<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_rwmd_8h">
<title>/Users/bernard/b20/bsoft/include/rwmd.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/rwmd.h</primary></indexterm>
<para>

<para>Header to read and write molecular dynamics parameters in STAR format. </para>
 
</para>
<programlisting>#include &quot;rwatomprop.h&quot;
#include &quot;Vector3.h&quot;
</programlisting><simplesect>
    <title>Classes    </title>
        <itemizedlist>
            <listitem><para>struct <link linkend="_struct_bbondtype">Bbondtype</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bangletype">Bangletype</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bmd">Bmd</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_bmd">Bmd</link> * <link linkend="_rwmd_8h_1a22923138de0def9578861ac65b276eee">md_init</link> ()</para>

<para>Initializes a molecular dynamics structure. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmd">Bmd</link> * <link linkend="_rwmd_8h_1a38b152c20e607fe4a762d31ed9e7f69e">md_init_with_types</link> ()</para>

<para>Initializes a molecular dynamics structure. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmd">Bmd</link> * <link linkend="_rwmd_8h_1af80e13ca3191b777db0e02e62585b193">read_md_parameters</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename)</para>

<para>Reading molecular dynamics parameters from STAR files. </para>
</listitem>
            <listitem><para>int <link linkend="_rwmd_8h_1a49ef3ca86ebe19c2b21685ef45015418">write_md_parameters</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bmd">Bmd</link> *md)</para>

<para>Writing molecular dynamics parameters to a STAR file. </para>
</listitem>
            <listitem><para>int <link linkend="_rwmd_8h_1a213d9b9a83f477cd75c53d8371b4ef95">md_kill</link> (<link linkend="_struct_bmd">Bmd</link> *md)</para>

<para>Deallocates a molecular dynamics structure. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header to read and write molecular dynamics parameters in STAR format. </para>

<para><formalpara><title>Author: </title>

<para>Bernard Heymann </para>
</formalpara>
<formalpara><title>Date: </title>

<para>Created: 20030919 </para>

<para>Modified: 20060424 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_rwmd_8h_1a22923138de0def9578861ac65b276eee"/>    <section>
    <title>md_init()</title>
<indexterm><primary>md_init</primary><secondary>rwmd.h</secondary></indexterm>
<indexterm><primary>rwmd.h</primary><secondary>md_init</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmd">Bmd</link>* md_init ( )</computeroutput></para><para>

<para>Initializes a molecular dynamics structure. </para>
</para>

<para><formalpara><title>Returns: </title>

<para>Bmd* molecular dynamics structure. <literallayout><computeroutput>The coefficients for the Lennard-Jones Van der Waals interaction are
defined as:
    VdWcoeff1 = 1/12
    VdWcoeff2 = 1/6
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 28 of file rwmd.cpp.</para>
    </section><anchor xml:id="_rwmd_8h_1a38b152c20e607fe4a762d31ed9e7f69e"/>    <section>
    <title>md_init_with_types()</title>
<indexterm><primary>md_init_with_types</primary><secondary>rwmd.h</secondary></indexterm>
<indexterm><primary>rwmd.h</primary><secondary>md_init_with_types</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmd">Bmd</link>* md_init_with_types ( )</computeroutput></para><para>

<para>Initializes a molecular dynamics structure. </para>
</para>

<para><formalpara><title>Returns: </title>

<para>Bmd* molecular dynamics structure. <literallayout><computeroutput>The coefficients for the Lennard-Jones Van der Waals interaction are
defined as:
    VdWcoeff1 = 1/12
    VdWcoeff2 = 1/6
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 51 of file rwmd.cpp.</para>
    </section><anchor xml:id="_rwmd_8h_1a213d9b9a83f477cd75c53d8371b4ef95"/>    <section>
    <title>md_kill()</title>
<indexterm><primary>md_kill</primary><secondary>rwmd.h</secondary></indexterm>
<indexterm><primary>rwmd.h</primary><secondary>md_kill</secondary></indexterm>
<para><computeroutput>int md_kill (<link linkend="_struct_bmd">Bmd</link> * md)</computeroutput></para><para>

<para>Deallocates a molecular dynamics structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>molecular dynamics structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>All linked lists within the structure is also deallocated.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 417 of file rwmd.cpp.</para>
    </section><anchor xml:id="_rwmd_8h_1af80e13ca3191b777db0e02e62585b193"/>    <section>
    <title>read_md_parameters()</title>
<indexterm><primary>read_md_parameters</primary><secondary>rwmd.h</secondary></indexterm>
<indexterm><primary>rwmd.h</primary><secondary>read_md_parameters</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmd">Bmd</link>* read_md_parameters (<link linkend="_class_bstring">Bstring</link> &amp; filename)</computeroutput></para><para>

<para>Reading molecular dynamics parameters from STAR files. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>file name (or comma-delimited list). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmd* molecular dynamics structure. </para>
</formalpara>
</para>
<para>
Definition at line 80 of file rwmd.cpp.</para>
    </section><anchor xml:id="_rwmd_8h_1a49ef3ca86ebe19c2b21685ef45015418"/>    <section>
    <title>write_md_parameters()</title>
<indexterm><primary>write_md_parameters</primary><secondary>rwmd.h</secondary></indexterm>
<indexterm><primary>rwmd.h</primary><secondary>write_md_parameters</secondary></indexterm>
<para><computeroutput>int write_md_parameters (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bmd">Bmd</link> * md)</computeroutput></para><para>

<para>Writing molecular dynamics parameters to a STAR file. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>file name (or comma-delimited list). </para>
</entry>
                            </row>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>molecular dynamics parameters structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int error code (&lt;0 means failure). </para>
</formalpara>
</para>
<para>
Definition at line 237 of file rwmd.cpp.</para>
</section>
</section>
</section>
