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gaussiandata Struct Reference

#include <gaussianplugin.h>

List of all members.

Public Attributes
FILE *	file
int	numatoms
int	runtyp
char	gbasis [20]
char	basis_string [MOLFILE_BUFSIZ]
char	runtitle [MOLFILE_BUFSIZ]
char	geometry [MOLFILE_BUFSIZ]
char	guess [MOLFILE_BUFSIZ]
char	version_string [MOLFILE_BUFSIZ]
int	version
char *	file_name
int	scftyp
char	scftyp_string [MOLFILE_BUFSIZ]
int	totalcharge
int	multiplicity
int	num_electrons
int	nimag
int *	nimag_modes
float *	wavenumbers
float *	intensities
float *	normal_modes
int	nproc
int	memory
int	have_wavefunction
int	have_basis
int	have_cart_basis
double *	mulliken_charges
int	have_mulliken
int	have_normal_modes
int	have_internals
int	have_cart_hessian
int	nintcoords
int	nbonds
int	nangles
int	ndiheds
int	nimprops
int *	bonds
int *	angles
int *	dihedrals
int *	impropers
double *	internal_coordinates
double *	carthessian
double *	inthessian
float *	basis
basis_atom_t *	basis_set
int	num_basis_funcs
int	num_basis_atoms
int *	atomicnum_per_basisatom
int	num_shells
int *	num_shells_per_atom
int *	num_prim_per_shell
int *	shell_symmetry
int	occ_orbitals_A
int	occ_orbitals_B
int	wavef_size
int	num_orbitals
int *	angular_momentum
int	converged
int	opt_status
qm_atom_t *	initatoms
float	initcell [6]
qm_timestep_t *	qm_timestep
int	num_frames
int	num_frames_sent
int	num_frames_read
int	end_of_trajectory

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Detailed Description

main gaussian plugin data structure

Definition at line 128 of file gaussianplugin.h.

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Member Data Documentation

int* gaussiandata::angles

Definition at line 240 of file gaussianplugin.h.

int* gaussiandata::angular_momentum

Array of length 3*num_wave_f containing the exponents describing the cartesian components of the angular momentum. E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}. Definition at line 304 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, get_wavefunction, read_cpmdlog_rundata, read_first_frame, and read_gaussian_rundata.

int* gaussiandata::atomicnum_per_basisatom

atomic number per atom in basis set Definition at line 279 of file gaussianplugin.h.

float* gaussiandata::basis

Definition at line 271 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, read_cpmdlog_rundata, and read_gaussian_rundata.

basis_atom_t* gaussiandata::basis_set

Definition at line 273 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, get_basis, and get_internal_basis.

char gaussiandata::basis_string[MOLFILE_BUFSIZ]

Definition at line 136 of file gaussianplugin.h. Referenced by get_basis_options, get_contrl, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int* gaussiandata::bonds

Definition at line 239 of file gaussianplugin.h.

double* gaussiandata::carthessian

Definition at line 250 of file gaussianplugin.h.

int gaussiandata::converged

this flag tells if the geometry search converged Definition at line 307 of file gaussianplugin.h.

int* gaussiandata::dihedrals

Definition at line 241 of file gaussianplugin.h.

int gaussiandata::end_of_trajectory

Definition at line 335 of file gaussianplugin.h. Referenced by get_traj_frame.

FILE* gaussiandata::file

Definition at line 130 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, find_traj_end, get_basis, get_basis_options, get_contrl, get_final_info, get_input_structure, get_population, get_proc_mem, get_runtitle, get_traj_frame, get_wavefunction, have_cpmd, have_gaussian, open_cpmdlog_read, open_gaussian_read, and parse_static_data.

char* gaussiandata::file_name

Definition at line 160 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, have_cpmd, have_gaussian, open_cpmdlog_read, and open_gaussian_read.

char gaussiandata::gbasis[20]

Definition at line 133 of file gaussianplugin.h. Referenced by get_basis, get_basis_options, get_contrl, get_internal_basis, and parse_static_data.

char gaussiandata::geometry[MOLFILE_BUFSIZ]

Definition at line 140 of file gaussianplugin.h. Referenced by read_cpmdlog_rundata, and read_gaussian_rundata.

char gaussiandata::guess[MOLFILE_BUFSIZ]

Definition at line 141 of file gaussianplugin.h.

int gaussiandata::have_basis

TRUE/FALSE flag indicating if we should try searching for wavefunction data. Gaussian needs IOP(6/7=3) to do this. if it is not set, we can save time searching. should help a lot with large log files... Definition at line 191 of file gaussianplugin.h. Referenced by get_basis, get_contrl, get_internal_basis, and parse_static_data.

int gaussiandata::have_cart_basis

TRUE/FALSE flag initially indicating if we should try searching for basis set data. Gaussian needs GFINPUT to print the data in a form that we can parse. If it is not set, we can save time searching. Should help a lot with large log files. If there is no basis in the log, we try reading the basis set from a local database. After initial parse it indicates whether basis set data is available. Definition at line 202 of file gaussianplugin.h. Referenced by get_contrl.

int gaussiandata::have_cart_hessian

Definition at line 229 of file gaussianplugin.h.

int gaussiandata::have_internals

TRUE/FALSE flag indicating if we could properly read normal modes, wavenumbers and intensities. Definition at line 225 of file gaussianplugin.h.

int gaussiandata::have_mulliken

Definition at line 215 of file gaussianplugin.h. Referenced by get_population, read_cpmdlog_structure, and read_gaussian_structure.

int gaussiandata::have_normal_modes

Definition at line 217 of file gaussianplugin.h.

int gaussiandata::have_wavefunction

Definition at line 185 of file gaussianplugin.h. Referenced by get_contrl, get_traj_frame, get_wavefunction, and parse_static_data.

int* gaussiandata::impropers

Definition at line 242 of file gaussianplugin.h.

qm_atom_t* gaussiandata::initatoms

Definition at line 321 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, get_basis, get_input_structure, get_internal_basis, get_traj_frame, parse_static_data, read_cpmdlog_structure, and read_gaussian_structure.

float gaussiandata::initcell[6]

initial cell info (in cpmd notation)": a, b/a, c/a, cos(alpha), cos(beta), cos(gamma) Definition at line 325 of file gaussianplugin.h. Referenced by parse_static_data.

float* gaussiandata::intensities

Definition at line 178 of file gaussianplugin.h. Referenced by close_cpmdlog_read, and close_gaussian_read.

double* gaussiandata::internal_coordinates

Definition at line 244 of file gaussianplugin.h. Referenced by close_cpmdlog_read, and close_gaussian_read.

double* gaussiandata::inthessian

Definition at line 256 of file gaussianplugin.h.

int gaussiandata::memory

Definition at line 183 of file gaussianplugin.h. Referenced by get_proc_mem, read_cpmdlog_rundata, and read_gaussian_rundata.

double* gaussiandata::mulliken_charges

flag indicating if we have a cartesian basis set. this is additive. 0 = none (can only visualize up to P) 1 = have cartesian (6 instead of 5) d-functions) 2 = have cartesian (10 instead of 7) f-functions) 4 = have cartesian (XX instead of X) g-functions) basis transferred to VMD is always cartesian, so wavefunctions expanded in pure atomic orbitals will have to be converted. Definition at line 214 of file gaussianplugin.h. Referenced by close_cpmdlog_read, and close_gaussian_read.

int gaussiandata::multiplicity

Definition at line 170 of file gaussianplugin.h. Referenced by get_basis_options, get_contrl, get_input_structure, and parse_static_data.

int gaussiandata::nangles

Definition at line 235 of file gaussianplugin.h.

int gaussiandata::nbonds

Definition at line 234 of file gaussianplugin.h.

int gaussiandata::ndiheds

Definition at line 236 of file gaussianplugin.h.

int gaussiandata::nimag

Definition at line 172 of file gaussianplugin.h.

int* gaussiandata::nimag_modes

Definition at line 173 of file gaussianplugin.h.

int gaussiandata::nimprops

Definition at line 237 of file gaussianplugin.h.

int gaussiandata::nintcoords

Definition at line 233 of file gaussianplugin.h.

float* gaussiandata::normal_modes

Definition at line 180 of file gaussianplugin.h. Referenced by close_cpmdlog_read, and close_gaussian_read.

int gaussiandata::nproc

Definition at line 182 of file gaussianplugin.h. Referenced by get_proc_mem, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::num_basis_atoms

total number of primitive basis functions Definition at line 276 of file gaussianplugin.h. Referenced by fill_basis_arrays, get_basis, get_basis_options, get_internal_basis, get_population, read_gaussian_metadata, and read_gaussian_rundata.

int gaussiandata::num_basis_funcs

Definition at line 275 of file gaussianplugin.h. Referenced by fill_basis_arrays, get_basis, get_basis_options, get_internal_basis, read_cpmdlog_metadata, read_cpmdlog_rundata, read_gaussian_metadata, and read_gaussian_rundata.

int gaussiandata::num_electrons

Definition at line 171 of file gaussianplugin.h. Referenced by get_basis_options, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::num_frames

number of trajectory points; single point corresponds to 1 Definition at line 331 of file gaussianplugin.h. Referenced by find_traj_end, parse_static_data, and read_first_frame.

int gaussiandata::num_frames_read

Definition at line 333 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, get_traj_frame, parse_static_data, and read_first_frame.

int gaussiandata::num_frames_sent

Definition at line 332 of file gaussianplugin.h. Referenced by parse_static_data.

int gaussiandata::num_orbitals

Definition at line 299 of file gaussianplugin.h. Referenced by get_basis_options, and get_wavefunction.

int* gaussiandata::num_prim_per_shell

number of primitives in shell i Definition at line 286 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::num_shells

the total number of atomic shells Definition at line 282 of file gaussianplugin.h. Referenced by fill_basis_arrays, get_basis, get_basis_options, get_internal_basis, read_cpmdlog_metadata, read_cpmdlog_rundata, read_gaussian_metadata, and read_gaussian_rundata.

int* gaussiandata::num_shells_per_atom

number of shells per atom i Definition at line 284 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, get_basis, get_internal_basis, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::numatoms

Definition at line 131 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, get_input_structure, get_internal_basis, get_population, get_traj_frame, parse_static_data, read_cpmdlog_rundata, read_cpmdlog_structure, and read_gaussian_structure.

int gaussiandata::occ_orbitals_A

number of occupied spin alpha and beta orbitals Definition at line 291 of file gaussianplugin.h. Referenced by get_basis_options, get_wavefunction, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::occ_orbitals_B

Definition at line 292 of file gaussianplugin.h. Referenced by get_basis_options, get_wavefunction, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::opt_status

Definition at line 308 of file gaussianplugin.h. Referenced by find_traj_end.

qm_timestep_t* gaussiandata::qm_timestep

per timestep data like wavefunctions and scf iterations Definition at line 328 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, get_traj_frame, read_cpmdlog_structure, read_first_frame, and read_gaussian_structure.

char gaussiandata::runtitle[MOLFILE_BUFSIZ]

Definition at line 138 of file gaussianplugin.h. Referenced by get_runtitle, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::runtyp

Definition at line 132 of file gaussianplugin.h. Referenced by get_contrl, get_final_info, open_cpmdlog_read, open_gaussian_read, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::scftyp

Definition at line 166 of file gaussianplugin.h. Referenced by get_contrl, get_traj_frame, get_wavefunction, open_cpmdlog_read, open_gaussian_read, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

char gaussiandata::scftyp_string[MOLFILE_BUFSIZ]

Definition at line 168 of file gaussianplugin.h.

int* gaussiandata::shell_symmetry

symmetry type of each shell Definition at line 288 of file gaussianplugin.h. Referenced by close_cpmdlog_read, close_gaussian_read, fill_basis_arrays, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::totalcharge

Definition at line 169 of file gaussianplugin.h. Referenced by get_input_structure, parse_static_data, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::version

Definition at line 144 of file gaussianplugin.h. Referenced by get_basis, have_cpmd, have_gaussian, open_cpmdlog_read, open_gaussian_read, parse_static_data, and read_first_frame.

char gaussiandata::version_string[MOLFILE_BUFSIZ]

Definition at line 143 of file gaussianplugin.h. Referenced by have_cpmd, have_gaussian, open_cpmdlog_read, open_gaussian_read, read_cpmdlog_rundata, and read_gaussian_rundata.

int gaussiandata::wavef_size

Max. rank of the wave_function matrix. While the actual number of MOs present can be different for each frame, this is the maximum number of possible occupied and virtual orbitals. Definition at line 298 of file gaussianplugin.h. Referenced by get_basis_options, get_internal_basis, get_traj_frame, get_wavefunction, read_cpmdlog_metadata, read_cpmdlog_rundata, read_first_frame, read_gaussian_metadata, and read_gaussian_rundata.

float* gaussiandata::wavenumbers

Definition at line 175 of file gaussianplugin.h. Referenced by close_cpmdlog_read, and close_gaussian_read.

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The documentation for this struct was generated from the following file:

• gaussianplugin.h

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