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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><HTML><HEAD> <META NAME="GENERATOR" CONTENT="SGML-Tools 1.0.9"> <TITLE>XMD - Molecular Dynamics Program: Write Command</TITLE> <LINK HREF="xmd-11.html" REL=next> <LINK HREF="xmd-9.html" REL=previous> <LINK HREF="xmd.html#toc10" REL=contents></HEAD><BODY><A HREF="xmd-11.html">Next</A><A HREF="xmd-9.html">Previous</A><A HREF="xmd.html#toc10">Contents</A><HR><H2><A NAME="s10">10. Write Command</A></H2><P><P>The WRITE command is used to write all information from XMD (with theexception of the ESAVE, BSAVE, SSAVE and TSAVE commands).There are two modifiers that can beused with some write options: SEL and FILE.<P><P><P>The <CODE>SEL</CODE> option causes only those values that belong to selectedatoms to be written out (see SELECT above).<P><P><P>The <CODE>FILE [+]filename</CODE>option directs the output to the specified file. Theoption <CODE>+</CODE> causes the output to be appended to the end of the specifiedfile. Otherwise, the output overwrites any previously existing file.<P><P><P>A detailed description of each parameter follows.<P><P><P><DL><P><DT><B>WRITE [FILE [+]filename] BOX</B><DD><P>Writes the corresponding parameter. Note that each of the aboveparameters are constants that are set either by the user or by default.All of these values are described above under there command forms.<P><DT><B>WRITE [SEL] COR [+]filename</B><DD><P>Writes the current step information in COR format to the file filename.If the [+] is included, the information is appended to the file end.Otherwise the file is over written.<P><DT><B>WRITE [FILE [+]filename] CSTEP</B><DD><P>Writes the value of cstep from the CLAMP command.<P><DT><B>WRITE [SEL] [FILE [+]filename] DISP</B><DD><P>Writes the displacement of each particle or selected particle relativeto the reference step. Note that you must first create the displacementsusing the DISP command(see section on the<A HREF="xmd-8.html#command-disp">DISP command</A>).<P><DT><B>WRITE [FILE [+]filename] DTIME</B><DD><P>Writes the value of dtime from DTIME command.<P><DT><B>WRITE [FILE [+]filename] [SEL] EATOM</B><DD><P>Writes the indices and energies for each atom or selected atom.<P><DT><B>WRITE [FILE [+]filename] EKIN</B><DD><P>Writes the average kinetic energy per atom. This value of kineticenergy is produced either by the ITEMP command or the CMD command, whichever was executed last. Units are in the units specified by EUNITcommand.<P><DT><B>WRITE [FILE [+]filename] ENERGY</B><DD><P>Writes the average potential energy per atom (the average taken is overall the atoms, but not over time steps). Units are in the unitsspecified by EUNIT command. This energy is the internal energy. Itincludes only the energy due to the interatomic potential, and notexternally applied forces (see the EXTFORCE and EXTSPRING commands).<P><DT><B>WRITE [FILE [+]filename] EPOT</B><DD><P>Same as WRITE ENERGY above.<P><DT><B>WRITE [FILE [+]filename] ETOT</B><DD><P>Writes the sum of the EKIN and EPOT.<P><DT><B>WRITE [FILE [+]filename] [SEL] STRESS</B><DD><P>Writes the product of the internal stress and the atomic volumeaveraged over either all the atoms or the selected atoms. The units are (erg cm). The actual stress per atom can be obtained by dividing the printedvalue by the atomic volume. Since XMD cannot always know the atomic volume(due to the presence of free surfaces and/or void in the lattice) XMDdoes not perform the division automatically.XMD writes 6 products, one for each of the Voight stresses.<P><DT><B>WRITE [FILE [+]filename] [SEL] EXTFORCE</B><DD><P>Writes the atom type and the x, y and z components of the external forceon the atom for every atom or selected atom. Units are the currentenergy units (determined by EUNIT command) divided by centimeters. Seealso the following command, WRITE FORCE.<P><DT><B>WRITE [ FILE [+]filename] [SEL] EXTSPRING</B><DD><P>Writes the atom type and the x, y and z components of the externalspring on the atom for every atom or selected atom. Units are thecurrent energy units (determined by EUNIT command) divided bycentimeters squared.<P><DT><B>WRITE [ FILE [+]filename] [SEL] FORCE</B><DD><P>Writes the atom type and the x, y and z components of force on the atomfor every atom or selected atom. Units are the current energy units(determined by EUNIT command) divided by centimeters. This force is theinternal force, and does not include the external force (which is setwith the EXTFORCE command. Use <DT><B>WRITE EXTFORCE to write theexternal force).</B><DD><P><DT><B>WRITE ILIST [+]file</B><DD><P>Writes a list of atom indices corresponding to the currently selectedatoms. This list can be used by the WMOVIE program (see section onCompanion Utilities, page 29), and with a little modification can beread in by the SELECT command.<P><DT><B>WRITE [ FILE [+]filename ] NP</B><DD><P>Writes number of particles<P><DT><B>WRITE [ FILE [+]filename ] [SEL] PARTICLE</B><DD><P>Writes the type and coordinates of each particle or selected particle.The units for a coordinate is angstroms.<P><DT><B>WRITE [ FILE [+]filename ] [SEL] POSVEL </B><DD><P>Writes the type, coordinates and velocity of each particle or selected particle. Coordinate units are angstroms, velocity units are cm/sec.<P><P><DT><B>WRITE [ FILE [+]filename ] STEP</B><DD><P>Writes out the current value of STEP.<P><DT><B>WRITE [SEL] RCV [+]filename</B><DD><P>Writes the current step information in RCV format to the file filename.If the [+] is included, the information is appended to the file end.Otherwise the file is over written. Note: This command is obsolete,use the WRITE COR command instead.<P><DT><B>WRITE [ FILE [+]filename ] RDF nbin rmin rmax [type1 type2] </B><DD><P>Writes a table of the Radial Distribution Function. This table is ahistogram of the number of atom pairs between a given range ofseparations. nbin is the number of bins in the histogram, and rmin andrmax are the minimum and maximum value of separation included in thetable (units are in angstroms). The output from this command is theheader line of the format.<P>If the optional type fields type1 and type2 are supplied, then only theRDF between these two types of atoms is written.<P><BLOCKQUOTE><CODE><PRE>RDF nbin rmin rmax</PRE></CODE></BLOCKQUOTE><P>which echoes back the input parameters followed by nbin lines. Eachline has two number on it, the first is the value of the separation atthe center of the bin, and the second is the number of atom pairs inthat bin.<P><DT><B>WRITE [ FILE [+]filename ] RUN</B><DD><P>Writes out the current value of RUN.<P><DT><B>WRITE STATE file</B><DD><P>Writes all information needed to recreate the current CMD step. Thisfile can be read by the STATE command.<P><DT><B>WRITE [ FILE [+]filename ] TEMP</B><DD><P>Writes out the current value of the temperature, as set by either theITEMP or CMD command.<P><DT><B>WRITE [ FILE [+]filename ] TEMPC</B><DD><P>Writes out the value of tempc from the CLAMP command.<P><DT><B>WRITE [SEL] TYPELIST [+]file</B><DD><P>Writes out a list of atom types of all atoms or selected atoms. Can beused by WMOVIE program (see section on Companion Utilities, page 29).<P><DT><B>WRITE [ FILE [+]filename ] [SEL] VELOCITY</B><DD><P>Writes out the [selected] velocities in units of cm/sec.<P><DT><B>WRITE [ FILE [+]filename ] string</B><DD><P>Any string which is not an option specified above is interpreted to be avariable that has been set by the CALC command. The value of thisvariable is then written out. If a variable by this name does notexist, it will be created and set to zero. You can also put in a validCALC expression such as "2*cos(pi/4)". It will be evaluated andwritten.<P><DT><B>WRITE [SEL] { XMOL | PDB } [+]file</B><DD><P>Writes the current particle coordinates (or the selected coordinates ifSEL is specified) to file in XMOL or PDB format. The + sign indicatesthat the information should be appended to file. XMOL is the programfor viewing atoms under X-Windows and is freely available on theInternet. Writing with the XMOL option creates a text file than can beread in by the XMOL program. PDB stands for Protein Data Bank. This isa data format use by many chemistry based program. XMD writes anon-standard PDB format file that has be tested sucessfully with thecommercial chemistry modeling program Cerius2, but may not be compatiblewith other programs. Both XMOL and PDB use standard elementabbreviations to label the atom. For instance, FE for iron, NA forsodium. Many potential files will configure XMD to use the correct typename. However, by default XMD will not know the correct element namesand so will write the type numbers instaed. You can set the correctelement names using the TYPENAME command.<P></DL><P><P><P><HR><A HREF="xmd-11.html">Next</A><A HREF="xmd-9.html">Previous</A><A HREF="xmd.html#toc10">Contents</A></BODY></HTML>⌨️ 快捷键说明
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