Psi4
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
opt Namespace Reference

Namespaces

 v3d
 

Classes

class  BEND
 
class  CART
 
class  COMBO_COORDINATES
 
class  FB_FRAG
 
class  FRAG
 A group of atoms, its geometry, and its internal coordinates. More...
 
struct  fixed_coord
 
struct  frozen_cart
 
class  INTERFRAG
 
class  IRC_POINT
 
class  IRC_DATA
 
class  MOLECULE
 
class  OOFP
 
class  STEP_DATA
 
class  OPT_DATA
 
class  INTCO_EXCEPT
 Exception class for problems with internal coordinates. More...
 
class  BAD_STEP_EXCEPT
 
class  BROKEN_SYMMETRY_EXCEPT
 
struct  OPT_PARAMS
 
class  SIMPLE_COORDINATE
 
class  STRE
 
class  TORS
 

Typedefs

typedef const double *const *const GeomType
 

Enumerations

enum  OPT_IO_FILE_STATUS { OPT_IO_OPEN_NEW, OPT_IO_OPEN_OLD }
 
enum  INTCO_TYPE {
  min_type, stre_type, bend_type, tors_type,
  oofp_type, cart_type, max_type
}
 

Functions

psi::PsiReturnType optking (psi::Options &)
 
void opt_clean (void)
 
map< string, double > create_element_to_Z_map ()
 
double Element_to_Z (std::string lbl)
 
int zeta (const int a, const int m, const int n)
 
int delta (const int i, const int j)
 
std::vector< int > split_to_ints (string &s)
 
std::vector< fixed_coordsplit_to_fixed_coord (string &str, int N)
 
std::vector< frozen_cartsplit_to_frozen_cart (string &str)
 
template<typename T >
StringToNumber (const string &Text)
 
static int period (int Z)
 
static double r_ref_table (int perA, int perB)
 
static double alpha_table (int perA, int perB)
 
static double Rcov (double ZA, double ZB)
 
bool int_compare (int i, int j)
 
bool is_integer (const char *check)
 
int read_natoms (void)
 
void zmat_point (double *A, double *B, double *C, double R_CD, double theta_BCD, double phi_ABCD, double *D)
 
void rotate_vecs (double *w, double phi, double **v, int num_v)
 Rotate a set of vectors around an arbitrary axis Vectors are rows of input matrix. More...
 
bool opt_io_is_present (void)
 
void opt_io_remove (bool force=false)
 
void opt_io_open (OPT_IO_FILE_STATUS status)
 
void opt_io_close (int keep)
 
void opt_io_read_entry (const char *key, char *buffer, size_t size)
 
void opt_io_write_entry (const char *key, char *buffer, size_t size)
 
void opt_intco_dat_remove (void)
 
double ** symm_matrix_inv (double **A, int dim, bool redundant)
 
double ** matrix_return_copy (double **A, int nr, int nc)
 
bool ** matrix_return_copy (bool **A, int nr, int nc)
 
void array_copy (double *v_from, double *v_to, int n)
 
void matrix_copy (double **from, double **to, int nr, int nc)
 
double array_dot (double *v1, double *v2, int n)
 
void array_normalize (double *v1, int n)
 
double array_norm (double *v1, int n)
 
void array_scm (double *v1, double a, int n)
 
double array_abs_max (double *v1, int n)
 
double array_max (double *v1, int n)
 
double array_rms (double *v1, int n)
 
void matrix_root (double **A, int dim, bool inverse)
 
void zero_array (double *A, long int n)
 
void zero_matrix (double **A, long int m, long int n)
 
void zero_int_array (int *A, long int n)
 
void zero_bool_array (bool *A, long int n)
 
double * init_array (long int m)
 
int * init_int_array (int m)
 
bool * init_bool_array (int m)
 
void free_array (double *f)
 
void free_int_array (int *f)
 
void free_bool_array (bool *f)
 
double ** init_matrix (long int m, long int n)
 
double ** unit_matrix (long int m)
 
void unit_matrix (double **A, long int m)
 
void free_matrix (double **A)
 
int ** init_int_matrix (long int m, long int n)
 
void free_int_matrix (int **A)
 
bool ** init_bool_matrix (long int m, long int n)
 
void free_bool_matrix (bool **A)
 
double DE_nr_energy (double step, double grad, double hess)
 
double DE_rfo_energy (double rfo_t, double rfo_g, double rfo_h)
 
double step_N_factor (double **G, double *g, int Nintco)
 
double * lowest_evector (double **H, int Nintco)
 
void GS_interpolation (double *p, double *p_0, double *g, double *g_0, int dim)
 
void interpolation (double *p, double *p_0, double *g, double *g_0, int dim)
 
double lag_function (double l, double *f, double *h, double *p, double *g, int dim, double s)
 
bool stoi (std::string s, int *a)
 
bool stob (std::string s, bool *a)
 
bool stof (std::string s, double *val)
 
bool has_asterisk (std::string &s)
 
bool myline (std::ifstream &fin, std::vector< std::string > &tokens, int &line_num)
 
double DE_quadratic_energy (double step, double grad, double hess)
 
int sign_of_double (double d)
 
void open_output_dat (void)
 
void close_output_dat (void)
 
void print_title_out (void)
 
void print_end_out (void)
 
void init_ioff (void)
 
void set_params (psi::Options &options)
 
void oprintf (const std::string psi_fp, const FILE *qc_fp, const char *format,...)
 
void offlush_out (void)
 
void oprintf_out (const char *format,...)
 
void oprint_matrix (const std::string psi_fp, const FILE *qc_fp, double **A, const int nrow, const int ncol)
 
void oprint_matrix_out (double **A, const int nrow, const int ncol)
 
void oprint_matrix_out_precise (double **A, const int nrow, const int ncol)
 
void oprint_array (const std::string psi_fp, const FILE *qc_fp, double *A, const int ncol)
 
void oprint_array_out (double *A, const int ncol)
 
void oprint_array_out_precise (double *A, const int ncol)
 
void print_params_out (void)
 

Variables

const char * Z_to_symbol []
 
const double Z_to_mass []
 
static map< string, double > element_to_Z_map = create_element_to_Z_map()
 
EXTERN std::string psi_outfile
 
EXTERN FILE * qc_outfile
 
EXTERN int * ioff
 
EXTERN OPT_PARAMS Opt_params
 
EXTERN OPT_DATAp_Opt_data
 
EXTERN IRC_DATAp_irc_data
 

Typedef Documentation

typedef const double* const* const opt::GeomType

Enumeration Type Documentation

Enumerator
min_type 
stre_type 
bend_type 
tors_type 
oofp_type 
cart_type 
max_type 
Enumerator
OPT_IO_OPEN_NEW 
OPT_IO_OPEN_OLD 

Function Documentation

double opt::alpha_table ( int  perA,
int  perB 
)
inlinestatic
double opt::array_abs_max ( double *  v1,
int  n 
)
void opt::array_copy ( double *  v_from,
double *  v_to,
int  n 
)
double opt::array_dot ( double *  v1,
double *  v2,
int  n 
)
double opt::array_max ( double *  v1,
int  n 
)
double opt::array_norm ( double *  v1,
int  n 
)
void opt::array_normalize ( double *  v1,
int  n 
)
double opt::array_rms ( double *  v1,
int  n 
)
void opt::array_scm ( double *  v1,
double  a,
int  n 
)
void opt::close_output_dat ( void  )
map<string,double> opt::create_element_to_Z_map ( )
double opt::DE_nr_energy ( double  step,
double  grad,
double  hess 
)
inline
double opt::DE_quadratic_energy ( double  step,
double  grad,
double  hess 
)
inline
double opt::DE_rfo_energy ( double  rfo_t,
double  rfo_g,
double  rfo_h 
)
inline
int opt::delta ( const int  i,
const int  j 
)
inline
double opt::Element_to_Z ( std::string  lbl)
void opt::free_array ( double *  f)
void opt::free_bool_array ( bool *  f)
void opt::free_bool_matrix ( bool **  A)
void opt::free_int_array ( int *  f)
void opt::free_int_matrix ( int **  A)
void opt::free_matrix ( double **  A)
void opt::GS_interpolation ( double *  p,
double *  p_0,
double *  g,
double *  g_0,
int  dim 
)
bool opt::has_asterisk ( std::string &  s)
double * opt::init_array ( long int  m)
bool * opt::init_bool_array ( int  m)
bool ** opt::init_bool_matrix ( long int  m,
long int  n 
)
int * opt::init_int_array ( int  m)
int ** opt::init_int_matrix ( long int  m,
long int  n 
)
void opt::init_ioff ( void  )
double ** opt::init_matrix ( long int  m,
long int  n 
)
bool opt::int_compare ( int  i,
int  j 
)
void opt::interpolation ( double *  p,
double *  p_0,
double *  g,
double *  g_0,
int  dim 
)
bool opt::is_integer ( const char *  check)
double opt::lag_function ( double  l,
double *  f,
double *  h,
double *  p,
double *  g,
int  dim,
double  s 
)
double * opt::lowest_evector ( double **  H,
int  Nintco 
)
void opt::matrix_copy ( double **  from,
double **  to,
int  nr,
int  nc 
)
double ** opt::matrix_return_copy ( double **  A,
int  nr,
int  nc 
)
bool ** opt::matrix_return_copy ( bool **  A,
int  nr,
int  nc 
)
void opt::matrix_root ( double **  A,
int  dim,
bool  inverse 
)
bool opt::myline ( std::ifstream &  fin,
std::vector< std::string > &  tokens,
int &  line_num 
)
void opt::offlush_out ( void  )
void opt::open_output_dat ( void  )
void opt::oprint_array ( const std::string  psi_fp,
const FILE *  qc_fp,
double *  A,
const int  ncol 
)
void opt::oprint_array_out ( double *  A,
const int  ncol 
)
void opt::oprint_array_out_precise ( double *  A,
const int  ncol 
)
void opt::oprint_matrix ( const std::string  psi_fp,
const FILE *  qc_fp,
double **  A,
const int  nrow,
const int  ncol 
)
void opt::oprint_matrix_out ( double **  A,
const int  nrow,
const int  ncol 
)
void opt::oprint_matrix_out_precise ( double **  A,
const int  nrow,
const int  ncol 
)
void opt::oprintf ( const std::string  psi_fp,
const FILE *  qc_fp,
const char *  format,
  ... 
)
void opt::oprintf_out ( const char *  format,
  ... 
)
void opt::opt_clean ( void  )
void opt::opt_intco_dat_remove ( void  )
void opt::opt_io_close ( int  keep)
bool opt::opt_io_is_present ( void  )
void opt::opt_io_open ( OPT_IO_FILE_STATUS  status)
void opt::opt_io_read_entry ( const char *  key,
char *  buffer,
size_t  size 
)
void opt::opt_io_remove ( bool  force = false)
void opt::opt_io_write_entry ( const char *  key,
char *  buffer,
size_t  size 
)
OptReturnType opt::optking ( psi::Options options)
int opt::period ( int  Z)
inlinestatic
void opt::print_end_out ( void  )
void opt::print_params_out ( void  )
void opt::print_title_out ( void  )
double opt::r_ref_table ( int  perA,
int  perB 
)
inlinestatic
static double opt::Rcov ( double  ZA,
double  ZB 
)
inlinestatic
int opt::read_natoms ( void  )
void opt::rotate_vecs ( double *  w,
double  phi,
double **  v,
int  num_v 
)

Rotate a set of vectors around an arbitrary axis Vectors are rows of input matrix.

rotate_vecs(): Rotate a set of vectors around an arbitrary axis

Parameters
wdouble * : axis to rotate around (wx, wy, wz) - gets normalized here
phidouble : magnitude of rotation
vdouble ** : points to rotate - column dim is 3; overwritten on exit
num_vint :

Returns: none

Rollin King, Feb. 2008

void opt::set_params ( psi::Options options)
int opt::sign_of_double ( double  d)
inline
std::vector< fixed_coord > opt::split_to_fixed_coord ( string &  str,
int  N 
)
std::vector< frozen_cart > opt::split_to_frozen_cart ( string &  str)
std::vector< int > opt::split_to_ints ( string &  s)
double opt::step_N_factor ( double **  G,
double *  g,
int  Nintco 
)
bool opt::stob ( std::string  s,
bool *  a 
)
bool opt::stof ( std::string  s,
double *  val 
)
bool opt::stoi ( std::string  s,
int *  a 
)
template<typename T >
T opt::StringToNumber ( const string &  Text)
double ** opt::symm_matrix_inv ( double **  A,
int  dim,
bool  redundant 
)
double ** opt::unit_matrix ( long int  m)
void opt::unit_matrix ( double **  A,
long int  m 
)
void opt::zero_array ( double *  A,
long int  n 
)
void opt::zero_bool_array ( bool *  A,
long int  n 
)
void opt::zero_int_array ( int *  A,
long int  n 
)
void opt::zero_matrix ( double **  A,
long int  m,
long int  n 
)
int opt::zeta ( const int  a,
const int  m,
const int  n 
)
inline
void opt::zmat_point ( double *  A,
double *  B,
double *  C,
double  R_CD,
double  theta_BCD,
double  phi_ABCD,
double *  D 
)

Variable Documentation

map<string,double> opt::element_to_Z_map = create_element_to_Z_map()
static
EXTERN int* opt::ioff
OPT_PARAMS opt::Opt_params
EXTERN IRC_DATA* opt::p_irc_data
EXTERN OPT_DATA* opt::p_Opt_data
EXTERN std::string opt::psi_outfile
EXTERN FILE* opt::qc_outfile
const double opt::Z_to_mass
Initial value:
= {
0.,1.00782503207,4.00260325415,7.016004548,9.012182201,11.009305406,
12,14.00307400478,15.99491461956,18.998403224,19.99244017542,
22.98976928087,23.985041699,26.981538627,27.97692653246,30.973761629,
31.972070999,34.968852682,39.96238312251,38.963706679,39.962590983,
44.955911909,47.947946281,50.943959507,51.940507472,54.938045141,
55.934937475,58.933195048,57.935342907,62.929597474,63.929142222,
68.925573587,73.921177767,74.921596478,79.916521271,78.918337087,
85.910610729,84.911789737,87.905612124,88.905848295,89.904704416,
92.906378058,97.905408169,98.906254747,101.904349312,102.905504292,
105.903485715,106.90509682,113.90335854,114.903878484,119.902194676,
120.903815686,129.906224399,126.904472681,131.904153457,132.905451932,
137.905247237,138.906353267,139.905438706,140.907652769,141.907723297,
144.912749023,151.919732425,152.921230339,157.924103912,158.925346757,
163.929174751,164.93032207,165.930293061,168.93421325,173.938862089,
174.940771819,179.946549953,180.947995763,183.950931188,186.955753109,
191.96148069,192.96292643,194.964791134,196.966568662,201.970643011,
204.974427541,207.976652071,208.980398734,208.982430435,210.987496271,
222.017577738,222.01755173,228.031070292,227.027752127,232.038055325,
231.03588399,238.050788247,237.048173444,242.058742611,243.06138108,
247.07035354,247.07030708,251.079586788,252.082978512,257.095104724,
258.098431319,255.093241131,260.105504,263.112547,255.107398,259.114500,
262.122892,263.128558,265.136151,281.162061,272.153615,283.171792,283.176451,
285.183698,287.191186,292.199786,291.206564,293.214670}
const char * opt::Z_to_symbol
Initial value:
= {
"X","H","HE","LI","BE","B","C","N","O","F","NE","NA","MG","AL","SI",
"P","S","CL","AR","K","CA","SC","TI","V","CR","MN","FE","CO","NI",
"CU","ZN","GA","GE","AS","SE","BR","KR","RB","SR","Y","ZR","NB","MO",
"TC","RU","RH","PD","AG","CD","IN","SN","SB","TE","I","XE","CS","BA",
"LA","CE","PR","ND","PM","SM","EU","GD","TB","DY","HO","ER","TM","YB",
"LU","HF","TA","W","RE","OS","IR","PT","AU","HG","TL","PB","BI","PO",
"AT","RN","FR","RA","AC","TH","PA","U","NP","PU","AM","CM","BK","CF",
"ES","FM","MD","NO","LR","RF","DB","SG","BH","HS","MT","DS","RG",
"UUB","UUT","UUQ","UUP","UUH","UUS","UUO"}