FILE *fflib_open(const char *file)
{
char *file_fullpath;
FILE *fp;
file_fullpath = gmxlibfn(file);
fprintf(stderr,"Opening force field file %s\n",file_fullpath);
fp = ffopen(file_fullpath,"r");
sfree(file_fullpath);
return fp;
}
static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
int ePBC, matrix box,
gmx_atomprop_t aps, real r_distance, int *atoms_added,
int *residues_added, real rshell, int max_sol,
const output_env_t oenv)
{
int i, nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt, *v_solvt = NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr, onres;
char *lfn;
lfn = gmxlibfn(fn);
strncpy(filename, lfn, STRLEN);
sfree(lfn);
snew(atoms_solvt, 1);
get_stx_coordnum(filename, &(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
{
gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
}
snew(x_solvt, atoms_solvt->nr);
if (v)
{
snew(v_solvt, atoms_solvt->nr);
}
snew(r_solvt, atoms_solvt->nr);
snew(atoms_solvt->resinfo, atoms_solvt->nr);
snew(atoms_solvt->atomname, atoms_solvt->nr);
snew(atoms_solvt->atom, atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr, "Reading solvent configuration%s\n",
v_solvt ? " and velocities" : "");
read_stx_conf(filename, title_solvt, atoms_solvt, x_solvt, v_solvt,
&ePBC_solvt, box_solvt);
fprintf(stderr, "\"%s\"\n", title_solvt);
fprintf(stderr, "solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr, atoms_solvt->nres);
fprintf(stderr, "\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt, r_solvt, aps, r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol = 1;
for (i = 0; (i < DIM); i++)
{
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
{
n_box[i]++;
}
nmol *= n_box[i];
}
fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX], n_box[YY], n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resinfo, atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname, atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom, atoms_solvt->nr*nmol);
srenew(x_solvt, atoms_solvt->nr*nmol);
if (v_solvt)
{
srenew(v_solvt, atoms_solvt->nr*nmol);
}
srenew(r_solvt, atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt, x_solvt, v_solvt, r_solvt, box_solvt, n_box);
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt, x_solvt, v_solvt, r_solvt);
/* add the two configurations */
onr = atoms->nr;
onres = atoms->nres;
add_conf(atoms, x, v, r, TRUE, ePBC, box, FALSE,
atoms_solvt, x_solvt, v_solvt, r_solvt, TRUE, rshell, max_sol, oenv);
*atoms_added = atoms->nr-onr;
*residues_added = atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
*atoms_added, *residues_added);
}
static int low_fflib_search_file_end(const char *ffdir,
gmx_bool bAddCWD,
const char *file_end,
gmx_bool bFatalError,
char ***filenames,
char ***filenames_short)
{
char *ret=NULL;
char *lib,*dir;
char buf[1024];
char *libpath;
gmx_bool env_is_set;
int len_fe,len_name;
char **fns,**fns_short;
char dir_print[GMX_PATH_MAX];
char *pdum;
char *s,fn_dir[GMX_PATH_MAX];
gmx_directory_t dirhandle;
char nextname[STRLEN];
int n,n_thisdir,rc;
len_fe = strlen(file_end);
env_is_set = FALSE;
if (ffdir != NULL)
{
/* Search in current dir and ffdir */
libpath = gmxlibfn(ffdir);
}
else
{
/* GMXLIB can be a path now */
lib = getenv("GMXLIB");
snew(libpath,GMX_PATH_MAX);
if (bAddCWD)
{
sprintf(libpath,"%s%s",".",PATH_SEPARATOR);
}
if (lib != NULL)
{
env_is_set = TRUE;
strncat(libpath,lib,GMX_PATH_MAX);
}
else if (!get_libdir(libpath+strlen(libpath)))
{
strncat(libpath,GMXLIBDIR,GMX_PATH_MAX);
}
}
s = libpath;
n = 0;
fns = NULL;
fns_short = NULL;
/* Loop over all the entries in libpath */
while ((dir=gmx_strsep(&s, PATH_SEPARATOR)) != NULL)
{
rc = gmx_directory_open(&dirhandle,dir);
if (rc==0)
{
strcpy(dir_print,dir);
n_thisdir = 0;
while (gmx_directory_nextfile(dirhandle,nextname,STRLEN-1)==0)
{
nextname[STRLEN-1]=0;
if (debug)
{
fprintf(debug,"dir '%s' %d file '%s'\n",
dir,n_thisdir,nextname);
}
len_name = strlen(nextname);
/* What about case sensitivity? */
if (len_name >= len_fe &&
strcmp(nextname+len_name-len_fe,file_end) == 0)
{
/* We have a match */
srenew(fns,n+1);
sprintf(fn_dir,"%s%c%s",
dir_print,DIR_SEPARATOR,nextname);
/* Copy the file name, possibly including the path. */
fns[n] = strdup(fn_dir);
if (ffdir == NULL)
{
/* We are searching in a path.
* Use the relative path when we use share/top
* from the installation.
* Add the full path when we use the current
* working directory of GMXLIB.
*/
srenew(fns_short,n+1);
if (strcmp(dir,".") == 0 || env_is_set)
{
fns_short[n] = strdup(fn_dir);
}
else
{
fns_short[n] = strdup(nextname);
}
}
n++;
n_thisdir++;
}
}
gmx_directory_close(dirhandle);
sort_filenames(n_thisdir,
fns+n-n_thisdir,
fns_short==NULL ? NULL : fns_short+n-n_thisdir);
}
}
sfree(libpath);
if (n == 0 && bFatalError)
{
if (ffdir != NULL)
{
gmx_fatal(FARGS,"Could not find any files ending on '%s' in the force field directory '%s'",file_end,ffdir);
}
else
{
gmx_fatal(FARGS,"Could not find any files ending on '%s' in the current directory or the GROMACS library search path",file_end);
}
}
*filenames = fns;
if (ffdir == NULL)
{
*filenames_short = fns_short;
}
return n;
}
static void read_tables(FILE *fp,const char *fn,
int ntab,int angle,t_tabledata td[])
{
char *libfn;
char buf[STRLEN];
double **yy=NULL,start,end,dx0,dx1,ssd,vm,vp,f,numf;
int k,i,nx,nx0=0,ny,nny,ns;
gmx_bool bAllZero,bZeroV,bZeroF;
double tabscale;
nny = 2*ntab+1;
libfn = gmxlibfn(fn);
nx = read_xvg(libfn,&yy,&ny);
if (ny != nny)
gmx_fatal(FARGS,"Trying to read file %s, but nr columns = %d, should be %d",
libfn,ny,nny);
if (angle == 0) {
if (yy[0][0] != 0.0)
gmx_fatal(FARGS,
"The first distance in file %s is %f nm instead of %f nm",
libfn,yy[0][0],0.0);
} else {
if (angle == 1)
start = 0.0;
else
start = -180.0;
end = 180.0;
if (yy[0][0] != start || yy[0][nx-1] != end)
gmx_fatal(FARGS,"The angles in file %s should go from %f to %f instead of %f to %f\n",
libfn,start,end,yy[0][0],yy[0][nx-1]);
}
tabscale = (nx-1)/(yy[0][nx-1] - yy[0][0]);
if (fp) {
fprintf(fp,"Read user tables from %s with %d data points.\n",libfn,nx);
if (angle == 0)
fprintf(fp,"Tabscale = %g points/nm\n",tabscale);
}
bAllZero = TRUE;
for(k=0; k<ntab; k++) {
bZeroV = TRUE;
bZeroF = TRUE;
for(i=0; (i < nx); i++) {
if (i >= 2) {
dx0 = yy[0][i-1] - yy[0][i-2];
dx1 = yy[0][i] - yy[0][i-1];
/* Check for 1% deviation in spacing */
if (fabs(dx1 - dx0) >= 0.005*(fabs(dx0) + fabs(dx1))) {
gmx_fatal(FARGS,"In table file '%s' the x values are not equally spaced: %f %f %f",fn,yy[0][i-2],yy[0][i-1],yy[0][i]);
}
}
if (yy[1+k*2][i] != 0) {
bZeroV = FALSE;
if (bAllZero) {
bAllZero = FALSE;
nx0 = i;
}
if (yy[1+k*2][i] > 0.01*GMX_REAL_MAX ||
yy[1+k*2][i] < -0.01*GMX_REAL_MAX) {
gmx_fatal(FARGS,"Out of range potential value %g in file '%s'",
yy[1+k*2][i],fn);
}
}
if (yy[1+k*2+1][i] != 0) {
bZeroF = FALSE;
if (bAllZero) {
bAllZero = FALSE;
nx0 = i;
}
if (yy[1+k*2+1][i] > 0.01*GMX_REAL_MAX ||
yy[1+k*2+1][i] < -0.01*GMX_REAL_MAX) {
gmx_fatal(FARGS,"Out of range force value %g in file '%s'",
yy[1+k*2+1][i],fn);
}
}
}
if (!bZeroV && bZeroF) {
set_forces(fp,angle,nx,1/tabscale,yy[1+k*2],yy[1+k*2+1],k);
} else {
/* Check if the second column is close to minus the numerical
* derivative of the first column.
*/
ssd = 0;
ns = 0;
for(i=1; (i < nx-1); i++) {
vm = yy[1+2*k][i-1];
vp = yy[1+2*k][i+1];
f = yy[1+2*k+1][i];
if (vm != 0 && vp != 0 && f != 0) {
/* Take the centered difference */
numf = -(vp - vm)*0.5*tabscale;
ssd += fabs(2*(f - numf)/(f + numf));
ns++;
}
}
if (ns > 0) {
ssd /= ns;
sprintf(buf,"For the %d non-zero entries for table %d in %s the forces deviate on average %d%% from minus the numerical derivative of the potential\n",ns,k,libfn,(int)(100*ssd+0.5));
if (debug)
fprintf(debug,"%s",buf);
if (ssd > 0.2) {
if (fp)
fprintf(fp,"\nWARNING: %s\n",buf);
fprintf(stderr,"\nWARNING: %s\n",buf);
}
}
}
}
if (bAllZero && fp) {
fprintf(fp,"\nNOTE: All elements in table %s are zero\n\n",libfn);
}
for(k=0; (k<ntab); k++) {
init_table(fp,nx,nx0,tabscale,&(td[k]),TRUE);
for(i=0; (i<nx); i++) {
td[k].x[i] = yy[0][i];
td[k].v[i] = yy[2*k+1][i];
td[k].f[i] = yy[2*k+2][i];
}
}
for(i=0; (i<ny); i++)
sfree(yy[i]);
sfree(yy);
sfree(libfn);
}
static int low_fflib_search_file_end(const char *ffdir,
gmx_bool bAddCWD,
const char *file_end,
gmx_bool bFatalError,
char ***filenames,
char ***filenames_short)
{
char **fns = NULL, **fns_short = NULL;
int n = 0;
try
{
std::vector<std::string> libPaths;
bool bEnvIsSet = false;
if (ffdir != NULL)
{
/* Search ffdir in current dir and library dirs */
libPaths.push_back(gmxlibfn(ffdir));
}
else
{
/* GMXLIB can be a path now */
if (bAddCWD)
{
libPaths.push_back(".");
}
const char *lib = getenv("GMXLIB");
if (lib != NULL)
{
bEnvIsSet = true;
gmx::Path::splitPathEnvironment(lib, &libPaths);
}
else
{
libPaths.push_back(gmx::getProgramContext().defaultLibraryDataPath());
}
}
const int len_fe = strlen(file_end);
std::vector<std::string>::const_iterator i;
for (i = libPaths.begin(); i != libPaths.end(); ++i)
{
const char *dir = i->c_str();
gmx_directory_t dirhandle;
const int rc = gmx_directory_open(&dirhandle, dir);
if (rc == 0)
{
char nextname[STRLEN];
int n_thisdir = 0;
while (gmx_directory_nextfile(dirhandle, nextname, STRLEN-1) == 0)
{
nextname[STRLEN-1] = 0;
if (debug)
{
fprintf(debug, "dir '%s' %d file '%s'\n",
dir, n_thisdir, nextname);
}
const int len_name = strlen(nextname);
/* What about case sensitivity? */
if (len_name >= len_fe &&
strcmp(nextname+len_name-len_fe, file_end) == 0)
{
char fn_dir[GMX_PATH_MAX];
/* We have a match */
srenew(fns, n+1);
sprintf(fn_dir, "%s%c%s", dir, DIR_SEPARATOR, nextname);
/* Copy the file name, possibly including the path. */
fns[n] = gmx_strdup(fn_dir);
if (ffdir == NULL)
{
/* We are searching in a path.
* Use the relative path when we use share/top
* from the installation.
* Add the full path when we use the current
* working directory of GMXLIB.
*/
srenew(fns_short, n+1);
if (strcmp(dir, ".") == 0 || bEnvIsSet)
{
fns_short[n] = gmx_strdup(fn_dir);
}
else
{
fns_short[n] = gmx_strdup(nextname);
}
}
n++;
n_thisdir++;
}
}
gmx_directory_close(dirhandle);
sort_filenames(n_thisdir,
fns+n-n_thisdir,
fns_short == NULL ? NULL : fns_short+n-n_thisdir);
}
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (n == 0 && bFatalError)
{
if (ffdir != NULL)
{
gmx_fatal(FARGS, "Could not find any files ending on '%s' in the force field directory '%s'", file_end, ffdir);
}
else
{
gmx_fatal(FARGS, "Could not find any files ending on '%s' in the current directory or the GROMACS library search path", file_end);
}
}
*filenames = fns;
if (ffdir == NULL)
{
*filenames_short = fns_short;
}
return n;
}
void ps_mat(const char *outf, int nmat, t_matrix mat[], t_matrix mat2[],
gmx_bool bFrame, gmx_bool bDiag, gmx_bool bFirstDiag,
gmx_bool bTitle, gmx_bool bTitleOnce, gmx_bool bYonce, int elegend,
real size, real boxx, real boxy, const char *m2p, const char *m2pout,
int mapoffset)
{
const char *libm2p;
char buf[256], *legend;
t_psdata out;
t_psrec psrec, *psr;
int W, H;
int i, j, x, y, col, leg = 0;
real x0, y0, xx;
real w, h, dw, dh;
int nmap1 = 0, nmap2 = 0, leg_nmap;
t_mapping *map1 = NULL, *map2 = NULL, *leg_map;
gmx_bool bMap1, bNextMap1, bDiscrete;
/* memory leak: */
libm2p = m2p ? gmxlibfn(m2p) : m2p;
get_params(libm2p, m2pout, &psrec);
psr = &psrec;
if (psr->X.major <= 0)
{
tick_spacing((mat[0].flags & MAT_SPATIAL_X) ? mat[0].nx + 1 : mat[0].nx,
mat[0].axis_x, psr->X.offset, 'X',
&(psr->X.major), &(psr->X.minor) );
}
if (psr->X.minor <= 0)
{
psr->X.minor = psr->X.major / 2;
}
if (psr->Y.major <= 0)
{
tick_spacing((mat[0].flags & MAT_SPATIAL_Y) ? mat[0].ny + 1 : mat[0].ny,
mat[0].axis_y, psr->Y.offset, 'Y',
&(psr->Y.major), &(psr->Y.minor) );
}
if (psr->Y.minor <= 0)
{
psr->Y.minor = psr->Y.major / 2;
}
if (boxx > 0)
{
psr->xboxsize = boxx;
psr->yboxsize = boxx;
}
if (boxy > 0)
{
psr->yboxsize = boxy;
}
if (psr->xboxsize == 0)
{
psr->xboxsize = size/mat[0].nx;
printf("Set the x-size of the box to %.3f\n", psr->xboxsize);
}
if (psr->yboxsize == 0)
{
psr->yboxsize = size/mat[0].nx;
printf("Set the y-size of the box to %.3f\n", psr->yboxsize);
}
nmap1 = 0;
for (i = 0; (i < nmat); i++)
{
if (mat[i].nmap > nmap1)
{
nmap1 = mat[i].nmap;
map1 = mat[i].map;
leg = i+1;
}
}
if (leg != 1)
{
printf("Selected legend of matrix # %d for display\n", leg);
}
if (mat2)
{
nmap2 = 0;
for (i = 0; (i < nmat); i++)
{
if (mat2[i].nmap > nmap2)
{
nmap2 = mat2[i].nmap;
map2 = mat2[i].map;
leg = i+1;
}
}
if (leg != 1)
{
printf("Selected legend of matrix # %d for second display\n", leg);
}
}
if ( (mat[0].legend[0] == 0) && psr->legend)
{
strcpy(mat[0].legend, psr->leglabel);
}
bTitle = bTitle && mat[nmat-1].title[0];
bTitleOnce = bTitleOnce && mat[nmat-1].title[0];
psr->bTitle = bTitle;
psr->bTitleOnce = bTitleOnce;
psr->bYonce = bYonce;
/* Set up size of box for nice colors */
box_dim(nmat, mat, mat2, psr, elegend, bFrame, &w, &h, &dw, &dh);
/* Set up bounding box */
W = w+dw;
H = h+dh;
/* Start box at */
x0 = dw;
y0 = dh;
x = W+psr->xoffs;
y = H+psr->yoffs;
if (bFrame)
{
x += 5*DDD;
y += 4*DDD;
}
out = ps_open(outf, 0, 0, x, y);
ps_linewidth(out, psr->linewidth);
ps_init_rgb_box(out, psr->xboxsize, psr->yboxsize);
ps_init_rgb_nbox(out, psr->xboxsize, psr->yboxsize);
ps_translate(out, psr->xoffs, psr->yoffs);
if (bFrame)
{
ps_comment(out, "Here starts the BOX drawing");
draw_boxes(out, x0, y0, w, nmat, mat, psr);
}
for (i = 0; (i < nmat); i++)
{
if (bTitle || (bTitleOnce && i == nmat-1) )
{
/* Print title, if any */
ps_rgb(out, BLACK);
ps_strfont(out, psr->titfont, psr->titfontsize);
if (!mat2 || (strcmp(mat[i].title, mat2[i].title) == 0))
{
strcpy(buf, mat[i].title);
}
else
{
sprintf(buf, "%s / %s", mat[i].title, mat2[i].title);
}
ps_ctext(out, x0+w/2, y0+box_height(&(mat[i]), psr)+psr->titfontsize,
buf, eXCenter);
}
sprintf(buf, "Here starts the filling of box #%d", i);
ps_comment(out, buf);
for (x = 0; (x < mat[i].nx); x++)
{
int nexty;
int nextcol;
xx = x0+x*psr->xboxsize;
ps_moveto(out, xx, y0);
y = 0;
bMap1 = (!mat2 || (x < y || (x == y && bFirstDiag)));
if ((bDiag) || (x != y))
{
col = mat[i].matrix[x][y];
}
else
{
col = -1;
}
for (nexty = 1; (nexty <= mat[i].ny); nexty++)
{
bNextMap1 = (!mat2 || (x < nexty || (x == nexty && bFirstDiag)));
/* TRUE: upper left -> map1 */
/* FALSE: lower right -> map2 */
if ((nexty == mat[i].ny) || (!bDiag && (x == nexty)))
{
nextcol = -1;
}
else
{
nextcol = mat[i].matrix[x][nexty];
}
if ( (nexty == mat[i].ny) || (col != nextcol) || (bMap1 != bNextMap1) )
{
if (col >= 0)
{
if (bMap1)
{
ps_rgb_nbox(out, &(mat[i].map[col].rgb), nexty-y);
}
else
{
ps_rgb_nbox(out, &(mat2[i].map[col].rgb), nexty-y);
}
}
else
{
ps_moverel(out, 0, psr->yboxsize);
}
y = nexty;
bMap1 = bNextMap1;
col = nextcol;
}
}
}
y0 += box_height(&(mat[i]), psr)+box_dh(psr)+box_dh_top(IS_ONCE, psr);
}
if (psr->X.lineatzero || psr->Y.lineatzero)
{
/* reset y0 for first box */
y0 = dh;
ps_comment(out, "Here starts the zero lines drawing");
draw_zerolines(out, x0, y0, w, nmat, mat, psr);
}
if (elegend != elNone)
{
ps_comment(out, "Now it's legend time!");
ps_linewidth(out, psr->linewidth);
if (mat2 == NULL || elegend != elSecond)
{
bDiscrete = mat[0].bDiscrete;
legend = mat[0].legend;
leg_nmap = nmap1;
leg_map = map1;
}
else
{
bDiscrete = mat2[0].bDiscrete;
legend = mat2[0].legend;
leg_nmap = nmap2;
leg_map = map2;
}
if (bDiscrete)
{
leg_discrete(out, psr->legfontsize, DDD, legend,
psr->legfontsize, psr->legfont, leg_nmap, leg_map);
}
else
{
if (elegend != elBoth)
{
leg_continuous(out, x0+w/2, w/2, DDD, legend,
psr->legfontsize, psr->legfont, leg_nmap, leg_map,
mapoffset);
}
else
{
leg_bicontinuous(out, x0+w/2, w, DDD, mat[0].legend, mat2[0].legend,
psr->legfontsize, psr->legfont, nmap1, map1, nmap2, map2);
}
}
ps_comment(out, "Were there, dude");
}
ps_close(out);
}
