int gmx_densorder(int argc,char *argv[])
{
static const char *desc[] = {
"A small program to reduce 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 -tavg"
};
/* Extra arguments - but note how you always get the begin/end
* options when running the program, without mentioning them here!
*/
output_env_t oenv;
t_topology *top;
char title[STRLEN],**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 char *axtitle="Z";
static int ngrps=1;
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,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[] = {
{ efTPX, "-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)
CopyRight(stderr,argv[0]);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
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(efTPX,NFILE,fnm),&ePBC);
snew(grpname,ngrps);
snew(index,ngrps);
snew(ngx,ngrps);
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
get_index(&top->atoms,ftp2fn_null(efNDX,NFILE,fnm),ngrps,ngx,index,grpname);
density_in_time(ftp2fn(efTRX,NFILE,fnm),index,ngx,ngrps,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);
}
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);
}
thanx(stderr);
return 0;
}
void writeDVDraw (const unsigned char *data1, int length1,
const unsigned char *data2, int length2,
struct cc_subtitle *sub)
{
/* these are only used by DVD raw mode: */
static int loopcount = 1; /* loop 1: 5 elements, loop 2: 8 elements,
loop 3: 11 elements, rest: 15 elements */
static int datacount = 0; /* counts within loop */
if (datacount==0)
{
writeraw (DVD_HEADER, sizeof (DVD_HEADER), NULL, sub);
if (loopcount==1)
writeraw (lc1, sizeof (lc1), NULL, sub);
if (loopcount==2)
writeraw (lc2, sizeof (lc2), NULL, sub);
if (loopcount==3)
{
writeraw (lc3, sizeof (lc3), NULL, sub);
if (data2 && length2)
writeraw (data2, length2, NULL, sub);
}
if (loopcount>3)
{
writeraw (lc4, sizeof (lc4), NULL, sub);
if (data2 && length2)
writeraw (data2, length2, NULL, sub);
}
}
datacount++;
writeraw (lc5, sizeof (lc5), NULL, sub);
if (data1 && length1)
writeraw (data1, length1, NULL, sub);
if (((loopcount == 1) && (datacount < 5)) || ((loopcount == 2) &&
(datacount < 8)) || (( loopcount == 3) && (datacount < 11)) ||
((loopcount > 3) && (datacount < 15)))
{
writeraw (lc6, sizeof(lc6), NULL, sub);
if (data2 && length2)
writeraw (data2, length2, NULL, sub);
}
else
{
if (loopcount==1)
{
writeraw (lc6, sizeof(lc6), NULL, sub);
if (data2 && length2)
writeraw (data2, length2, NULL, sub);
}
loopcount++;
datacount=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;
}
/* Buffer data with the same FTS and write when a new FTS or data==NULL
* is encountered */
void writercwtdata (struct lib_ccx_ctx *ctx, const unsigned char *data)
{
static LLONG prevfts = -1;
LLONG currfts = fts_now + fts_global;
static uint16_t cbcount = 0;
static int cbempty=0;
static unsigned char cbbuffer[0xFFFF*3]; // TODO: use malloc
static unsigned char cbheader[8+2];
if ( (prevfts != currfts && prevfts != -1)
|| data == NULL
|| cbcount == 0xFFFF)
{
// Remove trailing empty or 608 padding caption blocks
if ( cbcount != 0xFFFF)
{
unsigned char cc_valid;
unsigned char cc_type;
int storecbcount=cbcount;
for( int cb = cbcount-1; cb >= 0 ; cb-- )
{
cc_valid = (*(cbbuffer+3*cb) & 4) >>2;
cc_type = *(cbbuffer+3*cb) & 3;
// The -fullbin option disables pruning of 608 padding blocks
if ( (cc_valid && cc_type <= 1 // Only skip NTSC padding packets
&& !ccx_options.fullbin // Unless we want to keep them
&& *(cbbuffer+3*cb+1)==0x80
&& *(cbbuffer+3*cb+2)==0x80)
|| !(cc_valid || cc_type==3) ) // or unused packets
{
cbcount--;
}
else
{
cb = -1;
}
}
dbg_print(CCX_DMT_CBRAW, "%s Write %d RCWT blocks - skipped %d padding / %d unused blocks.\n",
print_mstime(prevfts), cbcount, storecbcount - cbcount, cbempty);
}
// New FTS, write data header
// RCWT data header (10 bytes):
//byte(s) value description
//0-7 FTS int64_t number with current FTS
//8-9 blocks Number of 3 byte data blocks with the same FTS that are
// following this header
memcpy(cbheader,&prevfts,8);
memcpy(cbheader+8,&cbcount,2);
if (cbcount > 0)
{
if (ccx_options.send_to_srv)
{
net_send_cc(cbheader, 10);
net_send_cc(cbbuffer, 3*cbcount);
}
else
{
writeraw(cbheader,10,&ctx->wbout1);
writeraw(cbbuffer,3*cbcount, &ctx->wbout1);
}
}
cbcount = 0;
cbempty = 0;
}
