Files | |
file | vpmg.h |
Contains declarations for class Vpmg. | |
Data Structures | |
struct | sVpmg |
Contains public data members for Vpmg class/module. More... | |
Defines | |
#define | VPMGMAXPART 2000 |
Typedefs | |
typedef sVpmg | Vpmg |
Declaration of the Vpmg class as the Vpmg structure. | |
Functions | |
int | Vpmg_memChk (Vpmg *thee) |
Return the memory used by this structure (and its contents) in bytes. | |
Vpmg * | Vpmg_ctor (Vpmgp *parms, Vpbe *pbe) |
Constructor for the Vpmg class (no focusing). | |
int | Vpmg_ctor2 (Vpmg *thee, Vpmgp *parms, Vpbe *pbe) |
FORTRAN stub constructor for the Vpmg class (no focusing). | |
Vpmg * | Vpmg_ctorFocus (Vpmgp *parms, Vpbe *pbe, Vpmg *pmgOLD, int energyFlag) |
Constructor for the Vpmg class (with focusing). | |
int | Vpmg_ctor2Focus (Vpmg *thee, Vpmgp *parms, Vpbe *pbe, Vpmg *pmgOLD, int energyFlag) |
FORTRAN stub bonstructor for the Vpmg class (with focusing). | |
void | Vpmg_dtor (Vpmg **thee) |
Object destructor. | |
void | Vpmg_dtor2 (Vpmg *thee) |
FORTRAN stub object destructor. | |
void | Vpmg_fillco (Vpmg *thee, Vsurf_Meth surfMeth, double splineWin, Vchrg_Meth chargeMeth, int useDielXMap, Vgrid *dielXMap, int useDielYMap, Vgrid *dielYMap, int useDielZMap, Vgrid *dielZMap, int useKappaMap, Vgrid *kappaMap, int useChargeMap, Vgrid *chargeMap) |
Fill the coefficient arrays prior to solving the equation. | |
void | Vpmg_solve (Vpmg *thee) |
Solve the PBE using PMG. | |
double | Vpmg_energy (Vpmg *thee, int extFlag) |
Get the total electrostatic energy. | |
double | Vpmg_qfEnergy (Vpmg *thee, int extFlag) |
Get the "fixed charge" contribution to the electrostatic energy. | |
double | Vpmg_qfAtomEnergy (Vpmg *thee, Vatom *atom) |
Get the per-atom "fixed charge" contribution to the electrostatic energy. | |
double | Vpmg_qmEnergy (Vpmg *thee, int extFlag) |
Get the "mobile charge" contribution to the electrostatic energy. | |
double | Vpmg_dielEnergy (Vpmg *thee, int extFlag) |
Get the "polarization" contribution to the electrostatic energy. | |
double | Vpmg_npEnergy (Vpmg *thee, int extFlag) |
Get the "apolar" energy. | |
double | Vpmg_dielGradNorm (Vpmg *thee) |
Get the integral of the gradient of the dielectric function. | |
void | Vpmg_force (Vpmg *thee, double *force, int atomID, Vsurf_Meth srfm, Vchrg_Meth chgm) |
Calculate the total force on the specified atom in units of ![]() | |
void | Vpmg_qfForce (Vpmg *thee, double *force, int atomID, Vchrg_Meth chgm) |
Calculate the "charge-field" force on the specified atom in units of ![]() | |
void | Vpmg_dbnpForce (Vpmg *thee, double *dbForce, double *npForce, int atomID, Vsurf_Meth srfm) |
Calculate the dielectric boundary and apolar forces on the specified atom in units of ![]() | |
void | Vpmg_ibForce (Vpmg *thee, double *force, int atomID, Vsurf_Meth srfm) |
Calculate the osmotic pressure on the specified atom in units of ![]() | |
void | Vpmg_setPart (Vpmg *thee, double lowerCorner[3], double upperCorner[3], int bflags[6]) |
Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain. | |
void | Vpmg_unsetPart (Vpmg *thee) |
Remove partition restrictions. | |
void | Vpmg_fillArray (Vpmg *thee, double *vec, Vdata_Type type, double parm) |
Fill the specified array with accessibility values. | |
void | Vpmg_printColComp (Vpmg *thee, char path[72], char title[72], char mxtype[3], int flag) |
Print out a column-compressed sparse matrix in Harwell-Boeing format. |
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The maximum number of partitions the mesh can be divided into |
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Constructor for the Vpmg class (no focusing).
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FORTRAN stub constructor for the Vpmg class (no focusing).
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FORTRAN stub bonstructor for the Vpmg class (with focusing).
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Constructor for the Vpmg class (with focusing).
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Calculate the dielectric boundary and apolar forces on the specified atom in units of
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Get the "polarization" contribution to the electrostatic energy. Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the mobile charges with the potential: ![]()
where
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Get the integral of the gradient of the dielectric function. Using the dielectric map at the finest mesh level, calculate the integral of the norm of the dielectric function gradient routines of Im et al (see Vpmg_dbnpForce for reference): ![]()
where
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Object destructor.
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FORTRAN stub object destructor.
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Get the total electrostatic energy.
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Fill the specified array with accessibility values.
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Fill the coefficient arrays prior to solving the equation.
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Calculate the total force on the specified atom in units of
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Calculate the osmotic pressure on the specified atom in units of
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Return the memory used by this structure (and its contents) in bytes.
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Get the "apolar" energy. Using the dielectric map at the finest mesh level, calculate the surface area in a manner consistent with the force evaluation routines of Im et al (see Vpmg_dbnpForce and Vpmg_dielGradNorm): ![]()
where ![]()
where
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Print out a column-compressed sparse matrix in Harwell-Boeing format.
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Get the per-atom "fixed charge" contribution to the electrostatic energy. Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the fixed charges with the potential: ![]()
where
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Get the "fixed charge" contribution to the electrostatic energy. Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the fixed charges with the potential: ![]()
and return the result in units of
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Calculate the "charge-field" force on the specified atom in units of
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Get the "mobile charge" contribution to the electrostatic energy. Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the mobile charges with the potential: ![]() for the NPBE and ![]()
for the LPBE. Here
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Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain.
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Solve the PBE using PMG.
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Remove partition restrictions.
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