3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
9 * VERSION 3.3.99_development_20071104
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * Groningen Machine for Chemical Simulation
40 #include "gromacs/utility/smalloc.h"
42 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/fileio/matio.h"
48 #include "gromacs/fileio/futil.h"
52 #include "gromacs/fileio/tpxio.h"
54 int main(int argc,char *argv[])
56 static char *desc[] = {
57 "[TT]g_anavel[tt] computes temperature profiles in a sample. The sample",
58 "can be analysed radial, i.e. the temperature as a function of",
59 "distance from the center, cylindrical, i.e. as a function of distance",
60 "from the vector (0,0,1) through the center of the box, or otherwise",
61 "(will be specified later)"
64 { efTRN, "-f", NULL, ffREAD },
65 { efTPX, "-s", NULL, ffREAD },
66 { efXPM, "-o", "xcm", ffWRITE }
68 #define NFILE asize(fnm)
70 static int mode = 0, nlevels = 10;
71 static real tmax = 300, xmax = -1;
73 { "-mode", FALSE, etINT, {&mode}, "mode" },
74 { "-nlevels", FALSE, etINT, {&nlevels}, "number of levels" },
75 { "-tmax", FALSE, etREAL, {&tmax}, "max temperature in output" },
76 { "-xmax", FALSE, etREAL, {&xmax}, "max distance from center" }
82 int i,j,idum,step,nframe=0,index;
83 real temp,rdum,hboxx,hboxy,scale,xnorm=0;
85 real *t_x=NULL,*t_y,hi=0;
90 gmx_bool bHaveV,bReadV;
91 t_rgb rgblo = { 0, 0, 1 },rgbhi = { 1, 0, 0 };
92 int flags = TRX_READ_X | TRX_READ_V;
96 CopyRight(stderr,argv[0]);
97 parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE ,NFILE,fnm,
98 asize(pa),pa,asize(desc),desc,0,NULL);
100 top = read_top(ftp2fn(efTPX,NFILE,fnm));
102 read_first_frame(&status,ftp2fn(efTRX,NFILE,fnm),&fr,flags);
110 nmax = (0.5*sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])))*scale;
114 for(i=0; (i<=nmax); i++) {
119 srenew(profile,++nframe);
120 snew(profile[nframe-1],nmax+1);
122 t_x[nframe-1] = fr.time*1000;
123 hboxx = box[XX][XX]/2;
124 hboxy = box[YY][YY]/2;
125 for(i=0; (i<fr.natoms); i++) {
126 /* determine position dependent on mode */
129 xnorm = sqrt(sqr(fr.x[i][XX]-hboxx) + sqr(fr.x[i][YY]-hboxy));
132 gmx_fatal(FARGS,"Unknown mode %d",mode);
136 temp = top->atoms.atom[i].m*iprod(fr.v[i],fr.v[i])/(2*BOLTZ);
140 profile[nframe-1][index] += temp;
143 for(i=0; (i<=nmax); i++) {
145 profile[nframe-1][i] /= npts[i];
148 } while (read_next_frame(status,&fr));
151 fp = ftp2FILE(efXPM,NFILE,fnm,"w");
152 write_xpm(fp,0,"Temp. profile","T (a.u.)",
154 nframe,nmax+1,t_x,t_y,profile,0,tmax,
155 rgblo,rgbhi,&nlevels);