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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: Command Summary</TITLE> <LINK HREF="xmd-8.html" REL=next> <LINK HREF="xmd-6.html" REL=previous> <LINK HREF="xmd.html#toc7" REL=contents></HEAD><BODY><A HREF="xmd-8.html">Next</A><A HREF="xmd-6.html">Previous</A><A HREF="xmd.html#toc7">Contents</A><HR><H2><A NAME="s7">7. Command Summary</A></H2><P>In this section is listed the commands to XMD. Some of these commands are shared by previous programs,namely CDCMD (an older version of XMD) and PLOTL (the PC lattice manipulation program used for creatingand printing lattices). The command descriptions below adhere to the following syntax:<P><UL><LI> The command lines are written in bold.</LI><LI> Items in UPPERCASE must be entered exactly as shown (althoughthe case entered is irrelevant). </LI><LI> Items in lower case are to besubstituted with the appropriate value.</LI><LI> Items enclosed in square brackets [ ] are optional.</LI><LI> Items separated by vertical bars | are choices.</LI><LI> Choices enclosed by curly brackets { } are required, one mustbe entered.</LI></UL><P><P><PRE># (comment)* (comment)BOX [SCALE] xbox ybox zboxBSAVE nskip fileCALC {expression..}CLAMP [SEL] { temp cstep | OFF }CMD nstepCONSTRAIN OFFCONSTRAIN { LINE | PLANE } xdir ydir zdir xpnt ypnt zpntCONSTRAIN CAVITY ELLIPSOID xc yc zc xa ya za springCONSTRAIN CAVITY SPHERE xc yc zc radius springCOR file [ [ run ] step ]DAMP { OFF | ON [ [ formula [ formula .. ] ] damp] }DISP [SEL] { CLEAR | MOVE [scale] | READ n | REFCALC | SCALE scale }DTIME dtimeDUP ndup xdisp ydisp zdispECHO { ON | OFF }ERASE fileESAVE nskip fileEUNITEXTFORCE { CLEAR | [ formula [ formula .. ] ] fx fy fz }EXTSPRING { CLEAR | [ formula [ formula .. ] ] kx ky kz }FIX {ON | OFF }FIX { ON | OFF }FILL ALIGN x y zFILL BOUNDARY BOX x1 y1 z1 x2 y2 z2FILL BOUNDARY SPHERE radius xcenter ycenter zcenterFILL BOUNDARY CYLINDER r length xc yc zc xorient yorient zorientFILL CELL ax ay az bx by bz cx cy czFILL GOFILL MARGIN marginFILL ORIENT ax ay az bx by bz cx cy czFILL PARTICLE n type x y z ....ITEMP [SEL] temp [ X | Y | Z ] [ X | Y | Z ] ...LABEL nlabel ... (up to 8 lines)MACRO name valueMACROF name format valueMASS massMC nstep dtempMOVE [ formula [ formula .. ] ] xdisp ydisp zdispNRANGE ratioPARTICLE [ADD] np .. type x y zPLOT BOND { OFF | ON lo hi }PLOT DEVICE { CANON | POSTSCRIPT }PLOT DISP { ON | OFF | SCALE scale }PLOT LAYER nlayer [ l1 [ l2 [ l3 .. ] ] ]PLOT ORIENT { y/z z/y x/z z/x x/y y/x }PLOT PAGE npagePLOT SIZE xinch yinchPLOT SYMBOL [FILL] [ RGB red green blue | HSB hue saturation brightness ] { NON | CIR | CRO | TRI | ITR | DIA | AST | SQU | NUM } radiusPLOT WRITE [SEL] [+]filePOSITION [ADD] np .. type x y zPOSVEL [ADD] np .. type x y zPOTENTIAL SET { EAM ntype | PAIR ntype | STILL | TERSOFF }PRESSURE ANDERSEN xmass [ymass [zmass]] PRESSURE CLAMP bulkmodulus [cstep] (bulk in units of MBAR)PRESSURE EXTERNAL pressureX [ pressureY [ pressureZ ] ] (Units of MBAR)PRESSURE { ISOTROPIC | ORTHORHOMBIC }PRESSURE OFFPSTRAIN e dx dy dz nx ny nzQUENCH nstep [nquench]RCV file [ [run] step ]READ fileREFSTEP [CLEAR | COPY | SWAP]REMOVEREPEAT nrepeat ... ENDREPEAT { COR | RCV } filename [ step1 [ step2 ] ] ... ENDROTATE xaxis yaxis zaxis xcenter ycenter zcenter angleRUN runSCALE xscale [yscale [zscale]]SCREW xburgers yburgers zburgers xorg yorg zorg [ xref yref zerf ]SEED seedSELECT [AND | OR | NOT | XOR ] { ALL | BOX x1 y1 z1 x2 y2 z2 | EATOM lo hi | ELLIPSE xc yc zc xr yr zr | ILIST nlist i1 i2 i3 ..... | INDEX i1 [i2 [iskip]] | NEAR n x y z | NONE | PLANE xn yn zn x1 y1 z1 x2 y2 z2 | SET set | TAG tag | TYPE type | VELOCITY [ ABS ] { X | Y | Z | MAG } lo hiSELECT KEEP { ON | OFF }SET { ADD | SUB | CLEAR } setSIZE sizeSSAVE nskip fileSTATESTEP stepSTRESS THERMAL { ON | OFF }SURFACE { ON | OFF } { X | Y | Z } [ X | Y | Z | ON | OFF ] ...TAG tagTYPE typeTYPELIST [ SEL ] ntypeTYPENAME t1 name1 [ t2 name2 ] [ t3 name3 ] ... [tn namen]VELOCITY { LINEAR | ANGULAR } dx dy dz magnitudeVERBOSE { ON | OFF }WAVE phase dx dy dz kx ky kzWRITE [SEL] COR [+]fnameWRITE [SEL] PDB [+]fnameWRITE [SEL] RCV [+]fnameWRITE [SEL] XMOL [+]fnameWRITE [SEL] {ILIST | TYPELIST} [ [+]fname ]WRITE [SEL] [FILE [+]fname] { STRESS }WRITE [SEL] [FILE [+]fname] [AVG] [MIN] [MAX] { FORCE | PARTICLE | POSTVEL | VELOCITY }WRITE [SEL] [FILE [+]fname] { DISP | EXTFORCE | EXTSPRING }WRITE [SEL] [FILE [+]fname] EATOMWRITE [SEL] [FILE [+]fname] { TEMP | EKIN | EPOT | ENERGY }WRITE [FILE [+]fname] RDF ntable rmin rmax [type1 type2]WRITE [FILE [+]fname] { BOX | RUN | STEP }WRITE STATE fname</PRE><P><P><P><P><HR><A HREF="xmd-8.html">Next</A><A HREF="xmd-6.html">Previous</A><A HREF="xmd.html#toc7">Contents</A></BODY></HTML>⌨️ 快捷键说明
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