33 #define cbrt(x) pow((double)x,(double)(1.0/3.0))
70 #define MAX_MULTIPLICITY 6
73 #define MAX_ATOMTYPE_CHARS 6
279 int *maxDihedralMults;
281 int *maxImproperMults;
284 void skip_stream_read(
char *, FILE *);
286 void add_bond_param(
const char *,
Bool);
290 void add_angle_param(
char *);
294 void add_dihedral_param(
char *, FILE *);
298 void add_improper_param(
char *, FILE *);
301 void add_crossterm_param(
char *, FILE *);
304 void add_vdw_param(
char *);
308 void add_vdw_pair_param(
char *);
309 void add_nbthole_pair_param(
char *);
310 void add_table_pair_param(
char *);
315 void add_hb_pair_param(
char *);
321 void traverse_vdw_params(
struct vdw_params *);
334 void index_dihedrals();
335 void index_impropers();
336 void index_crossterms();
338 void convert_vdw_pairs();
339 void convert_nbthole_pairs();
340 void convert_table_pairs();
363 void free_vdw_pair_list();
364 void free_nbthole_pair_list();
419 #ifdef MEM_OPT_VERSION
480 NAMD_die(
"Bad mult index in Parameters::get_improper_params");
493 NAMD_die(
"Bad mult index in Parameters::get_dihedral_params");
514 *sigma = sqrt(
cbrt(A)) / sqrt(
cbrt(B));
515 *epsilon = B*B / (4*
A);
518 *sigma = 0; *epsilon = 0;
521 *sigma14 = sqrt(
cbrt(A14)) / sqrt(
cbrt(B14));
522 *epsilon14 = B14*B14 / (4*A14);
525 *sigma14 = 0; *epsilon14 = 0;
528 else {
NAMD_die (
"Function get_vdw_params failed to derive Lennard-Jones sigma and epsilon from A and B values\n");}
GromacsPairValue * gromacsPair_array
void assign_improper_index(const char *, const char *, const char *, const char *, Improper *, int)
CrosstermData c[dim][dim]
void assign_vdw_index(const char *, Atom *)
void print_crossterm_params()
void read_charmm_parameter_file(char *)
struct indexed_vdw_pair * right
void assign_bond_index(const char *, const char *, Bond *)
struct indexed_table_pair * right
struct indexed_table_pair IndexedTablePair
int get_improper_multiplicity(Index index)
void get_dihedral_params(Real *k, int *n, Real *delta, Index index, int mult)
int read_energy_type_cubspline(FILE *, const int, BigReal *, const float, const float)
DihedralValue * dihedral_array
CrosstermValue * crossterm_array
IndexedVdwPair * vdw_pair_tree
int read_energy_type(FILE *, const int, BigReal *, const float, const float)
void print_param_summary()
IndexedNbtholePair * nbthole_pair_tree
void read_parameter_file(char *)
FourBodyConsts values[MAX_MULTIPLICITY]
struct indexed_vdw_pair * left
int get_int_table_type(char *)
void get_angle_params(Real *k, Real *theta0, Real *k_ub, Real *r_ub, Index index)
void get_improper_params(Real *k, int *n, Real *delta, Index index, int mult)
void assign_crossterm_index(const char *, const char *, const char *, const char *, const char *, const char *, const char *, const char *, Crossterm *)
void print_vdw_pair_params()
struct indexed_table_pair * left
void print_dihedral_params()
struct four_body_consts FourBodyConsts
struct indexed_vdw_pair IndexedVdwPair
ImproperValue * improper_array
int get_vdw_pair_params(Index ind1, Index ind2, Real *, Real *, Real *, Real *)
void NAMD_die(const char *err_msg)
NbtholePairValue * nbthole_array
char * atom_type_name(Index a)
int get_num_vdw_params(void)
FourBodyConsts values[MAX_MULTIPLICITY]
struct indexed_nbthole_pair * right
int get_table_pair_params(Index, Index, int *)
void send_Parameters(MOStream *)
void done_reading_files(Bool)
void print_nbthole_pair_params()
void read_ener_table(SimParameters *)
void print_improper_params()
int read_energy_type_bothcubspline(FILE *, const int, BigReal *, const float, const float)
void assign_dihedral_index(const char *, const char *, const char *, const char *, Dihedral *, int, int)
void done_reading_structure()
void assign_angle_index(const char *, const char *, const char *, Angle *, int)
struct indexed_nbthole_pair * left
void print_angle_params()
void get_bond_params(Real *k, Real *x0, Index index)
struct nbthole_pair_value NbtholePairValue
void get_vdw_params(Real *sigma, Real *epsilon, Real *sigma14, Real *epsilon14, Index index)
int get_dihedral_multiplicity(Index index)
IndexedTablePair * tab_pair_tree
#define MAX_ATOMTYPE_CHARS
struct indexed_nbthole_pair IndexedNbtholePair
void receive_Parameters(MIStream *)