xmd Code

/*
xmd - molecular dynamics for metals and ceramics
By Jonathan Rifkin <jon.rifkin@uconn.edu>
Copyright 1995-2004 Jonathan Rifkin

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
*/


#include <stdio.h>

#define NLINE 21       /*  NUMBER OF USED FOR DISPLAY  */

char *Usage[] =
   {
   "",
   "Usage",
	"",
	"",
   " XMD [-p nproc][-h?]   infile|-",
   "",
	"   Parameters",
	"   ----------",
   "   input_file     Input file containing commands",
	"",
	"   Options",
	"   -------",
	"   -p nproc  Use nproc processors (for multiprocessor systems)",
	"   -h -?     Print out command summary",
	"",
	"   Debug options",
	"   -------------",
	"   -c        Turns on memory leak check and fills output",
	"             with CHECK messages.  Use 'CheckMem' to analyze.",
   "   -d        Turns on any other debug output (version dependent)",
	"",
   NULL
   };

char *Doc[] =
{
   "COMMAND SUMMARY",
   "",
   "# (comment)",
   "* (comment)",
   "BOX       [SCALE] xbox ybox zbox",
   "BSAVE     nskip file",
   "CALC      (expression..)",
	"CLAMP     [SEL] { temp cstep | OFF }",
	"CLAMP     INFO",
   "CMD       nstep",
   "COR       file [ [run] step]]",
   "COMPARE   { ON | OFF }  [INV]  crad  cfile",
	"CONSTRAIN OFF | { LINE | PLANE } [ formula ... ] xd yd zd  xc yc zc",
	"CONSTRAIN CAVITY ELLIPSOID spring xcenter ycenter zcenter xaxis yaxis zaxis",
	"CONSTRAIN CAVITY SPHERE    spring xcenter ycenter radius",
	"DAMP      [ formula ] [ formula ... ]  damp",
   "DISP      [SEL] { CLEAR | MOVE [scale] | READ n | REFCALC | SCALE scale }",
   "DTIME     dtime",
   "DUP       ndup xmove ymove zmove",
   "ECHO      { ON | OFF }",
   "ERASE     file",
	"ERASE     file",
	"ESAVE     nskip file",
   "EUNIT     { EV | ERG | JOULE | K | uname uvalue }",
   "EXTFORCE  { CLEAR | [ formula ] [ formula ... ]  fx fy fz }",
   "EXTSPRING { CLEAR | [ formula ] [ formula ... ]  kx ky kz }",
   "FIX       { ON | OFF }",
   "FILL      ALIGN              x y z",
   "FILL      BOUNDARY BOX       x1 y1 z1  x2 y2 z2",
   "FILL      BOUNDARY SPHERE    radius xcenter ycenter zcenter",
   "FILL      BOUNDARY CYLINDER  r length xc yc zc xorient yorient zorient",
	"FILL      GO",
	"FILL      MARGIN             margin",
   "FILL      ORIENT             ax ay az  bx by bz  cx cy cz",
	"FILL      PARTICLE n",
	"   type x y z",
	" ....",
   "ITEMP     [SEL] temp [X] [Y] [Z]",
   "LABEL     nlabel",
   " .... (up to 8 lines)",
   "MACRO     name value",
   "MACROF    name format value",
   "MASS      mass",
	"MC        nstep temp",
   "MOVE      [ formula ] [ formula ... ]  xmove ymove zmove",
   "NRANGE    nrange",
   "NSEARCH   SORT | CELL",
   "PARTICLE  [ADD] np",
   "          type x y z",
   "",
   "PLOT      BOND    { ON | OFF } [ lo hi ]",
   "PLOT      DEVICE  { CANON | POSTSCRIPT }",
   "PLOT      DISP    { ON | OFF | SCALE scale }",
   "PLOT      LAYER     nlayer  [ l1 [ l2 [ l3 ... ] ] ]",
   "PLOT      ORIENT    x/y | y/x | x/z | z/x | y/z | z/y",
   "PLOT      PAGE      page",
	"PLOT      SIZE      xinch yinch",
   "PLOT      SYMBOL    [FILL] ",
   "            [ RGB red green blue | HSB hue saturation brightness ]",
   "            { NON | CIR | TRI | ITR | DIA | CRO | SQU | AST | NUM } radius",
   "PLOT      WRITE [SEL] [[+]file]",
   "POSITION  [ADD] np",
   "          type x y z",
   "",
	"POSVEL    [ADD] np",
   "POTENTIAL SET  STILL",
	"          (Stillinger-Weber, all atom types are Silicon)",
   "POTENTIAL SET  TERSOFF",
	"          (Tersoff CSi, types (1,2) are (C,Si)",
   "POTENTIAL SET  EAM ntype",
   "PRESSURE  ANDERSEN xmass [ ymass [ zmass ] ]",
	"PRESSURE  CLAMP  bulkmodulus [ cstep ]  (bulkmodulus in MBAR units)",
	"PRESSURE  EXTERNAL  pressureX [ pressureY [ pressureZ ] ] (Units of MBAR)",
   "PRESSURE  { ISOTROPIC | ORTHORHOMBIC }",
   "PRESSURE  OFF",
	"PSTRAIN   strain  dx dy dz   nx ny nz",
   "QUENCH    nstep [qtype]",
   "RCV       [file [ [run] step]]",
   "READ      file",
   "REFSTEP   [CLEAR | COPY | SWAP]",
   "REMOVE",
   "REPEAT    n\n...\nEND",
	"REPEAT    { COR | RCV } filename [ step1 [ step2 | * [ skip ] ]\n...\nEND",
   "ROTATE    xaxis yaxis zaxis  xcenter ycenter zcenter angle",
   "RUN       run",
   "SCALE     { xyzscale | xscale yzscale | xscale yscale zscale }",
	"SCREW     xburgers yburgers zburgers  xorg yorg zorg  [refX refY refZ]",
   "SELECT    [OR | AND | NOT | XOR]",
   "     ALL",
   "   | BOX     x1 y1 z1 x2 y2 z2",
   "   | EATOM   lo hi",
   "   | ELLIPSE xc yc zc xr yr zr",
   "   | ILIST   n",
   "     i1 i2 i3 ..in",
   "",
   "   | INDEX   i1 i2 iskip",
   "   | LAYER   X|Y|Z nlayer layer1 layer2 ..",
   "   | NEAR     n                 [ INDEX index | POINT x y z | SET set ]", 
   "   | NEAR   [ n ] RADIUS r1 r2  [ INDEX index | POINT x y z | SET set ]",
   "   | NONE",
   "   | PLANE   nx ny nz x1 y1 z1 x2 y2 z2",
   "   | SET     set",
   "   | TAG     tag",
   "   | TYPE    ntype",
   "   | VELOCITY [ABS] {X|Y|Z|MAG} lo hi",
   "SELECT    KEEP { ON|OFF }",
   "SEED      seed",
   "SET       {SUB | ADD | CLEAR} set",
	"SIZE      size",
   "SSAVE     nskip file",
   "STRESS    THERMAL { ON|OFF }",
   "STATE     file",
   "STEP      step",
   "SURFACE   ON|OFF X|Y|Z",
   "TAG       tag",
	"TSAVE     nskip file",
   "TYPE      type",
   "TYPELIST  [SEL] n",
   "          t1 t2 t3 ... tn",
   "",
	"TYPENAME  type name [ type name ] ...",
	"VERBOSE   { INFO | FILE } { ON | OFF }",
	"VELOCITY  { LINEAR | ANGULAR } dx dy dz mag",
	"WAVE      phase   dx dy dz   kx ky kz",
   "WRITE     [SEL] [TAG] COR  [+]fname",
	"WRITE     [SEL]       PDB  [+]fname",
   "WRITE     [SEL]       RCV  [+]fname",
	"WRITE     [SEL]       XMOL [+]fname",
   "WRITE     [SEL] {ILIST | TYPELIST} [ [+]fname ]",
   "WRITE     [SEL] [FILE [+]fname]  { STRESS }",
   "WRITE     [SEL] [FILE [+]fname]  [AVG] [MIN] [MAX] ",
	"                        { FORCE | PARTICLE | POSVEL | VELOCITY }",
   "WRITE     [SEL] [FILE [+]fname] [FORMAT format] [AVG] [MIN] [MAX] PARTICLE",
   "WRITE     [SEL] [FILE [+]fname]  { DISP | EXTFORCE | EXTSPRING }",
   "WRITE     [SEL] [FILE [+]fname]    EATOM",
   "WRITE     [SEL] [FILE [+]fname]  { TEMP | EKIN | EPOT | ENERGY }",
   "WRITE     [SEL] [FILE [+]fname]    MASS",
   "WRITE     [SEL] [FILE [+]fname]    VAR [i|t|df|g|m|x|y|z|vx|vy|vz|ep|ek] ...",
   "WRITE     [FILE [+]fname] RDF ntable rmin rmax [type1 type2]",
   "WRITE     [FILE [+]fname] { BOX |  RUN | STEP }",
   "WRITE     STATE fname",
	"WRITE     [SEL] XMOL [+]fname",
   "WRITE     [FILE [+]fname] SEED",
   NULL
}
;

void write_more (char **s, int rflag)
{
   char c;
   int n;
   char  **t = s;
   n = NLINE;
   c='0';
   while ((rflag || *t) && c!='q')
   {
      /*  PRINT CHARACTER - COUNT LINEFEEDS  */
      puts (*t);
      t++;
      n--;
      /*  END OF TEXT  */
      if (rflag && *t==NULL)
      {
         t = s;
         n = 0;  /*  SIGNAL TO WAIT FOR KEYPRESS  */
      }
      if (!n)
      {
         printf ("\n(q/ret):");
         c = getchar();
         printf ("\n\n\n");
         n = NLINE;
      }
   }
}

void write_usage (void)
{
   write_more (Usage, 0);
}

void write_doc  (void)
{
   write_more (Doc,   1);
}