;
- t_molinfo *mi0 = nullptr;
- DirStack *DS;
- Directive d, newd;
- t_nbparam **nbparam, **pair;
- gmx::ExclusionBlocks *exclusionBlocks;
- real fudgeLJ = -1; /* Multiplication factor to generate 1-4 from LJ */
- bool bReadDefaults, bReadMolType, bGenPairs, bWarn_copy_A_B;
- double qt = 0, qBt = 0; /* total charge */
- gpp_bond_atomtype *batype;
- int lastcg = -1;
- int dcatt = -1, nmol_couple;
+ FILE *out;
+ int sl, nb_funct;
+ char *pline = nullptr, **title = nullptr;
+ char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
+ char genpairs[32];
+ char *dirstr, *dummy2;
+ int nrcopies, nmol, nscan, ncombs, ncopy;
+ double fLJ, fQQ, fPOW;
+ MoleculeInformation *mi0 = nullptr;
+ DirStack *DS;
+ Directive d, newd;
+ t_nbparam **nbparam, **pair;
+ gmx::ExclusionBlocks *exclusionBlocks;
+ real fudgeLJ = -1; /* Multiplication factor to generate 1-4 from LJ */
+ bool bReadDefaults, bReadMolType, bGenPairs, bWarn_copy_A_B;
+ double qt = 0, qBt = 0; /* total charge */
+ gpp_bond_atomtype *batype;
+ int lastcg = -1;
+ int dcatt = -1, nmol_couple;
/* File handling variables */
- int status;
- bool done;
- gmx_cpp_t handle;
- char *tmp_line = nullptr;
- char warn_buf[STRLEN];
- const char *floating_point_arithmetic_tip =
+ int status;
+ bool done;
+ gmx_cpp_t handle;
+ char *tmp_line = nullptr;
+ char warn_buf[STRLEN];
+ const char *floating_point_arithmetic_tip =
"Total charge should normally be an integer. See\n"
"http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n"
"for discussion on how close it should be to an integer.\n";
*reppow = 12.0; /* Default value for repulsion power */
- *intermolecular_interactions = nullptr;
-
/* Init the number of CMAP torsion angles and grid spacing */
plist[F_CMAP].grid_spacing = 0;
plist[F_CMAP].nc = 0;
* to process the intermolecular interactions
* by making a "molecule" of the size of the system.
*/
- snew(*intermolecular_interactions, 1);
- init_molinfo(*intermolecular_interactions);
- mi0 = *intermolecular_interactions;
+ *intermolecular_interactions = std::make_unique<MoleculeInformation>( );
+ mi0 = intermolecular_interactions->get();
+ mi0->initMolInfo();
make_atoms_sys(*molblock, *molinfo,
&mi0->atoms);
}
bReadMolType = TRUE;
}
- push_molt(symtab, &nmol, molinfo, pline, wi);
+ push_molt(symtab, molinfo, pline, wi);
+ nmol = molinfo->size();
srenew(exclusionBlocks, nmol);
exclusionBlocks[nmol-1].nr = 0;
- mi0 = &((*molinfo)[nmol-1]);
+ mi0 = &molinfo->back();
mi0->atoms.haveMass = TRUE;
mi0->atoms.haveCharge = TRUE;
mi0->atoms.haveType = TRUE;
int whichmol;
bool bCouple;
- push_mol(nmol, *molinfo, pline, &whichmol, &nrcopies, wi);
+ push_mol(*molinfo, pline, &whichmol, &nrcopies, wi);
mi0 = &((*molinfo)[whichmol]);
molblock->resize(molblock->size() + 1);
molblock->back().type = whichmol;
}
DS_Done (&DS);
- for (i = 0; i < nmol; i++)
+ for (int i = 0; i < gmx::index(molinfo->size()); i++)
{
gmx::doneExclusionBlocks(&(exclusionBlocks[i]));
}
if (*intermolecular_interactions != nullptr)
{
- sfree(mi0->atoms.atom);
+ sfree(intermolecular_interactions->get()->atoms.atom);
}
*nrmols = nmol;
return title;
}
-char **do_top(bool bVerbose,
- const char *topfile,
- const char *topppfile,
- t_gromppopts *opts,
- bool bZero,
- t_symtab *symtab,
- t_params plist[],
- int *combination_rule,
- double *repulsion_power,
- real *fudgeQQ,
- gpp_atomtype *atype,
- int *nrmols,
- t_molinfo **molinfo,
- t_molinfo **intermolecular_interactions,
- const t_inputrec *ir,
- std::vector<gmx_molblock_t> *molblock,
- bool *ffParametrizedWithHBondConstraints,
- warninp *wi)
+char **do_top(bool bVerbose,
+ const char *topfile,
+ const char *topppfile,
+ t_gromppopts *opts,
+ bool bZero,
+ t_symtab *symtab,
+ t_params plist[],
+ int *combination_rule,
+ double *repulsion_power,
+ real *fudgeQQ,
+ gpp_atomtype *atype,
+ int *nrmols,
+ std::vector<MoleculeInformation> *molinfo,
+ std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
+ const t_inputrec *ir,
+ std::vector<gmx_molblock_t> *molblock,
+ bool *ffParametrizedWithHBondConstraints,
+ warninp *wi)
{
/* Tmpfile might contain a long path */
const char *tmpfile;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff