static void write_hconf_mtop(FILE *out,char *title,gmx_mtop_t *mtop,
int pr,
rvec *x,rvec *v,matrix box)
{
char format[100];
int i,resnr;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
char *atomname,*resname;
bromacs(format,99);
fprintf (out,"%s\n",(title && title[0])?title:format);
fprintf (out,"%5d\n",mtop->natoms);
make_hconf_format(pr,v!=NULL,format);
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
gmx_mtop_atomloop_all_names(aloop,&atomname,&resnr,&resname);
fprintf(out,"%5d%-5.5s%5.5s%5d",
(resnr+1)%100000,resname,atomname,(i+1)%100000);
/* next fprintf uses built format string */
if (v)
fprintf(out,format,
x[i][XX], x[i][YY], x[i][ZZ], v[i][XX],v[i][YY],v[i][ZZ]);
else
fprintf(out,format,
x[i][XX], x[i][YY], x[i][ZZ]);
}
write_hconf_box(out,pr,box);
fflush(out);
}
void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
int nx, const atom_id index[], int pr,
rvec *x, rvec *v, matrix box)
{
char resnm[6], nm[6], format[100];
int ai, i, resind, resnr;
bromacs(format, 99);
fprintf (out, "%s\n", (title && title[0]) ? title : format);
fprintf (out, "%5d\n", nx);
make_hconf_format(pr, v != NULL, format);
for (i = 0; (i < nx); i++)
{
ai = index[i];
resind = atoms->atom[ai].resind;
strncpy(resnm, " ??? ", sizeof(resnm)-1);
if (resind < atoms->nres)
{
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
resnr = atoms->resinfo[resind].nr;
}
else
{
strncpy(resnm, " ??? ", sizeof(resnm)-1);
resnr = resind + 1;
}
if (atoms->atom)
{
strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
}
else
{
strncpy(nm, " ??? ", sizeof(nm)-1);
}
fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000);
/* next fprintf uses built format string */
if (v)
{
fprintf(out, format,
x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX], v[ai][YY], v[ai][ZZ]);
}
else
{
fprintf(out, format,
x[ai][XX], x[ai][YY], x[ai][ZZ]);
}
}
write_hconf_box(out, pr, box);
fflush(out);
}
void write_hconf_indexed_p(FILE *out,char *title,t_atoms *atoms,
int nx,atom_id index[], int pr,
rvec *x,rvec *v,matrix box)
{
char resnm[6],nm[6],format[100];
int ai,i,resnr;
bromacs(format,99);
fprintf (out,"%s\n",(title && title[0])?title:format);
fprintf (out,"%5d\n",nx);
make_hconf_format(pr,v!=NULL,format);
for (i=0; (i<nx); i++) {
ai=index[i];
resnr=atoms->atom[ai].resnr;
strcpy(resnm," ??? ");
if (resnr < atoms->nres)
strcpy(resnm,*atoms->resname[resnr]);
if (atoms->atom)
strcpy(nm,*atoms->atomname[ai]);
else
strcpy(nm," ??? ");
fprintf(out,"%5d%-5.5s%5.5s%5d",(resnr+1)%100000,resnm,nm,(ai+1)%100000);
/* next fprintf uses built format string */
if (v)
fprintf(out,format,
x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX],v[ai][YY],v[ai][ZZ]);
else
fprintf(out,format,
x[ai][XX], x[ai][YY], x[ai][ZZ]);
}
write_hconf_box(out,pr,box);
fflush(out);
}
int gmx_insert_dummy_atom(int argc, char *argv[])
{
const char *desc[] = {
"\tAdd a dummy atom between atoms -a1 and -a2",
};
gmx_bool bVerbose = FALSE;
int a1=-1,a2=-1;
int insert_at=-1;
const char *tpr_file, *traj_file, *out_file;
t_pargs pa[] = {
{ "-a1", TRUE, etINT,
{&a1}, "Starting atom for bond vector--ie: CD in CNC"},
{ "-a2", TRUE, etINT,
{&a2}, "Ending atom for bond vector--ie: NE in CNC"},
{ "-insert_at", TRUE, etINT,
{&insert_at}, "Desired index for dummy atom. Default = 0"},
{ "-v", FALSE, etBOOL,
{&bVerbose}, "Be slightly more verbose"}
};
t_filenm fnm[] = {
{efTPS, NULL, NULL, ffREAD},
{efTRX, NULL, NULL, ffREAD},
{efTRO, "-o","tilt",ffWRITE},
};
#define NFILE asize(fnm)
#define NPA asize(pa)
output_env_t oenv;
int ngrps, nrefgrps;
t_topology top;
t_atoms *atoms=NULL;
t_trxframe fr,frout;
t_trxstatus *status;
rvec *xtop;
matrix box;
int ePBC;
int flags=TRX_READ_X;
char buffer[1024];
int ftp;
FILE *out_gro = NULL;
t_trxstatus *trxout = NULL;
CopyRight(stderr,argv[0]);
parse_common_args(&argc, argv,
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT | PCA_BE_NICE | PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv);
/* Get inputs */
tpr_file = ftp2fn(efTPS, NFILE, fnm);
traj_file = opt2fn( "-f", NFILE, fnm);
out_file = opt2fn("-o", NFILE, fnm);
ftp = fn2ftp(out_file);
std::cout << "\n\n" << out_file << " " << ftp << std::endl;
/* Open inputs */
read_tps_conf(tpr_file, buffer, &top, &ePBC,
&xtop, NULL, box, TRUE);
sfree(xtop);
atoms = &top.atoms;
gmx_conect gc = NULL;
gc = gmx_conect_generate(&top);
/* Make sure -a1 and -a2 are included and increment by -1 to match internal numbering */
if ( a1<1 || a2<1 || a1==a2 || a1>top.atoms.nr || a2>top.atoms.nr ) {
gmx_fatal(FARGS, "\nAtom numbers -a1 and -a2 defining the bond vector must be specified and different\n");
}
a1--; a2--;
/* Read first frame */
gmx_bool bHaveFirstFrame = read_first_frame(oenv, &status, traj_file, &fr, flags);
if (bHaveFirstFrame) {
set_trxframe_ePBC(&fr,ePBC);
}
if (ftp == efGRO) {
out_gro = ffopen(out_file,"w");
}
else if (ftp == efXTC) {
trxout = open_trx(out_file,"w");
}
/* read file and loop through frames */
int frameN = 0;
do {
if (ftp == efGRO) {
fprintf(out_gro,"Dummy atom inserted into %s, FRAME %i\n",traj_file,frameN);
fprintf(out_gro,"%i\n",top.atoms.nr+1);
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
float MP[3] ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
// GRO format:
// RESID, RESNAME, ATOM, INDEX, X, Y, Z, vX, vY, vZ
//"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
int index = 1;
if (insert_at <= 0) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
0,"TCHG","TCHG",0,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
}
/* Loop over atoms */
int i;
int resid_offset = 0;
for (i=0;i<top.atoms.nr;i++){
if (insert_at == index) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i-1].resind+2,"TCHG","TCHG",index,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
resid_offset++;
}
// Ignoring velocities since I'm using this with mdrun -rerun for
// force calculations only, which don't care about velocities
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i].resind+1 + resid_offset,
*top.atoms.resinfo[top.atoms.atom[i].resind].name,
*top.atoms.atomname[i],
index,
fr.x[i][0], fr.x[i][1], fr.x[i][2],
0.0f,0.0f,0.0f);
index++;
if (index > 99999) {
index = 0;
}
}
/* Get box information */
write_hconf_box(out_gro,1,box);
}
else if (ftp == efXTC) {
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
rvec MP ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
rvec * newX = new rvec [top.atoms.nr+1];
int i = 0;
int offset = 0;
if (insert_at <= 0) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (i=0; i<top.atoms.nr; i++) {
if (insert_at == i) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (int j=0;j<3;j++) {
newX[i+offset][j] = fr.x[i][j];
}
}
frout = fr;
frout.x = newX;
frout.natoms++;
write_trxframe(trxout,&frout,gc);
delete[] newX;
}
frameN++;
} while(read_next_frame(oenv, status, &fr));
if (trxout) {
close_trx(trxout);
}
if (out_gro) {
ffclose(out_gro);
}
return 0;
}
