sc::VDWShape Class Reference
The VDWShape class describes the surface of a molecule as the union of atom centered spheres, each the van der Waals radius of the atom. More...
#include <chemistry/molecule/molshape.h>
Inheritance diagram for sc::VDWShape:
Public Member Functions | |
| VDWShape (const Ref< Molecule > &, double radius_scale_factor=1.0) | |
| VDWShape (const Ref< KeyVal > &) | |
| void | initialize (const Ref< Molecule > &, double radius_scale_factor=1.0) |
 Public Member Functions inherited from sc::UnionShape | |
| void | add_shape (Ref< Shape >) |
| double | distance_to_surface (const SCVector3 &r, SCVector3 *grad=0) const |
| int | is_outside (const SCVector3 &r) const |
| void | boundingbox (double valuemin, double valuemax, SCVector3 &p1, SCVector3 &p2) |
| int | gradient_implemented () const |
| Public Member Functions inherited from sc::Shape | |
| Shape (const Ref< KeyVal > &keyval) | |
| void | compute () |
| Recompute at least the results that have compute true and are not already computed. More... | |
| void | interpolate (const SCVector3 &p1, const SCVector3 &p2, double val, SCVector3 &result) |
| int | value_implemented () const |
| Public Member Functions inherited from sc::Volume | |
| Volume (const Ref< KeyVal > &) | |
| void | set_gradient (const SCVector3 &g) |
| void | set_gradient (RefSCVector &g) |
| void | get_gradient (SCVector3 &g) |
| void | set_x (const SCVector3 &x) |
| void | set_x (const RefSCVector &x) |
| Set and retrieve the coordinate values. | |
| void | get_x (SCVector3 &x) |
| virtual void | solve (const SCVector3 &p, const SCVector3 &grad, double value, SCVector3 &result) |
| Public Member Functions inherited from sc::Function | |
| virtual RefSCVector | gradient () |
| int | gradient_needed () const |
| int | do_gradient (int) |
| virtual void | set_desired_gradient_accuracy (double) |
| virtual double | actual_gradient_accuracy () const |
| virtual double | desired_gradient_accuracy () const |
| AccResultRefSCVector & | gradient_result () |
| virtual RefSymmSCMatrix | hessian () |
| int | hessian_needed () const |
| int | do_hessian (int) |
| virtual void | set_desired_hessian_accuracy (double) |
| virtual double | actual_hessian_accuracy () const |
| virtual double | desired_hessian_accuracy () const |
| AccResultRefSymmSCMatrix & | hessian_result () |
| virtual bool | desired_value_accuracy_set_to_default () const |
| virtual bool | desired_gradient_accuracy_set_to_default () const |
| virtual bool | desired_hessian_accuracy_set_to_default () const |
| virtual void | guess_hessian (RefSymmSCMatrix &) |
| Compute a quick, approximate hessian. | |
| virtual RefSymmSCMatrix | inverse_hessian (RefSymmSCMatrix &) |
| virtual int | hessian_implemented () const |
| RefSCVector | get_x () const |
| const RefSCVector & | get_x_no_copy () const |
| virtual Ref< NonlinearTransform > | change_coordinates () |
| An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. More... | |
| virtual void | print (std::ostream &=ExEnv::out0()) const |
| Print information about the object. | |
| void | print_desired_accuracy (std::ostream &=ExEnv::out0()) const |
| similar to print(), but only prins desired accuracies | |
| virtual bool | throw_if_tolerance_exceeded () const |
| Overridden Compute member. | |
| Function () | |
| Function (StateIn &) | |
| Function (const Function &) | |
| Function (const Ref< KeyVal > &, double funcacc=DBL_EPSILON, double gradacc=DBL_EPSILON, double hessacc=DBL_EPSILON) | |
| The keyval constructor reads the following keywords: More... | |
| virtual | ~Function () |
| Function & | operator= (const Function &) |
| Ref< SCMatrixKit > | matrixkit () const |
| Return the SCMatrixKit used to construct vectors and matrices. | |
| RefSCDimension | dimension () const |
| Return the SCDimension of the problem. | |
| virtual void | save_data_state (StateOut &) |
| Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More... | |
| virtual double | value () |
| Return the value of the function. | |
| int | value_needed () const |
| Returns nonzero if the current value is not up-to-date. | |
| int | do_value (int) |
| If passed a nonzero number, compute the value the next time compute() is called. More... | |
| AccResultdouble & | value_result () |
| virtual void | set_desired_value_accuracy (double) |
| Set the accuracy to which the value is to be computed. | |
| virtual double | actual_value_accuracy () const |
| Return the accuracy with which the value has been computed. | |
| virtual double | desired_value_accuracy () const |
| Return the accuracy with which the value is to be computed. | |
| 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... | |
| Public Member Functions inherited from sc::Compute | |
| virtual void | obsolete () |
| Marks all results as being out of date. 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) |
| Protected Member Functions inherited from sc::Volume | |
| double & | interpolation_accuracy () |
| virtual void | failure (const char *) |
| Protected Member Functions inherited from sc::Function | |
| virtual void | set_value (double) |
| virtual void | set_hessian (RefSymmSCMatrix &) |
| virtual void | set_matrixkit (const Ref< SCMatrixKit > &) |
| Set the SCMatrixKit that should be used to construct the requisite vectors and matrices. | |
| virtual void | set_dimension (const RefSCDimension &) |
| virtual void | set_actual_value_accuracy (double) |
| virtual void | set_actual_gradient_accuracy (double) |
| virtual void | set_actual_hessian_accuracy (double) |
| RefSCVector & | get_x_reference () |
| Get read/write access to the coordinates for modification. | |
| void | do_change_coordinates (const Ref< NonlinearTransform > &) |
| Change the coordinate system and apply the given transform to intermediates matrices and vectors. | |
| 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 inherited from sc::UnionShape | |
| std::set< Ref< Shape > > | _shapes |
| Protected Attributes inherited from sc::Function | |
| Ref< SCMatrixKit > | matrixkit_ |
| Used to construct new matrices. | |
| RefSCVector | x_ |
| The variables. | |
| RefSCDimension | dim_ |
| The dimension of x_. | |
| AccResultdouble | value_ |
| The value of the function at x_. | |
| AccResultRefSCVector | gradient_ |
| The gradient at x_. | |
| AccResultRefSymmSCMatrix | hessian_ |
| The hessian at x_. | |
| bool | desired_value_accuracy_set_to_default_ |
| bool | desired_gradient_accuracy_set_to_default_ |
| bool | desired_hessian_accuracy_set_to_default_ |
| bool | throw_if_tolerance_exceeded_ |
Detailed Description
The VDWShape class describes the surface of a molecule as the union of atom centered spheres, each the van der Waals radius of the atom.
The documentation for this class was generated from the following file:
- src/lib/chemistry/molecule/molshape.h