File: elec.xml

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<cmdsynopsis>
	<command>ELEC</command>
	<arg choice="opt" id="elec-name">name <replaceable>id</replaceable></arg>
	<arg choice="req"><replaceable>type</replaceable></arg>
	<arg choice="opt" rep="repeat"><replaceable>keywords</replaceable></arg>
	<command>END</command>
</cmdsynopsis>
<para>This section is the main component for polar solvation calculations in
	APBS runs. There may be several <command>ELEC</command> sections,
	operating on different molecules or using different parameters for
	multiple runs on the same molecule. The order of the
	<command>ELEC</command> statement matters (see above); the arguments
	are:
	<variablelist>
		<varlistentry>
			<term> name <replaceable>id</replaceable> </term>
			<listitem>
				<para>This optional command allows users to
					assign an alphanumeric string to the
					calculation to facilitate later
					operations (particularly in the 
					<link linkend="print"><command>PRINT</command></link> statements).
				</para>
			</listitem>
		</varlistentry>
		<varlistentry>
			<term> <replaceable>type</replaceable> </term>
			<listitem>
				<para>Specify the type of electrostatics calculation to perform (these are described in greater detail below):
					<itemizedlist>
						<listitem>
							<para><command><link linkend="mg-auto">mg-auto</link></command>
								for automatically-configured sequential focusing multigrid
								calculations.</para> 
						</listitem>
						<listitem>
							<para><command><link linkend="mg-para">mg-para</link></command> 
								for automatically-configured parallel focusing multigrid
								calculations.</para> 
						</listitem>
						<listitem>
							<para><command><link linkend="mg-manual">mg-manual</link></command> 
								for manually-configured multigrid calculations.</para> 
						</listitem>
						<listitem>
							<para><command><link linkend="fe-manual">fe-manual</link></command> 
								for manually-configured adaptive finite element
								calculations.</para> 
						</listitem>
						<listitem>
							<para><command><link linkend="mg-dummy">mg-dummy</link></command>
								for calculations of surface and charge distribution properties
								which do not require solution of the PBE.</para> 
						</listitem>
					</itemizedlist>
				</para>
			</listitem>
		</varlistentry>
		<varlistentry>
			<term> <replaceable>keywords</replaceable> </term>
			<listitem>
				<para>Keywords describing the parameters of the electrostatic
					calculation.  These are described in the 
					<link linkend="elec-keywords-sect">Keywords section</link> below.
				</para>
			</listitem>
		</varlistentry>
	</variablelist>
</para>

<sect3 id="mg-auto"> <title>Automatic sequential focusing multigrid
		calculation (<command>mg-auto</command>)</title>
	<para> This automatically sets up and performs a string of single-point PBE
		calculations to "focus" on a region of interest (binding site, etc.) in a
		system. It is basically an automated version of mg-manual designed for
		easier use. Most users should probably use this version of
		<command>ELEC</command>.</para>
	<para> The keywords for this command (described in more detail in the 
		<link linkend="elec-keywords-sect">Keywords section</link>) are listed
		below.  All keywords are required (no default values!) unless otherwise
		noted:
		<simplelist type="inline">  
			<member>
				<command><link linkend="elec-dime">dime</link></command>
			</member>
			<member>
				<command><link linkend="elec-cglen">cglen</link></command>
			</member>
			<member>
				<command><link linkend="elec-fglen">fglen</link></command>
			</member>
			<member>
				<command><link linkend="elec-cgcent">cgcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-fgcent">fgcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-mol">mol</link></command>
			</member>
			<member>
				<command><link linkend="elec-lpbe">lpbe</link></command>
				or
				<command><link linkend="elec-npbe">npbe</link></command>
				or
				<command><link linkend="elec-smpbe">smpbe</link></command>
			</member>
			<member>
				<command><link linkend="elec-bcfl">bcfl</link></command>
			</member>
			<member>
				<command><link linkend="elec-ion">ion</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-pdie">pdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-sdie">sdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-chgm">chgm</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemap">usemap</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-useaqua">useaqua</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-sdens">sdens</link></command>
			</member>
			<member>
				<command><link linkend="elec-srfm">srfm</link></command>
			</member>
			<member>
				<command><link linkend="elec-srad">srad</link></command>
			</member>
			<member>
				<command><link linkend="elec-swin">swin</link></command>
			</member>
			<member>
				<command><link linkend="elec-temp">temp</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcenergy">calcenergy</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcforce">calcforce</link></command>
			</member>
			<member>
				<command><link linkend="elec-write">write</link></command>
			</member>
			<member>
				<command><link linkend="elec-writemat">writemat</link></command>
			</member>
		</simplelist>
	</para>
</sect3>

<sect3 id="mg-para"> <title>Automatic parallel focusing multigrid calculation
		(<command>mg-para</command>)</title>
	<para> This calculation closely resembles 
		<link linkend="mg-auto"><command>mg-auto</command></link> in syntax.
		However, it is basically designed to perform single-point calculations on
		systems in a parallel focusing fashion. While this method does provide
		support for decreasing the domain size from a coarse (large) global grid to
		a fine (smaller) global grid, it should not be used to look at subsets of
		biomolecules such as titration sites, etc. Such subset calculations require
		more complicated energy evaluation which is not yet supported by
		<command>mg-para</command>. However, since parallel focusing was designed
		to provide detailed evaluation of the electrostatic potential on a large
		scale, such subset calculations are better left to traditional focusing via
		the <command>mg-auto</command> keyword.
		<important>
			<para> Please note that some of the parameters change
				in meaning a bit for this type of calculation.
				In particular, <link linkend="elec-dime">dime</link>
				should be interpreted as the number of grid
				points <emphasis>per processor</emphasis>.
				This interpretation helps manage the amount of
				memory per-processor -- generally the limiting
				resource for most calculations. </para>
		</important>
	</para>
	<para> The keywords for this command (described in more detail in the 
		<link linkend="elec-keywords-sect">Keywords section</link>) are listed
		below.  All keywords are required (no default values!) unless otherwise
		noted:
		<simplelist type="inline">  
			<member>
				<command><link linkend="elec-dime">dime</link></command>
			</member>
			<member>
				<command><link linkend="elec-ofrac">ofrac</link></command>
			</member>
			<member>
				<command><link linkend="elec-pdime">pdime</link></command>
			</member>
			<member>
				<command><link linkend="elec-async">async</link></command>
			</member>
			<member>
				<command><link linkend="elec-cglen">cglen</link></command>
			</member>
			<member>
				<command><link linkend="elec-fglen">fglen</link></command>
			</member>
			<member>
				<command><link linkend="elec-cgcent">cgcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-fgcent">fgcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-mol">mol</link></command>
			</member>
			<member>
				<command><link linkend="elec-lpbe">lpbe</link></command>
				or
				<command><link linkend="elec-npbe">npbe</link></command>
				or
				<command><link linkend="elec-smpbe">smpbe</link></command>
			</member>
			<member>
				<command><link linkend="elec-bcfl">bcfl</link></command>
			</member>
			<member>
				<command><link linkend="elec-ion">ion</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-pdie">pdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-sdie">sdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-chgm">chgm</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemap">usemap</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-useaqua">useaqua</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-sdens">sdens</link></command>
			</member>
			<member>
				<command><link linkend="elec-srfm">srfm</link></command>
			</member>
			<member>
				<command><link linkend="elec-srad">srad</link></command>
			</member>
			<member>
				<command><link linkend="elec-swin">swin</link></command>
			</member>
			<member>
				<command><link linkend="elec-temp">temp</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcenergy">calcenergy</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcforce">calcforce</link></command>
			</member>
			<member>
				<command><link linkend="elec-write">write</link></command>
			</member>
			<member>
				<command><link linkend="elec-writemat">writemat</link></command>
			</member>
		</simplelist>
	</para>
</sect3>

<sect3 id="mg-manual"> <title>Manual multigrid calculation
		(<command>mg-manual</command>)</title> 
	<para>This is the standard single-point PBE calculation performed by
		most solvers. The <command>mg-manual</command> calculation
		offers the most control of parameters to the user. Several of
		these calculations can be strung together to perform focusing
		calculations by judicious choice of the <link
			linkend="elec-bcfl"><command>bcfl</command></link> flag,
		however, the setup of the focusing is not automated as it is in
		<link linkend="mg-auto"><command>mg-auto</command></link> and
		<link linkend="mg-para"><command>mg-para</command></link>
		calculations and therefore this command should only be used by
		more experienced users.</para>
	<para> The keywords for this command (described in more detail in the 
		<link linkend="elec-keywords-sect">Keywords section</link>) are listed
		below.  All keywords are required (no default values!) unless otherwise
		noted:
		<simplelist type="inline">  
			<member>
				<command><link linkend="elec-dime">dime</link></command>
			</member>
			<member>
				<command><link linkend="elec-nlev">nlev</link></command>
			</member>
			<member>
				<command><link linkend="elec-glen">glen</link></command> or
				<command><link linkend="elec-grid">grid</link></command> 
			</member>
			<member>
				<command><link linkend="elec-gcent">gcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-mol">mol</link></command>
			</member>
			<member>
				<command><link linkend="elec-lpbe">lpbe</link></command>
				or
				<command><link linkend="elec-npbe">npbe</link></command>
				or
				<command><link linkend="elec-smpbe">smpbe</link></command>
			</member>
			<member>
				<command><link linkend="elec-bcfl">bcfl</link></command>
			</member>
			<member>
				<command><link linkend="elec-ion">ion</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-pdie">pdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-sdie">sdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-chgm">chgm</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemap">usemap</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-useaqua">useaqua</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-sdens">sdens</link></command>
			</member>
			<member>
				<command><link linkend="elec-srfm">srfm</link></command>
			</member>
			<member>
				<command><link linkend="elec-srad">srad</link></command>
			</member>
			<member>
				<command><link linkend="elec-swin">swin</link></command>
			</member>
			<member>
				<command><link linkend="elec-temp">temp</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcenergy">calcenergy</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcforce">calcforce</link></command>
			</member>
			<member>
				<command><link linkend="elec-write">write</link></command>
			</member>
			<member>
				<command><link linkend="elec-writemat">writemat</link></command>
			</member>
		</simplelist>
	</para>
</sect3>

<sect3 id="fe-manual"> <title>Manual adaptive finite element calculation
		(<command>fe-manual</command>)</title> 
	<para>This is a single-point PBE calculation performed by our adaptive
		finite element PBE solver.  It requires that APBS was linked to the
		Holst group FEtk finite element library 
		(<ulink url="http://www.fetk.org/">http://www.fetk.org</ulink>) during
		compilation. 
	</para>
	<para>
		The finite element solver uses a "solve-estimate-refine" cycle.
		Specifically, starting from an initial mesh, it performs the following
		iteration:
		<orderedlist>
			<listitem> <para> solve the problem </para> </listitem>
			<listitem> <para> estimate the error in the solution </para> </listitem>
			<listitem> <para> adaptively refine the mesh </para> </listitem> 
		</orderedlist>
		until a global error tolerance is reached.
	</para>
	<para>
		<note>
			<para>These methods are most useful for a select set of problems which
				can benefit from adaptive refinement of the solution.  Furthermore,
				this implementation is experimental.   In general, the sequential and
				parallel focusing multigrid methods offer the most efficient solution
				of the PBE for most systems</para>
		</note>
	</para>
	<para> The keywords for this command (described in more detail in the 
		<link linkend="elec-keywords-sect">Keywords section</link>) are listed
		below.  All keywords are required (no default values!) unless otherwise
		noted:
		<simplelist type="inline">  
			<member>
				<command><link linkend="elec-domainLength">domainLength</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemesh">usemesh</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-etol">etol</link></command>
			</member>
			<member>
				<command><link linkend="elec-ekey">ekey</link></command>
			</member>
			<member>
				<command><link linkend="elec-akeyPRE">akeyPRE</link></command>
			</member>
			<member>
				<command><link linkend="elec-akeySOLVE">akeySOLVE</link></command>
			</member>
			<member>
				<command><link linkend="elec-targetNum">targetNum</link></command>
			</member>
			<member>
				<command><link linkend="elec-targetRes">targetRes</link></command>
			</member>
			<member>
				<command><link linkend="elec-maxsolve">maxsolve</link></command>
			</member>
			<member>
				<command><link linkend="elec-maxvert">maxvert</link></command>
			</member>
			<member>
				<command><link linkend="elec-mol">mol</link></command>
			</member>
			<member>
				<command><link linkend="elec-lpbe">lpbe</link></command>
				or
				<command><link linkend="elec-npbe">npbe</link></command>
				or
				<command><link linkend="elec-lrpbe">lrpbe</link></command>
				or
				<command><link linkend="elec-nrpbe">nrpbe</link></command>
			</member>
			<member>
				<command><link linkend="elec-bcfl">bcfl</link></command>
			</member>
			<member>
				<command><link linkend="elec-ion">ion</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-pdie">pdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-sdie">sdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-chgm">chgm</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemap">usemap</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-useaqua">useaqua</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-sdens">sdens</link></command>
			</member>
			<member>
				<command><link linkend="elec-srfm">srfm</link></command>
			</member>
			<member>
				<command><link linkend="elec-srad">srad</link></command>
			</member>
			<member>
				<command><link linkend="elec-swin">swin</link></command>
			</member>
			<member>
				<command><link linkend="elec-temp">temp</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcenergy">calcenergy</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcforce">calcforce</link></command>
			</member>
			<member>
				<command><link linkend="elec-write">write</link></command>
			</member>
			<member>
				<command><link linkend="elec-writemat">writemat</link></command>
			</member>
		</simplelist>
	</para>
</sect3>

<sect3 id="mg-dummy"> <title>Manual non-numerical calculations
		(<command>mg-dummy</command>)</title> 
	<para>This allows users to write out 
		<link linkend="diel">dielectric</link>, 
		<link linkend="kappa">ion-accessibility</link>, and
		<link linkend="charge">charge distribution</link> maps based on
		biomolecular geometry without actually solving the PB equation.
		The syntax is identical to <link linkend="mg-dummy">mg-dummy</link>.
	</para>
	<para> The keywords for this command (described in more detail in the 
		<link linkend="elec-keywords-sect">Keywords section</link>) are listed
		below.  All keywords are required (no default values!) unless otherwise
		noted:
		<simplelist type="inline">  
			<member>
				<command><link linkend="elec-dime">dime</link></command>
			</member>
			<member>
				<command><link linkend="elec-nlev">nlev</link></command>
			</member>
			<member>
				<command><link linkend="elec-glen">cglen</link></command> or
				<command><link linkend="elec-grid">grid</link></command> 
			</member>
			<member>
				<command><link linkend="elec-gcent">gcent</link></command>
			</member>
			<member>
				<command><link linkend="elec-mol">mol</link></command>
			</member>
			<member>
				<command><link linkend="elec-lpbe">lpbe</link></command>
				or
				<command><link linkend="elec-npbe">npbe</link></command>
				or
				<command><link linkend="elec-smpbe">smpbe</link></command>
			</member>
			<member>
				<command><link linkend="elec-bcfl">bcfl</link></command>
			</member>
			<member>
				<command><link linkend="elec-ion">ion</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-pdie">pdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-sdie">sdie</link></command>
			</member>
			<member>
				<command><link linkend="elec-chgm">chgm</link></command>
			</member>
			<member>
				<command><link linkend="elec-usemap">usemap</link></command>
				(optional)
			</member>
			<member>
				<command><link linkend="elec-useaqua">useaqua</link></command> (optional)
			</member>
			<member>
				<command><link linkend="elec-sdens">sdens</link></command>
			</member>
			<member>
				<command><link linkend="elec-srfm">srfm</link></command>
			</member>
			<member>
				<command><link linkend="elec-srad">srad</link></command>
			</member>
			<member>
				<command><link linkend="elec-swin">swin</link></command>
			</member>
			<member>
				<command><link linkend="elec-temp">temp</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcenergy">calcenergy</link></command>
			</member>
			<member>
				<command><link linkend="elec-calcforce">calcforce</link></command>
			</member>
			<member>
				<command><link linkend="elec-write">write</link></command>
			</member>
			<member>
				<command><link linkend="elec-writemat">writemat</link></command>
			</member>
		</simplelist>
	</para>
</sect3>

<sect3 id="elec-keywords-sect"> <title>Keyword descriptions</title>
	<para>
		This is a list of keywords used in the <command>ELEC</command> statements
		of APBS.  Note that not all keywords are used in every
		<command>ELEC</command> statement; see above.
	</para>
	<itemizedlist>

		<listitem id="elec-akeyPRE">
			<cmdsynopsis>
				<command>akeyPRE</command>
				<arg choice="req"><replaceable>key</replaceable></arg>
			</cmdsynopsis>
			<para>Specify how the initial finite element mesh should be constructed
				(from refinement of a very coarse 8-tetrahedron mesh prior to the
				solve-estimate-refine iteration.  This allows for various
				<foreignphrase>a priori</foreignphrase> refinement schemes.
				<variablelist>
					<varlistentry>
						<term> <replaceable>key</replaceable> </term>
						<listitem>
							<para>The method used to guide initial refinement:
								<variablelist>
									<varlistentry>
										<term> unif </term>
										<listitem> <para>Uniform refinement</para> </listitem>
									</varlistentry>
									<varlistentry>
										<term> geom </term>
										<listitem> 
											<para>Geometry-based refinement at molecular surfaces
												and charges</para> 
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-akeySOLVE">
			<cmdsynopsis>
				<command>akeySOLVE</command>
				<arg choice="req"><replaceable>key</replaceable></arg>
			</cmdsynopsis>
			<para>Specify how the the finite element mesh should be adaptively
				subdivided during the solve-estimate-refine iterations.  This allows
				for various <foreignphrase>a posteriori</foreignphrase> refinement
				schemes.  
				<variablelist>
					<varlistentry>
						<term> <replaceable>key</replaceable> </term>
						<listitem>
							<para>The method used to guide adpative refinement:
								<variablelist>
									<varlistentry>
										<term> resi </term>
										<listitem> 
											<para>Residual-based <foreignphrase>a
													posteriori</foreignphrase> refinement</para> 
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-async">
			<cmdsynopsis>
				<command>async</command>
				<arg choice="req"> <replaceable>rank</replaceable> </arg>
			</cmdsynopsis>
			<para> This optional keyword allows users to perform the different tasks
				in a parallel run asynchronously. Specifically, a processor masquerades
				as process <replaceable>rank</replaceable> in a parallel focusing run
				and provides output (data files and energies/forces) appropriate to
				that processor's local partition. The user must then assemble the
				results after all processes complete. First, this option is useful for
				scheduling on-demand resources: this makes it easy for users to
				backfill into the available processes in a queue.  Second, this option
				is useful for running on limited resources: this enables users without
				access to large parallel machines to still perform the same
				calculations. 
				<variablelist>
					<varlistentry>
						<term> <replaceable>rank</replaceable> </term>
						<listitem>
							<para> The ID of the particular processor to masquerade as.
								Processor IDs range from 0 to <replaceable>N</replaceable>-1,
								where <replaceable>N</replaceable> is the total number of
								processors in the run (see 
								<link
									linkend="elec-pdime"><command>pdime</command></link>).
								Processor ranks are related to their position in the overall
								grid by
								<informalequation>
									<alt>p = n_x n_y k + n_x j + i</alt>
									<graphic fileref="images/proc_rank.gif"/>
								</informalequation>
								where 
								n<subscript>x</subscript> is the number of processors in the
								x-direction,
								n<subscript>y</subscript> is the number of processors in the
								y-direction,
								n<subscript>z</subscript> is the number of processors in the
								z-direction,
								i is the index of the processor in the x-direction,
								j is the index of the processor in the y-direction,
								k is the index of the processor in the z-direction, and
								p is the overall rank of the processor.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-bcfl">
			<cmdsynopsis>
				<command>bcfl</command>
				<arg choice="req"><replaceable>flag</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the type of boundary conditions used to solve the
				Poisson-Boltzmann equation:
				<variablelist>
					<varlistentry>
						<term><replaceable>flag</replaceable></term>
						<listitem>
							<para>The flag specifying the boundary condition definition:
								<variablelist>
									<varlistentry>
										<term>zero</term>
										<listitem>
											<para>"Zero" boundary condition.  Potential at boundary
												is set to zero.  This condition is not commonly used
												and can result in large errors if used
												inappropriately.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>sdh</term>
										<listitem>
											<para>"Single Debye-H&uuml;ckel" boundary condition.
												Potential at boundary is set to the values prescribed
												by a Debye-H&uuml;ckel model for a single sphere with a
												point charge, dipole, and quadrupole.  The sphere 
												radius is set to the radius of the biomolecule and the 
												sphere charge, dipole, and quadrupole are set to the
												total moments of the protein.  This condition works 
												best when the boundary is sufficiently far from the
												biomolecule.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>mdh</term>
										<listitem>
											<para>"Multiple Debye-H&uuml;ckel" boundary condition.
												Potential at boundary is set to the values prescribed
												by a Debye-H&uuml;ckel model for a multiple,
												non-interacting spheres with a point charges.  The
												sphere radii are set to the atomic radii of the
												biomolecule and the sphere charges are set to the total
												charge of the protein.  This condition works better
												than sdh for closer boundaries but can be
												<emphasis>very slow</emphasis> for large
												biomolecules.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>focus</term>
										<listitem>
											<para>"Focusing" boundary condition.
												Potential at boundary is set to the values computed by
												the previous (usually lower-resolution) PB calculation.
												This is used in sequential focusing performed manually
												in 
												<link linkend="mg-manual"><command>mg-manual</command></link>
												calculations.  All of the boundary points should lie
												within the domain of the previous calculation for best
												accuracy; if any boundary points lie outside, their
												values are computed using single Debye-H&uuml;ckel
												boundary conditions (see above).</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-calcenergy">
			<cmdsynopsis>
				<command>calcenergy</command>
				<arg choice="req"> <replaceable>flag</replaceable> </arg>
			</cmdsynopsis>
			<para>
				This optional keyword controls electrostatic energy output from a PBE
				calculation.
				<note>
					<para> Note that this option must be used consistently for all
						calculations that will appear in subsequent 
						<link linkend="print"><command>PRINT</command></link> statements.
						For example, if the statement <literal>print energy 1 - 2
							end</literal> appears in the input file, then both calculations 1
						and 2 must have <command>calcenergy</command> keywords present with
						the same values for <replaceable>flag</replaceable>.
					</para>
				</note>
				<variablelist>
					<varlistentry>
						<term> <replaceable>flag</replaceable> </term>
						<listitem>
							<para>Specify the types of energy values to be returned:
								<variablelist>
									<varlistentry>
										<term>no</term>
										<listitem>
											<para>(Deprecated) don't calculate any energies.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>total</term>
										<listitem>
											<para>Calculate and return total electrostatic energy for
												the entire molecule.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>comps</term>
										<listitem>
											<para>Calculate and return total electrostatic energy for
												the entire molecule as well as electrostatic energy
												components for each atom.</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-calcforce">
			<cmdsynopsis>
				<command>calcforce</command>
				<arg choice="req"> <replaceable>flag</replaceable> </arg>
			</cmdsynopsis>
			<para>
				This optional keyword controls electrostatic and apolar force output
				from a PBE calculation.
				<note>
					<para> Note that this option must be used consistently for all
						calculations that will appear in subsequent 
						<link linkend="print"><command>PRINT</command></link> statements.
						For example, if the statement <literal>print force 1 - 2
							end</literal> appears in the input file, then both calculations 1
						and 2 must have <command>calcforce</command> keywords present with
						the same values for <replaceable>flag</replaceable>.
					</para>
				</note>
				<variablelist>
					<varlistentry>
						<term> <replaceable>flag</replaceable> </term>
						<listitem>
							<para>Specify the types of force values to be returned:
								<variablelist>
									<varlistentry>
										<term>no</term>
										<listitem>
											<para>(Deprecated) don't calculate any forces.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>total</term>
										<listitem>
											<para>Calculate and return total electrostatic and apolar
												forces for the entire molecule.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>comps</term>
										<listitem>
											<para>Calculate and return total electrostatic and apolar
												forces for the entire molecule as well as force
												components for each atom.</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-cgcent">
			<cmdsynopsis>
				<command>cgcent</command>
				<group choice="req">
					<arg choice="plain">mol <replaceable>id</replaceable></arg>
					<arg choice="plain"><replaceable>xcent ycent zcent</replaceable></arg>
				</group>
			</cmdsynopsis>
			<para>Specify the center of the coarse grid (in a focusing calculation)
				based on a molecule's center or absolute coordinates. The arguments for
				this keyword are:
				<variablelist>
					<varlistentry>
						<term>mol <replaceable>id</replaceable></term>
						<listitem>
							<para>Center the grid on molecule with ID
								<replaceable>id</replaceable>; as assigned in the 
								<link linkend="read"><command>READ</command></link> section.
								Molecule IDs are assigned in the order they're read, starting
								at 1. 
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>xcent ycent zcent</replaceable></term>
						<listitem>
							<para>The coordinates (in &Aring;) at which the grid is
								centered.  Based on the PDB coordinate frame.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-cglen">
			<cmdsynopsis>
				<command>cglen</command>
				<arg choice="req"><replaceable>xlen ylen zlen</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the coarse mesh domain lengths in a focusing calculation;
				this may be different in each direction.  This is the starting mesh, so
				it should be large enough to complete enclose the biomolecule
				<emphasis>and</emphasis> ensure that the chosen boundary condition (see
				<link linkend="elec-bcfl"><command>bcfl</command></link>) is appropriate.
				<variablelist>
					<varlistentry>
						<term><replaceable>xlen ylen zlen</replaceable></term>
						<listitem>
							<para>Grid lengths in the x-, y-, and z-directions in &Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


		<listitem id="elec-chgm">
			<cmdsynopsis>
				<command>chgm</command>
				<arg choice="req"><replaceable>flag</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the method by which the biomolecular point charges (i.e.,
				Dirac delta functions) are mapped onto the grid.  As we are
				attempting to model delta functions, the support (domain) of these
				discretized charge distributions is always a function of the grid
				spacing.
				<variablelist>
					<varlistentry>
						<term><replaceable>flag</replaceable></term>
						<listitem>
							<para>
								Discretization method (options have multiple declarations for
								backward-compatibility):
								<variablelist>
									<varlistentry>
										<term> spl0 </term>
										<listitem>
											<para>
												Traditional trilinear interpolation (linear splines).
												The charge is mapped onto the nearest-neighbor grid
												points.  Resulting potentials are very sensitive to
												grid spacing, length, and position.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> spl2 </term>
										<listitem>
											<para>
												Cubic B-spline discretization.
												The charge is mapped onto the nearest- and
												next-nearest-neighbor grid points.  Resulting
												potentials are somewhat less sensitive (than spl0) to
												grid spacing, length, and position.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> spl4 </term>
										<listitem>
											<para>
												Quintic B-spline discretization. Similar to spl2, 
												except the charge/multipole is additionally mapped to 
												include next-next-nearest neighbors (125 grid points 
												receive charge density).
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-dime">
			<cmdsynopsis>
				<command>dime</command>
				<arg choice="req"><replaceable>nx ny nz</replaceable></arg>
			</cmdsynopsis>
			<para>Number of grid points <emphasis>per
					processor</emphasis> for grid-based discretization.  For 
				<link linkend="mg-manual"><command>mg-manual</command></link>, the
				arguments are dependent on the choice of 
				<link linkend="elec-nlev"><command>nlev</command></link> by the formula
				<informalequation>
					<alt>n = c 2^{l+1} + 1</alt>
					<graphic fileref="images/nlev_dime.gif"/>
				</informalequation>
				where <varname>n</varname> is the <command>dime</command> argument,
				<varname>c</varname> is a non-zero integer, <varname>l</varname> is the
				<command>nlev</command> value.  The most common values for grid
				dimensions are 65, 97, 129, and 161 (they can be different in each
				direction); these are all compatible with a <command>nlev</command>
				value of 4.  If you happen to pick a "bad" value for the dimensions
				(i.e., mismatch with <command>nlev</command>), the code will adjust the
				specified dime downwards to more appropriate values. This means that
				"bad" values will typically result in lower resolution/accuracy
				calculations!  The arguments for this keyword are:
				<variablelist>
					<varlistentry>
						<term><replaceable>nx ny nz</replaceable></term>
						<listitem>
							<para>Number of grid points in the x-, y-, and z-directions.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
			<important>
				<para> Please note that some of the parameters change in meaning a bit for this <link linkend="mg-para">mg-para</link> calculations.  In particular, <link linkend="elec-dime">dime</link> should be interpreted as the number of grid points <emphasis>per processor</emphasis>.  This interpretation helps manage the amount of memory per-processor -- generally the limiting resource for most calculations. </para>
			</important>
		</listitem>

		<listitem id="elec-domainLength">
			<cmdsynopsis>
				<command>domainLength</command>
				<arg choice="req"><replaceable>xlen ylen zlen</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the rectangular finite element mesh domain lengths; this may be different in each
				direction.  If the <link linkend="elec-usemesh"><command>usemesh</command></link> keyword is included, then this command is ignored.
				<variablelist>
					<varlistentry>
						<term><replaceable>xlen ylen zlen</replaceable></term>
						<listitem>
							<para>Mesh lengths in the x-, y-, and z-directions in &Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


		<listitem id="elec-ekey">
			<cmdsynopsis>
				<command>ekey</command>
				<arg choice="req"> <replaceable>flag</replaceable> </arg>
			</cmdsynopsis>
			<para>
				Specify the method used to determine the error tolerance in the
				solve-estimate-refine iterations of the finite element solver.
				<variablelist>
					<varlistentry>
						<term> <replaceable>flag</replaceable> </term>
						<listitem>
							<para>Tolerance is interpreted as...
								<variablelist>
									<varlistentry>
										<term> simp </term>
										<listitem>
											<para>
												...per-simplex error limit
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> global </term>
										<listitem>
											<para>
												...global (whole domain) error limit
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> frac </term>
										<listitem>
											<para>
												...fraction of simplices you'd like to see refined
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-etol">
			<cmdsynopsis>
				<command>etol</command>
				<arg choice="req"> <replaceable>tol</replaceable> </arg>
			</cmdsynopsis>
			<para>Specify the tolerance for error-based adaptive refinement during
				the solve-estimate-refine iterations of the finite element solver.  See
				also:  <link linkend="elec-ekey"><command>ekey</command></link>.
			</para>
			<variablelist>
				<varlistentry>
					<term> <replaceable>tol</replaceable> </term>
					<listitem>
						<para>The error tolerance for adaptive finite element refinement.
							The exact definition of this tolerance is determined by the value
							of <command>ekey</command>.</para>
					</listitem>
				</varlistentry>
			</variablelist>
		</listitem>

		<listitem id="elec-fgcent">
			<cmdsynopsis>
				<command>fgcent</command>
				<group choice="req">
					<arg choice="plain">mol <replaceable>id</replaceable></arg>
					<arg choice="plain"><replaceable>xcent ycent zcent</replaceable></arg>
				</group>
			</cmdsynopsis>
			<para>Specify the center of the fine grid (in a focusing calculation)
				based on a molecule's center or absolute coordinates. The arguments for
				this keyword are:
				<variablelist>
					<varlistentry>
						<term>mol <replaceable>id</replaceable></term>
						<listitem>
							<para>Center the grid on molecule with ID
								<replaceable>id</replaceable>; as assigned in the 
								<link linkend="read"><command>READ</command></link> section.
								Molecule IDs are assigned in the order they're read, starting
								at 1. 
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>xcent ycent zcent</replaceable></term>
						<listitem>
							<para>The coordinates (in &Aring;) at which the grid is
								centered.  Based on the PDB coordinate frame.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-fglen">
			<cmdsynopsis>
				<command>fglen</command>
				<arg choice="req"><replaceable>xlen ylen zlen</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the fine mesh domain lengths in a focusing calculation;
				this may be different in each direction.  This should enclose the
				region of interest in the molecule.
				<variablelist>
					<varlistentry>
						<term><replaceable>xlen ylen zlen</replaceable></term>
						<listitem>
							<para>Grid lengths in the x-, y-, and z-directions in &Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<!--
		<listitem id="gamma">
			<cmdsynopsis>
				<command>gamma</command>
				<arg choice="req"> <replaceable>value</replaceable> </arg>
			</cmdsynopsis>
			<para>
				The coefficient (surface tension) for solvent-accesisble surface area
				(SASA) models of apolar forces.  This term <emphasis>only</emphasis>
				enters into force calculations; SASA-based energies must be computed
				separately (see <link linkend="acc"><filename>acc</filename></link>).
				<variablelist>
					<varlistentry>
						<term><replaceable>value</replaceable></term>
						<listitem>
							<para>SASA-based apolar coefficient (in kJ/mol/&Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>
		-->

		<listitem id="elec-gcent">
			<cmdsynopsis>
				<command>gcent</command>
				<group choice="req">
					<arg choice="plain">mol <replaceable>id</replaceable></arg>
					<arg choice="plain"><replaceable>xcent ycent zcent</replaceable></arg>
				</group>
			</cmdsynopsis>
			<para>Specify the center of the grid based on a molecule's center or
				absolute coordinates. The arguments for this keyword are:
				<variablelist>
					<varlistentry>
						<term>mol <replaceable>id</replaceable></term>
						<listitem>
							<para>Center the grid on molecule with ID
								<replaceable>id</replaceable>; as assigned in the 
								<link linkend="read"><command>READ</command></link> section.
								Molecule IDs are assigned in the order they're read, starting
								at 1. 
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>xcent ycent zcent</replaceable></term>
						<listitem>
							<para>The coordinates (in &Aring;) at which the grid is
								centered.  Based on the PDB coordinate frame.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-glen">
			<cmdsynopsis>
				<command>glen</command>
				<arg choice="req"><replaceable>xlen ylen zlen</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the mesh domain lengths; this may be different in each
				direction.  For some invocations of APBS, either this key or 
				<link linkend="elec-grid"><command>grid</command></link> must be specified.
				<variablelist>
					<varlistentry>
						<term><replaceable>xlen ylen zlen</replaceable></term>
						<listitem>
							<para>Grid lengths in the x-, y-, and z-directions in &Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-grid">
			<cmdsynopsis>
				<command>grid</command>
				<arg choice="req"><replaceable>hx hy hz</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the mesh grid spacings; this may be different in each
				direction.  For some invocations of APBS, either this key or 
				<link linkend="elec-glen"><command>glen</command></link> must be specified.
				<variablelist>
					<varlistentry>
						<term><replaceable>hx hy hz</replaceable></term>
						<listitem>
							<para>Grid spacings in the x-, y-, and z-directions in
								&Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-ion">
			<cmdsynopsis>
				<command>ion</command>
				<command>charge</command>
				<arg choice="req"><replaceable>charge</replaceable></arg>
				<command>charge</command>
				<arg choice="req"><replaceable>conc</replaceable></arg>
				<command>radius</command>
				<arg choice="req"><replaceable>radius</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the mobile ion species present in the system.  This command
				can be repeated as necessary to specify multiple types of ions;
				however, only the largest ionic radius is used to determine the
				ion-accessibility function. 
				<variablelist>
					<varlistentry>
						<term><replaceable>charge</replaceable></term>
						<listitem>
							<para>Mobile ion species charge (in
								e<subscript>c</subscript>)</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>conc</replaceable></term>
						<listitem>
							<para>Mobile ion species concentration (in M)</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>radius</replaceable></term>
						<listitem>
							<para>Mobile ion species radius (in &Aring;)</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
			<warning>
				<para>Note that the old command syntax of
					<command>ion</command>
					<arg choice="req"><replaceable>charge</replaceable></arg>
					<arg choice="req"><replaceable>conc</replaceable></arg>
					<arg choice="req"><replaceable>radius</replaceable></arg>
					is deprecated and will go away "soon".
				</para>
			</warning>
		</listitem>

		<listitem id="elec-lpbe">
			<cmdsynopsis>
				<command>lpbe</command>
			</cmdsynopsis>
			<para>Specifies that the linearized PBE should be solved. Either this
				keyword or
				<itemizedlist>
					<listitem> <link linkend="elec-npbe"><command>npbe</command></link> </listitem>
					<listitem> <link linkend="elec-nrpbe"><command>nrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-lrpbe"><command>lrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-smpbe"><command>smpbe</command></link> </listitem>
				</itemizedlist>
				must be present (based on the calculation type).</para>
		</listitem>

		<listitem id="elec-lrpbe">
			<cmdsynopsis>
				<command>lrpbe</command>
			</cmdsynopsis>
			<para> Specifies the linearized form of the regularized PBE equation
				(RPBE). The regularized PBE equation replaces the point charge
				distribution with the corresponding Green's function. As a result of
				this replacement, the solution corresponds to the reaction field
				instead of the total potential; the total potential can be recovered by
				adding the appropriate Coulombic terms to the solution. Likewise, this
				equation immediately yields the solvation energy without the need for
				reference calculations. Either this keyword or 
				<itemizedlist>
					<listitem> <link linkend="elec-npbe"><command>npbe</command></link> </listitem>
					<listitem> <link linkend="elec-nrpbe"><command>nrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-lrpbe"><command>lrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-smpbe"><command>smpbe</command></link> </listitem>
				</itemizedlist>
				must be present (based on the calculation type).
				<note>
					<para>This function is only available for FEM-based solvers.</para>
				</note>
			</para>
		</listitem>

		<listitem id="elec-maxsolve">
			<cmdsynopsis>
				<command>maxsolve</command>
				<arg choice="req"> <replaceable>num</replaceable> </arg>
			</cmdsynopsis>
			<para>Specify the number of times to perform the solve-estimate-refine
				iteration of the finite element solver.  
				See also:  
				<link linkend="elec-maxvert"><command>maxvert</command></link>,
				<link linkend="elec-targetRes"><command>targetRes</command></link>,
				<variablelist>
					<varlistentry>
						<term> <replaceable>num</replaceable> </term>
						<listitem>
							<para>Maximum number of iterations.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-maxvert">
			<cmdsynopsis>
				<command>maxvert</command>
				<arg choice="req"> <replaceable> num </replaceable> </arg>
			</cmdsynopsis>
			<para>
				Specify the maximum number of vertices to allow during
				solve-estimate-refine cycle of finite element solver.  This places a
				limit on the memory that can be used by the solver.
				See also:  
				<link linkend="elec-targetRes"><command>targetRes</command></link>,
				<link linkend="elec-maxsolve"><command>maxsolve</command></link>.
				<variablelist>
					<varlistentry>
						<term> <replaceable>num</replaceable> </term>
						<listitem>
							<para>Maximum number of vertices.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-mol">
			<cmdsynopsis>
				<command>mol</command>
				<arg choice="req"><replaceable>id</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the molecule for which the PBE is to be solved.  IDs are
				based on the order in which molecules are read by 
				<link linkend="read-mol"><command>read mol</command></link> statements,
				starting from 1.
				<variablelist>
					<varlistentry>
						<term><replaceable>id</replaceable></term>
						<listitem>
							<para>The ID of the molecule for which the PBE is to be
								solved.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-nlev">
			<cmdsynopsis>
				<command>nlev</command>
				<arg choice="req"><replaceable>lev</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the depth of the multilevel hierarchy used in the multigrid
				solver.  See <link linkend="elec-dime"><command>dime</command></link> for a
				discussion of how <command>nlev</command> relates to grid
				dimensions.
				<variablelist>
					<varlistentry>
						<term><replaceable>lev</replaceable></term>
						<listitem>
							<para>Depth of the multigrid hierarchy.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-npbe">
			<cmdsynopsis>
				<command>npbe</command>
			</cmdsynopsis>
			<para>Specifies that the nonlinear (full) PBE should be solved. Either
				this keyword or 
				<itemizedlist>
					<listitem> <link linkend="elec-npbe"><command>npbe</command></link> </listitem>
					<listitem> <link linkend="elec-nrpbe"><command>nrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-lrpbe"><command>lrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-smpbe"><command>smpbe</command></link> </listitem>
				</itemizedlist>
				must be present (based on the calculation type).</para>
		</listitem>

		<listitem id="elec-nrpbe">
			<cmdsynopsis>
				<command>nrpbe</command>
			</cmdsynopsis>
			<para> Specifies the nonlinear form of the regularized PBE equation
				(RPBE). The regularized PBE equation replaces the point charge
				distribution with the corresponding Green's function. As a result of
				this replacement, the solution corresponds to the reaction field
				instead of the total potential; the total potential can be recovered by
				adding the appropriate Coulombic terms to the solution. Likewise, this
				equation immediately yields the solvation energy without the need for
				reference calculations. Either this keyword or 
				<itemizedlist>
					<listitem> <link linkend="elec-npbe"><command>npbe</command></link> </listitem>
					<listitem> <link linkend="elec-nrpbe"><command>nrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-lrpbe"><command>lrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-smpbe"><command>smpbe</command></link> </listitem>
				</itemizedlist>
				must be present (based on the calculation type).
				<note>
					<para>This function is only available for FEM-based solvers.</para>
				</note>
			</para>
		</listitem>

		<listitem id="elec-pdie">
			<cmdsynopsis>
				<command>pdie</command>
				<arg choice="req"><replaceable>diel</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the dielectric constant of the biomolecule.  This is
				usually a value between 2 to 20, where lower values consider only
				electronic polarization and higher values consider additional
				polarization due to intramolecular motion.
				<variablelist>
					<varlistentry>
						<term><replaceable>diel</replaceable></term>
						<listitem>
							<para>Biomolecular dielectric constant (unitless)</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-pdime">
			<cmdsynopsis>
				<command>pdime</command>
				<arg choice="req"><replaceable>npx npy npz</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the processor array to be used in a parallel focusing
				calculation.  The product 
				<replaceable>npx</replaceable> &times;
				<replaceable>npy</replaceable> &times;
				<replaceable>npz</replaceable> should be less than or equal to the
				total number of processors with which APBS was invoked (usually via
				<command>mpirun</command>).  If more processors are provided at
				invocation than actually used during the run, the extra processors are
				not used in the calculation.  The processors are tiled across the
				domain in a Cartesian fashion with a specified amount of overlap (see
				<link linkend="elec-ofrac"><command>ofrac</command></link>) between each
				processor to ensure continuity of the solution.  Each processor's subdomain will contain the number of grid points specified by the <link linkend="elec-dime">dime</link> keyword.
				<variablelist>
					<varlistentry>
						<term> <replaceable>npx npy npz</replaceable> </term>
						<listitem>
							<para>The number of processors to be used in the x-, y- and
								z-directions of the system.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-ofrac">
			<cmdsynopsis>
				<command>ofrac</command>
				<arg choice="req"><replaceable>frac</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the amount of overlap to include between the individual
				processors meshes in a parallel focusing calculation (see 
				<link linkend="elec-ofrac"><command>ofrac</command></link>).  This should be
				a value between 0 and 1.
				<variablelist>
					<varlistentry>
						<term> <replaceable>frac</replaceable> </term>
						<listitem>
							<para>Amount of overlap between processor meshes; a value between
								0 and 1.</para>
						</listitem>
					</varlistentry>
				</variablelist>
				<tip>
					<para>
						Empirical evidence suggests that an <command>ofrac</command> value
						of 0.1 is sufficient to generate stable energies.  However, this
						value may not be sufficient to generate stable forces and/or good
						quality isocontours.  For example, the following table illustrates
						the change in energies and visual artifacts in isocontours as a
						function of <command>ofrac</command> values for a small peptide 
						(<ulink url="http://www.rcsb.org/pdb/cgi/explore.cgi?job=chains&amp;pdbId=2PHK">2PHK</ulink>:B).
						<table> <title>Sensitivity of 2PHK:B solvation energy calculations
								to <command>ofrac</command> values.</title>
							<tgroup cols="3">
								<thead>
									<row>
										<entry><command>ofrac</command> value</entry>
										<entry>Energy (kJ/mol)</entry>
										<entry>Visual artifact in &plusmn; 1 kT/e iscontour?</entry>
									</row>
								</thead>
								<tbody>
									<row>
										<entry>0.05</entry> 
										<entry>342.79</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.06</entry>
										<entry>342.00</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.07</entry>
										<entry>341.12</entry>
										<entry>Yes</entry>
									</row>
									<row>
										<entry>0.08</entry>
										<entry>341.14</entry>
										<entry>Yes</entry>
									</row>
									<row>
										<entry>0.09</entry>
										<entry>342.02</entry>
										<entry>Yes</entry>
									</row>
									<row>
										<entry>0.10</entry>
										<entry>340.84</entry>
										<entry>Yes</entry>
									</row>
									<row>
										<entry>0.11</entry>
										<entry>339.67</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.12</entry>
										<entry>341.10</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.13</entry>
										<entry>341.10</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.14</entry>
										<entry>341.32</entry>
										<entry>No</entry>
									</row>
									<row>
										<entry>0.15</entry>
										<entry>341.54</entry>
										<entry>No</entry>
									</row>
								</tbody>
							</tgroup>
						</table>
					</para>
				</tip>
			</para>
		</listitem>


		<listitem id="elec-sdie">
			<cmdsynopsis>
				<command>sdie</command>
				<arg choice="req"><replaceable>diel</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the dielectric constant of the solvent.  Bulk water at
				biologically-relevant temperatures is usually modeled with a dielectric
				constant of 78-80.
				<variablelist>
					<varlistentry>
						<term><replaceable>diel</replaceable></term>
						<listitem>
							<para>Solvent dielectric constant (unitless)</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-sdens">
			<cmdsynopsis>
				<command>sdens</command>
				<arg choice="req"><replaceable>density</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the number of grid points per square-angstrom to use 
				in surface constructions (e.g., molecular
				surface, solvent-accessible surface, etc.). Ignored when srad is 0.0 (see 
				<link linkend="elec-srad"><command>srad</command></link>) or srfm is 
				spl2 (see <link linkend="elec-srfm"><command>srfm</command></link>).
				There is a direct correlation between this value 
				used for the surface sphere density, the
				accuracy of the surface calculations,, 
				and the APBS calculation time.  APBS
				"suggested" value is 10.0.
				<variablelist>
					<varlistentry>
						<term><replaceable>density</replaceable></term>
						<listitem>
							<para>Surface sphere density (in grid points/&Aring;<superscript>2
							</superscript>).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>
		
		<listitem id="elec-smpbe">
			<cmdsynopsis>
				<command>smpbe</command>
				<command>vol</command>
				<arg choice="req"> <replaceable>volume</replaceable> </arg>
				<command>size</command>
				<arg choice="req"> <replaceable>number</replaceable> </arg>
			</cmdsynopsis>
			<para>
				Specifies that the size-modified PBE should be solved as described by Chu V, et al <citetitle>Biophys J</citetitle>, in press (<ulink url="http://dx.doi.org/10.1529/biophysj.106.099168">doi:10.1529/biophysj.106.099168</ulink>).
				The parameter <replaceable>radius</replaceable> controls the lattice size (in Angstroms) used in the SMPBE formalism; each lattice site has a volume equal to <replaceable>radius</replaceable><superscript>3</superscript>.  The parameter <replaceable>size</replaceable> controls the relative size of the ions (in Angstroms) such that each lattice site can contain a single ion of volume <replaceable>radius</replaceable><superscript>3</superscript> or <replaceable>size</replaceable> ions of volume <replaceable>radius</replaceable><superscript>3</superscript>/<replaceable>size</replaceable>.
				Either this keyword or
				<itemizedlist>
					<listitem> <link linkend="elec-npbe"><command>npbe</command></link> </listitem>
					<listitem> <link linkend="elec-nrpbe"><command>nrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-lrpbe"><command>lrpbe</command></link> </listitem>
					<listitem> <link linkend="elec-smpbe"><command>smpbe</command></link> </listitem>
				</itemizedlist>
				must be present (based on the calculation type).</para>
		</listitem>
		

		<listitem id="elec-srad">
			<cmdsynopsis>
				<command>srad</command>
				<arg choice="req"><replaceable>radius</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the radius of the solvent molecules; this parameter is used
				to define the dielectric function (see 
				<link linkend="elec-srfm"><command>srfm</command></link>).  This value is
				usually set to 1.4 &Aring; for water.  This keyword is ignored when any of the spline-based surfaces are used (e.g., spl2, see <link linkend="elec-srfm"><command>srfm</command></link>).
				<variablelist>
					<varlistentry>
						<term><replaceable>radius</replaceable></term>
						<listitem>
							<para>Solvent radius (in &Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-swin">
			<cmdsynopsis>
				<command>swin</command>
				<arg choice="req"><replaceable>win</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the size of the support (i.e., the rate of change) for
				spline-based surface definitions 
				(see <link linkend="elec-srfm"><command>srfm</command></link>).  
				Usually 0.3 &Aring;.
				<variablelist>
					<varlistentry>
						<term><replaceable>win</replaceable></term>
						<listitem>
							<para>Spline window (in &Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-srfm">
			<cmdsynopsis>
				<command>srfm</command>
				<arg choice="req"><replaceable>flag</replaceable></arg>
			</cmdsynopsis>
			<para>
				Specify the model used to construct the dielectric ion-accessibility
				coefficients.  
				<variablelist>
					<varlistentry>
						<term><replaceable>flag</replaceable></term>
						<listitem>
							<para>
								The coefficient model:
								<variablelist>
									<varlistentry>
										<term>mol</term>
										<listitem>
											<para>The dielectric coefficient 
												<inlineequation>
													<alt>\epsilon(x)</alt>
													<graphic fileref="images/epsilon_of_x.gif" valign="bottom" />
												</inlineequation>
												is defined based on 
												a molecular surface definition.  The problem domain is
												divided into two spaces.  The "free volume" space is
												defined by the union of solvent-sized spheres (see 
												<link
													linkend="elec-srad"><command>srad</command></link>)
												which do not overlap with biomolecular atoms.  This
												free volume is assigned bulk solvent dielectric values.
												The complement of this space is assigned biomolecular
												dielectric values.  With a non-zero solvent radius
												(<command>srad</command>), this choice of coefficient
												corresponds to the traditional definition used for PB
												calculations.  When the solvent radius is set to zero,
												this corresponds to a van der Waals surface
												definition.</para>
											<para>The ion-accessibility coefficient
												<inlineequation>
													<alt>\overline{\kappa}^2(x)</alt>
													<graphic fileref="images/overline_kappa_2_of_x.gif" valign="bottom" />
												</inlineequation>
												is defined by an "inflated" van der Waals model.
												Specifically, the radius of each biomolecular atom is
												increased by the radius of the ion species.  The
												problem domain is then divided into two spaces.  The
												space inside the union of these inflated atomic spheres
												is assigned an ion-accessibility value of 0; the
												complement space is assigned bulk ion accessibility
												values.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>smol</term>
										<listitem>
											<para>
												The dielectric and ion-accessibility coefficients are
												defined as for mol (see above).  However, they are then
												"smoothed" by a 9-point harmonic averaging to somewhat
												reduce sensitivity to the grid setup as described by
												Bruccoleri et al. <citetitle>J Comput Chem</citetitle> 
												18 268-276, 1997 (<ulink
													url="http://dx.doi.org/10.1002/(SICI)1096-987X(19970130)18:2&gt;268::AID-JCC11>3.0.CO;2-E">doi:10.1002/(SICI)1096-987X(19970130)18:2&gt;268::AID-JCC11>3.0.CO;2-E</ulink>).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>spl2</term>
										<listitem>
											<para>
												The dielectric 
												<inlineequation>
													<alt>\epsilon(x)</alt>
													<graphic fileref="images/epsilon_of_x.gif" valign="bottom" />
												</inlineequation>
												and ion-accessibility
												<inlineequation>
													<alt>\overline{\kappa}^2(x)</alt>
													<graphic fileref="images/overline_kappa_2_of_x.gif" valign="bottom" />
												</inlineequation>
												coefficients are defined by a cubic-spline surface as
												described by Im et al, <citetitle>Comp Phys
													Commun</citetitle> 111 (1-3) 59-75, 1998 
												(<ulink url="http://dx.doi.org/10.1016/S0010-4655(98)00016-2">doi:10.1016/S0010-4655(98)00016-2</ulink>).
												These spline-based surface definitions are very stable
												with respect to grid parameters and therefore ideal for
												calculating forces.  However, they require substantial
												reparameterization of the force field; interested users
												should consult Nina et al, <citetitle>Biophys
													Chem</citetitle> 78 (1-2) 89-96, 1999 
												(<ulink url="http://dx.doi.org/10.1016/S0301-4622(98)00236-1">doi:10.1016/S0301-4622(98)00236-1</ulink>).
												Additionally, these surfaces can generate unphysical
												results with non-zero ionic strengths; this is an
												on-going area of development.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>spl4</term>
										<listitem>
											<para>
												The dielectric and ion-accessibility coefficients are 
												defined by a 7th order polynomial. This surface 
												definition has characteristics similar to spl2, but
												provides higher order continuity necessary for stable 
												force calculations with atomic multipole force fields 
												(up to quadrupole).
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-targetRes">
			<cmdsynopsis>
				<command>targetRes</command>
				<arg choice="req"> <replaceable>res</replaceable> </arg>
			</cmdsynopsis>
			<para>
				Specify the target resolution of the simplices in the mesh; refinement
				will continue until the longest edge of every simplex is below this
				value.  See also:
				<link linkend="elec-maxvert"><command>maxvert</command></link>,
				<link linkend="elec-maxsolve"><command>maxsolve</command></link>,
				<link linkend="elec-targetNum"><command>targetNum</command></link>
				<variablelist>
					<varlistentry>
						<term> <replaceable>res</replaceable> </term>
						<listitem>
							<para>
								Target resolution for longest edges of simplices in mesh (in
								&Aring;).
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-targetNum">
			<cmdsynopsis>
				<command>targetNum</command>
				<arg choice="req"> <replaceable>num</replaceable> </arg>
			</cmdsynopsis>
			<para>
				Specify the target number of vertices in the
				<emphasis>initial</emphasis> mesh; intiial refinement
				will continue until this number is reached or the the longest edge of
				every simplex is below 
				<link linkend="elec-targetNum"><command>targetNum</command>.</link>
				See also:
				<link linkend="elec-targetRes"><command>targetRes</command></link>
				<variablelist>
					<varlistentry>
						<term> <replaceable>num</replaceable> </term>
						<listitem>
							<para>
								Target number of vertices in initial mesh.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


		<listitem id="elec-temp">
			<cmdsynopsis>
				<command>temp</command>
				<arg choice="req"> <replaceable>T</replaceable> </arg>
			</cmdsynopsis>
			<para>Temperature for PBE calculation.
				<variablelist>
					<varlistentry>
						<term><replaceable>T</replaceable></term>
						<listitem>
							<para>Temperature (in K)</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


		<listitem id="elec-useaqua">
			<cmdsynopsis>
				<command>useaqua</command>
			</cmdsynopsis>
			<para>This enables <emphasis>experimental</emphasis> support for Aqua, a verison of the Holst group <ulink url="http://www.fetk.org/">FEtk PMG</ulink> multigrid library optimized by <ulink url="http://koehllab.genomecenter.ucdavis.edu/">Patrice Koehl</ulink> for improved memory usage and speed when solving the Poisson-Boltzmann equation.  <emphasis>This keyword is temporary and will eventually disappear as Aqua becomes the default multigrid solver for APBS.</emphasis>
			</para>
		</listitem>

		<listitem id="elec-usemap">
			<cmdsynopsis>
				<command>usemap</command>
				<arg choice="req"><replaceable>type</replaceable></arg>
				<arg choice="req"><replaceable>id</replaceable></arg>
			</cmdsynopsis>
			<para>Specify pre-calculated coefficient maps to be used in the PB
				calculation.  These must have been input via an earlier 
				<link linkend="read"><command>read map</command></link> statement.
				<variablelist>
					<varlistentry>
						<term><replaceable>type</replaceable></term>
						<listitem>
							<para>
								Specify the type of pre-calculated map to be read in:
								<variablelist>
									<varlistentry>
										<term>diel</term>
										<listitem>
											<para>Dielectric function map (as read by <command>read
													map</command> <replaceable>dielx diely
													dielx</replaceable>); this causes the
												<link
													linkend="elec-pdie"><command>pdie</command></link>,
												<link
													linkend="elec-sdie"><command>sdie</command></link>,
												<link
													linkend="elec-srad"><command>srad</command></link>, 
												<link
													linkend="elec-swin"><command>swin</command></link>, and
												<link
													linkend="elec-srfm"><command>srfm</command></link>
												parameters and the radii of the biomolecular atoms to be
												ignored when computing dielectric values for the PBE.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>kappa</term>
										<listitem>
											<para>Mobile ion-accessibility function map (as read by
												<command>read map</command>
												<replaceable>kappa</replaceable>); this causes the
												<link
													linkend="elec-swin"><command>swin</command></link> and 
												<link
													linkend="elec-srfm"><command>srfm</command></link>
												parameters and the radii of the biomolecular atoms to be
												ignored when computing mobile ion values for the PBE.
												The 
												<link
													linkend="elec-ion"><command>ion</command></link>
												parameter is not ignored and will still be used.
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>charge</term>
										<listitem>
											<para>Charge distribution map (as read by 
												<command>read map</command>
												<replaceable>charge</replaceable>); this causes the
												<link
													linkend="elec-chgm"><command>chgm</command></link>
												parameter and the charges of the biomolecular atoms to
												be ignored when assembling the fixed charge
												distribution for the PBE.
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>id</replaceable></term>
						<listitem>
							<para>
								This ID specifies the particular map read in with <command>read
									map</command>.  These IDs are assigned sequentially, starting
								from 1, for each map type read by APBS.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


		<listitem id="elec-usemesh">
			<cmdsynopsis>
				<command>usemesh</command>
				<arg choice="req"><replaceable>id</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the external finite element mesh to be used in the <link linkend="fe-manual">finite element</link> PB calculation.  These must have been input via an earlier <link linkend="read"><command>read mesh</command></link> statement.
				<variablelist>
					<varlistentry>
						<term><replaceable>id</replaceable></term>
						<listitem>
							<para>
								This ID specifies the particular map read in with <command>read
									mesh</command>.  These IDs are assigned sequentially, starting
								from 1, for each mesh read by APBS.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-write">
			<cmdsynopsis>
				<command>write</command>
				<arg choice="req">type</arg>
				<arg choice="req">format</arg>
				<arg choice="req">stem</arg>
			</cmdsynopsis>
			<para>
				This controls the output of scalar data calculated during the PB run.
				This keyword can be repeated several times to provide various types of
				data.
				<variablelist>
					<varlistentry>
						<term> <replaceable>type</replaceable> </term>
						<listitem>
							<para>
								What type of data to output:
								<variablelist>
									<varlistentry>
										<term>charge</term>
										<listitem>
											<para>
												Write out the biomolecular charge distribution in
												units of e<subscript>c</subscript> (electron charge)
												per Angstrom<superscript>3</superscript> (multigrid
												only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>pot</term>
										<listitem>
											<para>
												Write out the electrostatic potential in units of
												k<subscript>b</subscript>T/e<subscript>c</subscript>
												(multigrid and finite element)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>smol</term>
										<listitem>
											<para>
												Write out the solvent accessibility defined by the
												molecular surface definition (see 
												<link
													linkend="elec-srfm"><command>srfm</command> 
													smol</link>).
												Values are unitless and range from 0 (inaccessible) to 1
												(accessible).  (multigrid and finite element)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>sspl</term>
										<listitem>
											<para>
												Write out the spline-based solvent accessibility
												(see
												<link
													linkend="elec-srfm"><command>srfm</command> 
													spl2</link>).
												Values are unitless and range from 0 (inaccessible) to
												1 (accessible).  (multigrid and finite element)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>vdw</term>
										<listitem>
											<para>
												Write out the van der Waals-based solvent
												accessibility (see 
												<link
													linkend="elec-srfm"><command>srfm</command> 
													smol</link>
												with
												<link
													linkend="elec-srad"><command>srad</command>
													smol</link>).  Values are unitless and range from 0
												(inaccessible) to 1 (accessible).  (multigrid and
												finite element)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>ivdw</term>
										<listitem>
											<para>
												Write out the inflated van der Waals-based ion
												accessibility (see 
												<link
													linkend="elec-srfm"><command>srfm</command> 
													smol</link>).
												Values are unitless and range from 0 (inaccessible) to 1
												(accessible).  (multigrid and finite element)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>lap</term>
										<listitem>
											<para>
												Write out the Laplacian of the potential
												<informalequation>
													<alt>\nabla^2 \phi(x)</alt>
													<graphic fileref="images/lap.gif"/>
												</informalequation>
												in units of
												k<subscript>B</subscript>T/e<subscript>c</subscript>/&Aring;<superscript>2</superscript>
												(multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>edens</term>
										<listitem>
											<para>
												Write out the "energy density"
												<informalequation>
													<alt>\epsilon(x) \left( \nabla \phi \right)^2</alt>
													<graphic fileref="images/edens.gif"/>
												</informalequation>
												in units of
												k<subscript>B</subscript>T/e<subscript>c</subscript>/&Aring;<superscript>2</superscript>
												(multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>ndens</term>
										<listitem>
											<para>
												Write out the mobile ion number density
												<informalequation>
													<alt>\sum_i^m \overline{c}_i e^{-\beta q_i \phi(x)}</alt>
													<graphic fileref="images/ndens.gif"/>
												</informalequation>
												for <replaceable>m</replaceable> ion species
												in units of M (multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>qdens</term>
										<listitem>
											<para>
												Write out the mobile charge density
												<informalequation>
													<alt>\sum_i^m q_i \overline{c}_i e^{-\beta q_i \phi(x)}</alt>
													<graphic fileref="images/qdens.gif"/>
												</informalequation>
												for <replaceable>m</replaceable> ion species in units
												of e<subscript>c</subscript> M (multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>dielx</term>
										<listitem>
											<para>Write out the dielectric map shifted by 1/2 grid
												spacing in the x-direction (see 
												<link linkend="read"><command>read</command> 
													diel</link>).
												The values are unitless (multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>diely</term>
										<listitem>
											<para>Write out the dielectric map shifted by 1/2 grid
												spacing in the y-direction (see 
												<link linkend="read"><command>read</command> 
													diel</link>).
												The values are unitless (multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>dielz</term>
										<listitem>
											<para>Write out the dielectric map shifted by 1/2 grid
												spacing in the z-direction (see 
												<link linkend="read"><command>read</command> 
													diel</link>).
												The values are unitless (multigrid only).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>kappa</term>
										<listitem>
											<para>Write out the ion-accessibility kappa map (see 
												<link linkend="read"><command>read</command> 
													kappa</link>).
												The values are in units of
												&Aring;<superscript>-2</superscript> (multigrid only).
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term> <replaceable>format</replaceable> </term>
						<listitem>
							<para>Specify the format for writing out the data.
								<variablelist>
									<varlistentry>
										<term> dx </term>
										<listitem>
											<para>Write out data in 
												<link linkend="opendx-format">OpenDX format</link>.
												This is the preferred format for APBS I/O. (multigrid
												and finite element).
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> avs </term>
										<listitem>
											<para>Write out data in 
												<ulink url="http://www.avs.com">AVS UCD
													format</ulink>.  (finite element only)
											</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term> uhbd </term>
										<listitem>
											<para>Write out data in UHBD format.  (multigrid only)
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term> <replaceable>stem</replaceable> </term>
						<listitem>
							<para>
								Specify the path for the output; files are written to
								<replaceable>stem</replaceable><filename>.XXX</filename>, where
								<filename>XXX</filename> is determined by the file format (and
								processor rank for parallel calculations).  This pathname should not include spaces.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="elec-writemat">
			<cmdsynopsis>
				<command>writemat</command>
				<arg choice="req">type</arg>
				<arg choice="req">stem</arg>
			</cmdsynopsis>
			<para>
				This controls the output of the mathematical operators in the PBE as
				matrices in <link linkend="hb-format">Harwell-Boeing format</link>
				(multigrid only)
				<variablelist>
					<varlistentry>
						<term> <replaceable>type</replaceable> </term>
						<listitem>
							<para>
								What type of operator to output:
								<variablelist>
									<varlistentry>
										<term>poission</term>
										<listitem>
											<para>Write out the Poisson operator.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>pot</term>
										<listitem>
											<para>Write out the Gateaux (functional) derivative of the
												full PBE operator evaluated at the current
												solution.</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term> <replaceable>stem</replaceable> </term>
						<listitem>
							<para>
								Specify the path for the output; files are written to
								<replaceable>stem</replaceable><filename>.mat</filename>.  This pathname should not include spaces.
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


	</itemizedlist>


</sect3>