Files | |
file | vpmg-private.h |
Class Vpmg private method declaration. | |
file | vpmg.c |
Class Vpmg methods. | |
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 | |
unsigned long int | Vpmg_memChk (Vpmg *thee) |
Return the memory used by this structure (and its contents) in bytes. | |
Vpmg * | Vpmg_ctor (Vpmgp *parms, Vpbe *pbe, int focusFlag, Vpmg *pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag) |
Constructor for the Vpmg class (allocates new memory). | |
int | Vpmg_ctor2 (Vpmg *thee, Vpmgp *parms, Vpbe *pbe, int focusFlag, Vpmg *pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag) |
FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory). | |
void | Vpmg_dtor (Vpmg **thee) |
Object destructor. | |
void | Vpmg_dtor2 (Vpmg *thee) |
FORTRAN stub object destructor. | |
int | 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. | |
int | Vpmg_solve (Vpmg *thee) |
Solve the PBE using PMG. | |
int | Vpmg_solveLaplace (Vpmg *thee) |
Solve Poisson's equation with a homogeneous Laplacian operator using the solvent dielectric constant. This solution is performed by a sine wave decomposition. | |
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_dielGradNorm (Vpmg *thee) |
Get the integral of the gradient of the dielectric function. | |
int | 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 k_B T/AA. | |
int | Vpmg_qfForce (Vpmg *thee, double *force, int atomID, Vchrg_Meth chgm) |
Calculate the "charge-field" force on the specified atom in units of k_B T/AA. | |
int | Vpmg_dbForce (Vpmg *thee, double *dbForce, int atomID, Vsurf_Meth srfm) |
Calculate the dielectric boundary forces on the specified atom in units of k_B T/AA. | |
int | Vpmg_ibForce (Vpmg *thee, double *force, int atomID, Vsurf_Meth srfm) |
Calculate the osmotic pressure on the specified atom in units of k_B T/AA. | |
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. | |
int | Vpmg_fillArray (Vpmg *thee, double *vec, Vdata_Type type, double parm, Vhal_PBEType pbetype) |
Fill the specified array with accessibility values. | |
VPUBLIC void | Vpmg_fieldSpline4 (Vpmg *thee, int atomID, double field[3]) |
Computes the field at an atomic center using a stencil based on the first derivative of a 5th order B-spline. | |
double | Vpmg_qfPermanentMultipoleEnergy (Vpmg *thee, int atomID) |
Computes the permanent multipole electrostatic hydration energy (the polarization component of the hydration energy currently computed in TINKER). | |
void | Vpmg_qfPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3], double torque[3]) |
Computes the q-Phi Force for permanent multipoles based on 5th order B-splines. | |
void | Vpmg_ibPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3]) |
Compute the ionic boundary force for permanent multipoles. | |
void | Vpmg_dbPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3]) |
Compute the dielectric boundary force for permanent multipoles. | |
void | Vpmg_qfDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *induced, int atomID, double force[3], double torque[3]) |
q-Phi direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field. | |
void | Vpmg_qfNLDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *nlInduced, int atomID, double force[3], double torque[3]) |
q-Phi direct polarization force between permanent multipoles and non-local induced dipoles based on 5th Order B-Splines. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy. | |
void | Vpmg_ibDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *induced, int atomID, double force[3]) |
Ionic boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field. | |
void | Vpmg_ibNLDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *nlInduced, int atomID, double force[3]) |
Ionic boundary direct polarization force between permanent multipoles and non-local induced dipoles based on 5th order Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy. | |
void | Vpmg_dbDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *induced, int atomID, double force[3]) |
Dielectric boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field. | |
void | Vpmg_dbNLDirectPolForce (Vpmg *thee, Vgrid *perm, Vgrid *nlInduced, int atomID, double force[3]) |
Dielectric bounday direct polarization force between permanent multipoles and non-local induced dipoles. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy. | |
void | Vpmg_qfMutualPolForce (Vpmg *thee, Vgrid *induced, Vgrid *nlInduced, int atomID, double force[3]) |
Mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field. | |
void | Vpmg_ibMutualPolForce (Vpmg *thee, Vgrid *induced, Vgrid *nlInduced, int atomID, double force[3]) |
Ionic boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field. | |
void | Vpmg_dbMutualPolForce (Vpmg *thee, Vgrid *induced, Vgrid *nlInduced, int atomID, double force[3]) |
Dielectric boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field. | |
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. |
|
The maximum number of partitions the mesh can be divided into |
|
Constructor for the Vpmg class (allocates new memory).
|
Here is the call graph for this function:
|
FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory).
|
Here is the call graph for this function:
|
Dielectric boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
|
|
Calculate the dielectric boundary forces on the specified atom in units of k_B T/AA.
|
Here is the call graph for this function:
|
Dielectric boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
|
|
Dielectric bounday direct polarization force between permanent multipoles and non-local induced dipoles. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
|
|
Compute the dielectric boundary force for permanent multipoles.
|
|
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 epsilon is the dielectric parameter and u(x) is the dimensionless electrostatic potential. The energy is scaled to units of k_b T.
|
Here is the call graph for this function:
|
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_dbForce for reference):
where epsilon is the dielectric parameter. The integral is returned in units of A^2.
|
|
Object destructor.
|
Here is the call graph for this function:
|
FORTRAN stub object destructor.
|
|
Get the total electrostatic energy.
|
Here is the call graph for this function:
|
Computes the field at an atomic center using a stencil based on the first derivative of a 5th order B-spline.
|
|
Fill the specified array with accessibility values.
|
Here is the call graph for this function:
|
Fill the coefficient arrays prior to solving the equation.
|
Here is the call graph for this function:
|
Calculate the total force on the specified atom in units of k_B T/AA.
|
Here is the call graph for this function:
|
Ionic boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
|
|
Calculate the osmotic pressure on the specified atom in units of k_B T/AA.
|
Here is the call graph for this function:
|
Ionic boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
|
|
Ionic boundary direct polarization force between permanent multipoles and non-local induced dipoles based on 5th order Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
|
|
Compute the ionic boundary force for permanent multipoles.
|
|
Return the memory used by this structure (and its contents) in bytes.
|
|
Print out a column-compressed sparse matrix in Harwell-Boeing format.
|
|
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 q$ is the charge and r is the location of the atom of interest. The result is returned in units of k_B T. Clearly, no self-interaction terms are removed. A factor a 1/2 has to be included to convert this to a real energy.
|
Here is the call graph for this function:
|
q-Phi direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
|
|
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 k_B T. Clearly, no self-interaction terms are removed. A factor a 1/2 has to be included to convert this to a real energy.
|
Here is the call graph for this function:
|
Calculate the "charge-field" force on the specified atom in units of k_B T/AA.
|
Here is the call graph for this function:
|
Mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
|
|
q-Phi direct polarization force between permanent multipoles and non-local induced dipoles based on 5th Order B-Splines. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
|
|
Computes the permanent multipole electrostatic hydration energy (the polarization component of the hydration energy currently computed in TINKER).
|
|
Computes the q-Phi Force for permanent multipoles based on 5th order B-splines.
|
|
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 i denotes the counterion species, I_s is the bulk ionic strength, kappa^2(x) is the modified Debye-Huckel parameter, c_i is the concentration of species i, q_i is the charge of species i, and u(x) is the dimensionless electrostatic potential. The energy is scaled to units of k_b T.
|
Here is the call graph for this function:
|
Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain.
|
Here is the call graph for this function:
|
Solve the PBE using PMG.
|
Here is the call graph for this function:
|
Solve Poisson's equation with a homogeneous Laplacian operator using the solvent dielectric constant. This solution is performed by a sine wave decomposition.
|
Here is the call graph for this function:
|
Remove partition restrictions.
|
Here is the call graph for this function: