void powerspectavg_intf(t_interf ***if1, t_interf ***if2, int t, int xb, int yb, char **fnms)
{
real ***surf;
int xy = xb*yb;
int i, n;
snew(surf, 2);
snew(surf[0], t);
snew(surf[1], t);
for (n = 0; n < t; n++)
{
snew(surf[0][n], xy);
snew(surf[1][n], xy);
for (i = 0; i < xy; i++)
{
surf[0][n][i] = if1[n][i]->Z;
surf[1][n][i] = if2[n][i]->Z;
}
}
powerspectavg(surf, t, xb, yb, fnms);
}
void powerspectavg_intf(t_interf ***if1, t_interf ***if2, int t, int xb, int yb,
gmx::ArrayRef<const std::string> outfiles)
{
real ***surf;
int xy = xb*yb;
int i, n;
snew(surf, 2);
snew(surf[0], t);
snew(surf[1], t);
for (n = 0; n < t; n++)
{
snew(surf[0][n], xy);
snew(surf[1][n], xy);
for (i = 0; i < xy; i++)
{
surf[0][n][i] = if1[n][i]->Z;
surf[1][n][i] = if2[n][i]->Z;
}
}
powerspectavg(surf, t, xb, yb, outfiles);
}
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;
}
