File: print.xml

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<cmdsynopsis>
	<command>PRINT</command>
	<arg choice="req"><replaceable>what</replaceable></arg>
	<arg choice="opt" rep="repeat"><replaceable>id op id op</replaceable></arg>
	<command>END</command>
</cmdsynopsis>
<para>
	This is a very simple section that allows linear combinations of calculated
	properties to be written to standard output.  It has the following variables:
	<variablelist>
		<varlistentry>
			<term> <replaceable>what</replaceable> </term>
			<listitem>
				<para>
					Specify which quantities to manipulate/print:
					<variablelist>
						<varlistentry>
							<term> energy </term>
							<listitem>
								<para>
									Print energies as calculated with an earlier
									<link linkend="elec-calcenergy"><command>calcenergy</command></link>
									<link linkend="elec"><command>ELEC</command></link> command.
								</para>
								<warning> <para>This usage is deprecated and will be replaced in the next release.  Please use "elecEnergy" or "apolEnergy" as appropriate.  For now, this will return the old results of "elecEnergy".</para> </warning>
							</listitem>
						</varlistentry>
						<varlistentry>
							<term> force </term>
							<listitem>
								<para>
									Print forces as calculated with an earlier
									<link linkend="elec-calcforce"><command>calcforce</command></link>
									<command>ELEC</command> command.
								</para>
								<warning> <para>This usage is deprecated and will be replaced in the next release.  Please use "elecForce" or "apolForce" as appropriate.  For now, this will return the old results of "elecEnergy".</para> </warning>
							</listitem>
						</varlistentry>
						<varlistentry>
							<term> elecEnergy </term>
							<listitem>
								<para>
									Print energies as calculated with an earlier
									<link linkend="elec-calcenergy"><command>calcenergy</command></link>
									<link linkend="elec"><command>ELEC</command></link> command.
								</para>
							</listitem>
						</varlistentry>
						<varlistentry>
							<term> elecForce </term>
							<listitem>
								<para>
									Print forces as calculated with an earlier
									<link linkend="elec-calcforce"><command>calcforce</command></link>
									<link linkend="elec"><command>ELEC</command></link> command.
								</para>
							</listitem>
						</varlistentry>
						<varlistentry>
							<term> apolEnergy </term>
							<listitem>
								<para>
									Print energies as calculated with an earlier
									<link linkend="apolar-calcenergy"><command>calcenergy</command></link>
									<link linkend="apolar"><command>APOLAR</command></link> command.
								</para>
							</listitem>
						</varlistentry>
						<varlistentry>
							<term> apolForce </term>
							<listitem>
								<para>
									Print forces as calculated with an earlier
									<link linkend="apolar-calcforce"><command>calcforce</command></link>
									<link linkend="apolar"><command>APOLAR</command></link> command.
								</para>
							</listitem>
						</varlistentry>
					</variablelist>
				</para>
			</listitem>
		</varlistentry>
		<varlistentry>
			<term> <replaceable>id</replaceable> </term>
			<listitem>
				<para>The ID of a particular <command>ELEC</command> calculation as
					specified with the 
					<link linkend="elec"><command>ELEC name</command></link>
					<replaceable>id</replaceable> command.  If the
					<replaceable>id</replaceable> variables are not set explicitly, they
					are assigned sequential integers, starting at 1, based on the order of
					the <command>ELEC</command> statements.
				</para>
			</listitem>
		</varlistentry>
		<varlistentry>
			<term> <replaceable>op</replaceable> </term>
			<listitem>
				<para>Specify the arthimetic operation to be performed on the calculated
					quantities:
					<variablelist>
						<varlistentry>
							<term> + </term>
							<listitem> <para>Addition</para> </listitem>
						</varlistentry>
						<varlistentry>
							<term> - </term>
							<listitem> <para>Subtraction</para> </listitem>
						</varlistentry>
					</variablelist>
				</para>
			</listitem>
		</varlistentry>
	</variablelist>
</para>

<para>Given all these options, a typical declaration might look like:</para>
<example> <title>PRINT statement example</title>
	<programlisting>
		# Energy change due to binding
		print energy complex - ligand - protein end
		# Energy change due to solvation
		print energy solvated - reference end
		# Solvation energy change due to binding
		print energy 
		complex_solv - complex_ref 
		- ligand_solv + ligand_ref 
		- protein_solv + protein_ref 
		end
	</programlisting>
</example>
<para>
	See the APBS <filename>examples/</filename> directory for more examples.
</para>