#include <delphi_datamarshal.h>
Inherits IDataMarshal.
class CDelphiDataMarshal is an implementation of the interface IDataMarshal. It provides not only a particular set of statements and functions allowed in the parameter file, but also the set of variables contained in the private map of class CDelphiDtata and their default values.
- Note
- This class must be paired with the class CDelphiData for practical uses. They together define the particular application, namely the delphicpp.
| CDelphiDataMarshal::CDelphiDataMarshal |
( |
int |
argc, |
|
|
char * |
argv[], |
|
|
shared_ptr< CTimer > |
pt |
|
) |
| |
|
inline |
constructor to generate regular stand-alone executable delphicpp.
- Parameters
-
| [in] | argc | Number of parameters in the command line |
| [in] | argv[] | paraemters in the command line |
| [in] | pt | pointer to an object of class CTimer to report execution time |
| CDelphiDataMarshal::CDelphiDataMarshal |
( |
shared_ptr< CTimer > |
pt | ) |
|
|
inline |
constructor to allow delphicpp to be compiled with mcce in order to avoid intensive IO operations.
- Parameters
-
| [in] | mcce_data | A pointer to the interface struct SMCCE |
| [in] | pt | pointer to an object of class CTimer to report execution time |
| CDelphiDataMarshal::~CDelphiDataMarshal |
( |
| ) |
|
|
inline |
| void CDelphiDataMarshal::setDefault |
( |
| ) |
|
set default values for all variables contained in data container
| void CDelphiDataMarshal::updateParameters |
( |
| ) |
|
|
virtual |
function implementing post-reading updates of parameters
Implements IDataMarshal.
| bool CDelphiDataMarshal::bAnalyEng |
- F95 var.: loga
- Set by func.: ENERGY
- Default : FALSE
- Description:
flag for calculating analytic energy
| bool CDelphiDataMarshal::bAnalySurfEng |
- F95 var.: logas
- Set by func.: ENERGY
- Default : FALSE
- Description:
flag for analytic surface
| bool CDelphiDataMarshal::bAtomCoordInSite |
- F95 var.: isitx
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report atomic coordinate information in site function
| bool CDelphiDataMarshal::bAtomInSite |
- F95 var.: isita
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report atom info in site function.
| bool CDelphiDataMarshal::bAtomPotentialInSite |
- F95 var.: isitap
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report atomic potential info in site function
| bool CDelphiDataMarshal::bAutoConverge |
- Long form :
- AUTOCON
- AUTOCONVERGENCE
- AUTOMATICCONVERGENCE
- Short form :
- AUTOC
- 2L abbrev. :
- AC
- F95 var.: iautocon
- Default : TRUE
- Description:
A flag for automatic convergence. The program by default will automatically calculate the number of iterations needed to attain convergence. It is automatically set if no number of iteration is specified otherwise.
- Note
- When AUTOC = FLASE, either LINIT or NONIT must be set nonzero so that the solver knows which solver to use and how many iterations to take.
| bool CDelphiDataMarshal::bBemSrfOut |
- F95 var.: ibem
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for saving vertices, normals and triangles in the bem.srf file
| bool CDelphiDataMarshal::bBiosystemOut |
- F95 var.: ibios
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
Flag for format of output file fort.14. = .false. to output in DELPHI format, = .true. to output in INSIGHT format.
| bool CDelphiDataMarshal::bCoulombEng |
- F95 var.: logc
- Set by func.: ENERGY
- Default : FALSE
- Description:
flag for calculating coulombic energy
| bool CDelphiDataMarshal::bCoulombForceInSite |
- F95 var.: isitcf
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report coulombic force info in site function
| bool CDelphiDataMarshal::bCoulombPotentialInSite |
- F95 var.: isitc
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report coulombic potential info in site function
| bool CDelphiDataMarshal::bCrgInSite |
- F95 var.: isitq
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report charge in site function
| bool CDelphiDataMarshal::bCrgInterplateType |
- Long form :
- FANCYCHARGE
- SPHERICALCHARGEDISTRIBUTION
- Short form :
- FCRG
- 2L abbrev. :
- FC
- F95 var.: isph
- Default : FALSE
- Description:
A flag, normally set to false indicating a linear cubic interpolation of charges to grid points; set to true this turns on a spherical charge interpolation. If an atomic charge does not lie exactly on a grid point, then it must somehow be distributed onto the grid points. If this flag is set false, the standard algorithm is used which distributes a charge to the nearest 8 grid points (quick and simple, see the Proteins paper of Klapper et al.). If this flag is set true, then an algorithm is used which gives a more spherically symmetric charge distribution, although the charge is now spread over a wider region of space. For certain cases this gives higher accuracy for potentials less than 3 grid units from a charge (see Gilson et al. J.Comp. Chem paper), although this point has not been exhaustively explored.
| bool CDelphiDataMarshal::bDbOut |
- F95 var.: idbwrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing DELPHI DB file, containing Debye factor
| bool CDelphiDataMarshal::bDebyeFractionInSite |
- F95 var.: isitdeb
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report debye fraction map info in site function
| bool CDelphiDataMarshal::bEngOut |
- F95 var.: inrgwrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing energy in unit 42 file
| bool CDelphiDataMarshal::bEpsOut |
- F95 var.: epswrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing epsilon map
| bool CDelphiDataMarshal::bExitUniformDielect |
- Long form :
- EXITUNIFORMDIELECTRIC
- Short form :
- EXITUN
- 2L abbrev. :
- XU
- F95 var.: iexun
- Default : FALSE
- Description:
A flag to terminate the program if uniform dielectric is present (INDI=EXDI). Usually not modified.
| bool CDelphiDataMarshal::bFieldInSite |
- F95 var.: isitf
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report field info in site function
| bool CDelphiDataMarshal::bFixedRelaxParam |
- Long form :
- CHEBIT
- Short form :
- CHEBIT
- 2L abbrev. :
- CI
- F95 var.: icheb
- Default : FALSE
- Description:
A flag, that if it is true the relaxation parameter for linear convergence process is set equal to 1 (usually not modified from default).
| bool CDelphiDataMarshal::bFrcUnformatIn |
- F95 var.: ifrcrd
- Default : FALSE
- Description:
flag for reading unformatted frc file
| bool CDelphiDataMarshal::bGridCrgOut |
- F95 var.: iwgcrg
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing grid charge file
| bool CDelphiDataMarshal::bGridEng |
- F95 var.: logg
- Set by func.: ENERGY
- Default : FALSE
- Description:
flag for calculating grid energy
| bool CDelphiDataMarshal::bGridPotentialInSite |
- F95 var.: isitp
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report grid potential info in site function
| bool CDelphiDataMarshal::bHsurf2DatOut |
- F95 var.: iacs
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for importing exposed vertices from thehsurf2.dat file
| bool CDelphiDataMarshal::bIonsEng |
- F95 var.: logions
- Set by func.: ENERGY
- Default : FALSE
- Description:
Flag for energy calculation of contribution by the solvent
| bool CDelphiDataMarshal::bIsAcent |
- F95 var.: iacent
- Set by func.: ACENTER or ACENT
- Default : FALSE
- Description:
flag for Acent(x,y,z) function
| bool CDelphiDataMarshal::bIsBuffz |
- F95 var.: ibufz
- Set by func.: BUFFZ
- Default : FALSE
- Description:
flag activating the BUFFZ feature for reaction field energy
| bool CDelphiDataMarshal::bLogGraph |
- Long form :
- LOGFILECONVERGENCE
- Short form :
- LOGGRP
- 2L abbrev. :
- LG
- F95 var.: igraph
- Default : FALSE
- Description:
A flag that activates the convergence plot during the run.
| bool CDelphiDataMarshal::bLogPotential |
- Long form :
- LOGFILEPOTENTIALS
- Short form :
- LOGPOT
- 2L abbrev. :
- LP
- F95 var.: ipoten
- Default : FALSE
- Description:
A flag that activates the potential listing during the run.
| bool CDelphiDataMarshal::bManualRelaxParam |
- F95 var.: imanual
- Default : FALSE
- Description:
flag for manual assignment of relaxation parameter
| bool CDelphiDataMarshal::bMDInSite |
- F95 var.: isitmd
- Set by func.: SITE
- Default : FALSE
- Description:
flag for producing molecular dynamics data for future implementation
| bool CDelphiDataMarshal::bModPdbOut |
- F95 var.: iatout
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
Flag controlling outputting modified PDB file in UNIT 19
| bool CDelphiDataMarshal::bNonlinearEng |
- F95 var.: lognl
- Default : FALSE
- Description:
Flag for non linear energy calculation.
| bool CDelphiDataMarshal::bOnlyMolecule |
- F95 var.: ionlymol
- Default : TRUE
- Description:
true if there are only molecules in the system (no objects)
| bool CDelphiDataMarshal::bOutCrgDensity |
- Long form :
- PHICON
- Short form :
- PHICON
- 2L abbrev. :
- N.A.
- F95 var.: iconc
- Default : FALSE
- Description:
A flag, that maps charge density in a .phi file, with a procedure that is equivalent to the one that saves the potential map. phicon=f produces standard potential output in kT/e (approximately equal to 25.6 mV at 25oC, or to 0.593 kcal/mole of charge). phicon=t will give net solvent ion concentration output in M/l, where for every lattice point inside the molecule the concentration is 0, and the outside concentration is obtained from: (-ionic strength*2*sinh(potential)) or its linearized version if linear PBE is used.
| bool CDelphiDataMarshal::bOutGraspSurf |
- Long form :
- CLCSRF
- Short form :
- CLCSRF
- 2L abbrev. :
- CS
- F95 var.: isrf
- Default : FALSE
- Description:
A flag, that when set to true, outputs a GRASP viewable surface file in the file named grasp.srf.
| bool CDelphiDataMarshal::bPDB2FRCInSite |
- F95 var.: iself
- Set by func.: SITE
- Default : FALSE
- Description:
flag to use processed pdb as frc field for site function activation
| bool CDelphiDataMarshal::bPdbUnformatIn |
- F95 var.: ipdbrd
- Set by func.: READ or IN
- Default : FALSE
- Description:
flag for reading unformatted pdb file
| bool CDelphiDataMarshal::bPhimapOut |
- F95 var.: phiwrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing potential map
| bool CDelphiDataMarshal::bPotentialInSite |
- F95 var.: isitpot
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report potential info in site function
| bool CDelphiDataMarshal::bReactFieldInFRC |
- F95 var.: irea
- Set by func.: SITE
- Default : FALSE
- Description:
flag for calculating reaction field and output it in formatted frc file
| bool CDelphiDataMarshal::bReactForceInSite |
- F95 var.: isitrf
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report reaction force info in site function
| bool CDelphiDataMarshal::bReactPotentialInSite |
- F95 var.: isitr
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report reaction potential info in site function
| bool CDelphiDataMarshal::bSaltInSite |
- F95 var.: isiti
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report salt concentration info in site function
| bool CDelphiDataMarshal::bSiteOut |
- F95 var.: isite
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for outputting site potential
| bool CDelphiDataMarshal::bSolvEng |
- F95 var.: logs
- Set by func.: ENERGY
- Default : FALSE
- Description:
flag for calculating solvation energy
| bool CDelphiDataMarshal::bSolvePB |
- Long form :
- SOLVPB
- Short form :
- SOLVPB
- 2L abbrev. :
- SP
- F95 var.: isolv
- Default : TRUE
- Description:
A flag, which controls the Poisson-Boltzmann solver. Normally DelPhi will invoke the Poisson-Boltzmann solver but if you are interested in using DelPhi for other things such as calculating surface area or producing a GRASP viewable surface file, you can turn off the solver using this option.
| bool CDelphiDataMarshal::bSpectralRadius |
- F95 var.: iuspec
- Default : FALSE
- Description:
flag for using relaxation factor from prm file
| bool CDelphiDataMarshal::bSurfCrgInSite |
- F95 var.: isitsf
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report site surface charge and electric field at site's Solvent Accessible Surface
| bool CDelphiDataMarshal::bSurfCrgOut |
- F95 var.: isch
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for outputting surface charge file
| bool CDelphiDataMarshal::bSurfEngOut |
- F95 var.: isen
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for calculating surface energy positions and values
| bool CDelphiDataMarshal::bTotalForceInSite |
- F95 var.: isittf
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report total force info in site function
| bool CDelphiDataMarshal::bTotalPotentialInSite |
- F95 var.: isitt
- Set by func.: SITE
- Default : FALSE
- Description:
flag to report total potential info in site function
| bool CDelphiDataMarshal::bUnformatFrcOut |
- F95 var.: ifrcwrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing unformatted frc file
| bool CDelphiDataMarshal::bUnformatPdbOut |
- F95 var.: ipdbwrt
- Set by func.: WRITE or OUT
- Default : FALSE
- Description:
flag for writing unformatted pdb file
| bool CDelphiDataMarshal::bUniformDielec |
- F95 var.: uniformdiel
- Default : TRUE
- Description:
true if the dielectric in the system is uniform
| SExtrema<delphi_integer> CDelphiDataMarshal::eiBuffz |
- F95 var.: bufz
- Set by func.: BUFFZ
- Default : {0,0,0,0,0,0}
- Description:
Defines a box with sides parallel to grid unit vectors that the reaction field energy will then be calculated using ONLY the polarization charges contained in that box. The fixed format is BUFFZ(6i3).
| delphi_real CDelphiDataMarshal::fDebyeLength |
- F95 var.: deblen
- Default : 0.0
- Description:
Debye Length value
| delphi_real CDelphiDataMarshal::fEngCorrect |
- F95 var.: test_ergs
- Default : 0.0
- Description:
corrected reaction field energy
| delphi_real CDelphiDataMarshal::fEngCoul |
- F95 var.: test_ergc
- Default : 0.0
- Description:
coulombic energy
| delphi_real CDelphiDataMarshal::fEngGrid |
- F95 var.: test_ergg
- Default : 0.0
- Description:
total grid energy
| delphi_real CDelphiDataMarshal::fEngIons |
- F95 var.: test_ergions
- Default : 0.0
- Description:
total ionic direct contribution
| delphi_real CDelphiDataMarshal::fEngReact |
- F95 var.: test_ergr
- Default : 0.0
- Description:
total reaction field energy
| delphi_real CDelphiDataMarshal::fEPKT |
- F95 var.: epkt
- Default : 0.0
- Description:
EPKT
| delphi_real CDelphiDataMarshal::fEpsIn |
- F95 var.: epsin
- Default : 2.0
- Description:
repsin/epkt
| delphi_real CDelphiDataMarshal::fEpsOut |
- F95 var.: epsout
- Default : 80.0
- Description:
repsout/epkt
| delphi_real CDelphiDataMarshal::fExDielec |
- Long form :
- EXTERIORDIELECTRIC
- EXTERNALDIELECTRIC
- Short form :
- EXDI
- 2L abbrev. :
- ED
- F95 var.: repsout
- Default : 80.0
- Description:
The external (solution) dielectric constant. A value of EXDI=1 corresponds to the molecule in vacuum, EXDI=80 to the molecule in water. Depending on the application runs with EXDI equal to either of these values may be used to represent different states in a thermodynamic cycle.
| delphi_real CDelphiDataMarshal::fGridConverge |
- Long form :
- GRIDCONVERGENCE
- Short form :
- GRDCON
- 2L abbrev. :
- GC
- F95 var.: gten
- Default : 0.0
- Description:
The value for grid convergence. When set, the criterion used to stop the iterative process is the difference on values of grid energy, this option might slow down the calculation a bit, but provides a very strong criterion.
| delphi_real CDelphiDataMarshal::fInDielec |
- Long form :
- INTERIORDIELECTRIC
- Short form :
- INDI
- 2L abbrev. :
- ID
- F95 var.: repsin
- Default : 2.0
- Description:
The internal (molecules) dielectric constant. It is used only in single molecule systems for compatibility with the old version. A value of INDI=1 corresponds to a molecule with no polarizability- the state assumed in most molecular mechanics applications. INDI=2 represents a molecule with only electronic polarizability (i.e. assuming no reorientation of fixed dipoles, peptide bonds, etc). A value of 2 is based on the experimentally observed high frequency dielectric behavior of essentially all organic materials. INDI=4-6 represents a process where some small reorganization of molecular dipoles occurs which is not represented explicitly (for example in modeling the effects of site directed mutagenesis experiments, when the structure of the wild type, but not mutant protein is known). According to M.K. Gilson and B. Honig, Biopolymers, 25:2097 (1986) for instance, materials having similar dipole density, dipole moment and flexibility as globular proteins have a dielectric between 4 and 6. In modeling any process where large reorientations of dipoles, or large conformational change occurs, i.e. upon folding or denaturation, using a simple dielectric constant for the molecule would be inappropriate, and the change in conformation should be modeled explicitly.
| delphi_real CDelphiDataMarshal::fIonRadius |
- Long form :
- IONRADIUS
- Short form :
- IONRAD
- 2L abbrev. :
- IR
- F95 var.: exrad
- Default : 2.0
- Description:
The thickness of the ion exclusion layer around molecule (Å). IONRAD, in combination with the atomic van der Waals radii in the siz file, determines the regions of space, and hence the lattice points, which are inaccessible to solvent ions. Suggested values is IONRAD = 2.0 for sodium chloride. For the purpose of DelPhi, a solvent ion is considered as a point charge, which can approach no closer than its ionic radius, IONRAD, to any atoms van der Waals surface. The ion excluded volume is thus bounded by the contact surface, which is the locus of the ion centres when in van der Waals contact with any accessible atom of the molecule. A zero value for IONRAD will just yield the van der Waals surface. A non zero value of IONRAD will thus introduce a Stern, or ion exclusion layer, around the molecule where the solvent ion concentration will be zero and whose dielectric constant is that of the solvent, EXDI.
| delphi_real CDelphiDataMarshal::fIonStrength |
- F95 var.: rionst
- Default : 0.0
- Description:
ionic strength
| delphi_real CDelphiDataMarshal::fMaxc |
- Long form :
- MAXC
- Short form :
- MAXC
- 2L abbrev. :
- XC
- F95 var.: res2
- Default : 0.0
- Description:
The convergence threshold value based on maximum change of potential (suggested).
| delphi_real CDelphiDataMarshal::fMaxDimension |
- F95 var.: rmaxdim
- Default : 0.0
- Description:
largest dimension
| delphi_real CDelphiDataMarshal::fMaxRadius |
- F95 var.: rdmx
- Default : 0.01
- Description:
max among the radii
| delphi_real CDelphiDataMarshal::fMinusCrg |
- F95 var.: qmin
- Default : 0.0
- Description:
assigned negative charge
| delphi_real CDelphiDataMarshal::fNetCrg |
- F95 var.: qnet
- Default : 0.0
- Description:
net assigned charge
| delphi_real CDelphiDataMarshal::fPercentageFill |
- Long form :
- BOXFILL
- PERCENTFILL
- PERCENTBOXFILL
- Short form :
- PERFIL
- 2L abbrev. :
- PF
- F95 var.: perfil
- Default : 80.0
- Description:
A percentage of the object longest linear dimension to the lattice linear dimension. This will affect the scale of the lattice (grids/angstrom). The percentage fill of the lattice will depend on the application. A large percentage fill will provide a more detailed mapping of the molecular shape onto the lattice. A perfil less than 20% is not usually necessary or advisable. A very large filling will bring the dielectric boundary of the molecule closer to the lattice edge. This will cause larger errors arising from the boundary potential estimates, which are set to zero or approximated by coulombic/Debye-Huckel-type functions using a uniform solvent dielectric. The error will be minimal for higher salt concentrations or weakly charged molecules. Smaller percentages will increase the accuracy of the boundary conditions, but result in a coarser representation of the molecule. Higher resolution can be achieved more efficiently using focusing.
- Note
- If the molecule is not centered in the origin of the coordinate system, the perfil reflects the percentage of the system that is actually contained in the lattice. For example, if the maximum dimension of a molecule is 100Å, there is no offset and perfil is 50%, then the box side will be 200Å; but if there is an offset of 20Å in the maximum dimension direction, then the box side will be 280Å.
Scale, grid size and perfil are not independent variables so they cannot all be assigned simultaneously in a single run. In any quantitative calculation, the largest possible scale should be used, preferably greater than 2 grids/angstrom. Without focusing, a perfil of around 50% or 60% is reasonable. For example, if scale is set to 2 and perfil is set to 50, the grid size is calculated automatically given the size of the structure. For larger molecules this could mean a prohibitively large memory requirement. In this case a compromise must be found or focusing could be used. Regardless of grid scale, calculations should be repeated at different scales to assess the size of lattice resolution errors.
A good approach to the calculation could start with a small percentage, say 20%, using Debye-Huckel boundary conditions, and then focus in to say 90% or more, in one (or two) stages, using focusing boundary conditions for the second (and third) runs. It is not necessary for the molecule to lie completely within the grid although then the potential boundary conditions must be generated by focusing. However when calculating solvation energies with box fills of > 100% remember that unexpected results may be obtained since parts of the surface, (and perhaps some charges) are not included in the grid.
| delphi_real CDelphiDataMarshal::fPlusCrg |
- F95 var.: qplus
- Default : 0.0
- Description:
assigned positive charge
| delphi_real CDelphiDataMarshal::fPotentialUpperBond |
- Long form :
- N.A.
- Short form :
- ATPODS
- 2L abbrev. :
- N.A.
- F95 var.: atompotdist
- Default : 0.5
- Description:
upper bound of atomic potential for charged atoms (averaged over a spherical surface)
| delphi_real CDelphiDataMarshal::fRelaxParam |
- Long form :
- RELPAR
- Short form :
- RELPAR
- 2L abbrev. :
- RR
- F95 var.: relpar
- Default : 1.0
- Description:
A manually assigned value for relaxation parameter in non-linear iteration convergence process.
| delphi_real CDelphiDataMarshal::fRmsc |
- Long form :
- RMSC
- Short form :
- RMSC
- 2L abbrev. :
- MC
- F95 var.: res1
- Default : 0.0
- Description:
The convergence threshold value based on maximum change of potential (suggested).
| delphi_real CDelphiDataMarshal::fScale |
- Long form :
- SCALE
- Short form :
- SCALE
- 2L abbrev. :
- SC
- F95 var.: scale
- Default : 1.2
- Description:
The reciprocal of one grid spacing (grids/angstrom).
| delphi_real CDelphiDataMarshal::fSpectralRadius |
- Long form :
- RELAXATIONFACTOR
- Short form :
- RELFAC
- 2L abbrev. :
- RF
- F95 var.: uspec
- Default : 0.9975
- Description:
The externally assigned value for spectral radius (define spectral radius) (usually not modified from default).
| delphi_real CDelphiDataMarshal::fTaylorCoeff1 |
- F95 var.: chi1
- Default : 0.0
- Description:
Coefficient of x^1 term in Taylor series of the charge concentration.
| delphi_real CDelphiDataMarshal::fTaylorCoeff2 |
- F95 var.: chi2
- Default : 0.0
- Description:
Coefficient of x^2 term in Taylor series of the charge concentration.
| delphi_real CDelphiDataMarshal::fTaylorCoeff3 |
- F95 var.: chi3
- Default : 0.0
- Description:
Coefficient of x^3 term in Taylor series of the charge concentration.
| delphi_real CDelphiDataMarshal::fTaylorCoeff4 |
- F95 var.: chi4
- Default : 0.0
- Description:
Coefficient of x^4 term in Taylor series of the charge concentration.
| delphi_real CDelphiDataMarshal::fTaylorCoeff5 |
- F95 var.: chi5
- Default : 0.0
- Description:
Coefficient of x^5 term in Taylor series of the charge concentration.
| delphi_real CDelphiDataMarshal::fTemper |
- Long form :
- N.A.
- Short form :
- TEMPER
- 2L abbrev. :
- N.A.
- F95 var.: temperature
- Default : 297.3342119
- Description:
temperature in absolute degree
| SGrid<delphi_real> CDelphiDataMarshal::gfAcent |
- F95 var.: acent
- Set by func.: ACENTER or ACENT
- Default : {0.0,0.0,0.0}
- Description:
Used to set oldmid when iacent = .true.
| SGrid<delphi_real> CDelphiDataMarshal::gfBoxCenter |
- F95 var.: oldmid
- Default : {0.0,0.0,0.0}
- Description:
grid box center
| SGrid<delphi_real> CDelphiDataMarshal::gfCoordinateRange |
- F95 var.: cran
- Default : {0.0,0.0,0.0}
- Description:
range of x-, y- and z- coordinates
| SGrid<delphi_real> CDelphiDataMarshal::gfGeometricCenter |
- F95 var.: pmid
- Default : {0.0,0.0,0.0}
- Description:
system geometric center
| SGrid<delphi_real> CDelphiDataMarshal::gfMaxCoordinate |
- F95 var.: cmax
- Default : {-6000.0,-6000.0,-6000.0}
- Description:
maximal x-, y- and z- coordinates
| SGrid<delphi_real> CDelphiDataMarshal::gfMinCoordinate |
- F95 var.: cmin
- Default : {6000.0,6000.0,6000.0}
- Description:
minimal x-, y- and z- coordinates
| SGrid<delphi_real> CDelphiDataMarshal::gfMinusCrgCenter |
- F95 var.: cqmin
- Default : {0.0,0.0,0.0}
- Description:
Center of assigned negative charge
| SGrid<delphi_real> CDelphiDataMarshal::gfOffCenter |
- F95 var.: offset
- Set by func.: CENTER or CENT
- Default : {0.0,0.0,0.0}
- Description:
| SGrid<delphi_real> CDelphiDataMarshal::gfPlusCrgCenter |
- F95 var.: cqplus
- Default : {0.0,0.0,0.0}
- Description:
Center of assigned positive charge
| SGrid<delphi_real> CDelphiDataMarshal::gfPotentialDrop |
- Long form :
- N.A.
- Short form :
- VDROPX/VDROPY/VDROPZ
- 2L abbrev. :
- N.A.
- F95 var.: vdrop
- Default : 0.0/0.0/0.0
- Description:
vdropx = “VDROPX”; iper(4)=.true. vdropy = “VDROPY”; iper(5)=.true. vdropz = “VDROPZ”; iper(6)=.true.
| delphi_integer CDelphiDataMarshal::iAtomNum |
- F95 var.: natom
- Default : 0
- Description:
of atoms
| delphi_integer CDelphiDataMarshal::iBndyGridNum |
- F95 var.: ibnum
- Default : 0
- Description:
of boundary grid points
| int CDelphiDataMarshal::iBndyType |
- Long form :
- BOUNDARYCONDITION
- BOUNDARYCONDITIONS
- Short form :
- BNDCON
- 2L abbrev. :
- BC
- F95 var.: ibctyp
- Default : 2(=DIPOLAR)
- Description:
An integer flag specifying the type of boundary condition imposed on the edge of the lattice. Allowed options:
(1) potential is zero.
(2) dipolar. The boundary potentials are approximated by the Debye-Huckel potential of the equivalent dipole to the molecular charge distribution. Phi is the potential estimated at a given lattice boundary point, q+ (q-) is the sum of all positive (negative) charges, and r+(r-) is distance from the point to the center of positive (negative) charge, lambda is the Debye length.
(3) focusing. The potential map from a previous calculation is read in unit 18, and values for the potential at the lattice edge are interpolated from this map- clearly the first map should have been generated with a coarser grid (greater distance between lattice points) and positioned such that current lattice lies completely within old lattice or the program will protest. For focusing boundary conditions, the program reads in a potential map from a previous run, and compares the scale of the focusing map with that for the current run. If they are the same, it assumes that this is a continuation of a previous run, and iteration of the potentials contained in the previous potential map is continued. If the scale is not the same, it checks to ensure that the new lattice lies completely within the old lattice before interpolating the boundary conditions.
(4) coulombic. They are approximated by the sum of Debye-Huckel potentials of all the charges. qi is the i'th charge, and ri is the distance from the lattice boundary point to the charge.
| int CDelphiDataMarshal::iConvergeFract |
- Long form :
- CONVERGENCEFRACTION
- Short form :
- CONFRA
- 2L abbrev. :
- CF
- F95 var.: icon2
- Default : 1
- Description:
A flag that determines the convergence fraction. It decides what fraction of grid points are used in assessing convergence (1=all, 2=half, 5=fifth etc). By default it equals 1 (usually not modified from default).
| delphi_integer CDelphiDataMarshal::iCrg2GridNum |
- F95 var.: nqgrd
- Default : 0
- Description:
number of charges which will be charging the grid
| delphi_integer CDelphiDataMarshal::iCrgBdyGrid |
- F95 var.: ibc
- Default : 0
- Description:
number of charged boundary grid points
| delphi_integer CDelphiDataMarshal::iCrgedGridSum |
- F95 var.: icount1b
- Default : 0
- Description:
total charged grid points
| delphi_integer CDelphiDataMarshal::iCrgGridNum |
- F95 var.: nqass
- Default : 0
- Description:
number of assigned charges
| delphi_integer CDelphiDataMarshal::iDielecBndySum |
- F95 var.: icount2b
- Default : 0
- Description:
used for realigning idpos and db,compressing to contiguous space
| int CDelphiDataMarshal::iDirectEpsMap |
- F95 var.: idirectalg
- Default : 1
- Description:
Direct mapping of epsilon: (0/1)(n/y)
| int CDelphiDataMarshal::iFrcFormatOut |
- F95 var.: frcfrm
- Set by func.: WRITE or OUT
- Default : 0
- Description:
Format of file frcnam, = 0 if unknown format, = 1 if “RC”, = 2 if “R”, = 3 if “UN”
| delphi_integer CDelphiDataMarshal::iGrid |
- Long form :
- GRIDSIZE
- Short form :
- GSIZE
- 2L abbrev. :
- GS
- F95 var.: igrid
- Default : 0.0
- Description:
An odd integer number of points per side of the cubic lattice, min=5, max=571 (=NGRID, platform dependent). A larger grid size will in general mean a better resolution representation of the molecule on the lattice. This will results in more accurate potentials, but will require more time. The number of iterations required to reach a certain convergence will increase approximately linearly with parameter GS. Since the time per iteration will go up as the cube of this parameter the amount of calculation will thus increase at about the fourth power of GS.
| int CDelphiDataMarshal::iIterateInterval |
- Long form :
- CONVERGENCEINTERVAL
- Short form :
- CONINT
- 2L abbrev. :
- CI
- F95 var.: icon1
- Default : 10
- Description:
A flag that determines at what iteration interval convergence is checked, by default it equals 10.(usually not modified from default) The idea behind this parameter is to allow convergence to be checked less frequently to reduce the amount of time spent.
| int CDelphiDataMarshal::iLinIterateNum |
- Long form :
- ITERATION
- ITERATIONS
- LINEARITERATION
- Short form :
- LINIT
- 2L abbrev. :
- LI
- F95 var.: nlit
- Default : 0
- Description:
An integer number (> 3) of iterations with linear equation. The convergence behavior of the finite difference procedure is reported in the log file as both the mean and maximum absolute change in potential at the grid points between successive iterations. The latter is probably more important since it puts an upper bound on how much the potential is changing at the grid points. It is suggested that sufficient iterations be performed to give a final maximum change of less than 0.001 kT/e. The number of iterations per se is not important, as long as its sufficient to give the required convergence. The convergence behavior can also be judged from the slope of the semi-log plot of the mean and max changes given in the log file. LINIT is best determined by experience, since the convergence rate depends on several factors. Start with say 100 iterations, and then increase the number of iterations until sufficient. Note that a run can be restarted by using focusing boundary conditions with exactly the same SCALE, PERFIL and ACENTER values (see note 5). Some guidelines are: The number of iterations needed will increase with grid size (GSIZE). It will decrease with decreasing PERFIL, since the potentials converge more rapidly in the solvent. It will decrease with increasing ionic strength. The number is fairly insensitive to the size and number of charges on the molecule.
| delphi_integer CDelphiDataMarshal::iMediaNum |
- F95 var.: nmedia
- Default : 1
- Description:
of media
| int CDelphiDataMarshal::iModPdbFormatOut |
- F95 var.: mpdbfrm
- Set by func.: WRITE or OUT
- Default : 0
- Description:
Format of file mpdbnam, = 0 if unknown format, = 1 if “PQR”.
| delphi_integer CDelphiDataMarshal::iMoleculeNum |
- F95 var.: numbmol
- Default : 0
- Description:
of molecules
| int CDelphiDataMarshal::iNonIterateNum |
- Long form :
- NONLINEARITERATION
- NONLINEARITERATIONS
- Short form :
- NONIT
- 2L abbrev. :
- NI
- F95 var.: nnit
- Default : 0
- Description:
An integer number (> = 0) of non-linear iterations. If linear PB equation only is required, NONIT is set to be 0.
| delphi_integer CDelphiDataMarshal::iObjectNum |
- F95 var.: nobject
- Default : 1
- Description:
of objects
| int CDelphiDataMarshal::iPdbFormatIn |
- F95 var.: pdbfrm
- Set by func.: READ or IN
- Default : 10
- Description:
pdb file format, = 0 if unknown format, = 1 if “UN”, = 2 if “MOD”, = 3 if "PQR"
| int CDelphiDataMarshal::iPhiFormatOut |
- F95 var.: phifrm
- Set by func.: WRITE or OUT
- Default : 0
- Description:
Format of file phinam, = 0 if unknown format,= 1 if “BIOSYS”, = 2 if “GRASP”, = 3 if “CCP4”, = 4 if “DIFF”, = 5 if “CUBE”.
| delphi_integer CDelphiDataMarshal::iResidueNum |
- F95 var.: resnummax
- Default : 0
- Description:
maximum residue number
| int CDelphiDataMarshal::iSurfCrgFormatOut |
- F95 var.: scrgfrm
- Set by func.: WRITE or OUT
- Default : 0
- Description:
Format of file scrgnam, = 0 if unknown format, = 1 if “PDB”.
| int CDelphiDataMarshal::iTypeSurf |
- F95 var.: iTypeSurf
- Set by func.: SURFACE
- Default : -1
- Description:
flag for surface type
| string CDelphiDataMarshal::strCentFile |
- F95 var.: centnam
- Default : fort.27
- Description:
Site coordinates file. List of coordinates where site potentials are output in Unit 16. Format as for Unit 13.
| string CDelphiDataMarshal::strCrgFile |
- IO type : IN
- F95 var.: crgnam
- Default : fort.12
- Description:
Default extension crg. List of the atomic charges to be assigned to each atom/residue/number/chain pdb record type. A sample file is provided together with the code. The ascii fields for atom, residue, number and chain ignore case and leading blanks. Any field except the atom name may be left blank and will be treated as a wild card. Records of greater specificity override those of lesser specificity as for the siz file above.
| string CDelphiDataMarshal::strEnergyFile |
- F95 var.: nrgnam
- Default : energy.dat
- Description:
Ouput energy file
- Note
- NOT described in manual!
| string CDelphiDataMarshal::strEpsFile |
- IO type : OUT
- F95 var.: epsnam
- Default : fort.17
- Description:
Dielectric bit map, default extension: eps. If grid size=65, there are 3*65*65*65 lines joining neighboring grid points, 65*65*65 each in of the x,y,z directions. The midpoint of each line is given a value of 1 if it lies within the solvent accessible volume of the system, 0 if outside. This defines the shape of the molecule and separates the space into different dielectric regions. The format of the output files is described below in case that the user wants to build own software to visualize the map. For compact output purposes the array of INTEGER*4, epsmap(65,65,65,3), is compressed into an INTEGER*2 array, neps(5,65,65), by bit-mapping: the first index of epsmap, range 1-65 is compressed into the first index of neps, range 1-5, where the indices 1-16 go into bits 0-15 of the word with index 1, indices 17-32 -> bits 0-15 of word with index 2 etc. The array neps is then written to an unformatted binary file: write (17) imap, scale, oldmid
write (17) neps
- Note
- In the case that the solute is composed of more than one dielectric media, in this release (v.6.1 up to rel. 1.1) the additional information is not included in the fort.17, in order to maintain compatibility with software packages that take it as an input.
| string CDelphiDataMarshal::strFrcFile |
- IO type : OUT
- F95 var.: frcnam
- Default : fort.16
- Description:
Default extension frc. A list of potentials and fields at coordinates in pdb file read on unit 15. Format: 12 lines of ascii header information, followed by a variable number of records written as:
230 format(8G10.3) \n
write(16,230)xo,chrgv,phiv,fx,fy,fz \n
| string CDelphiDataMarshal::strFrciFile |
- IO type : IN
- F95 var.: frcinam
- Default : fort.15
- Description:
Default extension: pdb or frc. List of coordinates where site potentials are output in Unit
- Format as for Unit 13.
| string CDelphiDataMarshal::strGraspFile |
- F95 var.: srfnam
- Default : grasp.srf
- Description:
Output grasp surface file
- Note
- NOT described in manual!
| string CDelphiDataMarshal::strModifiedPdbFile |
- IO type : OUT
- F95 var.: mpdbnam
- Default : fort.19
- Description:
If the "modified pdb file" option is activated in a WRITE/OUT function, a logical flag (t/f), iatout, will be set to true and will produce a modified PDB file written on unit 19, containing the: radius and charge assigned to each atom written after the coordinates, in the fields used for occupancy and B factor. It is recommended that this option be set initially so that the user can check that all the radius and charge assignments are correct. An additional check on the charge assignment can be made by looking at the total charge written to the log file.
| string CDelphiDataMarshal::strPdbFile |
- IO type : IN
- F95 var.: pdbnam
- Default : fort.13
- Description:
A Brookhaven protein data bank standard format file containing atom labels and coordinates, or a modified OBJECTFILE. Only records starting with ATOM or HETATM are read; if objects or multi-dielectric option are used, also the keywords MEDIA, OBJECT, CRGDST, DATA are also read. The default extension is pdb. The precise format is essential; using Fortran syntax, (6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,1X,I3) is used for the atom record. From left to right, the fields contain 'ATOM–' or 'HETATM' atom serial number, atom name, alternate location indicator, residue name, chain identifier, residue sequence number, residue insertion code, x, y, and z coordinates, occupancy, temperature factor, footnote number.
- Note
- The program treats the residue number as an ascii string, not as an integer. As a warning to the user, there are many variations, and even outright errors found in the format of pdb files obtained from the web. It would be wise to double-check the contents of a file to save any heartache.
| string CDelphiDataMarshal::strPhiFile |
- IO type : OUT
- F95 var.: phinam
- Default : fort.14
- Description:
If the flag IBIOS (BIOSYM) is false, then output is in DELPHI format, default extension phi. The output can be either a potential map or a concentration map, with format same as for unit 18 above. The output phi map has the same scale as used in the calculation (i.e, variable) unless format=grasp is specified. The grasp-style phi map format will always interpolate to a 65 x 65 x 65 grid for use in Grasp (or other hardwired display/analysis programs). If the flag IBIOS (BIOSYM) is true, then output is in INSIGHT format, default extension ins. This is an unformatted (binary) file. As it was explained above, the format is provided only for completeness in case that one wants to visualize the file with different than Insight software.
- Note
- Note that for grid sizes less than 65, INSIGHT format files will occupy less disk space than the corresponding DELPHI files. ins files are designed as input to a Biosym Corp. stand alone utility called CONTOUR, supplied with INSIGHT Version 2.4. This program will produce contour files for display with INSIGHT.33
If the flag CUBE is true, then output is in CUBE format (Gaussian Cube). Example: Out(phi,file=’phimap.txt’,form=’cube’)
| string CDelphiDataMarshal::strPhiiFile |
- IO type : IN
- F95 var.: phiinam
- Default : fort.18
- Description:
Default extension phi, potential map for focusing boundary conditions. Potentials are in kT/e (25.6mV, 0.593 kcal/mole/charge at 25°C).
The format of the file is given below in case that the user wants to adopt the file to its own software. If the users wants to visualize the file with Grasp or Insight, no action should be taken. unformatted (binary file)
character*20 uplbl
character*10 nxtlbl,character*60 toplbl
real*4 phi(65,65,65)
character*16 botlbl
real*4 scale,oldmid(3)
x = (IX - 33)/scale + oldmid(1)
y = (IY - 33)/scale + oldmid(2)
z = (IZ - 33)/scale + oldmid(3)
| string CDelphiDataMarshal::strScrgFile |
- F95 var.: scrgnam
- Default : scrg.dat
- Description:
Output surface charge file. Only PDB format is supported.
- Note
- NOT described in manual!
| string CDelphiDataMarshal::strSizeFile |
- IO type : IN
- F95 var.: siznam
- Default : fort.11
- Description:
Default extension siz. List describing the van der Waals radii to be assigned to each atom/residue pdb record type. A sample file is provided together with the code. Note the atom and residue fields ignore case and leading blanks. The residue field may be left blank (wild card), causing a match with the given atom type of any residue. ONLY if the residue field is left blank, the LAST 5 characters of the atom record may be left blank. In this case all atom types beginning with the letter in column 1 will be matched. Records of greater specificity override those of less specificity. Beware of ambiguities like calcium (ca) and alpha carbon! All atoms of an input pdb file must be assigned a radius through the siz file, even if it is 0, or the output will be flagged with a warning.
| string CDelphiDataMarshal::strUnformatFrcFile |
- F95 var.: ufrcnam
- Default : fort.21
- Description:
Output unformatted frc file
- Note
- NOT described in manual!
| string CDelphiDataMarshal::strUnformatPdbFile |
- F95 var.: updbnam
- Default : fort.20
- Description:
Output unformatted pdb file
- Note
- NOT described in manual!
| vector<CAtomPdb> CDelphiDataMarshal::vctapAtomPdb |
- F95 var.: delphipdb(natom)
- Default : AUTOMATIC
- Description:
array of structure to store info read from pdb file
| vector<bool> CDelphiDataMarshal::vctbDielecMap |
- F95 var.: idebmap(igrid,igrid,igrid)
- Default : AUTOMATIC
- Description:
logical 3D array for assigning dielectric constants used for the molecular surface scaling
| vector<bool> CDelphiDataMarshal::vctbPeriodicBndy |
- Long form :
- PERIODICBOUNDARYX/PERIODICBOUNDARYY/PERIODICBOUNDARYZ
- Short form :
- PBX/PBY/PBZ
- 2L abbrev. :
- PX/PY/PZ
- F95 var.: iper
- Default : FALSE/FALSE/FALSE
- Description:
They are the three logical flags (t/f) for periodic boundary conditions for the x,y,z edges of the lattice respectively. Note that periodic boundary conditions will override other boundary conditions on edges to which they are applied. Periodic boundary conditions can be applied in one or more of the x, y or z directions. When applied, the potential at each periodic lattice boundary point is iterated by supplying its missing neighbor(s) from the corresponding point on the opposite edge of the lattice. This can be used for example to model an infinite length of DNA. Assume that the helical axis of the DNA in the pdb file is aligned along the Z axis. The periodic boundary flags are set to false, false, true, and the percent fill of the box, PERFIL, is adjusted so that an integral number of turns just fill the box in the Z direction. Normal boundary conditions are applied to the X,Y boundaries. By setting two, or three of the boundary flags to true, one can simulate 2 * dimensional or 3 dimensional cubic lattices of molecules.
- Note
- iper(1:3) are for periodic boundary conditions on the x,y,z edges and iper(4:6) are for corresponding voltage drop.
- F95 var.: cgbp(ibc)
- Default : AUTOMATIC
- Description:
information on the charged boundary grid points
| vector< SExtrema<delphi_real> > CDelphiDataMarshal::vctefExtrema |
- F95 var.: limobject(Nobject)
- Default : AUTOMATIC
- Description:
contains extreme values of each object, for a molecule it has extreme but without radii
| vector<delphi_real> CDelphiDataMarshal::vctfAtomEps |
- F95 var.: atmeps(nqass)
- Default : AUTOMATIC
- Description:
| vector<delphi_real> CDelphiDataMarshal::vctfGridCrg |
- F95 var.: gchrg(icount1b)
- Default : AUTOMATIC
- Description:
fractional charge in electron units assigned to each grid point
| vector<delphi_real> CDelphiDataMarshal::vctfMediaEps |
- F95 var.: medeps(0:nmedia)
- Default : AUTOMATIC
- Description:
vector containing correspondence media<->epsilon/epkt
| vector<delphi_real> CDelphiDataMarshal::vctfPhiMap |
- F95 var.: phimap(igrid,igrid,igrid)
- Default : AUTOMATIC
- Description:
3D potential map
| vector<delphi_real> CDelphiDataMarshal::vctfProbeRadius |
- Long form :
- PROBERADIUS/RADPR2
- Short form :
- PRBRAD/RADPR2
- 2L abbrev. :
- PR/R2
- F95 var.: radprb
- Default : 1.4/-1.0
- Description:
A radius (Å) of probe molecule that will define solvent accessible surface in the Lee and Richard's sense (relative to the part of the molecule which is internal to an object). In combination with the atomic van der Waals radii in the siz file, PRBRAD determines the regions of space, and hence the lattice points, that are inaccessible to solvent molecules (water). Suggested value is PRBRAD 1.4 for water. To understand how these parameters work, you should be familiar with the concepts of contact and solvent accessible surface, as discussed by Lee and Richards, and by Mike Connolly. For the purpose of DelPhi, any region of space that is accessible to any part of a solvent (water) molecule is considered as having a dielectric of EXDI. A value of zero for PRBRAD used with a siz file containing the standard van der Waals radii values will assign any region of space not inside any atom's van der Waals sphere to the solvent. For more details, please refer to Rocchia et al. J. Comp. Chem. paper.
| vector<delphi_real> CDelphiDataMarshal::vctfSalt |
- Long form :
- IONICSTRENGTH/SALT2
- SALTCONC
- SALTCONCENTRATION
- Short form :
- SALT/SALT2
- 2L abbrev. :
- IS/S2
- F95 var.: conc
- Default : 0.0/0.0
- Description:
The concentration of first and second kind of salt,(moles/liter). In the case of a single 1:1 salt, it coincides with ionic strength.
| vector<delphi_real> CDelphiDataMarshal::vctfSurfCrgE |
- F95 var.: schrg(ibnum)
- Default : AUTOMATIC
- Description:
the induced surface charges in electrons
| vector< SGrid<delphi_real> > CDelphiDataMarshal::vctgfAtomCoordA |
- F95 var.: xn1(natom)
- Default : AUTOMATIC
- Description:
atom coordinates in angstroms
| vector< SGrid<delphi_real> > CDelphiDataMarshal::vctgfAtomCoordG |
- F95 var.: xn2(natom)
- Default : AUTOMATIC
- Description:
atom coordinates in grid units
| vector< SGrid<delphi_real> > CDelphiDataMarshal::vctgfCrgPoseA |
- F95 var.: chgpos(nqass)
- Default : AUTOMATIC
- Description:
charge position in angstroms
| vector< SGrid<delphi_real> > CDelphiDataMarshal::vctgfSurfCrgA |
- F95 var.: scspos(ibnum)
- Default : AUTOMATIC
- Description:
position in angstroms of induced surface charges
| vector< SGrid<delphi_real> > CDelphiDataMarshal::vctgfSurfCrgE |
- F95 var.: scsnor(ibnum)
- Default : AUTOMATIC
- Description:
| vector< SGrid<delphi_integer> > CDelphiDataMarshal::vctgiBndyGrid |
- F95 var.: ibgrd(ibnum)
- Default : AUTOMATIC
- Description:
boundary grids
| vector< SGrid<delphi_integer> > CDelphiDataMarshal::vctgiEpsMap |
- F95 var.: iepsmp(igrid,igrid,igrid)
- Default : AUTOMATIC
- Description:
a listing of boundary elements 3D eps map, used to constrcut db array. (Can't get rid of for calculating the nonlinear energy)
| vector< SGrid<delphi_integer> > CDelphiDataMarshal::vctgiGridCrgPose |
- F95 var.: gchrgp(icount1b)
- Default : AUTOMATIC
- Description:
position of each such charge on the grid
| vector< SGridValue<delphi_real> > CDelphiDataMarshal::vctgvfAtomCrg |
- F95 var.: atmcrg(nqass)
- Default : AUTOMATIC
- Description:
atmcrg contains grid positions of all charges AND the charge in the 4th field
| vector< SGridValue<delphi_real> > CDelphiDataMarshal::vctgvfCrg2Grid |
- F95 var.: chrgv2(nqgrd)
- Default : AUTOMATIC
- Description:
charges which will be charging the grid
| vector<delphi_integer> CDelphiDataMarshal::vctiAtNdx |
- F95 var.: atndx(ibnum)
- Default : AUTOMATIC
- Description:
| vector<delphi_integer> CDelphiDataMarshal::vctiAtomMediaNum |
- F95 var.: iatmmed(Natom+Nobjectmax)
- Default : AUTOMATIC
- Description:
vector containing internal media-number per atom and object
| vector<delphi_integer> CDelphiDataMarshal::vctiAtSurf |
- F95 var.: atsurf(ibnum)
- Default : AUTOMATIC
- Description:
| vector<delphi_integer> CDelphiDataMarshal::vctiCrg2GridMap |
- F95 var.: nqgrdtonqass(nqgrd)
- Default : AUTOMATIC
- Description:
nqgrdtonqass maps ic2-th charge internal atmeps6 to ic1-th general charge
| vector<delphi_integer> CDelphiDataMarshal::vctiCrgAt |
- F95 var.: crgatn(nqass)
- Default : AUTOMATIC
- Description:
| vector<int> CDelphiDataMarshal::vctiValence1 |
- Long form :
- VAL+1/VAL-1
- Short form :
- VAL+1/VAL-1
- 2L abbrev. :
- +1/-1
- F95 var.: ival
- Default : 1/1
- Description:
A number > 0, valence of positive (negative) ion constituting salt one.
| vector<int> CDelphiDataMarshal::vctiValence2 |
- Long form :
- VAL+2/VAL-2
- Short form :
- VAL+2/VAL-2
- 2L abbrev. :
- +2/-2
- F95 var.: ival2
- Default : 0/0
- Description:
A number > 0, valence of positive (negative) ion constituting salt two.
| vector<string> CDelphiDataMarshal::vctstrObject |
- F95 var.: dataobject(nobject,2)
- Default : AUTOMATIC
- Description:
vector containing string with object data, and pre-elab data changed it to vctstrObject(2*nobjectmax)
The documentation for this class was generated from the following files:
- delphi_datamarshal.h
- delphi_datamarshal_getStatement.cpp
- delphi_datamarshal_getFunction.cpp
- delphi_datamarshal_showParameters.cpp
- delphi_datamarshal_updateParameters.cpp
- delphi_datamarshal_setDefault.cpp
Public Member Functions inherited from IDataMarshal
1.8.8 
