/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* 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.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#include "gmx_ana.h"
-int gmx_vanhove(int argc,char *argv[])
+int gmx_vanhove(int argc, char *argv[])
{
- const char *desc[] = {
- "[TT]g_vanhove[tt] computes the Van Hove correlation function.",
- "The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
- "at time zero can be found at position r[SUB]0[sub]+r at time t.",
- "[TT]g_vanhove[tt] determines G not for a vector r, but for the length of r.",
- "Thus it gives the probability that a particle moves a distance of r",
- "in time t.",
- "Jumps across the periodic boundaries are removed.",
- "Corrections are made for scaling due to isotropic",
- "or anisotropic pressure coupling.",
- "[PAR]",
- "With option [TT]-om[tt] the whole matrix can be written as a function",
- "of t and r or as a function of [SQRT]t[sqrt] and r (option [TT]-sqrt[tt]).",
- "[PAR]",
- "With option [TT]-or[tt] the Van Hove function is plotted for one",
- "or more values of t. Option [TT]-nr[tt] sets the number of times,",
- "option [TT]-fr[tt] the number spacing between the times.",
- "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
- "is determined automatically.",
- "[PAR]",
- "With option [TT]-ot[tt] the integral up to a certain distance",
- "(option [TT]-rt[tt]) is plotted as a function of time.",
- "[PAR]",
- "For all frames that are read the coordinates of the selected particles",
- "are stored in memory. Therefore the program may use a lot of memory.",
- "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
- "This is because the calculation scales as the number of frames times",
- "[TT]-fm[tt] or [TT]-ft[tt].",
- "Note that with the [TT]-dt[tt] option the memory usage and calculation",
- "time can be reduced."
- };
- static int fmmax=0,ftmax=0,nlev=81,nr=1,fshift=0;
- static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
- t_pargs pa[] = {
- { "-sqrt", FALSE, etREAL,{&sbin},
- "Use [SQRT]t[sqrt] on the matrix axis which binspacing # in [SQRT]ps[sqrt]" },
- { "-fm", FALSE, etINT, {&fmmax},
- "Number of frames in the matrix, 0 is plot all" },
- { "-rmax", FALSE, etREAL, {&rmax},
- "Maximum r in the matrix (nm)" },
- { "-rbin", FALSE, etREAL, {&rbin},
- "Binwidth in the matrix and for [TT]-or[tt] (nm)" },
- { "-mmax", FALSE, etREAL, {&mmax},
- "Maximum density in the matrix, 0 is calculate (1/nm)" },
- { "-nlevels" ,FALSE, etINT, {&nlev},
- "Number of levels in the matrix" },
- { "-nr", FALSE, etINT, {&nr},
- "Number of curves for the [TT]-or[tt] output" },
- { "-fr", FALSE, etINT, {&fshift},
- "Frame spacing for the [TT]-or[tt] output" },
- { "-rt", FALSE, etREAL, {&rint},
- "Integration limit for the [TT]-ot[tt] output (nm)" },
- { "-ft", FALSE, etINT, {&ftmax},
- "Number of frames in the [TT]-ot[tt] output, 0 is plot all" }
- };
+ const char *desc[] = {
+ "[TT]g_vanhove[tt] computes the Van Hove correlation function.",
+ "The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
+ "at time zero can be found at position r[SUB]0[sub]+r at time t.",
+ "[TT]g_vanhove[tt] determines G not for a vector r, but for the length of r.",
+ "Thus it gives the probability that a particle moves a distance of r",
+ "in time t.",
+ "Jumps across the periodic boundaries are removed.",
+ "Corrections are made for scaling due to isotropic",
+ "or anisotropic pressure coupling.",
+ "[PAR]",
+ "With option [TT]-om[tt] the whole matrix can be written as a function",
+ "of t and r or as a function of [SQRT]t[sqrt] and r (option [TT]-sqrt[tt]).",
+ "[PAR]",
+ "With option [TT]-or[tt] the Van Hove function is plotted for one",
+ "or more values of t. Option [TT]-nr[tt] sets the number of times,",
+ "option [TT]-fr[tt] the number spacing between the times.",
+ "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
+ "is determined automatically.",
+ "[PAR]",
+ "With option [TT]-ot[tt] the integral up to a certain distance",
+ "(option [TT]-rt[tt]) is plotted as a function of time.",
+ "[PAR]",
+ "For all frames that are read the coordinates of the selected particles",
+ "are stored in memory. Therefore the program may use a lot of memory.",
+ "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
+ "This is because the calculation scales as the number of frames times",
+ "[TT]-fm[tt] or [TT]-ft[tt].",
+ "Note that with the [TT]-dt[tt] option the memory usage and calculation",
+ "time can be reduced."
+ };
+ static int fmmax = 0, ftmax = 0, nlev = 81, nr = 1, fshift = 0;
+ static real sbin = 0, rmax = 2, rbin = 0.01, mmax = 0, rint = 0;
+ t_pargs pa[] = {
+ { "-sqrt", FALSE, etREAL, {&sbin},
+ "Use [SQRT]t[sqrt] on the matrix axis which binspacing # in [SQRT]ps[sqrt]" },
+ { "-fm", FALSE, etINT, {&fmmax},
+ "Number of frames in the matrix, 0 is plot all" },
+ { "-rmax", FALSE, etREAL, {&rmax},
+ "Maximum r in the matrix (nm)" },
+ { "-rbin", FALSE, etREAL, {&rbin},
+ "Binwidth in the matrix and for [TT]-or[tt] (nm)" },
+ { "-mmax", FALSE, etREAL, {&mmax},
+ "Maximum density in the matrix, 0 is calculate (1/nm)" },
+ { "-nlevels", FALSE, etINT, {&nlev},
+ "Number of levels in the matrix" },
+ { "-nr", FALSE, etINT, {&nr},
+ "Number of curves for the [TT]-or[tt] output" },
+ { "-fr", FALSE, etINT, {&fshift},
+ "Frame spacing for the [TT]-or[tt] output" },
+ { "-rt", FALSE, etREAL, {&rint},
+ "Integration limit for the [TT]-ot[tt] output (nm)" },
+ { "-ft", FALSE, etINT, {&ftmax},
+ "Number of frames in the [TT]-ot[tt] output, 0 is plot all" }
+ };
#define NPA asize(pa)
- t_filenm fnm[] = {
- { efTRX, NULL, NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXPM, "-om", "vanhove", ffOPTWR },
- { efXVG, "-or", "vanhove_r", ffOPTWR },
- { efXVG, "-ot", "vanhove_t", ffOPTWR }
- };
+ t_filenm fnm[] = {
+ { efTRX, NULL, NULL, ffREAD },
+ { efTPS, NULL, NULL, ffREAD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efXPM, "-om", "vanhove", ffOPTWR },
+ { efXVG, "-or", "vanhove_r", ffOPTWR },
+ { efXVG, "-ot", "vanhove_t", ffOPTWR }
+ };
#define NFILE asize(fnm)
- output_env_t oenv;
- const char *matfile,*otfile,*orfile;
- char title[256];
- t_topology top;
- int ePBC;
- matrix boxtop,box,*sbox,avbox,corr;
- rvec *xtop,*x,**sx;
- int isize,nalloc,nallocn,natom;
- t_trxstatus *status;
- atom_id *index;
- char *grpname;
- int nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
- real *time,t,invbin=0,rmax2=0,rint2=0,d2;
- real invsbin=0,matmax,normfac,dt,*tickx,*ticky;
- char buf[STRLEN],**legend;
- real **mat=NULL;
- int *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
- FILE *fp;
- t_rgb rlo={1,1,1}, rhi={0,0,0};
+ output_env_t oenv;
+ const char *matfile, *otfile, *orfile;
+ char title[256];
+ t_topology top;
+ int ePBC;
+ matrix boxtop, box, *sbox, avbox, corr;
+ rvec *xtop, *x, **sx;
+ int isize, nalloc, nallocn, natom;
+ t_trxstatus *status;
+ atom_id *index;
+ char *grpname;
+ int nfr, f, ff, i, m, mat_nx = 0, nbin = 0, bin, mbin, fbin;
+ real *time, t, invbin = 0, rmax2 = 0, rint2 = 0, d2;
+ real invsbin = 0, matmax, normfac, dt, *tickx, *ticky;
+ char buf[STRLEN], **legend;
+ real **mat = NULL;
+ int *pt = NULL, **pr = NULL, *mcount = NULL, *tcount = NULL, *rcount = NULL;
+ FILE *fp;
+ t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
-
- matfile = opt2fn_null("-om",NFILE,fnm);
- if (opt2parg_bSet("-fr",NPA,pa))
- orfile = opt2fn("-or",NFILE,fnm);
- else
- orfile = opt2fn_null("-or",NFILE,fnm);
- if (opt2parg_bSet("-rt",NPA,pa))
- otfile = opt2fn("-ot",NFILE,fnm);
- else
- otfile = opt2fn_null("-ot",NFILE,fnm);
-
- if (!matfile && !otfile && !orfile) {
- fprintf(stderr,
- "For output set one (or more) of the output file options\n");
- exit(0);
- }
-
- read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
- FALSE);
- get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
-
- nalloc = 0;
- time = NULL;
- sbox = NULL;
- sx = NULL;
- clear_mat(avbox);
+ parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
- natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
- nfr = 0;
- do {
- if (nfr >= nalloc) {
- nalloc += 100;
- srenew(time,nalloc);
- srenew(sbox,nalloc);
- srenew(sx,nalloc);
+ matfile = opt2fn_null("-om", NFILE, fnm);
+ if (opt2parg_bSet("-fr", NPA, pa))
+ {
+ orfile = opt2fn("-or", NFILE, fnm);
+ }
+ else
+ {
+ orfile = opt2fn_null("-or", NFILE, fnm);
+ }
+ if (opt2parg_bSet("-rt", NPA, pa))
+ {
+ otfile = opt2fn("-ot", NFILE, fnm);
+ }
+ else
+ {
+ otfile = opt2fn_null("-ot", NFILE, fnm);
}
-
- time[nfr] = t;
- copy_mat(box,sbox[nfr]);
- /* This assumes that the off-diagonal box elements
- * are not affected by jumps across the periodic boundaries.
- */
- m_add(avbox,box,avbox);
- snew(sx[nfr],isize);
- for(i=0; i<isize; i++)
- copy_rvec(x[index[i]],sx[nfr][i]);
-
- nfr++;
- } while (read_next_x(oenv,status,&t,natom,x,box));
- /* clean up */
- sfree(x);
- close_trj(status);
-
- fprintf(stderr,"Read %d frames\n",nfr);
+ if (!matfile && !otfile && !orfile)
+ {
+ fprintf(stderr,
+ "For output set one (or more) of the output file options\n");
+ exit(0);
+ }
+
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, boxtop,
+ FALSE);
+ get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
- dt = (time[nfr-1] - time[0])/(nfr - 1);
- /* Some ugly rounding to get nice nice times in the output */
- dt = (int)(10000.0*dt + 0.5)/10000.0;
+ nalloc = 0;
+ time = NULL;
+ sbox = NULL;
+ sx = NULL;
+ clear_mat(avbox);
- invbin = 1.0/rbin;
+ natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
+ nfr = 0;
+ do
+ {
+ if (nfr >= nalloc)
+ {
+ nalloc += 100;
+ srenew(time, nalloc);
+ srenew(sbox, nalloc);
+ srenew(sx, nalloc);
+ }
- if (matfile) {
- if (fmmax <= 0 || fmmax >= nfr)
- fmmax = nfr - 1;
- snew(mcount,fmmax);
- nbin = (int)(rmax*invbin + 0.5);
- if (sbin == 0) {
- mat_nx = fmmax + 1;
- } else {
- invsbin = 1.0/sbin;
- mat_nx = sqrt(fmmax*dt)*invsbin + 1;
+ time[nfr] = t;
+ copy_mat(box, sbox[nfr]);
+ /* This assumes that the off-diagonal box elements
+ * are not affected by jumps across the periodic boundaries.
+ */
+ m_add(avbox, box, avbox);
+ snew(sx[nfr], isize);
+ for (i = 0; i < isize; i++)
+ {
+ copy_rvec(x[index[i]], sx[nfr][i]);
+ }
+
+ nfr++;
}
- snew(mat,mat_nx);
- for(f=0; f<mat_nx; f++)
- snew(mat[f],nbin);
- rmax2 = sqr(nbin*rbin);
- /* Initialize time zero */
- mat[0][0] = nfr*isize;
- mcount[0] += nfr;
- } else {
- fmmax = 0;
- }
-
- if (orfile) {
- snew(pr,nr);
- nalloc = 0;
- snew(rcount,nr);
- }
-
- if (otfile) {
- if (ftmax <= 0)
- ftmax = nfr - 1;
- snew(tcount,ftmax);
- snew(pt,nfr);
- rint2 = rint*rint;
- /* Initialize time zero */
- pt[0] = nfr*isize;
- tcount[0] += nfr;
- } else {
- ftmax = 0;
- }
+ while (read_next_x(oenv, status, &t, natom, x, box));
+
+ /* clean up */
+ sfree(x);
+ close_trj(status);
+
+ fprintf(stderr, "Read %d frames\n", nfr);
+
+ dt = (time[nfr-1] - time[0])/(nfr - 1);
+ /* Some ugly rounding to get nice nice times in the output */
+ dt = (int)(10000.0*dt + 0.5)/10000.0;
- msmul(avbox,1.0/nfr,avbox);
- for(f=0; f<nfr; f++) {
- if (f % 100 == 0)
- fprintf(stderr,"\rProcessing frame %d",f);
- /* Scale all the configuration to the average box */
- m_inv_ur0(sbox[f],corr);
- mmul_ur0(avbox,corr,corr);
- for(i=0; i<isize; i++) {
- mvmul_ur0(corr,sx[f][i],sx[f][i]);
- if (f > 0) {
- /* Correct for periodic jumps */
- for(m=DIM-1; m>=0; m--) {
- while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
- rvec_dec(sx[f][i],avbox[m]);
- while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
- rvec_inc(sx[f][i],avbox[m]);
- }
- }
+ invbin = 1.0/rbin;
+
+ if (matfile)
+ {
+ if (fmmax <= 0 || fmmax >= nfr)
+ {
+ fmmax = nfr - 1;
+ }
+ snew(mcount, fmmax);
+ nbin = (int)(rmax*invbin + 0.5);
+ if (sbin == 0)
+ {
+ mat_nx = fmmax + 1;
+ }
+ else
+ {
+ invsbin = 1.0/sbin;
+ mat_nx = sqrt(fmmax*dt)*invsbin + 1;
+ }
+ snew(mat, mat_nx);
+ for (f = 0; f < mat_nx; f++)
+ {
+ snew(mat[f], nbin);
+ }
+ rmax2 = sqr(nbin*rbin);
+ /* Initialize time zero */
+ mat[0][0] = nfr*isize;
+ mcount[0] += nfr;
+ }
+ else
+ {
+ fmmax = 0;
}
- for(ff=0; ff<f; ff++) {
- fbin = f - ff;
- if (fbin <= fmmax || fbin <= ftmax) {
- if (sbin == 0)
- mbin = fbin;
- else
- mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
- for(i=0; i<isize; i++) {
- d2 = distance2(sx[f][i],sx[ff][i]);
- if (mbin < mat_nx && d2 < rmax2) {
- bin = (int)(sqrt(d2)*invbin + 0.5);
- if (bin < nbin) {
- mat[mbin][bin] += 1;
- }
- }
- if (fbin <= ftmax && d2 <= rint2)
- pt[fbin]++;
- }
- if (matfile)
- mcount[mbin]++;
- if (otfile)
- tcount[fbin]++;
- }
+
+ if (orfile)
+ {
+ snew(pr, nr);
+ nalloc = 0;
+ snew(rcount, nr);
+ }
+
+ if (otfile)
+ {
+ if (ftmax <= 0)
+ {
+ ftmax = nfr - 1;
+ }
+ snew(tcount, ftmax);
+ snew(pt, nfr);
+ rint2 = rint*rint;
+ /* Initialize time zero */
+ pt[0] = nfr*isize;
+ tcount[0] += nfr;
}
- if (orfile) {
- for(fbin=0; fbin<nr; fbin++) {
- ff = f - (fbin + 1)*fshift;
- if (ff >= 0) {
- for(i=0; i<isize; i++) {
- d2 = distance2(sx[f][i],sx[ff][i]);
- bin = (int)(sqrt(d2)*invbin);
- if (bin >= nalloc) {
- nallocn = 10*(bin/10) + 11;
- for(m=0; m<nr; m++) {
- srenew(pr[m],nallocn);
- for(i=nalloc; i<nallocn; i++)
- pr[m][i] = 0;
- }
- nalloc = nallocn;
- }
- pr[fbin][bin]++;
- }
- rcount[fbin]++;
- }
- }
+ else
+ {
+ ftmax = 0;
}
- }
- fprintf(stderr,"\n");
-
- if (matfile) {
- matmax = 0;
- for(f=0; f<mat_nx; f++) {
- normfac = 1.0/(mcount[f]*isize*rbin);
- for(i=0; i<nbin; i++) {
- mat[f][i] *= normfac;
- if (mat[f][i] > matmax && (f!=0 || i!=0))
- matmax = mat[f][i];
- }
+
+ msmul(avbox, 1.0/nfr, avbox);
+ for (f = 0; f < nfr; f++)
+ {
+ if (f % 100 == 0)
+ {
+ fprintf(stderr, "\rProcessing frame %d", f);
+ }
+ /* Scale all the configuration to the average box */
+ m_inv_ur0(sbox[f], corr);
+ mmul_ur0(avbox, corr, corr);
+ for (i = 0; i < isize; i++)
+ {
+ mvmul_ur0(corr, sx[f][i], sx[f][i]);
+ if (f > 0)
+ {
+ /* Correct for periodic jumps */
+ for (m = DIM-1; m >= 0; m--)
+ {
+ while (sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
+ {
+ rvec_dec(sx[f][i], avbox[m]);
+ }
+ while (sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
+ {
+ rvec_inc(sx[f][i], avbox[m]);
+ }
+ }
+ }
+ }
+ for (ff = 0; ff < f; ff++)
+ {
+ fbin = f - ff;
+ if (fbin <= fmmax || fbin <= ftmax)
+ {
+ if (sbin == 0)
+ {
+ mbin = fbin;
+ }
+ else
+ {
+ mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
+ }
+ for (i = 0; i < isize; i++)
+ {
+ d2 = distance2(sx[f][i], sx[ff][i]);
+ if (mbin < mat_nx && d2 < rmax2)
+ {
+ bin = (int)(sqrt(d2)*invbin + 0.5);
+ if (bin < nbin)
+ {
+ mat[mbin][bin] += 1;
+ }
+ }
+ if (fbin <= ftmax && d2 <= rint2)
+ {
+ pt[fbin]++;
+ }
+ }
+ if (matfile)
+ {
+ mcount[mbin]++;
+ }
+ if (otfile)
+ {
+ tcount[fbin]++;
+ }
+ }
+ }
+ if (orfile)
+ {
+ for (fbin = 0; fbin < nr; fbin++)
+ {
+ ff = f - (fbin + 1)*fshift;
+ if (ff >= 0)
+ {
+ for (i = 0; i < isize; i++)
+ {
+ d2 = distance2(sx[f][i], sx[ff][i]);
+ bin = (int)(sqrt(d2)*invbin);
+ if (bin >= nalloc)
+ {
+ nallocn = 10*(bin/10) + 11;
+ for (m = 0; m < nr; m++)
+ {
+ srenew(pr[m], nallocn);
+ for (i = nalloc; i < nallocn; i++)
+ {
+ pr[m][i] = 0;
+ }
+ }
+ nalloc = nallocn;
+ }
+ pr[fbin][bin]++;
+ }
+ rcount[fbin]++;
+ }
+ }
+ }
}
- fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
- mat[0][0],matmax);
- if (mmax > 0)
- matmax = mmax;
- snew(tickx,mat_nx);
- for(f=0; f<mat_nx; f++) {
- if (sbin == 0)
- tickx[f] = f*dt;
- else
- tickx[f] = f*sbin;
+ fprintf(stderr, "\n");
+
+ if (matfile)
+ {
+ matmax = 0;
+ for (f = 0; f < mat_nx; f++)
+ {
+ normfac = 1.0/(mcount[f]*isize*rbin);
+ for (i = 0; i < nbin; i++)
+ {
+ mat[f][i] *= normfac;
+ if (mat[f][i] > matmax && (f != 0 || i != 0))
+ {
+ matmax = mat[f][i];
+ }
+ }
+ }
+ fprintf(stdout, "Value at (0,0): %.3f, maximum of the rest %.3f\n",
+ mat[0][0], matmax);
+ if (mmax > 0)
+ {
+ matmax = mmax;
+ }
+ snew(tickx, mat_nx);
+ for (f = 0; f < mat_nx; f++)
+ {
+ if (sbin == 0)
+ {
+ tickx[f] = f*dt;
+ }
+ else
+ {
+ tickx[f] = f*sbin;
+ }
+ }
+ snew(ticky, nbin+1);
+ for (i = 0; i <= nbin; i++)
+ {
+ ticky[i] = i*rbin;
+ }
+ fp = ffopen(matfile, "w");
+ write_xpm(fp, MAT_SPATIAL_Y, "Van Hove function", "G (1/nm)",
+ sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)",
+ mat_nx, nbin, tickx, ticky, mat, 0, matmax, rlo, rhi, &nlev);
+ ffclose(fp);
}
- snew(ticky,nbin+1);
- for(i=0; i<=nbin; i++)
- ticky[i] = i*rbin;
- fp = ffopen(matfile,"w");
- write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
- sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
- mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);
- ffclose(fp);
- }
-
- if (orfile) {
- fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
- fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
- snew(legend,nr);
- for(fbin=0; fbin<nr; fbin++) {
- sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
- legend[fbin] = strdup(buf);
+
+ if (orfile)
+ {
+ fp = xvgropen(orfile, "Van Hove function", "r (nm)", "G (nm\\S-1\\N)", oenv);
+ fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ snew(legend, nr);
+ for (fbin = 0; fbin < nr; fbin++)
+ {
+ sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
+ legend[fbin] = strdup(buf);
+ }
+ xvgr_legend(fp, nr, (const char**)legend, oenv);
+ for (i = 0; i < nalloc; i++)
+ {
+ fprintf(fp, "%g", i*rbin);
+ for (fbin = 0; fbin < nr; fbin++)
+ {
+ fprintf(fp, " %g",
+ (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i == 0 ? 0.5 : 1)));
+ }
+ fprintf(fp, "\n");
+ }
+ ffclose(fp);
}
- xvgr_legend(fp,nr,(const char**)legend,oenv);
- for(i=0; i<nalloc; i++) {
- fprintf(fp,"%g",i*rbin);
- for(fbin=0; fbin<nr; fbin++)
- fprintf(fp," %g",
- (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
- fprintf(fp,"\n");
+
+ if (otfile)
+ {
+ sprintf(buf, "Probability of moving less than %g nm", rint);
+ fp = xvgropen(otfile, buf, "t (ps)", "", oenv);
+ fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ for (f = 0; f <= ftmax; f++)
+ {
+ fprintf(fp, "%g %g\n", f*dt, (real)pt[f]/(tcount[f]*isize));
+ }
+ ffclose(fp);
}
- ffclose(fp);
- }
-
- if (otfile) {
- sprintf(buf,"Probability of moving less than %g nm",rint);
- fp = xvgropen(otfile,buf,"t (ps)","",oenv);
- fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
- for(f=0; f<=ftmax; f++)
- fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
- ffclose(fp);
- }
- do_view(oenv, matfile,NULL);
- do_view(oenv, orfile,NULL);
- do_view(oenv, otfile,NULL);
+ do_view(oenv, matfile, NULL);
+ do_view(oenv, orfile, NULL);
+ do_view(oenv, otfile, NULL);
+
+ thanx(stderr);
- thanx(stderr);
-
- return 0;
+ return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff