本文整理汇总了C++中do_view函数的典型用法代码示例。如果您正苦于以下问题：C++ do_view函数的具体用法？C++ do_view怎么用？C++ do_view使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了do_view函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的C++代码示例。
示例1: dump_slab_dipoles
static void dump_slab_dipoles(const char *fn,int idim,int nslice,
rvec slab_dipole[], matrix box,int nframes,
const output_env_t oenv)
{
FILE *fp;
char buf[STRLEN];
int i;
real mutot;
const char *leg_dim[4] = {
"\\f{12}m\\f{4}\\sX\\N",
"\\f{12}m\\f{4}\\sY\\N",
"\\f{12}m\\f{4}\\sZ\\N",
"\\f{12}m\\f{4}\\stot\\N"
};
sprintf(buf,"Box-%c (nm)",'X'+idim);
fp = xvgropen(fn,"Average dipole moment per slab",buf,"\\f{12}m\\f{4} (D)",
oenv);
xvgr_legend(fp,DIM,leg_dim,oenv);
for(i=0; (i<nslice); i++) {
mutot = norm(slab_dipole[i])/nframes;
fprintf(fp,"%10.3f %10.3f %10.3f %10.3f %10.3f\n",
((i+0.5)*box[idim][idim])/nslice,
slab_dipole[i][XX]/nframes,
slab_dipole[i][YY]/nframes,
slab_dipole[i][ZZ]/nframes,
mutot);
}
ffclose(fp);
do_view(oenv,fn,"-autoscale xy -nxy");
}
开发者ID:BradleyDickson，项目名称:ABPenabledGROMACS，代码行数:31，代码来源:gmx_dipoles.c
示例2: view_all
void view_all(const output_env_t oenv,int nf, t_filenm fnm[])
{
int i;
for(i=0; i<nf; i++)
if ( can_view(fnm[i].ftp) && is_output(&(fnm[i])) &&
( ! is_optional(&(fnm[i])) || is_set(&(fnm[i])) ) )
do_view(oenv,fnm[i].fns[0], NULL);
}
开发者ID:TTarenzi，项目名称:MMCG-HAdResS，代码行数:9，代码来源:viewit.c
示例3: view_all
void view_all(int nf, t_filenm fnm[])
{
int i;
for(i=0; i<nf; i++)
if ( can_view(fnm[i].ftp) && is_output(&(fnm[i])) &&
( ! is_optional(&(fnm[i])) || is_set(&(fnm[i])) ) )
do_view(fnm[i].fn, NULL);
}
开发者ID:Chadi-akel，项目名称:cere，代码行数:9，代码来源:viewit.c
示例4: view_all
void view_all(const gmx_output_env_t *oenv, int nf, t_filenm fnm[])
{
int i;
for (i = 0; i < nf; i++)
{
if (can_view(fnm[i].ftp) && is_output(&(fnm[i])) &&
( !is_optional(&(fnm[i])) || is_set(&(fnm[i])) ) )
{
do_view(oenv, fnm[i].filenames[0].c_str(), nullptr);
}
}
}
开发者ID:friforever，项目名称:gromacs，代码行数:13，代码来源:viewit.cpp
示例5: gmx_rama
int gmx_rama(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_rama[tt] selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file",
"and computes these as a function of time.",
"Using simple Unix tools such as [IT]grep[it] you can select out",
"specific residues."
};
FILE *out;
t_xrama *xr;
int j;
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, NULL, "rama",ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL,&oenv);
snew(xr,1);
init_rama(oenv,ftp2fn(efTRX,NFILE,fnm),ftp2fn(efTPX,NFILE,fnm),xr,3);
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),"Ramachandran Plot","Phi","Psi",oenv);
xvgr_line_props(out,0,elNone,ecFrank,oenv);
xvgr_view(out,0.2,0.2,0.8,0.8,oenv);
xvgr_world(out,-180,-180,180,180,oenv);
fprintf(out,"@ xaxis tick on\[email protected] xaxis tick major 60\[email protected] xaxis tick minor 30\n");
fprintf(out,"@ yaxis tick on\[email protected] yaxis tick major 60\[email protected] yaxis tick minor 30\n");
fprintf(out,"@ s0 symbol 2\[email protected] s0 symbol size 0.4\[email protected] s0 symbol fill 1\n");
j=0;
do {
plot_rama(out,xr);
j++;
} while (new_data(xr));
fprintf(stderr,"\n");
ffclose(out);
do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);
thanx(stderr);
return 0;
}
开发者ID:martinhoefling，项目名称:gromacs，代码行数:49，代码来源:gmx_rama.c
示例6: gmx_rms
//.........这里部分代码省略.........
whatxvglabel[ewhat], oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n",
(nrms == 1) ? "" : "of ", gn_rms[0], fitgraphlabel[efit],
bFit ? " to " : "", bFit ? gn_fit : "");
}
if (nrms != 1)
{
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 &&
abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rls[j][i]);
if (bAv)
{
rlstot += rls[j][i];
}
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
if (bMirror)
{
/* Write the mirror RMSD's to file */
sprintf(buf, "%s with Mirror", whatxvgname[ewhat]);
sprintf(buf2, "Mirror %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
buf2, oenv);
if (nrms == 1)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n",
gn_rms[0], gn_fit);
}
}
else
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"after lsq fit to mirror %s\"\n", gn_fit);
}
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 && abs(time[i]) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rlsm[j][i]);
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
}
if (bAv)
{
sprintf(buf, "Average %s", whatxvgname[ewhat]);
sprintf(buf2, "Average %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-a", NFILE, fnm), buf, "Residue", buf2, oenv);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, "%10d %10g\n", j, rlstot/teller);
}
gmx_ffclose(fp);
}
if (bNorm)
{
fp = xvgropen("aver.xvg", gn_rms[0], "Residue", whatxvglabel[ewhat], oenv);
for (j = 0; (j < irms[0]); j++)
{
fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
}
gmx_ffclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-mir", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-m", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-bm", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-dist", NFILE, fnm), NULL);
return 0;
}
开发者ID:rbharath，项目名称:gromacs，代码行数:101，代码来源:gmx_rms.c
示例7: gmx_g_angle
//.........这里部分代码省略.........
}
if (bChandler)
{
mode = eacNormal;
}
else
{
mode = eacCos;
}
do_autocorr(opt2fn("-oc", NFILE, fnm), oenv,
"Dihedral Autocorrelation Function",
nframes, nangles, dih, dt, mode, bAverCorr);
}
}
/* Determine the non-zero part of the distribution */
for (first = 0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
{
;
}
for (last = maxangstat-1; (last > 0) && (angstat[last-1] == 0); last--)
{
;
}
aver = aver2 = 0;
for (i = 0; (i < nframes); i++)
{
aver += RAD2DEG*aver_angle[i];
aver2 += sqr(RAD2DEG*aver_angle[i]);
}
aver /= (real) nframes;
aver2 /= (real) nframes;
aversig = sqrt(aver2-sqr(aver));
printf("Found points in the range from %d to %d (max %d)\n",
first, last, maxangstat);
printf(" < angle > = %g\n", aver);
printf("< angle^2 > = %g\n", aver2);
printf("Std. Dev. = %g\n", aversig);
if (mult == 3)
{
sprintf(title, "Angle Distribution: %s", grpname);
}
else
{
sprintf(title, "Dihedral Distribution: %s", grpname);
calc_distribution_props(maxangstat, angstat, -180.0, 0, NULL, &S2);
fprintf(stderr, "Order parameter S^2 = %g\n", S2);
}
bPeriodic = (mult == 4) && (first == 0) && (last == maxangstat-1);
out = xvgropen(opt2fn("-od", NFILE, fnm), title, "Degrees", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"average angle: %g\\So\\N\"\n", aver);
}
norm_fac = 1.0/(nangles*nframes*binwidth);
if (bPeriodic)
{
maxstat = 0;
for (i = first; (i <= last); i++)
{
maxstat = max(maxstat, angstat[i]*norm_fac);
}
fprintf(out, "@with g0\n");
fprintf(out, "@ world xmin -180\n");
fprintf(out, "@ world xmax 180\n");
fprintf(out, "@ world ymin 0\n");
fprintf(out, "@ world ymax %g\n", maxstat*1.05);
fprintf(out, "@ xaxis tick major 60\n");
fprintf(out, "@ xaxis tick minor 30\n");
fprintf(out, "@ yaxis tick major 0.005\n");
fprintf(out, "@ yaxis tick minor 0.0025\n");
}
for (i = first; (i <= last); i++)
{
fprintf(out, "%10g %10f\n", i*binwidth+180.0-maxang, angstat[i]*norm_fac);
}
if (bPeriodic)
{
/* print first bin again as last one */
fprintf(out, "%10g %10f\n", 180.0, angstat[0]*norm_fac);
}
ffclose(out);
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
if (bAver)
{
do_view(oenv, opt2fn("-ov", NFILE, fnm), "-nxy");
}
thanx(stderr);
return 0;
}
开发者ID:smendozabarrera，项目名称:gromacs，代码行数:101，代码来源:gmx_angle.c
示例8: gmx_dos
//.........这里部分代码省略.........
dos[DOS][j] = bfac*dos[DOS][2*j];
}
}
/* Normalize it */
dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
if (bNormalizeDos)
{
for (j = 0; (j < nframes/4); j++)
{
dos[DOS][j] *= 3*Natom/dostot;
}
}
/* Now analyze it */
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
Delta = ((2*DoS0/(9*Natom))*std::sqrt(M_PI*BOLTZ*Temp*Natom/tmass)*
std::pow((Natom/V), 1.0/3.0)*std::pow(6.0/M_PI, 2.0/3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
Sig = BOLTZ*(5.0/2.0+std::log(2*M_PI*BOLTZ*Temp/(gmx::square(PLANCK))*V/(f*Natom)));
Shs = Sig+calc_Shs(f, y);
rho = (tmass*AMU)/(V*NANO*NANO*NANO);
sigHS = std::cbrt(6*y*V/(M_PI*Natom));
fprintf(fplog, "System = \"%s\"\n", *top.name);
fprintf(fplog, "Nmol = %d\n", Nmol);
fprintf(fplog, "Natom = %d\n", Natom);
fprintf(fplog, "dt = %g ps\n", dt);
fprintf(fplog, "tmass = %g amu\n", tmass);
fprintf(fplog, "V = %g nm^3\n", V);
fprintf(fplog, "rho = %g g/l\n", rho);
fprintf(fplog, "T = %g K\n", Temp);
fprintf(fplog, "beta = %g mol/kJ\n", beta);
fprintf(fplog, "\nDoS parameters\n");
fprintf(fplog, "Delta = %g\n", Delta);
fprintf(fplog, "fluidicity = %g\n", f);
fprintf(fplog, "hard sphere packing fraction = %g\n", y);
fprintf(fplog, "hard sphere compressibility = %g\n", z);
fprintf(fplog, "ideal gas entropy = %g\n", Sig);
fprintf(fplog, "hard sphere entropy = %g\n", Shs);
fprintf(fplog, "sigma_HS = %g nm\n", sigHS);
fprintf(fplog, "DoS0 = %g\n", DoS0);
fprintf(fplog, "Dos2 = %g\n", dos2);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
"\\f{4}S(\\f{12}n\\f{4})", oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_DIFF][j] = DoS0/(1+gmx::square(DoS0*M_PI*nu[j]/(6*f*Natom)));
dos[DOS_SOLID][j] = dos[DOS][j]-dos[DOS_DIFF][j];
fprintf(fp, "%10g %10g %10g %10g\n",
recip_fac*nu[j],
dos[DOS][j]/recip_fac,
dos[DOS_SOLID][j]/recip_fac,
dos[DOS_DIFF][j]/recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
wSdiff = Shs/(3*BOLTZ); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff-wSdiff;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_CP][j] = (dos[DOS_DIFF][j]*wCdiff +
dos[DOS_SOLID][j]*wCsolid(nu[j], beta));
dos[DOS_S][j] = (dos[DOS_DIFF][j]*wSdiff +
dos[DOS_SOLID][j]*wSsolid(nu[j], beta));
dos[DOS_A][j] = (dos[DOS_DIFF][j]*wAdiff +
dos[DOS_SOLID][j]*wAsolid(nu[j], beta));
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
开发者ID:wangxubo0201，项目名称:gromacs，代码行数:101，代码来源:gmx_dos.cpp
示例9: gmx_rmsf
//.........这里部分代码省略.........
xvgr_legend(fp, 2, leg, oenv);
for (i = 0; (i < isize); i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
resind = top.atoms.atom[index[i]].resind;
pdb_bfac = find_pdb_bfac(pdbatoms, &top.atoms.resinfo[resind],
*(top.atoms.atomname[index[i]]));
fprintf(fp, "%5d %10.5f %10.5f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, rmsf[i]*bfac,
pdb_bfac);
}
}
xvgrclose(fp);
}
else
{
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS fluctuation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
}
}
xvgrclose(fp);
}
for (i = 0; i < isize; i++)
{
pdbatoms->pdbinfo[index[i]].bfac = 800*M_PI*M_PI/3.0*rmsf[i];
}
if (devfn)
{
for (i = 0; i < isize; i++)
{
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
}
if (bRes)
{
average_residues(rmsf, nullptr, 0, isize, index, w_rls, &top.atoms);
}
/* Write RMSD output */
fp = xvgropen(devfn, "RMS Deviation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
}
}
xvgrclose(fp);
}
if (opt2bSet("-oq", NFILE, fnm))
{
/* Write a .pdb file with B-factors and optionally anisou records */
for (i = 0; i < isize; i++)
{
rvec_inc(pdbx[index[i]], xcm);
}
write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
nullptr, ePBC, pdbbox, isize, index);
}
if (opt2bSet("-ox", NFILE, fnm))
{
rvec *bFactorX;
snew(bFactorX, top.atoms.nr);
for (i = 0; i < isize; i++)
{
for (d = 0; d < DIM; d++)
{
bFactorX[index[i]][d] = xcm[d] + xav[i*DIM + d];
}
}
/* Write a .pdb file with B-factors and optionally anisou records */
write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr,
ePBC, pdbbox, isize, index);
sfree(bFactorX);
}
if (bAniso)
{
correlate_aniso(opt2fn("-oc", NFILE, fnm), refatoms, pdbatoms, oenv);
do_view(oenv, opt2fn("-oc", NFILE, fnm), "-nxy");
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (devfn)
{
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
}
return 0;
}
开发者ID:HITS-MBM，项目名称:gromacs-fda，代码行数:101，代码来源:gmx_rmsf.cpp
示例10: gmx_rotacf
//.........这里部分代码省略.........
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-o", "rotacf", ffWRITE }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
if (bVec)
nvec = isize/2;
else
nvec = isize/3;
if (((isize % 3) != 0) && !bVec)
gmx_fatal(FARGS,"number of index elements not multiple of 3, "
"these can not be atom triplets\n");
if (((isize % 2) != 0) && bVec)
gmx_fatal(FARGS,"number of index elements not multiple of 2, "
"these can not be atom doublets\n");
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
snew(c1,nvec);
for (i=0; (i<nvec); i++)
c1[i]=NULL;
n_alloc=0;
natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(x_s,natoms);
/* Start the loop over frames */
t1 = t0 = t;
teller = 0;
do {
if (teller >= n_alloc) {
n_alloc+=100;
for (i=0; (i<nvec); i++)
srenew(c1[i],DIM*n_alloc);
}
t1 = t;
/* Remove periodicity */
rm_pbc(&(top->idef),ePBC,natoms,box,x,x_s);
/* Compute crossproducts for all vectors, if triplets.
* else, just get the vectors in case of doublets.
*/
if (bVec == FALSE) {
for (i=0; (i<nvec); i++) {
ai=index[3*i];
aj=index[3*i+1];
ak=index[3*i+2];
rvec_sub(x_s[ai],x_s[aj],xij);
rvec_sub(x_s[aj],x_s[ak],xjk);
cprod(xij,xjk,n);
for(m=0; (m<DIM); m++)
c1[i][DIM*teller+m]=n[m];
}
}
else {
for (i=0; (i<nvec); i++) {
ai=index[2*i];
aj=index[2*i+1];
rvec_sub(x_s[ai],x_s[aj],n);
for(m=0; (m<DIM); m++)
c1[i][DIM*teller+m]=n[m];
}
}
/* Increment loop counter */
teller++;
} while (read_next_x(status,&t,natoms,x,box));
close_trj(status);
fprintf(stderr,"\nDone with trajectory\n");
/* Autocorrelation function */
if (teller < 2)
fprintf(stderr,"Not enough frames for correlation function\n");
else {
dt=(t1 - t0)/(teller-1);
mode = eacVector;
do_autocorr(ftp2fn(efXVG,NFILE,fnm),"Rotational Correlation Function",
teller,nvec,c1,dt,mode,bAver);
}
do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
thanx(stderr);
return 0;
}
开发者ID:BioinformaticsArchive，项目名称:GromPy，代码行数:101，代码来源:gmx_rotacf.c
示例11: gmx_densmap
//.........这里部分代码省略.........
vol = (j+1)/(invspz*invspa);
break;
default:
vol = j+1;
break;
}
if (bMirror)
k = j + nradial;
else
k = j;
grid[i][k] /= nfr*(vol - vol_old);
if (bMirror)
grid[i][nradial-1-j] = grid[i][k];
vol_old = vol;
if (grid[i][k] > maxgrid)
maxgrid = grid[i][k];
}
}
}
fprintf(stdout,"\n The maximum density is %f %s\n",maxgrid,unit);
if (dmax > 0)
maxgrid = dmax;
snew(tickx,n1+1);
snew(tickz,n2+1);
if (!bRadial) {
/* normalize box-axes */
box1 /= nfr;
box2 /= nfr;
for (i=0; i<=n1; i++)
tickx[i] = i*box1/n1;
for (i=0; i<=n2; i++)
tickz[i] = i*box2/n2;
} else {
for (i=0; i<=n1; i++)
tickx[i] = i/invspa - amax;
if (bMirror) {
for (i=0; i<=n2; i++)
tickz[i] = i/invspz - rmax;
} else {
for (i=0; i<=n2; i++)
tickz[i] = i/invspz;
}
}
if (bSums)
{
for (i=0; i<n1; ++i)
{
fprintf(stdout,"Density sums:\n");
rowsum=0;
for (j=0; j<n2; ++j)
rowsum+=grid[i][j];
fprintf(stdout,"%g\t",rowsum);
}
fprintf(stdout,"\n");
}
sprintf(buf,"%s number density",grpname[anagrp]);
if (!bRadial && (bXmin || bXmax)) {
if (!bXmax)
sprintf(buf+strlen(buf),", %c > %g nm",eaver[0][0],xmin);
else if (!bXmin)
sprintf(buf+strlen(buf),", %c < %g nm",eaver[0][0],xmax);
else
sprintf(buf+strlen(buf),", %c: %g - %g nm",eaver[0][0],xmin,xmax);
}
if (ftp2bSet(efDAT,NFILE,fnm))
{
fp = ffopen(ftp2fn(efDAT,NFILE,fnm),"w");
/*optional text form output: first row is tickz; first col is tickx */
fprintf(fp,"0\t");
for(j=0; j<n2; ++j)
fprintf(fp,"%g\t",tickz[j]);
fprintf(fp,"\n");
for (i=0; i<n1; ++i)
{
fprintf(fp,"%g\t",tickx[i]);
for (j=0; j<n2; ++j)
fprintf(fp,"%g\t",grid[i][j]);
fprintf(fp,"\n");
}
ffclose(fp);
}
else
{
fp = ffopen(ftp2fn(efXPM,NFILE,fnm),"w");
write_xpm(fp,MAT_SPATIAL_X | MAT_SPATIAL_Y,buf,unit,
bRadial ? "axial (nm)" : label[c1],bRadial ? "r (nm)" : label[c2],
n1,n2,tickx,tickz,grid,dmin,maxgrid,rlo,rhi,&nlev);
ffclose(fp);
}
thanx(stderr);
do_view(oenv,opt2fn("-o",NFILE,fnm),NULL);
return 0;
}
开发者ID:BradleyDickson，项目名称:ABPenabledGROMACS，代码行数:101，代码来源:gmx_densmap.c
示例12: gmx_polystat
//.........这里部分代码省略.........
sum_gyro_tot += sum_gyro;
if (outp)
{
i = -1;
for (j = 0; j < nat_min/2; j += 2)
{
sum_inp[j] /= ninp[j];
if (i == -1 && sum_inp[j] <= std::exp(-1.0))
{
i = j;
}
}
if (i == -1)
{
pers = j;
}
else
{
/* Do linear interpolation on a log scale */
pers = i - 2.0
+ 2.0*(std::log(sum_inp[i-2]) + 1.0)/(std::log(sum_inp[i-2]) - std::log(sum_inp[i]));
}
fprintf(outp, "%10.3f %8.4f\n", t*output_env_get_time_factor(oenv), pers);
sum_pers_tot += pers;
}
frame++;
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trx(status);
xvgrclose(out);
if (outv)
{
xvgrclose(outv);
}
if (outp)
{
xvgrclose(outp);
}
sum_eed2_tot /= frame;
sum_gyro_tot /= frame;
sum_pers_tot /= frame;
fprintf(stdout, "\nAverage end to end distance: %.3f (nm)\n",
std::sqrt(sum_eed2_tot));
fprintf(stdout, "\nAverage radius of gyration: %.3f (nm)\n",
std::sqrt(sum_gyro_tot));
if (opt2bSet("-p", NFILE, fnm))
{
fprintf(stdout, "\nAverage persistence length: %.2f bonds\n",
sum_pers_tot);
}
/* Handle printing of internal distances. */
if (outi)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(outi, "@ xaxes scale Logarithmic\n");
}
ymax = -1;
ymin = 1e300;
j = index[molind[1]-1] - index[molind[0]]; /* Polymer length -1. */
for (i = 0; i < j; i++)
{
intd[i] /= (i + 1) * frame * nmol;
if (intd[i] > ymax)
{
ymax = intd[i];
}
if (intd[i] < ymin)
{
ymin = intd[i];
}
}
xvgr_world(outi, 1, ymin, j, ymax, oenv);
for (i = 0; i < j; i++)
{
fprintf(outi, "%d %8.4f\n", i+1, intd[i]);
}
xvgrclose(outi);
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (opt2bSet("-v", NFILE, fnm))
{
do_view(oenv, opt2fn("-v", NFILE, fnm), "-nxy");
}
if (opt2bSet("-p", NFILE, fnm))
{
do_view(oenv, opt2fn("-p", NFILE, fnm), "-nxy");
}
return 0;
}
开发者ID:HITS-MBM，项目名称:gromacs-fda，代码行数:101，代码来源:gmx_polystat.cpp
示例13: gmx_editconf
//.........这里部分代码省略.........
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
if (opt2bSet("-bf",NFILE,fnm) || bLegend)
{
gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
}
if (outftp == efPDB)
{
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
ffclose(out);
}
else
{
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
ffclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(oenv,outfile,NULL);
thanx(stderr);
return 0;
}
开发者ID:andersx，项目名称:gmx-debug，代码行数:101，代码来源:gmx_editconf.c
示例14: gmx_rotmat
//.........这里部分代码省略.........
{ "-mw", FALSE, etBOOL, {&bMW},
"Use mass weighted fitting" }
};
FILE *out;
t_trxstatus *status;
t_topology top;
int ePBC;
rvec *x_ref, *x;
matrix box, R;
real t;
int natoms, i;
char *grpname, title[256];
int gnx;
gmx_rmpbc_t gpbc = NULL;
atom_id *index;
output_env_t oenv;
real *w_rls;
const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "rotmat", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (reffit[0][0] != 'n')
{
get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
gnx, index, bMW, &top, ePBC, x_ref);
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(w_rls, natoms);
for (i = 0; i < gnx; i++)
{
if (index[i] >= natoms)
{
gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
}
w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
}
if (reffit[0][0] == 'n')
{
reset_x(gnx, index, natoms, NULL, x_ref, w_rls);
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Fit matrix", "Time (ps)", "", oenv);
xvgr_legend(out, NLEG, leg, oenv);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
reset_x(gnx, index, natoms, NULL, x, w_rls);
if (bFitXY)
{
do_fit_ndim(2, natoms, w_rls, x_ref, x);
}
calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
fprintf(out,
"%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
t,
R[XX][XX], R[XX][YY], R[XX][ZZ],
R[YY][XX], R[YY][YY], R[YY][ZZ],
R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trj(status);
gmx_ffclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
开发者ID:ElsevierSoftwareX，项目名称:SOFTX-D-15-00003，代码行数:101，代码来源:gmx_rotmat.c
示例15: gmx_potential
int gmx_potential(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the electrostatical potential across the box. The potential is",
"calculated by first summing the charges per slice and then integrating",
"twice of this charge distribution. Periodic boundaries are not taken",
"into account. Reference of potential is taken to be the left side of",
"the box. It is also possible to calculate the potential in spherical",
"coordinates as function of r by calculating a charge distribution in",
"spherical slices and twice integrating them. epsilon_r is taken as 1,",
"but 2 is more appropriate in many cases."
};
gmx_output_env_t *oenv;
static int axis = 2; /* normal to memb. default z */
static const char *axtitle = "Z";
static int nslices = 10; /* nr of slices defined */
static int ngrps = 1;
static gmx_bool bSpherical = FALSE; /* default is bilayer types */
static real fudge_z = 0; /* translate coordinates */
static gmx_bool bCorrect = 0;
t_pargs pa [] = {
{ "-d", FALSE, etSTR, {&axtitle},
"Take the normal on the membrane in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate potential as function of boxlength, dividing the box"
" in this number of slices." },
{ "-cb", FALSE, etINT, {&cb},
"Discard this number of first slices of box for integration" },
{ "-ce", FALSE, etINT, {&ce},
"Discard this number of last slices of box for integration" },
{ "-tz", FALSE, etREAL, {&fudge_z},
"Translate all coordinates by this distance in the direction of the box" },
{ "-spherical", FALSE, etBOOL, {&bSpherical},
"Calculate spherical thingie" },
{ "-ng", FALSE, etINT, {&ngrps},
"Number of groups to consider" },
{ "-correct", FALSE, etBOOL, {&bCorrect},
"Assume net zero charge of groups to improve accuracy" }
};
const char *bugs[] = {
"Discarding slices for integration should not be necessary."
};
double **potential, /* potential per slice */
**charge, /* total charge per slice */
**field, /* field per slice */
slWidth; /* width of one slice */
char **grpname; /* groupnames */
int *ngx; /* sizes of groups */
t_topology *top; /* topology */
int ePBC;
int **index; /* indices for all groups */
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
{ efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "potential", ffWRITE }, /* xvgr output file */
{ efXVG, "-oc", "charge", ffWRITE }, /* xvgr output file */
{ efXVG, "-of", "field", ffWRITE }, /* xvgr output file */
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
return 0;
}
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
snew(grpname, ngrps);
snew(index, ngrps);
snew(ngx, ngrps);
rd_index(ftp2fn(efNDX, NFILE, fnm), ngrps, ngx, index, grpname);
calc_potential(ftp2fn(efTRX, NFILE, fnm), index, ngx,
&potential, &charge, &field,
&nslices, top, ePBC, axis, ngrps, &slWidth, fudge_z,
bSpherical, bCorrect, oenv);
plot_potential(potential, charge, field, opt2fn("-o", NFILE, fnm),
opt2fn("-oc", NFILE, fnm), opt2fn("-of", NFILE, fnm),
nslices, ngrps, (const char**)grpname, slWidth, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
do_view(oenv, opt2fn("-oc", NFILE, fnm), NULL); /* view xvgr file */
do_view(oenv, opt2fn("-of", NFILE, fnm), NULL); /* view xvgr file */
return 0;
}
开发者ID:MichalKononenko，项目名称:gromacs，代码行数:97，代码来源:gmx_potential.cpp
示例16: gmx_h2order
int gmx_h2order(int argc,char *argv[])
{
const char *desc[] = {
"Compute the orientation of water molecules with respect to the normal",
"of the box. The program determines the average cosine of the angle",
"between de dipole moment of water and an axis of the box. The box is",
"divided in slices and the average orientation per slice is printed.",
"Each water molecule is assigned to a slice, per time frame, based on the",
"position of the oxygen. When -nm is used the angle between the water",
"dipole and the axis from the center of mass to the oxygen is calculated",
"instead of the angle between the dipole and a box axis."
};
static int axis = 2; /* normal to memb. default z */
static const char *axtitle="Z";
static int nslices = 0; /* nr of slices defined */
t_pargs pa[] = {
{ "-d", FALSE, etSTR, {&axtitle},
"Take the normal on the membrane in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate order parameter as function of boxlength, dividing the box"
" in #nr slices."}
};
const char *bugs[] = {
"The program assigns whole water molecules to a slice, based on the first"
"atom of three in the index file group. It assumes an order O,H,H."
"Name is not important, but the order is. If this demand is not met,"
"assigning molecules to slices is different."
};
output_env_t oenv;
real *slOrder, /* av. cosine, per slice */
slWidth = 0.0; /* width of a slice */
rvec *slDipole;
char *grpname, /* groupnames */
*micname;
int ngx, /* nr. of atomsin sol group */
nmic; /* nr. of atoms in micelle */
t_topology *top; /* topology */
int ePBC;
atom_id *index, /* indices for solvent group */
*micelle;
gmx_bool bMicel = FALSE; /* think we're a micel */
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
{ efNDX, "-nm&qu
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