## Software

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### write

 This controls the output of scalar data calculated during the Poisson-Boltzmann run. This keyword can be repeated several times to provide various types of data output from APBS. The syntax is  write {type} {format} {stem} type A string indicating what type of data to output: charge Write out the biomolecular charge distribution in units of ec (electron charge) per Å3. (multigrid only) pot Write out the electrostatic potential in units of kb T ec-1. (multigrid and finite element) atompot Write out the electrostatic potential at each atom in units of kb T ec-1. The format for the output must be specified as flat. The values are listed sequentially from 1 to NATOMS. See below for more information about format types. (multigrid and finite element).  smol Write out the solvent accessibility defined by the molecular surface definition (see srfm smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) sspl Write out the spline-based solvent accessibility (see srfm spl2). Values are unitless and range from 0 (inaccessible) to 1 (accessible) (multigrid and finite element) vdw Write out the van der Waals-based solvent accessibility (see srfm smol with srad 0.0). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) ivdw Write out the inflated van der Waals-based ion accessibility (see srfm smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) lap Write out the Laplacian of the potential in units of kB T ec-1 Å-2. (multigrid only) edens Write out the "energy density" in units of kB T ec-1 Å-2. (multigrid only) ndens Write out the total mobile ion number density for all ion species in units of M. (multigrid only)  The output is calculated according to the formula (for nonlinear PB calculations)where M is the number of ionic species, c_i is the bulk concentration of each species, q_i is the charge of each species, \phi is the electrostatic potential, k_B is Boltzmann's constant, and T is the temperature. qdens Write out the total mobile charge density for all ion species in units of ec M. (multigrid only)  The output is calculated according to the formula (for nonlinear PB calculations)where M is the number of ionic species, c_i is the bulk concentration of each species, q_i is the charge of each species, \phi is the electrostatic potential, k_B is Boltzmann's constant, and T is the temperature. dielx Write out the dielectric map shifted by 1/2 grid spacing in the x-direction (see READ diel). The values are unitless. (multigrid only) diely Write out the dielectric map shifted by 1/2 grid spacing in the y-direction (see READ diel). The values are unitless. (multigrid only) dielz Write out the dielectric map shifted by 1/2 grid spacing in the z-direction (see READ diel). The values are unitless. (multigrid only) kappa Write out the ion-accessibility kappa map (see READ kappa). The values are in units of Å-2 (multigrid only) format A string that specifies the format for writing out the data. dx Write out data in OpenDX format. This is the preferred format for APBS I/O. (multigrid and finite element). avs Write out data in AVS UCD format. (finite element only) uhbd Write out data in UHBD format. (multigrid only) gz Write out OpenDX data in gzipped (zlib) compatible format. Appends .dx.gz to the filename. flat Write out data as a plain text file. (multigrid and finite element). stem A string that specifies the path for the output; files are written to stem.XYZ, where XYZ is determined by the file format (and processor rank for parallel calculations). If the pathname contains spaces, then it must be surrounded by double quotes; e.g., "/path with spaces/foo.in".