Vfetk class

FEtk master class (interface between FEtk and APBS). More...

Data Structures

struct  sVfetk
 Contains public data members for Vfetk class/module. More...
struct  sVfetk_LocalVar
 Vfetk LocalVar subclass. More...

Files

file  vfetk.h
 

Contains declarations for class Vfetk.


file  vfetk.c
 

Class Vfetk methods.


Defines

#define VRINGMAX   1000
 Maximum number of simplices in a simplex ring.
#define VATOMMAX   1000000
 Maximum number of atoms associated with a vertex.

Typedefs

typedef enum eVfetk_LsolvType Vfetk_LsolvType
 Declare FEMparm_LsolvType type.
typedef enum eVfetk_MeshLoad Vfetk_MeshLoad
 Declare FEMparm_GuessType type.
typedef enum eVfetk_NsolvType Vfetk_NsolvType
 Declare FEMparm_NsolvType type.
typedef enum eVfetk_GuessType Vfetk_GuessType
 Declare FEMparm_GuessType type.
typedef enum eVfetk_PrecType Vfetk_PrecType
 Declare FEMparm_GuessType type.
typedef struct sVfetk_LocalVar Vfetk_LocalVar
 Declaration of the Vfetk_LocalVar subclass as the Vfetk_LocalVar structure.
typedef struct sVfetk Vfetk
 Declaration of the Vfetk class as the Vfetk structure.

Enumerations

enum  eVfetk_LsolvType {
  VLT_SLU = 0,
  VLT_MG = 1,
  VLT_CG = 2,
  VLT_BCG = 3
}
 

Linear solver type.

More...
enum  eVfetk_MeshLoad {
  VML_DIRICUBE,
  VML_NEUMCUBE,
  VML_EXTERNAL
}
 

Mesh loading operation.

More...
enum  eVfetk_NsolvType {
  VNT_NEW = 0,
  VNT_INC = 1,
  VNT_ARC = 2
}
 

Non-linear solver type.

More...
enum  eVfetk_GuessType {
  VGT_ZERO = 0,
  VGT_DIRI = 1,
  VGT_PREV = 2
}
 

Initial guess type.

More...
enum  eVfetk_PrecType {
  VPT_IDEN = 0,
  VPT_DIAG = 1,
  VPT_MG = 2
}
 

Preconditioner type.

More...

Functions

Gem * Vfetk_getGem (Vfetk *thee)
 Get a pointer to the Gem (grid manager) object.
AM * Vfetk_getAM (Vfetk *thee)
 Get a pointer to the AM (algebra manager) object.
Vpbe * Vfetk_getVpbe (Vfetk *thee)
 Get a pointer to the Vpbe (PBE manager) object.
Vcsm * Vfetk_getVcsm (Vfetk *thee)
 Get a pointer to the Vcsm (charge-simplex map) object.
int Vfetk_getAtomColor (Vfetk *thee, int iatom)
 Get the partition information for a particular atom.
Vfetk * Vfetk_ctor (Vpbe *pbe, Vhal_PBEType type)
 Constructor for Vfetk object.
int Vfetk_ctor2 (Vfetk *thee, Vpbe *pbe, Vhal_PBEType type)
 FORTRAN stub constructor for Vfetk object.
void Vfetk_dtor (Vfetk **thee)
 Object destructor.
void Vfetk_dtor2 (Vfetk *thee)
 FORTRAN stub object destructor.
double * Vfetk_getSolution (Vfetk *thee, int *length)
 Create an array containing the solution (electrostatic potential in units of $k_B T/e$) at the finest mesh level.
void Vfetk_setParameters (Vfetk *thee, PBEparm *pbeparm, FEMparm *feparm)
 Set the parameter objects.
double Vfetk_energy (Vfetk *thee, int color, int nonlin)
 Return the total electrostatic energy.
double Vfetk_dqmEnergy (Vfetk *thee, int color)
 Get the "mobile charge" and "polarization" contributions to the electrostatic energy.
double Vfetk_qfEnergy (Vfetk *thee, int color)
 Get the "fixed charge" contribution to the electrostatic energy.
unsigned long int Vfetk_memChk (Vfetk *thee)
 Return the memory used by this structure (and its contents) in bytes.
void Vfetk_setAtomColors (Vfetk *thee)
 Transfer color (partition ID) information frmo a partitioned mesh to the atoms.
void Bmat_printHB (Bmat *thee, char *fname)
 Writes a Bmat to disk in Harwell-Boeing sparse matrix format.
Vrc_Codes Vfetk_genCube (Vfetk *thee, double center[3], double length[3], Vfetk_MeshLoad meshType)
 Construct a rectangular mesh (in the current Vfetk object).
Vrc_Codes Vfetk_loadMesh (Vfetk *thee, double center[3], double length[3], Vfetk_MeshLoad meshType, Vio *sock)
 Loads a mesh into the Vfetk (and associated) object(s).
PDE * Vfetk_PDE_ctor (Vfetk *fetk)
 Constructs the FEtk PDE object.
int Vfetk_PDE_ctor2 (PDE *thee, Vfetk *fetk)
 Intializes the FEtk PDE object.
void Vfetk_PDE_dtor (PDE **thee)
 Destroys FEtk PDE object.
void Vfetk_PDE_dtor2 (PDE *thee)
 FORTRAN stub: destroys FEtk PDE object.
void Vfetk_PDE_initAssemble (PDE *thee, int ip[], double rp[])
 Do once-per-assembly initialization.
void Vfetk_PDE_initElement (PDE *thee, int elementType, int chart, double tvx[][VAPBS_DIM], void *data)
 Do once-per-element initialization.
void Vfetk_PDE_initFace (PDE *thee, int faceType, int chart, double tnvec[])
 Do once-per-face initialization.
void Vfetk_PDE_initPoint (PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][VAPBS_DIM])
 Do once-per-point initialization.
void Vfetk_PDE_Fu (PDE *thee, int key, double F[])
 Evaluate strong form of PBE. For interior points, this is:

\[ -\nabla \cdot \epsilon \nabla u + b(u) - f \]

where $b(u)$ is the (possibly nonlinear) mobile ion term and $f$ is the source charge distribution term (for PBE) or the induced surface charge distribution (for RPBE). For an interior-boundary (simplex face) point, this is:

\[ [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^+} - [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^-} \]

where $n(x)$ is the normal to the simplex face and the term represents the jump in dielectric displacement across the face. There is no outer-boundary contribution for this problem.

double Vfetk_PDE_Fu_v (PDE *thee, int key, double V[], double dV[][VAPBS_DIM])
 This is the weak form of the PBE; i.e. the strong form integrated with a test function to give:

\[ \int_\Omega \left[ \epsilon \nabla u \cdot \nabla v + b(u) v - f v \right] dx \]

where $b(u)$ denotes the mobile ion term.

double Vfetk_PDE_DFu_wv (PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][VAPBS_DIM])
 This is the linearization of the weak form of the PBE; e.g., for use in a Newton iteration. This is the functional linearization of the strong form integrated with a test function to give:

\[ \int_\Omega \left[ \epsilon \nabla w \cdot \nabla v + b'(u) w v - f v \right] dx \]

where $b'(u)$ denotes the functional derivation of the mobile ion term.

void Vfetk_PDE_delta (PDE *thee, int type, int chart, double txq[], void *user, double F[])
 Evaluate a (discretized) delta function source term at the given point.
void Vfetk_PDE_u_D (PDE *thee, int type, int chart, double txq[], double F[])
 Evaluate the Dirichlet boundary condition at the given point.
void Vfetk_PDE_u_T (PDE *thee, int type, int chart, double txq[], double F[])
 Evaluate the "true solution" at the given point for comparison with the numerical solution.
void Vfetk_PDE_bisectEdge (int dim, int dimII, int edgeType, int chart[], double vx[][VAPBS_DIM])
 Define the way manifold edges are bisected.
void Vfetk_PDE_mapBoundary (int dim, int dimII, int vertexType, int chart, double vx[VAPBS_DIM])
 Map a boundary point to some pre-defined shape.
int Vfetk_PDE_markSimplex (int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][VAPBS_DIM], void *simplex)
 User-defined error estimator -- in our case, a geometry-based refinement method; forcing simplex refinement at the dielectric boundary and (for non-regularized PBE) the charges.
void Vfetk_PDE_oneChart (int dim, int dimII, int objType, int chart[], double vx[][VAPBS_DIM], int dimV)
 Unify the chart for different coordinate systems -- a no-op for us.
double Vfetk_PDE_Ju (PDE *thee, int key)
 Energy functional. This returns the energy (less delta function terms) in the form:

\[ c^{-1}/2 \int (\epsilon (\nabla u)^2 + \kappa^2 (cosh u - 1)) dx \]

for a 1:1 electrolyte where $c$ is the output from Vpbe_getZmagic.

void Vfetk_externalUpdateFunction (SS **simps, int num)
 External hook to simplex subdivision routines in Gem. Called each time a simplex is subdivided (we use it to update the charge-simplex map).
int Vfetk_PDE_simplexBasisInit (int key, int dim, int comp, int *ndof, int dof[])
 Initialize the bases for the trial or the test space, for a particular component of the system, at all quadrature points on the master simplex element.
void Vfetk_PDE_simplexBasisForm (int key, int dim, int comp, int pdkey, double xq[], double basis[])
 Evaluate the bases for the trial or test space, for a particular component of the system, at all quadrature points on the master simplex element.
void Vfetk_readMesh (Vfetk *thee, int skey, Vio *sock)
 Read in mesh and initialize associated internal structures.
void Vfetk_dumpLocalVar ()
 Debugging routine to print out local variables used by PDE object.
int Vfetk_fillArray (Vfetk *thee, Bvec *vec, Vdata_Type type)
 Fill an array with the specified data.
int Vfetk_write (Vfetk *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname, Bvec *vec, Vdata_Format format)
 Write out data.
Vrc_Codes Vfetk_loadGem (Vfetk *thee, Gem *gm)
 Load a Gem geometry manager object into Vfetk.

Detailed Description

FEtk master class (interface between FEtk and APBS).

Enumeration Type Documentation

enum eVfetk_GuessType

Initial guess type.

Note:
Do not change these values; they correspond to settings in FEtk
Enumerator:
VGT_ZERO 

Zero initial guess

VGT_DIRI 

Dirichlet boundary condition initial guess

VGT_PREV 

Previous level initial guess

enum eVfetk_LsolvType

Linear solver type.

Note:
Do not change these values; they correspond to settings in FEtk
Enumerator:
VLT_SLU 

SuperLU direct solve

VLT_MG 

Multigrid

VLT_CG 

Conjugate gradient

VLT_BCG 

BiCGStab

enum eVfetk_MeshLoad

Mesh loading operation.

Enumerator:
VML_DIRICUBE 

Dirichlet cube

VML_NEUMCUBE 

Neumann cube

VML_EXTERNAL 

External mesh (from socket)

enum eVfetk_NsolvType

Non-linear solver type.

Note:
Do not change these values; they correspond to settings in FEtk
Enumerator:
VNT_NEW 

Newton solver

VNT_INC 

Incremental

VNT_ARC 

Psuedo-arclength

enum eVfetk_PrecType

Preconditioner type.

Note:
Do not change these values; they correspond to settings in FEtk
Enumerator:
VPT_IDEN 

Identity matrix

VPT_DIAG 

Diagonal scaling

VPT_MG 

Multigrid

Function Documentation

void Bmat_printHB ( Bmat *  thee,
char *  fname 
)

Writes a Bmat to disk in Harwell-Boeing sparse matrix format.

Author:
Stephen Bond
Note:
This is a friend function of Bmat
Bug:
Hardwired to only handle the single block symmetric case.
Parameters:
fname The matrix to write Filename for output
Vfetk* Vfetk_ctor ( Vpbe *  pbe,
Vhal_PBEType  type 
)

Constructor for Vfetk object.

Author:
Nathan Baker
Returns:
Pointer to newly allocated Vfetk object
Note:
This sets up the Gem, AM, and Aprx FEtk objects but does not create a mesh. The easiest way to create a mesh is to then call Vfetk_genCube
Parameters:
type Vpbe (PBE manager object) Version of PBE to solve

References Vfetk_ctor2().

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int Vfetk_ctor2 ( Vfetk *  thee,
Vpbe *  pbe,
Vhal_PBEType  type 
)

FORTRAN stub constructor for Vfetk object.

Author:
Nathan Baker
Returns:
1 if successful, 0 otherwise
Note:
This sets up the Gem, AM, and Aprx FEtk objects but does not create a mesh. The easiest way to create a mesh is to then call Vfetk_genCube
Parameters:
pbe Vfetk object memory
type PBE manager object Version of PBE to solve

References sVpbe::acc, sVpbe::alist, sVfetk::am, sVfetk::aprx, sVfetk::csm, sVfetk::feparm, sVfetk_LocalVar::fetk, Gem_setExternalUpdateFunction(), sVfetk::gm, sVfetk::gues, sVfetk_LocalVar::initGreen, sVfetk_LocalVar::ionConc, sVfetk_LocalVar::ionQ, sVfetk_LocalVar::ionRadii, sVfetk_LocalVar::ionstr, sVfetk::level, sVfetk::lkey, sVfetk::lmax, sVfetk::lprec, sVfetk::ltol, sVfetk_LocalVar::nion, sVfetk::nkey, sVfetk::nmax, sVfetk::ntol, sVfetk::pbe, sVfetk::pbeparm, sVfetk::pde, sVfetk::pjac, sVfetk::type, VAPBS_DIM, Vfetk_externalUpdateFunction(), Vfetk_PDE_ctor(), VGT_ZERO, VLT_MG, sVfetk::vmem, VNT_NEW, Vpbe_getBulkIonicStrength(), Vpbe_getIons(), Vpbe_getZkappa2(), VPT_MG, sVfetk_LocalVar::zkappa2, and sVfetk_LocalVar::zks2.

Referenced by Vfetk_ctor().

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double Vfetk_dqmEnergy ( Vfetk *  thee,
int  color 
)

Get the "mobile charge" and "polarization" contributions 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 and polarization of the dielectric medium:

\[ G = \frac{1}{4 I_s} \sum_i c_i q_i^2 \int \overline{\kappa}^2(x) e^{-q_i u(x)} dx + \frac{1}{2} \int \epsilon ( \nabla u )^2 dx \]

for the NPBE and

\[ G = \frac{1}{2} \int \overline{\kappa}^2(x) u^2(x) dx + \frac{1}{2} \int \epsilon ( \nabla u )^2 dx \]

for the LPBE. Here $i$ denotes the counterion species, $I_s$ is the bulk ionic strength, $\overline{\kappa}^2(x)$ is the modified Debye-Huckel parameter, $c_i$ is the concentration of species $i$, $q_i$ is the charge of species $i$, $\epsilon$ is the dielectric function, and $u(x)$ is the dimensionless electrostatic potential. The energy is scaled to units of $k_b T$.

Author:
Nathan Baker
Parameters:
thee Vfetk object
color Partition restriction for energy evaluation, only used if non-negative
Returns:
The "mobile charge" and "polarization" contributions to the electrostatic energy in units of $k_B T$.
Parameters:
color The Vfetk object Partition restriction for energy calculation; if non-negative, energy calculation is restricted to the specified partition (indexed by simplex and atom colors

References sVfetk::am.

Referenced by Vfetk_energy().

void Vfetk_dtor ( Vfetk **  thee  ) 

Object destructor.

Author:
Nathan Baker
Parameters:
thee Pointer to memory location of Vfetk object

References Vfetk_dtor2().

Referenced by killFE().

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void Vfetk_dtor2 ( Vfetk *  thee  ) 

FORTRAN stub object destructor.

Author:
Nathan Baker
Parameters:
thee Pointer to Vfetk object to be destroyed

References sVfetk::am, sVfetk::aprx, sVfetk::csm, sVfetk::pde, Vcsm_dtor(), Vfetk_PDE_dtor(), and sVfetk::vmem.

Referenced by Vfetk_dtor().

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void Vfetk_dumpLocalVar (  ) 

Debugging routine to print out local variables used by PDE object.

Author:
Nathan Baker
Bug:
This function is not thread-safe

References sVfetk_LocalVar::A, sVfetk_LocalVar::B, sVfetk_LocalVar::d2W, sVfetk_LocalVar::DB, sVfetk_LocalVar::delta, sVfetk_LocalVar::DFu_wv, sVfetk_LocalVar::diel, sVfetk_LocalVar::dU, sVfetk_LocalVar::dW, sVfetk_LocalVar::F, sVfetk_LocalVar::fType, sVfetk_LocalVar::Fu_v, sVfetk_LocalVar::ionacc, sVfetk_LocalVar::ionConc, sVfetk_LocalVar::ionQ, sVfetk_LocalVar::ionRadii, sVfetk_LocalVar::nion, sVfetk_LocalVar::nvec, sVfetk_LocalVar::nverts, sVfetk_LocalVar::simp, sVfetk_LocalVar::sType, sVfetk_LocalVar::U, sVfetk_LocalVar::u_D, sVfetk_LocalVar::u_T, sVfetk_LocalVar::verts, sVfetk_LocalVar::vx, sVfetk_LocalVar::W, sVfetk_LocalVar::xq, sVfetk_LocalVar::zkappa2, and sVfetk_LocalVar::zks2.

double Vfetk_energy ( Vfetk *  thee,
int  color,
int  nonlin 
)

Return the total electrostatic energy.

Using the solution at the finest mesh level, get the electrostatic energy using the free energy functional for the Poisson-Boltzmann equation without removing any self-interaction terms (i.e., removing the reference state of isolated charges present in an infinite dielectric continuum with the same relative permittivity as the interior of the protein) and return the result in units of $k_B T$. The argument color allows the user to control the partition on which this energy is calculated; if (color == -1) no restrictions are used. The solution is obtained from the finest level of the passed AM object, but atomic data from the Vfetk object is used to calculate the energy.

Author:
Nathan Baker
Returns:
Total electrostatic energy in units of $k_B T$.
Parameters:
color THe Vfetk object
nonlin Partition restriction for energy calculation; if non-negative, energy calculation is restricted to the specified partition (indexed by simplex and atom colors If 1, the NPBE energy functional is used; otherwise, the LPBE energy functional is used. If -2, SMPBE is used.

References sVfetk::pbe, Vfetk_dqmEnergy(), Vfetk_qfEnergy(), and Vpbe_getBulkIonicStrength().

Referenced by energyFE().

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void Vfetk_externalUpdateFunction ( SS **  simps,
int  num 
)

External hook to simplex subdivision routines in Gem. Called each time a simplex is subdivided (we use it to update the charge-simplex map).

Author:
Nathan Baker
Bug:
This function is not thread-safe.
Parameters:
num List of parent (simps[0]) and children (remainder) simplices Number of simplices in list

References sVfetk_LocalVar::fetk, Vcsm_update(), and Vfetk_getVcsm().

Referenced by Vfetk_ctor2().

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int Vfetk_fillArray ( Vfetk *  thee,
Bvec *  vec,
Vdata_Type  type 
)

Fill an array with the specified data.

Author:
Nathan Baker
Note:
This function is thread-safe
Bug:
Several values of type are not implemented
Returns:
1 if successful, 0 otherwise
Parameters:
vec The Vfetk object with the data
type The vector to hold the data THe type of data to write

References sVpbe::acc, sVfetk::am, sVfetk::gm, sVcsm::gm, sVpbe::ionConc, sVpbe::ionQ, sVpbe::maxIonRadius, sVpbe::numIon, sVfetk::pbe, PBE_LPBE, PBE_NPBE, PBE_SMPBE, sVfetk::pbeparm, sVpbe::solventRadius, sPBEparm::swin, sVfetk::type, Vacc_ivdwAcc(), Vacc_molAcc(), Vacc_splineAcc(), Vacc_vdwAcc(), Vcap_exp(), VDT_CHARGE, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_EDENS, VDT_IVDW, VDT_KAPPA, VDT_LAP, VDT_NDENS, VDT_POT, VDT_QDENS, VDT_SMOL, VDT_SSPL, and VDT_VDW.

Referenced by writedataFE().

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Vrc_Codes Vfetk_genCube ( Vfetk *  thee,
double  center[3],
double  length[3],
Vfetk_MeshLoad  meshType 
)

Construct a rectangular mesh (in the current Vfetk object).

Author:
Nathan Baker
Parameters:
center Vfetk object
length Center for mesh
meshType Mesh lengths Mesh boundary conditions

References sVfetk::am, sVfetk::gm, sVcsm::gm, VML_DIRICUBE, VML_EXTERNAL, VML_NEUMCUBE, VRC_FAILURE, and VRC_SUCCESS.

Referenced by Vfetk_loadMesh().

AM* Vfetk_getAM ( Vfetk *  thee  ) 

Get a pointer to the AM (algebra manager) object.

Author:
Nathan Baker
Returns:
Pointer to the AM (algebra manager) object
Parameters:
thee The Vfetk object

References sVfetk::am.

int Vfetk_getAtomColor ( Vfetk *  thee,
int  iatom 
)

Get the partition information for a particular atom.

Author:
Nathan Baker
Note:
Friend function of Vatom
Parameters:
thee Vfetk object
iatom Valist atom ID
Returns:
Partition ID
Parameters:
iatom The Vfetk object Valist atom index

References sVfetk::pbe, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPartID(), and Vpbe_getValist().

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Gem* Vfetk_getGem ( Vfetk *  thee  ) 

Get a pointer to the Gem (grid manager) object.

Author:
Nathan Baker
Returns:
Pointer to the Gem (grid manager) object
Parameters:
thee Vfetk object

References sVfetk::gm.

Referenced by Vfetk_PDE_delta().

double* Vfetk_getSolution ( Vfetk *  thee,
int *  length 
)

Create an array containing the solution (electrostatic potential in units of $k_B T/e$) at the finest mesh level.

Author:
Nathan Baker and Michael Holst
Note:
The user is responsible for destroying the newly created array
Returns:
Newly created array of length "length" (see above); the user is responsible for destruction
Parameters:
length Vfetk object with solution Ste to length of the newly created solution array

References sVfetk::am.

Referenced by Vfetk_qfEnergy().

Vcsm* Vfetk_getVcsm ( Vfetk *  thee  ) 

Get a pointer to the Vcsm (charge-simplex map) object.

Author:
Nathan Baker
Returns:
Pointer to the Vcsm (charge-simplex map) object
Parameters:
thee The Vfetk object

References sVfetk::csm.

Referenced by Vfetk_externalUpdateFunction(), and Vfetk_PDE_delta().

Vpbe* Vfetk_getVpbe ( Vfetk *  thee  ) 

Get a pointer to the Vpbe (PBE manager) object.

Author:
Nathan Baker
Returns:
Pointer to the Vpbe (PBE manager) object
Parameters:
thee The Vfetk object

References sVfetk::pbe.

Vrc_Codes Vfetk_loadGem ( Vfetk *  thee,
Gem *  gm 
)

Load a Gem geometry manager object into Vfetk.

Author:
Nathan Baker
Parameters:
thee Destination
gm Geometry manager source
Vrc_Codes Vfetk_loadMesh ( Vfetk *  thee,
double  center[3],
double  length[3],
Vfetk_MeshLoad  meshType,
Vio *  sock 
)

Loads a mesh into the Vfetk (and associated) object(s).

Author:
Nathan Baker
Parameters:
center Vfetk object to load into
length Center for mesh (if constructed)
meshType Mesh lengths (if constructed)
sock Type of mesh to load Socket for external mesh data (NULL otherwise)

References sVfetk::am, sVfetk::csm, sVfetk::gm, sVfetk::pbe, Vcsm_ctor(), Vcsm_init(), Vfetk_genCube(), VML_DIRICUBE, VML_EXTERNAL, VML_NEUMCUBE, Vpbe_getValist(), VRC_FAILURE, and VRC_SUCCESS.

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unsigned long int Vfetk_memChk ( Vfetk *  thee  ) 

Return the memory used by this structure (and its contents) in bytes.

Author:
Nathan Baker
Returns:
The memory used by this structure and its contents in bytes
Parameters:
thee THe Vfetk object

References sVfetk::csm, and Vcsm_memChk().

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void Vfetk_PDE_bisectEdge ( int  dim,
int  dimII,
int  edgeType,
int  chart[],
double  vx[][VAPBS_DIM] 
)

Define the way manifold edges are bisected.

Author:
Nathan Baker and Mike Holst
Note:
This function is thread-safe.
Parameters:
dimII Intrinsic dimension of manifold
edgeType Embedding dimension of manifold
chart Type of edge being refined
vx Chart for edge vertices, used here as accessibility bitfields Edge vertex coordindates

Referenced by Vfetk_PDE_ctor2().

PDE* Vfetk_PDE_ctor ( Vfetk *  fetk  ) 

Constructs the FEtk PDE object.

Author:
Nathan Baker
Returns:
Newly-allocated PDE object
Bug:
Not thread-safe
Parameters:
fetk The Vfetk object

References Vfetk_PDE_ctor2(), and sVfetk::vmem.

Referenced by Vfetk_ctor2().

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int Vfetk_PDE_ctor2 ( PDE *  thee,
Vfetk *  fetk 
)

Intializes the FEtk PDE object.

Author:
Nathan Baker (with code by Mike Holst)
Returns:
1 if successful, 0 otherwise
Bug:
Not thread-safe
Parameters:
fetk The newly-allocated PDE object The parent Vfetk object

References sVfetk_LocalVar::fetk, Vfetk_PDE_bisectEdge(), Vfetk_PDE_delta(), Vfetk_PDE_DFu_wv(), Vfetk_PDE_Fu(), Vfetk_PDE_Fu_v(), Vfetk_PDE_initAssemble(), Vfetk_PDE_initElement(), Vfetk_PDE_initFace(), Vfetk_PDE_initPoint(), Vfetk_PDE_Ju(), Vfetk_PDE_mapBoundary(), Vfetk_PDE_markSimplex(), Vfetk_PDE_oneChart(), Vfetk_PDE_simplexBasisForm(), Vfetk_PDE_simplexBasisInit(), Vfetk_PDE_u_D(), and Vfetk_PDE_u_T().

Referenced by Vfetk_PDE_ctor().

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void Vfetk_PDE_delta ( PDE *  thee,
int  type,
int  chart,
double  txq[],
void *  user,
double  F[] 
)

Evaluate a (discretized) delta function source term at the given point.

Author:
Nathan Baker
Bug:
This function is not thread-safe
Parameters:
type PDE object
chart Vertex type
txq Chart for point coordinates
user Point coordinates
F Vertex object pointer Set to delta function value

References sVfetk_LocalVar::delta, sVfetk_LocalVar::fetk, sVfetk::pbe, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sVfetk::type, Vatom_getCharge(), Vatom_getPosition(), VATOMMAX, Vcsm_getAtom(), Vcsm_getAtomIndex(), Vcsm_getNumberAtoms(), Vfetk_getGem(), Vfetk_getVcsm(), Vpbe_getZmagic(), and VRINGMAX.

Referenced by Vfetk_PDE_ctor2().

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double Vfetk_PDE_DFu_wv ( PDE *  thee,
int  key,
double  W[],
double  dW[][VAPBS_DIM],
double  V[],
double  dV[][VAPBS_DIM] 
)

This is the linearization of the weak form of the PBE; e.g., for use in a Newton iteration. This is the functional linearization of the strong form integrated with a test function to give:

\[ \int_\Omega \left[ \epsilon \nabla w \cdot \nabla v + b'(u) w v - f v \right] dx \]

where $b'(u)$ denotes the functional derivation of the mobile ion term.

Author:
Nathan Baker and Mike Holst
Returns:
Integrand value
Bug:
This function is not thread-safe
Parameters:
key The PDE object
W Integrand to evaluate (0 = interior weak form, 1 = boundary weak form)
dW Trial function value at current point
V Trial function gradient at current point
dV Test function value at current point Test function gradient

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_dtor ( PDE **  thee  ) 

Destroys FEtk PDE object.

Author:
Nathan Baker
Note:
Thread-safe
Parameters:
thee Pointer to PDE object memory

References sVfetk_LocalVar::fetk, Vfetk_PDE_dtor2(), and sVfetk::vmem.

Referenced by Vfetk_dtor2().

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void Vfetk_PDE_dtor2 ( PDE *  thee  ) 

FORTRAN stub: destroys FEtk PDE object.

Author:
Nathan Baker
Note:
Thread-safe
Parameters:
thee PDE object memory

References sVfetk_LocalVar::fetk.

Referenced by Vfetk_PDE_dtor().

void Vfetk_PDE_Fu ( PDE *  thee,
int  key,
double  F[] 
)

Evaluate strong form of PBE. For interior points, this is:

\[ -\nabla \cdot \epsilon \nabla u + b(u) - f \]

where $b(u)$ is the (possibly nonlinear) mobile ion term and $f$ is the source charge distribution term (for PBE) or the induced surface charge distribution (for RPBE). For an interior-boundary (simplex face) point, this is:

\[ [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^+} - [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^-} \]

where $n(x)$ is the normal to the simplex face and the term represents the jump in dielectric displacement across the face. There is no outer-boundary contribution for this problem.

Author:
Nathan Baker
Bug:

This function is not thread-safe

This function is not implemented (sets error to zero)

Parameters:
key The PDE object
F Type of point (0 = interior, 1 = boundary, 2 = interior boundary Set to value of residual

Referenced by Vfetk_PDE_ctor2().

double Vfetk_PDE_Fu_v ( PDE *  thee,
int  key,
double  V[],
double  dV[][VAPBS_DIM] 
)

This is the weak form of the PBE; i.e. the strong form integrated with a test function to give:

\[ \int_\Omega \left[ \epsilon \nabla u \cdot \nabla v + b(u) v - f v \right] dx \]

where $b(u)$ denotes the mobile ion term.

Author:
Nathan Baker and Mike Holst
Returns:
Integrand value
Bug:
This function is not thread-safe
Parameters:
key The PDE object
V Integrand to evaluate (0 = interior weak form, 1 = boundary weak form
dV Test function at current point Test function derivative at current point

References sVfetk_LocalVar::A, sVfetk_LocalVar::B, sVfetk_LocalVar::dU, sVfetk_LocalVar::dW, sVfetk_LocalVar::F, sVfetk_LocalVar::fetk, sVfetk_LocalVar::Fu_v, PBE_LRPBE, and sVfetk::type.

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_initAssemble ( PDE *  thee,
int  ip[],
double  rp[] 
)

Do once-per-assembly initialization.

Author:
Nathan Baker and Mike Holst
Note:
Thread-safe
Parameters:
ip PDE object
rp Integer parameter array (not used) Double parameter array (not used)

References sVpbe::alist, sVfetk_LocalVar::fetk, sVfetk_LocalVar::green, sVfetk_LocalVar::initGreen, sVfetk::pbe, Vgreen_ctor(), and Vgreen_dtor().

Referenced by Vfetk_PDE_ctor2().

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void Vfetk_PDE_initElement ( PDE *  thee,
int  elementType,
int  chart,
double  tvx[][VAPBS_DIM],
void *  data 
)

Do once-per-element initialization.

Author:
Nathan Baker and Mike Holst
Todo:
Jump term is not implemented
Bug:
This function is not thread-safe
Parameters:
elementType PDE object
chart Material type (not used)
tvx Chart in which the vertex coordinates are provided, used here as a bitfield to store molecular accessibility
data Vertex coordinates Simplex pointer (hack)

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_initFace ( PDE *  thee,
int  faceType,
int  chart,
double  tnvec[] 
)

Do once-per-face initialization.

Author:
Nathan Baker and Mike Holst
Bug:
This function is not thread-safe
Parameters:
faceType THe PDE object
chart Simplex face type (interior or various boundary types)
tnvec Chart in which the vertex coordinates are provided, used here as a bitfield for molecular accessibility Coordinates of outward normal vector for face

References sVfetk_LocalVar::fType, and sVfetk_LocalVar::nvec.

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_initPoint ( PDE *  thee,
int  pointType,
int  chart,
double  txq[],
double  tU[],
double  tdU[][VAPBS_DIM] 
)

Do once-per-point initialization.

Author:
Nathan Baker
Bug:

This function is not thread-safe

This function uses pre-defined boudnary definitions for the molecular surface.

Parameters:
pointType The PDE object
chart The type of point -- interior or various faces
txq The chart in which the point coordinates are provided, used here as bitfield for molecular accessibility
tU Point coordinates
tdU Solution value at point Solution derivative at point

Referenced by Vfetk_PDE_ctor2().

double Vfetk_PDE_Ju ( PDE *  thee,
int  key 
)

Energy functional. This returns the energy (less delta function terms) in the form:

\[ c^{-1}/2 \int (\epsilon (\nabla u)^2 + \kappa^2 (cosh u - 1)) dx \]

for a 1:1 electrolyte where $c$ is the output from Vpbe_getZmagic.

Author:
Nathan Baker
Returns:
Energy value (in kT)
Bug:
This function is not thread-safe.
Parameters:
key The PDE object What to evluate: interior (0) or boundary (1)?

References sVfetk_LocalVar::diel, sVfetk_LocalVar::dU, sVfetk_LocalVar::fetk, sVfetk_LocalVar::ionacc, sVfetk_LocalVar::ionConc, sVfetk_LocalVar::ionQ, sVfetk_LocalVar::nion, sVfetk::pbe, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sVfetk::type, sVfetk_LocalVar::U, Vcap_exp(), Vpbe_getZmagic(), sVfetk_LocalVar::W, sVfetk_LocalVar::zkappa2, and sVfetk_LocalVar::zks2.

Referenced by Vfetk_PDE_ctor2().

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void Vfetk_PDE_mapBoundary ( int  dim,
int  dimII,
int  vertexType,
int  chart,
double  vx[VAPBS_DIM] 
)

Map a boundary point to some pre-defined shape.

Author:
Nathan Baker and Mike Holst
Note:
This function is thread-safe and is a no-op
Parameters:
dimII Intrinsic dimension of manifold
vertexType Embedding dimension of manifold
chart Type of vertex
vx Chart for vertex coordinates Vertex coordinates

Referenced by Vfetk_PDE_ctor2().

int Vfetk_PDE_markSimplex ( int  dim,
int  dimII,
int  simplexType,
int  faceType[VAPBS_NVS],
int  vertexType[VAPBS_NVS],
int  chart[],
double  vx[][VAPBS_DIM],
void *  simplex 
)

User-defined error estimator -- in our case, a geometry-based refinement method; forcing simplex refinement at the dielectric boundary and (for non-regularized PBE) the charges.

Author:
Nathan Baker
Returns:
1 if mark simplex for refinement, 0 otherwise
Bug:
This function is not thread-safe
Parameters:
dimII Intrinsic manifold dimension
simplexType Embedding manifold dimension
faceType Type of simplex being refined
vertexType Types of faces in simplex
chart Types of vertices in simplex
vx Charts for vertex coordinates
simplex Vertex coordinates Simplex pointer

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_oneChart ( int  dim,
int  dimII,
int  objType,
int  chart[],
double  vx[][VAPBS_DIM],
int  dimV 
)

Unify the chart for different coordinate systems -- a no-op for us.

Author:
Nathan Baker
Note:
Thread-safe; a no-op
Parameters:
dimII Intrinsic manifold dimension
objType Embedding manifold dimension
chart ???
vx Charts of vertices' coordinates
dimV Vertices' coordinates Number of vertices

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_simplexBasisForm ( int  key,
int  dim,
int  comp,
int  pdkey,
double  xq[],
double  basis[] 
)

Evaluate the bases for the trial or test space, for a particular component of the system, at all quadrature points on the master simplex element.

Author:
Mike Holst
Parameters:
dim Basis type to evaluate (0 = trial, 1 = test, 2 = trialB, 3 = testB)
comp Spatial dimension Which component of elliptic system to produce basis for
xq Basis partial differential equation evaluation key:

  • 0 = evaluate basis(x,y,z)
  • 1 = evaluate basis_x(x,y,z)
  • 2 = evaluate basis_y(x,y,z)
  • 3 = evaluate basis_z(x,y,z)
  • 4 = evaluate basis_xx(x,y,z)
  • 5 = evaluate basis_yy(x,y,z)
  • 6 = evaluate basis_zz(x,y,z)
  • 7 = etc...
basis Set to quad pt coordinate Set to all basis functions evaluated at all quadrature pts

Referenced by Vfetk_PDE_ctor2().

int Vfetk_PDE_simplexBasisInit ( int  key,
int  dim,
int  comp,
int *  ndof,
int  dof[] 
)

Initialize the bases for the trial or the test space, for a particular component of the system, at all quadrature points on the master simplex element.

Author:
Mike Holst
Note:
 *   The basis ordering is important.  For a fixed quadrature
 *   point iq, you must follow the following ordering in p[iq][],
 *   based on how you specify the degrees of freedom in dof[]:
 *   
 *   <v_0 vDF_0>,      <v_1 vDF_0>,      ..., <v_{nv} vDF_0>
 *   <v_0 vDF_1>,      <v_1 vDF_1>,      ..., <v_{nv} vDF_1>
 *                           ...
 *   <v_0 vDF_{nvDF}>, <v_0 vDF_{nvDF}>, ..., <v_{nv} vDF_{nvDF}>
 *   
 *   <e_0 eDF_0>,      <e_1 eDF_0>,      ..., <e_{ne} eDF_0>
 *   <e_0 eDF_1>,      <e_1 eDF_1>,      ..., <e_{ne} eDF_1>
 *                           ...
 *   <e_0 eDF_{neDF}>, <e_1 eDF_{neDF}>, ..., <e_{ne} eDF_{neDF}>
 *
 *   <f_0 fDF_0>,      <f_1 fDF_0>,      ..., <f_{nf} fDF_0>
 *   <f_0 fDF_1>,      <f_1 fDF_1>,      ..., <f_{nf} fDF_1>
 *                           ...
 *   <f_0 fDF_{nfDF}>, <f_1 fDF_{nfDF}>, ..., <f_{nf} fDF_{nfDF}>
 *
 *   <s_0 sDF_0>,      <s_1 sDF_0>,      ..., <s_{ns} sDF_0>
 *   <s_0 sDF_1>,      <s_1 sDF_1>,      ..., <s_{ns} sDF_1>
 *                           ...
 *   <s_0 sDF_{nsDF}>, <s_1 sDF_{nsDF}>, ..., <s_{ns} sDF_{nsDF}>
 *
 *   For example, linear elements in R^3, with one degree of freedom at each *
 *   vertex, would use the following ordering: 
 *
 *     <v_0 vDF_0>, <v_1 vDF_0>, <v_2 vDF_0>, <v_3 vDF_0> 
 *
 *   Quadratic elements in R^2, with one degree of freedom at each vertex and
 *   edge, would use the following ordering: 
 * 
 *     <v_0 vDF_0>, <v_1 vDF_0>, <v_2 vDF_0> 
 *     <e_0 eDF_0>, <e_1 eDF_0>, <e_2 eDF_0> 
 *
 *   You can use different trial and test spaces for each component of the
 *   elliptic system, thereby allowing for the use of Petrov-Galerkin methods.
 *   You MUST then tag the bilinear form symmetry entries as nonsymmetric in
 *   your PDE constructor to reflect that DF(u)(w,v) will be different from
 *   DF(u)(v,w), even if your form acts symmetrically when the same basis is
 *   used for w and v.
 * 
 *   You can also use different trial spaces for each component of the elliptic
 *   system, and different test spaces for each component of the elliptic
 *   system.  This allows you to e.g.  use a basis which is vertex-based for 
 *   one component, and a basis which is edge-based for another.  This is
 *   useful in fluid mechanics, eletromagnetics, or simply to play around with
 *   different elements.  
 *   
 *   This function is called by MC to build new master elements whenever it
 *   reads in a new mesh.  Therefore, this function does not have to be all
 *   that fast, and e.g.  could involve symbolic computation.
 *
Parameters:
dim Basis type to evaluate (0 = trial, 1 = test, 2 = trialB, 3 = testB)
comp Spatial dimension
ndof Which component of elliptic system to produce basis for?
dof Set to the number of degrees of freedom Set to degree of freedom per v/e/f/s

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_u_D ( PDE *  thee,
int  type,
int  chart,
double  txq[],
double  F[] 
)

Evaluate the Dirichlet boundary condition at the given point.

Author:
Nathan Baker
Bug:

This function is hard-coded to call only multiple-sphere Debye-Hü functions.

This function is not thread-safe.

Parameters:
type PDE object
chart Vertex boundary type
txq Chart for point coordinates
F Point coordinates Set to boundary values

References sVfetk_LocalVar::fetk, sVfetk::pbe, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sVfetk::type, and sVfetk_LocalVar::u_D.

Referenced by Vfetk_PDE_ctor2().

void Vfetk_PDE_u_T ( PDE *  thee,
int  type,
int  chart,
double  txq[],
double  F[] 
)

Evaluate the "true solution" at the given point for comparison with the numerical solution.

Author:
Nathan Baker
Note:
This function only returns zero.
Bug:
This function is not thread-safe.
Parameters:
type PDE object
chart Point type
txq Chart for point coordinates
F Point coordinates Set to value at point

References sVfetk_LocalVar::u_T.

Referenced by Vfetk_PDE_ctor2().

double Vfetk_qfEnergy ( Vfetk *  thee,
int  color 
)

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:

\[ G = \sum_i q_i u(r_i) \]

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.

Author:
Nathan Baker
Parameters:
thee Vfetk object
color Partition restriction for energy evaluation, only used if non-negative
Returns:
The fixed charge electrostatic energy in units of $k_B T$.
Parameters:
color The Vfetk object Partition restriction for energy evaluation, only used if non-negative

References sVpbe::alist, sVfetk::am, sVfetk::gm, sVfetk::pbe, Valist_getNumberAtoms(), and Vfetk_getSolution().

Referenced by Vfetk_energy().

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void Vfetk_readMesh ( Vfetk *  thee,
int  skey,
Vio *  sock 
)

Read in mesh and initialize associated internal structures.

Author:
Nathan Baker
Note:
See also:
Vfetk_genCube
Parameters:
skey THe Vfetk object
sock The sock format key (0 = MCSF simplex format) Socket object ready for reading
void Vfetk_setAtomColors ( Vfetk *  thee  ) 

Transfer color (partition ID) information frmo a partitioned mesh to the atoms.

Transfer color information from partitioned mesh to the atoms. In the case that a charge is shared between two partitions, the partition color of the first simplex is selected. Due to the arbitrary nature of this selection, THIS METHOD SHOULD ONLY BE USED IMMEDIATELY AFTER PARTITIONING!!!

Warning:
This function should only be used immediately after mesh partitioning
Author:
Nathan Baker
Note:
This is a friend function of Vcsm
Parameters:
thee THe Vfetk object

References sVpbe::alist, sVfetk::csm, sVfetk::pbe, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_setPartID(), and Vcsm_getSimplex().

Referenced by partFE().

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void Vfetk_setParameters ( Vfetk *  thee,
PBEparm *  pbeparm,
FEMparm *  feparm 
)

Set the parameter objects.

Author:
Nathan Baker
Parameters:
pbeparm The Vfetk object
feparm Parameters for solution of the PBE FEM-speecific solution parameters

References sVfetk::feparm, and sVfetk::pbeparm.

int Vfetk_write ( Vfetk *  thee,
const char *  iodev,
const char *  iofmt,
const char *  thost,
const char *  fname,
Bvec *  vec,
Vdata_Format  format 
)

Write out data.

Author:
Nathan Baker
Parameters:
thee Vfetk object
vec FEtk Bvec vector to use
format Format for data
iodev Output device type (FILE/BUFF/UNIX/INET)
iofmt Output device format (ASCII/XDR)
thost Output hostname (for sockets)
fname Output FILE/BUFF/UNIX/INET name
Note:
This function is thread-safe
Bug:
Some values of format are not implemented
Returns:
1 if successful, 0 otherwise
Parameters:
iodev The Vfetk object
iofmt Output device type (FILE = file, BUFF = buffer, UNIX = unix pipe, INET = network socket)
thost Output device format (ASCII = ascii/plaintext, XDR = xdr)
fname Output hostname for sockets
vec Output filename for other
format Data vector Data format

References sVfetk::aprx, sVfetk::gm, sVcsm::gm, VDF_AVS, VDF_DX, and VDF_UHBD.

Referenced by writedataFE().

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