File: invocation.xml

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apbs 1.0.0-2
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<sect1> <title>Invocation</title>

	<para>As mentioned in the 
		<link linkend="installation-sect">Installation intructions</link>, the main
		APBS binary is installed in
		<filename>${FETK_PREFIX}/bin/${prefix}/</filename> where
		<filename>${prefix}</filename> is a machine-specific directory.  Of course,
		you can move the binary to any directory you choose.  APBS is invoked with a
		very simple syntax:
		<cmdsynopsis>
			<command>apbs</command> <arg choice="opt">options</arg>
			<arg choice="plain"><link linkend="apbs-input">input-file</link></arg>
		</cmdsynopsis>

		Command line options include:
		<variablelist>
			<varlistentry>
				<term><literal>--outputfile=</literal><replaceable>name</replaceable></term>
				<listitem>
					<para>Sets the output logging path (as described in the 
						output logging section of 
						the manual) to <replaceable>name</replaceable>, or
						<replaceable>name_N</replaceable> for parallel runs, where 
						<literal>N</literal> is the processor ID.
						If <literal>--outputformat</literal> is not specified, flat-file
						format will be used as the default.
					</para>
				</listitem>
			</varlistentry>
			<varlistentry>
				<term><literal>--outputformat=</literal><replaceable>type</replaceable></term>
				<listitem>
					<para>Sets the output logging format.  Accepted values are:
						<variablelist>
							<varlistentry>
								<term><replaceable>flat</replaceable></term>
								<listitem>
									<para>Flat-file format (default).</para>
								</listitem>
							</varlistentry>
							<varlistentry>
								<term><replaceable>xml</replaceable></term>
								<listitem>
									<para>XML format</para>
								</listitem>
							</varlistentry>
						</variablelist>
					</para>
				</listitem>
			</varlistentry>
			<varlistentry>
				<term><literal>--help</literal></term>
				<listitem>                   
					<para>Displays command line usage</para>
				</listitem>
			</varlistentry>
			<varlistentry> 
				<term><literal>--version</literal></term>
				<listitem>
					<para>Displays the current APBS version</para>
				</listitem>
			</varlistentry>
		</variablelist>

		<parameter>input-file</parameter> is an input file with a
		specific syntax described in <xref linkend="apbs-input"/>.
		Besides the output files specified in
		<literal>input-file</literal> and optional logs as specified by
		use of the <literal>--output-file</literal> command line
		option, APBS writes data to three additional places:
		<itemizedlist>
			<listitem>
				<para>Standard output.  This will appear on your screen (if you don't
					redirect it somewhere) and will contain all the basic information about
					the electrostatics calculation.</para>
			</listitem>
			<listitem>
				<para>Standard error.  This will also appear on your screen (if you don't
					redirect it somewher) and will contain warnings and error
					messages.</para>
			</listitem>
			<listitem>
				<para>The file <filename>io.mc</filename> (or
					<filename>io.mc_N</filename> for parallel runs, where
					<literal>N</literal> is the processor ID.  This gives you detailed
					information about the progress of the run with a particular focus on
					the numerical solver.</para>
			</listitem>
		</itemizedlist>
	</para>
</sect1>