sc::GaussianBasisSet Class Reference

The GaussianBasisSet class is used describe a basis set composed of atomic gaussian orbitals. More...

#include <chemistry/qc/basis/gaussbas.h>

Inheritance diagram for sc::GaussianBasisSet:

Classes
class	Shell
	Shell is a GaussianShell that is part of GaussianBasisSet, i.e. has a center on which it's centered. More...
class	ValueData
	This holds scratch data needed to compute basis function values. More...

Public Member Functions
Ref< GaussianBasisSet >	operator+ (const Ref< GaussianBasisSet > &B)
	Uses UnionBasisSet to construct the sum of this and B. More...
GaussianBasisSet &	operator= (const GaussianBasisSet &A)
const std::string &	name () const
	Return the name of the basis set (is nonnull only if keyword "name" was provided)
const std::string &	label () const
	Return the label of the basis set. More...
Ref< Molecule >	molecule () const
	Return the Molecule object.
Ref< SCMatrixKit >	matrixkit ()
	Returns the SCMatrixKit that is to be used for AO bases.
Ref< SCMatrixKit >	so_matrixkit ()
	Returns the SCMatrixKit that is to be used for SO bases.
RefSCDimension	basisdim ()
	Returns the SCDimension object for the dimension.
unsigned int	ncenter () const
	Return the number of centers.
unsigned int	nshell () const
	Return the number of shells.
int	nshell_on_center (int icenter) const
	Return the number of shells on the given center.
int	shell_on_center (int icenter, int shell) const
	Return the overall shell number, given a center and the shell number on that center. More...
int	shell_to_center (int ishell) const
	Return the center on which the given shell is located. More...
unsigned int	nbasis () const
	Return the number of basis functions.
unsigned int	nbasis_on_center (int icenter) const
	Return the number of basis functions on the given center.
unsigned int	nprimitive () const
	Return the number of primitive Gaussians (sum of number of primitives for each Shell)
bool	has_pure () const
	Return true if basis contains solid harmonics Gaussians.
unsigned int	max_nfunction_in_shell () const
	Return the maximum number of functions that any shell has.
unsigned int	max_ncartesian_in_shell (int aminc=0) const
	Return the maximum number of Cartesian functions that any shell has. More...
unsigned int	max_nprimitive_in_shell () const
	Return the maximum number of primitive Gaussian that any shell has.
unsigned int	max_angular_momentum () const
	Return the highest angular momentum in any shell.
unsigned int	max_ncontraction () const
	Return the maximum number of Gaussians in a contraction in any shell.
unsigned int	max_am_for_contraction (int con) const
	Return the maximum angular momentum found in the given contraction number for any shell. More...
unsigned int	max_cartesian () const
	Return the maximum number of Cartesian functions in any shell.
int	shell_to_function (int i) const
	Return the number of the first function in the given shell.
int	function_to_shell (int i) const
	Return the shell to which the given function belongs.
const Shell &	operator() (int i) const
	Return a reference to Shell number i.
Shell &	operator() (int i)
	Return a reference to Shell number i.
const Shell &	operator[] (int i) const
	Return a reference to Shell number i.
Shell &	operator[] (int i)
	Return a reference to Shell number i.
const Shell &	shell (int i) const
	Return a reference to Shell number i.
Shell &	shell (int i)
	Return a reference to Shell number i.
const Shell &	operator() (int icenter, int ishell) const
	Return a reference to Shell number ishell on center icenter.
Shell &	operator() (int icenter, int ishell)
	Return a reference to Shell number ishell on center icenter.
const Shell &	shell (int i, int j) const
	Return a reference to Shell number j on center i.
Shell &	shell (int i, int j)
	Return a reference to Shell number j on center i.
int	find (int C, const GaussianShell &S) const
	Return the absolute index of shell S located at center C in this basis. If the shell is not found, returns -1.
double	r (int icenter, int xyz) const
	The location of center icenter. More...
int	values (const SCVector3 &r, ValueData *, double *basis_values) const
	Compute the values for this basis set at position r. More...
int	grad_values (const SCVector3 &r, ValueData *, double *g_values, double *basis_values=0) const
	Like values(...), but computes gradients of the basis function values, too. More...
int	hessian_values (const SCVector3 &r, ValueData *, double *h_values, double *g_values=0, double *basis_values=0) const
	Like values(...), but computes first and second derivatives of the basis function values, too. More...
int	shell_values (const SCVector3 &r, int sh, ValueData *, double *basis_values) const
	Compute the values for the given shell functions at position r. More...
int	grad_shell_values (const SCVector3 &r, int sh, ValueData *, double *g_values, double *basis_values=0) const
	Like values(...), but computes gradients of the shell function values, too. More...
int	hessian_shell_values (const SCVector3 &r, int sh, ValueData *, double *h_values, double *g_values=0, double *basis_values=0) const
	Like values(...), but computes first and second derivatives of the shell function values, too. More...
int	equiv (const Ref< GaussianBasisSet > &b)
	Returns true if this and the argument are equivalent.
void	print_brief (std::ostream &=ExEnv::out0()) const
	Print a brief description of the basis set.
virtual void	print (std::ostream &=ExEnv::out0()) const
	Print a detailed description of the basis set.
Serialization
	GaussianBasisSet (StateIn &si)
	restores this from si
void	save_data_state (StateOut &so)
	saves this to so
Public Member Functions inherited from sc::SavableState
SavableState &	operator= (const SavableState &)
void	save_state (StateOut &)
	Save the state of the object as specified by the StateOut object. More...
void	save_object_state (StateOut &)
	This can be used for saving state when the exact type of the object is known for both the save and the restore. More...
virtual void	save_vbase_state (StateOut &)
	Save the virtual bases for the object. More...
Public Member Functions inherited from sc::DescribedClass
	DescribedClass (const DescribedClass &)
DescribedClass &	operator= (const DescribedClass &)
ClassDesc *	class_desc () const MPQC__NOEXCEPT
	This returns the unique pointer to the ClassDesc corresponding to the given type_info object. More...
const char *	class_name () const
	Return the name of the object's exact type.
int	class_version () const
	Return the version of the class.
Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer. More...
Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types. More...
int	lock_ptr () const
	Lock this object.
int	unlock_ptr () const
	Unlock this object.
void	use_locks (bool inVal)
	start and stop using locks on this object
refcount_t	nreference () const
	Return the reference count.
refcount_t	reference ()
	Increment the reference count and return the new count.
refcount_t	dereference ()
	Decrement the reference count and return the new count.
int	managed () const
void	unmanage ()
	Turn off the reference counting mechanism for this object. More...

Protected Member Functions
virtual void	set_matrixkit (const Ref< SCMatrixKit > &)
void	init (std::string name, std::string label, const Ref< Molecule > &molecule, const std::vector< Shell > &shell)
	Initializes everything. More...
Protected Member Functions inherited from sc::SavableState
	SavableState (const SavableState &)
	SavableState (StateIn &)
	Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above. More...
Protected Member Functions inherited from sc::RefCount
	RefCount (const RefCount &)
RefCount &	operator= (const RefCount &)

Protected Attributes
Ref< Molecule >	molecule_

Friends
class	UnionBasisSet

Constructors
	GaussianBasisSet (const Ref< KeyVal > &)
	The KeyVal constructor. More...
	GaussianBasisSet (const Ref< Molecule > &molecule, const std::vector< GaussianShell > &shells, const std::vector< unsigned int > &shell_to_center, std::string name=std::string(), std::string label=std::string())
	Constructs GaussianBasisSet from a Molecule and a vector of GaussianShells. More...
	GaussianBasisSet (const GaussianBasisSet &)
static Ref< GaussianBasisSet >	unit ()
	This will produce a GaussianBasisSet object composed of a a single "unit" basis function, i.e. More...

Additional Inherited Members
Static Public Member Functions inherited from sc::SavableState
static void	save_state (SavableState *s, StateOut &)
static SavableState *	restore_state (StateIn &si)
	Restores objects saved with save_state. More...
static SavableState *	key_restore_state (StateIn &si, const char *keyword)
	Like restore_state, but keyword is used to override values while restoring.
static SavableState *	dir_restore_state (StateIn &si, const char *objectname, const char *keyword=0)

Detailed Description

The GaussianBasisSet class is used describe a basis set composed of atomic gaussian orbitals.

Inputs for common basis sets are included in the MPQC distribution. They have been obtained from the EMSL Basis Set Database and translated into the MPQC format. The citation for this database is below. The technical citation for each basis set is listed in the individual basis set data files, in MPQC's lib/basis directory.

Following is a table with available basis sets listing the supported elements for each basis and the number of basis functions for H, , first row, , and second row, , atoms. Basis sets with non-alpha-numerical characters in their name must be given in quotes.

Basis Set	Elements
STO-2G	H-Ca	1	5	9
STO-3G	H-Kr	1	5	9
STO-3G*	H-Ar	1	5	14
STO-6G	H-Kr	1	5	9
MINI (Huzinaga)	H-Ca	1	5	9
MINI (Scaled)	H-Ca	1	5	9
MIDI (Huzinaga)	H-Na, Al-K	2	9	13
DZ (Dunning)	H, Li, B-Ne, Al-Cl	2	10	18
DZP (Dunning)	H, Li, B-Ne, Al-Cl	5	16	24
DZP + Diffuse (Dunning)	H, B-Ne	6	19
3-21G	H-Kr	2	9	13
3-21G*	H-Ar	2	9	19
3-21++G	H-Ar	3	13	17
3-21++G*	H-Ar	3	13	23
4-31G	H-Ne, P-Cl	2	9	13
6-31G	H-Zn	2	9	13
6-31G*	H-Zn	2	15	19
6-31G**	H-Zn	5	15	19
6-31+G*	H-Ar	2	19	23
6-31++G	H-Ca	3	13	17
6-31++G*	H-Ar	3	19	23
6-31++G**	H-Ar	6	19	23
6-311G	H-Ca, Ga-Kr	3	13	21
6-311G*	H-Ca, Ga-Kr	3	18	26
6-311G**	H-Ca, Ga-Kr	6	18	26
6-311G(2df,2pd)	H-Ne, K, Ca	14	30
6-311++G**	H-Ne	7	22
6-311++G(2d,2p)	H-Ca	10	27	35
6-311++G(3df,3pd)	H-Ar	18	39	47
cc-pVDZ	H-Ar, Ca, Ga-Kr	5	14	18
cc-pVTZ	H-Ar, Ca, Ga-Kr	14	30	34
cc-pVQZ	H-Ar, Ca, Ga-Kr	30	55	59
cc-pV5Z	H-Ar, Ca, Ga-Kr	55	91	95
cc-pV6Z	H, He, B-Ne, Al-Ar	91	140	144
aug-cc-pVDZ	H, He, B-Ne, Al-Ar, Ga-Kr	9	23	27
aug-cc-pVTZ	H, He, B-Ne, Al-Ar, Ga-Kr	23	46	50
aug-cc-pVQZ	H, He, B-Ne, Al-Ar, Ga-Kr	46	80	84
aug-cc-pV5Z	H, He, B-Ne, Al-Ar, Ga-Kr	80	127	131
aug-cc-pV6Z	H, He, B-Ne, Al-Ar	127	189	193
cc-pCVDZ	Li, B-Ar		18	27
cc-pCVTZ	Li, B-Ar		43	59
cc-pCVQZ	Li, B-Ar		84	109
cc-pCV5Z	B-Ne		145
aug-cc-pCVDZ	B-F, Al-Ar		27	36
aug-cc-pCVTZ	B-Ne, Al-Ar		59	75
aug-cc-pCVQZ	B-Ne, Al-Ar		109	134
aug-cc-pCV5Z	B-F		181
NASA Ames ANO	H, B-Ne, Al, P, Ti, Fe, Ni	30	55	59
pc-0	H, C-F, Si-Cl	2	9	13
pc-1	H, C-F, Si-Cl	5	14	18
pc-2	H, C-F, Si-Cl	14	30	34
pc-3	H, C-F, Si-Cl	34	64	64
pc-4	H, C-F, Si-Cl	63	109	105
pc-0-aug	H, C-F, Si-Cl	3	13	17
pc-1-aug	H, C-F, Si-Cl	9	23	27
pc-2-aug	H, C-F, Si-Cl	23	46	50
pc-3-aug	H, C-F, Si-Cl	50	89	89
pc-4-aug	H, C-F, Si-Cl	88	145	141

All basis sets were obtained from the Extensible Computational Chemistry Environment Basis Set Database, Version 12/03/03, as developed and distributed by the Molecular Science Computing Facility, Environmental and Molecular Sciences Laboratory which is part of the Pacific Northwest Laboratory, P.O. Box 999, Richland, Washington 99352, USA, and funded by the U.S. Department of Energy. The Pacific Northwest Laboratory is a multi-program laboratory operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC06-76RLO 1830. Contact David Feller or Karen Schuchardt for further information.

Constructor & Destructor Documentation

GaussianBasisSet() [1/2]

sc::GaussianBasisSet::GaussianBasisSet

(

const Ref< KeyVal > &

)

The KeyVal constructor.

molecule

The gives a Molecule object. The is no default.

puream

If this boolean parameter is true then 5D, 7F, etc. will be used. Otherwise all cartesian functions will be used. The default depends on the particular basis set.

name

This is a string giving the name of the basis set. The above table of basis sets gives some of the recognized basis set names. It may be necessary to put the name in double quotes. There is no default.

basis

If the element vector is given, then this vector specifies the names of basis sets for each element. If the element vector is not given, this vector specifies basis set name for each atom in the molecule (note that the same basis name must be specified for each set of atoms related by symmetry). If this keyword omitted, the basis set specified in name will be used for all atoms.

element

This is a vector of elements. If it is given then it must have the same number of entries as the basis vector.

basisdir

A string giving a directory where basis set data files are to be sought. See the text below for a complete description of what directories are consulted.

basisfiles

Each keyword in this vector of files is appended to the directory specified with basisdir and basis set data is read from them.

Several files in various directories are checked for basis set data. First, basis sets can be given by the user in the basis section at the top level of the main input file. Next, if a path is given with the basisdir keyword, then all of the files given with the basisfiles keyword are read in after appending their names to the value of basisdir. Basis sets can be given in these files in the basis section at the top level as well. If the named basis set still cannot be found, then GaussianBasisSet will try convert the basis set name to a file name (see the note below for the rules of this conversion) and check first in the directory given by basisdir. Next it checks for the environment variable MPQC_DATA_PATH. If it is set it will look for the basis file in $MPQC_DATA_PATH/basis. Otherwise it will look in the source code distribution in the directory SC/lib/basis. If the executable has changed machines or the source code has be moved, then it may be necessary to copy the library files to your machine and set the MPQC_DATA_PATH environmental variable.

Note: translation of a basis name to a file name will convert upper-case letters(A-Z) to the lower-case letters, characters ',' and ' ' (whitespace) to '_', character '+' to 'P', character '*' to 'S', character '(' to 'L', and character ')' to 'R'.

The basis set itself is also given in the ParsedKeyVal format. There are two recognized formats for basis sets:

array of shells

One must specify the keyword :basis: followed by the lowercase atomic name followed by : followed by the basis set name (which may need to be placed inside double quotes). The value for the keyword is an array of shells. Each shell reads the following keywords:

type

This is a vector that describes each component of this shell. For each element the following two keywords are read:

am

The angular momentum of the component. This can be given as the letter designation, s, p, d, etc. There is no default.

puream

If this boolean parameter is true then 5D, 7F, etc. shells are used. The default is false. This parameter can be overridden in the GaussianBasisSet specification.

exp

This is a vector giving the exponents of the primitive Gaussian functions.

coef

This is a matrix giving the coeffients of the primitive Gaussian functions. The first index gives the component number of the shell and the second gives the primitive number.

An example might be easier to understand. This is a basis set specificition for STO-2G carbon:

basis: (
 carbon: "STO-2G": [
  (type: [(am = s)]
   {      exp      coef:0 } = {
      27.38503303 0.43012850
       4.87452205 0.67891353
   })
  (type: [(am = p) (am = s)]
   {     exp      coef:1     coef:0 } = {
       1.13674819 0.04947177 0.51154071
       0.28830936 0.96378241 0.61281990
   })
 ]
)

basis set of even-tempered primitive Gaussians

Such basis set format is given as a group of keywords. The name of the group is :basis: followed by the lowercase atomic name followed by : followed by the basis set name (which may need to be placed inside double quotes). The group of keywords must contain vectors am and nprim, which specify the angular momentum and the number of shells in each block of even-tempered primitives. In addition, one must provide any two of the following vectors:

first_exp

The exponent of the "tightest" primitive Gaussian in the block.

last_exp

The exponent of the most "diffuse" primitive Gaussian in the block.

exp_ratio

The ratio of exponents of consecutive primitive Gaussians in the block.

Note that the dimensions of each vector must be the same.

Here's an example of a basis set composed of 2 blocks of even-tempered s-functions and 1 block of even-tempered p-functions.

basis: (
 neon: "20s5s13p":(

   am = [ 0 0 1 ]
   nprim = [ 20 5 13 ]
   first_exp = [ 1000.0 0.1  70.0 ]
   last_exp =  [    1.0 0.01  0.1 ]

 )
)

GaussianBasisSet() [2/2]

sc::GaussianBasisSet::GaussianBasisSet	(	const Ref< Molecule > &	molecule,
		const std::vector< GaussianShell > &	shells,
		const std::vector< unsigned int > &	shell_to_center,
		std::string	name = std::string(),
		std::string	label = std::string()
	)

Constructs GaussianBasisSet from a Molecule and a vector of GaussianShells.

Parameters

molecule	molecule whose centers will serve as origins for shells
shells	vector of GaussianShell objects
shell_to_center	maps shell -> center; shells on the same center MUST appear in succession
name
label

Member Function Documentation

grad_shell_values()

int sc::GaussianBasisSet::grad_shell_values	(	const SCVector3 &	r,
		int	sh,
		ValueData *	,
		double *	g_values,
		double *	basis_values = 0
	)		const

Like values(...), but computes gradients of the shell function values, too.

See the other grad_values(...) members for more information.

grad_values()

int sc::GaussianBasisSet::grad_values	(	const SCVector3 &	r,
		ValueData *	,
		double *	g_values,
		double *	basis_values = 0
	)		const

Like values(...), but computes gradients of the basis function values, too.

The g_values argument must be vector of length 3*nbasis. The data will be written in the order bf1_x, bf1_y, bf1_z, ...

hessian_shell_values()

int sc::GaussianBasisSet::hessian_shell_values	(	const SCVector3 &	r,
		int	sh,
		ValueData *	,
		double *	h_values,
		double *	g_values = 0,
		double *	basis_values = 0
	)		const

Like values(...), but computes first and second derivatives of the shell function values, too.

See the other hessian_values(...) members for more information.

hessian_values()

int sc::GaussianBasisSet::hessian_values	(	const SCVector3 &	r,
		ValueData *	,
		double *	h_values,
		double *	g_values = 0,
		double *	basis_values = 0
	)		const

Like values(...), but computes first and second derivatives of the basis function values, too.

h_values must be vector of length 6*nbasis. The data will be written in the order bf1_xx, bf1_yx, bf1_yy, bf1_zx, bf1_zy, bf1_zz, ...

init()

void sc::GaussianBasisSet::init ( std::string  name, std::string  label, const Ref< Molecule > &  molecule, const std::vector< Shell > &  shell  )

protected

Initializes everything.

To be used by derived classes.

label()

const std::string& sc::GaussianBasisSet::label ( ) const

inline

Return the label of the basis set.

label() returns the same string as name() if keyword "name" was provided, otherwise it is a unique descriptive string which can be arbitrarily long.

max_am_for_contraction()

unsigned int sc::GaussianBasisSet::max_am_for_contraction

(

int

con

)

const

Return the maximum angular momentum found in the given contraction number for any shell.

max_ncartesian_in_shell()

unsigned int sc::GaussianBasisSet::max_ncartesian_in_shell

(

int

aminc = 0

)

const

Return the maximum number of Cartesian functions that any shell has.

The optional argument is an angular momentum increment.

operator+()

Ref<GaussianBasisSet> sc::GaussianBasisSet::operator+

(

const Ref< GaussianBasisSet > &

B

)

Uses UnionBasisSet to construct the sum of this and B.

r()

double sc::GaussianBasisSet::r	(	int	icenter,
		int	xyz
	)		const

The location of center icenter.

The xyz argument is 0 for x, 1 for y, and 2 for z.

shell_on_center()

int sc::GaussianBasisSet::shell_on_center	(	int	icenter,
		int	shell
	)		const

Return the overall shell number, given a center and the shell number on that center.

Shells on the same center have consecutive indices.

See also

shell_to_center()

shell_to_center()

int sc::GaussianBasisSet::shell_to_center ( int  ishell ) const

inline

Return the center on which the given shell is located.

Note

There are no guarantees about shell->center map, other than the shells on the same center are be consecutive.

shell_values()

int sc::GaussianBasisSet::shell_values	(	const SCVector3 &	r,
		int	sh,
		ValueData *	,
		double *	basis_values
	)		const

Compute the values for the given shell functions at position r.

See the other values(...) members for more information.

unit()

static Ref<GaussianBasisSet> sc::GaussianBasisSet::unit ( )

static

This will produce a GaussianBasisSet object composed of a a single "unit" basis function, i.e.

that is one everywhere. This can be used with integral evaluators to compute certain classes of integrals, with limitations.

values()

int sc::GaussianBasisSet::values	(	const SCVector3 &	r,
		ValueData *	,
		double *	basis_values
	)		const

Compute the values for this basis set at position r.

The basis_values argument must be vector of length nbasis.

---

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

• src/lib/chemistry/qc/basis/gaussbas.h