int gmx_gyrate(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the radius of gyration of a molecule",
"and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
"The axis components corresponds to the mass-weighted root-mean-square",
"of the radii components orthogonal to each axis, for example:[PAR]",
"Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
"With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
"of slices along the [IT]z[it]-axis are calculated."
};
static int nmol = 1, nz = 0;
static gmx_bool bQ = FALSE, bRot = FALSE, bMOI = FALSE;
t_pargs pa[] = {
{ "-nmol", FALSE, etINT, {&nmol},
"The number of molecules to analyze" },
{ "-q", FALSE, etBOOL, {&bQ},
"Use absolute value of the charge of an atom as weighting factor instead of mass" },
{ "-p", FALSE, etBOOL, {&bRot},
"Calculate the radii of gyration about the principal axes." },
{ "-moi", FALSE, etBOOL, {&bMOI},
"Calculate the moments of inertia (defined by the principal axes)." },
{ "-nz", FALSE, etINT, {&nz},
"Calculate the 2D radii of gyration of this number of slices along the z-axis" },
};
FILE *out;
t_trxstatus *status;
t_topology top;
int ePBC;
rvec *x, *x_s;
rvec xcm, gvec, gvec1;
matrix box, trans;
gmx_bool bACF;
real **moi_trans = NULL;
int max_moi = 0, delta_moi = 100;
rvec d, d1; /* eigenvalues of inertia tensor */
real t, t0, tm, gyro;
int natoms;
char *grpname;
int j, m, gnx, nam, mol;
atom_id *index;
gmx_output_env_t *oenv;
gmx_rmpbc_t gpbc = NULL;
const char *leg[] = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
const char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "gyrate", ffWRITE },
{ efXVG, "-acf", "moi-acf", ffOPTWR },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bACF = opt2bSet("-acf", NFILE, fnm);
if (bACF && nmol != 1)
{
gmx_fatal(FARGS, "Can only do acf with nmol=1");
}
bRot = bRot || bMOI || bACF;
/*
if (nz > 0)
bMOI = TRUE;
*/
if (bRot)
{
printf("Will rotate system along principal axes\n");
snew(moi_trans, DIM);
}
if (bMOI)
{
printf("Will print moments of inertia\n");
bQ = FALSE;
}
if (bQ)
{
printf("Will print radius normalised by charge\n");
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (nmol > gnx || gnx % nmol != 0)
{
gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
}
nam = gnx/nmol;
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(x_s, natoms);
j = 0;
t0 = t;
if (bQ)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Radius of Charge (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
else if (bMOI)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Moments of inertia (total and around axes)", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
}
else
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Radius of gyration (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
if (bMOI)
{
xvgr_legend(out, NLEG, legI, oenv);
}
else
{
if (bRot)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
}
}
xvgr_legend(out, NLEG, leg, oenv);
}
if (nz == 0)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
}
do
{
if (nz == 0)
{
gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
}
gyro = 0;
clear_rvec(gvec);
clear_rvec(gvec1);
clear_rvec(d);
clear_rvec(d1);
for (mol = 0; mol < nmol; mol++)
{
tm = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
if (nz == 0)
{
gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
tm, gvec1, d1, bQ, bRot, bMOI, trans);
}
else
{
calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
}
rvec_inc(gvec, gvec1);
rvec_inc(d, d1);
}
if (nmol > 0)
{
gyro /= nmol;
svmul(1.0/nmol, gvec, gvec);
svmul(1.0/nmol, d, d);
}
if (nz == 0)
{
if (bRot)
{
if (j >= max_moi)
{
max_moi += delta_moi;
for (m = 0; (m < DIM); m++)
{
srenew(moi_trans[m], max_moi*DIM);
}
}
for (m = 0; (m < DIM); m++)
{
copy_rvec(trans[m], moi_trans[m]+DIM*j);
}
fprintf(out, "%10g %10g %10g %10g %10g\n",
t, gyro, d[XX], d[YY], d[ZZ]);
}
else
{
fprintf(out, "%10g %10g %10g %10g %10g\n",
t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
}
}
j++;
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (nz == 0)
{
gmx_rmpbc_done(gpbc);
}
xvgrclose(out);
if (bACF)
{
int mode = eacVector;
do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
"Moment of inertia vector ACF",
j, 3, moi_trans, (t-t0)/j, mode, FALSE);
do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
int gmx_gyrate(int argc,char *argv[])
{
const char *desc[] = {
"g_gyrate computes the radius of gyration of a group of atoms",
"and the radii of gyration about the x, y and z axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
"With the option [TT]-nz[tt] 2D radii of gyration in the x-y plane",
"of slices along the z-axis are calculated."
};
static int nmol=1,nz=0;
static bool bQ=FALSE,bRot=FALSE,bMOI=FALSE;
t_pargs pa[] = {
{ "-nmol", FALSE, etINT, {&nmol},
"The number of molecules to analyze" },
{ "-q", FALSE, etBOOL, {&bQ},
"Use absolute value of the charge of an atom as weighting factor instead of mass" },
{ "-p", FALSE, etBOOL, {&bRot},
"Calculate the radii of gyration about the principal axes." },
{ "-moi", FALSE, etBOOL, {&bMOI},
"Calculate the moments of inertia (defined by the principal axes)." },
{ "-nz", FALSE, etINT, {&nz},
"Calculate the 2D radii of gyration of # slices along the z-axis" },
};
FILE *out;
int status;
t_topology top;
int ePBC;
rvec *x,*x_s;
rvec xcm,gvec,gvec1;
matrix box,trans;
bool bACF;
real **moi_trans=NULL;
int max_moi=0,delta_moi=100;
rvec d,d1; /* eigenvalues of inertia tensor */
real t,t0,tm,gyro;
int natoms;
char *grpname,title[256];
int i,j,m,gnx,nam,mol;
atom_id *index;
char *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "gyrate", ffWRITE },
{ efXVG, "-acf", "moi-acf", ffOPTWR },
};
#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_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
bACF = opt2bSet("-acf",NFILE,fnm);
if (bACF && nmol!=1)
gmx_fatal(FARGS,"Can only do acf with nmol=1");
bRot = bRot || bMOI || bACF;
/*
if (nz > 0)
bMOI = TRUE;
*/
if (bRot) {
printf("Will rotate system along principal axes\n");
snew(moi_trans,DIM);
}
if (bMOI) {
printf("Will print moments of inertia\n");
bQ = FALSE;
}
if (bQ)
printf("Will print radius normalised by charge\n");
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x,NULL,box,TRUE);
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
if (nmol > gnx || gnx % nmol != 0) {
gmx_fatal(FARGS,"The number of atoms in the group (%d) is not a multiple of nmol (%d)",gnx,nmol);
}
nam = gnx/nmol;
natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(x_s,natoms);
j = 0;
t0 = t;
if (bQ)
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Radius of Charge","Time (ps)","Rg (nm)");
else if (bMOI)
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Moments of inertia","Time (ps)","I (a.m.u. nm\\S2\\N)");
else
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Radius of gyration","Time (ps)","Rg (nm)");
if (bMOI)
xvgr_legend(out,NLEG,legI);
else {
if (bRot)
if (bPrintXvgrCodes())
fprintf(out,"@ subtitle \"Axes are principal component axes\"\n");
xvgr_legend(out,NLEG,leg);
}
do {
if (nz == 0)
rm_pbc(&top.idef,ePBC,natoms,box,x,x_s);
gyro = 0;
clear_rvec(gvec);
clear_rvec(d);
for(mol=0; mol<nmol; mol++) {
tm = sub_xcm(nz==0?x_s:x,nam,index+mol*nam,top.atoms.atom,xcm,bQ);
if (nz == 0)
gyro += calc_gyro(x_s,nam,index+mol*nam,top.atoms.atom,
tm,gvec1,d1,bQ,bRot,bMOI,trans);
else
calc_gyro_z(x,box,nam,index+mol*nam,top.atoms.atom,nz,t,out);
rvec_inc(gvec,gvec1);
rvec_inc(d,d1);
}
if (nmol > 0) {
gyro /= nmol;
svmul(1.0/nmol,gvec,gvec);
svmul(1.0/nmol,d,d);
}
if (nz == 0) {
if (bRot) {
if (j >= max_moi) {
max_moi += delta_moi;
for(m=0; (m<DIM); m++)
srenew(moi_trans[m],max_moi*DIM);
}
for(m=0; (m<DIM); m++)
copy_rvec(trans[m],moi_trans[m]+DIM*j);
fprintf(out,"%10g %10g %10g %10g %10g\n",
t,gyro,d[XX],d[YY],d[ZZ]); }
else {
fprintf(out,"%10g %10g %10g %10g %10g\n",
t,gyro,gvec[XX],gvec[YY],gvec[ZZ]); }
}
j++;
} while(read_next_x(status,&t,natoms,x,box));
close_trj(status);
fclose(out);
if (bACF) {
int mode = eacVector;
do_autocorr(opt2fn("-acf",NFILE,fnm),
"Moment of inertia vector ACF",
j,3,moi_trans,(t-t0)/j,mode,FALSE);
do_view(opt2fn("-acf",NFILE,fnm),"-nxy");
}
do_view(ftp2fn(efXVG,NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}