int gmx_densorder(int argc, char *argv[])
{
static const char *desc[] = {
"[THISMODULE] reduces a two-phase density distribution",
"along an axis, computed over a MD trajectory,",
"to 2D surfaces fluctuating in time, by a fit to",
"a functional profile for interfacial densities.",
"A time-averaged spatial representation of the",
"interfaces can be output with the option [TT]-tavg[tt]."
};
/* Extra arguments - but note how you always get the begin/end
* options when running the program, without mentioning them here!
*/
gmx_output_env_t *oenv;
t_topology *top;
char **grpname;
int ePBC, *ngx;
static real binw = 0.2;
static real binwz = 0.05;
static real dens1 = 0.00;
static real dens2 = 1000.00;
static int ftorder = 0;
static int nsttblock = 100;
static int axis = 2;
static const char *axtitle = "Z";
atom_id **index; /* Index list for single group*/
int xslices, yslices, zslices, tblock;
static gmx_bool bGraph = FALSE;
static gmx_bool bCenter = FALSE;
static gmx_bool bFourier = FALSE;
static gmx_bool bRawOut = FALSE;
static gmx_bool bOut = FALSE;
static gmx_bool b1d = FALSE;
static int nlevels = 100;
/*Densitymap - Densmap[t][x][y][z]*/
real ****Densmap = NULL;
/* Surfaces surf[t][surf_x,surf_y]*/
t_interf ***surf1, ***surf2;
static const char *meth[] = {NULL, "bisect", "functional", NULL};
int eMeth;
char **graphfiles, **rawfiles, **spectra; /* Filenames for xpm-surface maps, rawdata and powerspectra */
int nfxpm = -1, nfraw, nfspect; /* # files for interface maps and spectra = # interfaces */
t_pargs pa[] = {
{ "-1d", FALSE, etBOOL, {&b1d},
"Pseudo-1d interface geometry"},
{ "-bw", FALSE, etREAL, {&binw},
"Binwidth of density distribution tangential to interface"},
{ "-bwn", FALSE, etREAL, {&binwz},
"Binwidth of density distribution normal to interface"},
{ "-order", FALSE, etINT, {&ftorder},
"Order of Gaussian filter, order 0 equates to NO filtering"},
{"-axis", FALSE, etSTR, {&axtitle},
"Axis Direction - X, Y or Z"},
{"-method", FALSE, etENUM, {meth},
"Interface location method"},
{"-d1", FALSE, etREAL, {&dens1},
"Bulk density phase 1 (at small z)"},
{"-d2", FALSE, etREAL, {&dens2},
"Bulk density phase 2 (at large z)"},
{ "-tblock", FALSE, etINT, {&nsttblock},
"Number of frames in one time-block average"},
{ "-nlevel", FALSE, etINT, {&nlevels},
"Number of Height levels in 2D - XPixMaps"}
};
t_filenm fnm[] = {
{ efTPR, "-s", NULL, ffREAD }, /* this is for the topology */
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
{ efNDX, "-n", NULL, ffREAD}, /* this is to select groups */
{ efDAT, "-o", "Density4D", ffOPTWR}, /* This is for outputting the entire 4D densityfield in binary format */
{ efOUT, "-or", NULL, ffOPTWRMULT}, /* This is for writing out the entire information in the t_interf arrays */
{ efXPM, "-og", "interface", ffOPTWRMULT}, /* This is for writing out the interface meshes - one xpm-file per tblock*/
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* This is for the trajectory averaged Fourier-spectra*/
};
#define NFILE asize(fnm)
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
eMeth = nenum(meth);
bFourier = opt2bSet("-Spect", NFILE, fnm);
bRawOut = opt2bSet("-or", NFILE, fnm);
bGraph = opt2bSet("-og", NFILE, fnm);
bOut = opt2bSet("-o", NFILE, fnm);
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
snew(grpname, 1);
snew(index, 1);
snew(ngx, 1);
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
get_index(&top->atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, ngx, index, grpname);
density_in_time(ftp2fn(efTRX, NFILE, fnm), index, ngx, binw, binwz, nsttblock, &Densmap, &xslices, &yslices, &zslices, &tblock, top, ePBC, axis, bCenter, b1d, oenv);
if (ftorder > 0)
{
filterdensmap(Densmap, xslices, yslices, zslices, tblock, 2*ftorder+1);
}
if (bOut)
{
outputfield(opt2fn("-o", NFILE, fnm), Densmap, xslices, yslices, zslices, tblock);
}
interfaces_txy(Densmap, xslices, yslices, zslices, tblock, binwz, eMeth, dens1, dens2, &surf1, &surf2, oenv);
if (bGraph)
{
/*Output surface-xpms*/
nfxpm = opt2fns(&graphfiles, "-og", NFILE, fnm);
if (nfxpm != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
}
writesurftoxpms(surf1, surf2, tblock, xslices, yslices, zslices, binw, binwz, graphfiles, zslices);
}
/*Output raw-data*/
if (bRawOut)
{
nfraw = opt2fns(&rawfiles, "-or", NFILE, fnm);
if (nfraw != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
}
writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles, oenv);
}
if (bFourier)
{
nfspect = opt2fns(&spectra, "-Spect", NFILE, fnm);
if (nfspect != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-file-series: %d",
nfspect);
}
powerspectavg_intf(surf1, surf2, tblock, xslices, yslices, spectra);
}
sfree(Densmap);
if (bGraph || bFourier || bRawOut)
{
sfree(surf1);
sfree(surf2);
}
return 0;
}
int gmx_hydorder(int argc, char *argv[])
{
static const char *desc[] = {
"g_hydorder computes the tetrahedrality order parameters around a ",
"given atom. Both angle an distance order parameters are calculated. See",
"P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
"for more details.[BR]"
"This application calculates the orderparameter in a 3d-mesh in the box, and",
"with 2 phases in the box gives the user the option to define a 2D interface in time",
"separating the faces by specifying parameters -sgang1 and -sgang2 (It is important",
"to select these judiciously)"
};
int axis = 0;
static int nsttblock = 1;
static int nlevels = 100;
static real binwidth = 1.0; /* binwidth in mesh */
static real sg1 = 1;
static real sg2 = 1; /* order parameters for bulk phases */
static gmx_bool bFourier = FALSE;
static gmx_bool bRawOut = FALSE;
int frames, xslices, yslices; /* Dimensions of interface arrays*/
real ***intfpos; /* Interface arrays (intfnr,t,xy) -potentially large */
static char *normal_axis[] = { NULL, "z", "x", "y", NULL };
t_pargs pa[] = {
{ "-d", FALSE, etENUM, {normal_axis},
"Direction of the normal on the membrane" },
{ "-bw", FALSE, etREAL, {&binwidth},
"Binwidth of box mesh" },
{ "-sgang1", FALSE, etREAL, {&sg1},
"tetrahedral angle parameter in Phase 1 (bulk)" },
{ "-sgang2", FALSE, etREAL, {&sg2},
"tetrahedral angle parameter in Phase 2 (bulk)" },
{ "-tblock", FALSE, etINT, {&nsttblock},
"Number of frames in one time-block average"},
{ "-nlevel", FALSE, etINT, {&nlevels},
"Number of Height levels in 2D - XPixMaps"}
};
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
{ efTPX, "-s", NULL, ffREAD }, /* topology file */
{ efXPM, "-o", "intf", ffWRMULT}, /* XPM- surface maps */
{ efOUT, "-or", "raw", ffOPTWRMULT }, /* xvgr output file */
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
};
#define NFILE asize(fnm)
/*Filenames*/
const char *ndxfnm, *tpsfnm, *trxfnm;
char **spectra, **intfn, **raw;
int nfspect, nfxpm, nfraw;
output_env_t oenv;
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);
bFourier = opt2bSet("-Spect", NFILE, fnm);
bRawOut = opt2bSet("-or", NFILE, fnm);
if (binwidth < 0.0)
{
gmx_fatal(FARGS, "Can not have binwidth < 0");
}
ndxfnm = ftp2fn(efNDX, NFILE, fnm);
tpsfnm = ftp2fn(efTPX, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
if (strcmp(normal_axis[0], "x") == 0)
{
axis = XX;
}
else if (strcmp(normal_axis[0], "y") == 0)
{
axis = YY;
}
else if (strcmp(normal_axis[0], "z") == 0)
{
axis = ZZ;
}
else
{
gmx_fatal(FARGS, "Invalid axis, use x, y or z");
}
switch (axis)
{
case 0:
fprintf(stderr, "Taking x axis as normal to the membrane\n");
break;
case 1:
fprintf(stderr, "Taking y axis as normal to the membrane\n");
break;
case 2:
fprintf(stderr, "Taking z axis as normal to the membrane\n");
break;
}
/* tetraheder order parameter */
/* If either of the options is set we compute both */
nfxpm = opt2fns(&intfn, "-o", NFILE, fnm);
if (nfxpm != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
}
calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
if (bFourier)
{
nfspect = opt2fns(&spectra, "-Spect", NFILE, fnm);
if (nfspect != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfspect);
}
powerspectavg(intfpos, frames, xslices, yslices, spectra);
}
if (bRawOut)
{
nfraw = opt2fns(&raw, "-or", NFILE, fnm);
if (nfraw != 2)
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfraw);
}
writeraw(intfpos, frames, xslices, yslices, raw);
}
thanx(stderr);
return 0;
}