bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle)
{
t_tabledata td;
double start;
int i;
bondedtable_t tab;
if (angle < 2)
start = 0;
else
start = -180.0;
read_tables(fplog,fn,1,angle,&td);
if (angle > 0) {
/* Convert the table from degrees to radians */
for(i=0; i<td.nx; i++) {
td.x[i] *= DEG2RAD;
td.f[i] *= RAD2DEG;
}
td.tabscale *= RAD2DEG;
}
tab.n = td.nx;
tab.scale = td.tabscale;
snew(tab.tab,tab.n*4);
copy2table(tab.n,0,4,td.x,td.v,td.f,tab.tab);
done_tabledata(&td);
return tab;
}
t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
const t_forcerec *fr,
const char *fn,
real rtab)
{
const char *fns[3] = { "gbctab.xvg", "gbdtab.xvg", "gbrtab.xvg" };
const char *fns14[3] = { "gbctab14.xvg", "gbdtab14.xvg", "gbrtab14.xvg" };
FILE *fp;
t_tabledata *td;
gmx_bool bReadTab,bGenTab;
real x0,y0,yp;
int i,j,k,nx,nx0,tabsel[etiNR];
void * p_tmp;
double r,r2,Vtab,Ftab,expterm;
t_forcetable table;
double abs_error_r, abs_error_r2;
double rel_error_r, rel_error_r2;
double rel_error_r_old=0, rel_error_r2_old=0;
double x0_r_error, x0_r2_error;
/* Only set a Coulomb table for GB */
/*
tabsel[0]=etabGB;
tabsel[1]=-1;
tabsel[2]=-1;
*/
/* Set the table dimensions for GB, not really necessary to
* use etiNR (since we only have one table, but ...)
*/
snew(td,1);
table.r = fr->gbtabr;
table.scale = fr->gbtabscale;
table.scale_exp = 0;
table.n = table.scale*table.r;
nx0 = 0;
nx = table.scale*table.r;
/* Check whether we have to read or generate
* We will always generate a table, so remove the read code
* (Compare with original make_table function
*/
bReadTab = FALSE;
bGenTab = TRUE;
/* Each table type (e.g. coul,lj6,lj12) requires four
* numbers per datapoint. For performance reasons we want
* the table data to be aligned to 16-byte. This is accomplished
* by allocating 16 bytes extra to a temporary pointer, and then
* calculating an aligned pointer. This new pointer must not be
* used in a free() call, but thankfully we're sloppy enough not
* to do this :-)
*/
/* 4 fp entries per table point, nx+1 points, and 16 bytes extra
to align it. */
p_tmp = malloc(4*(nx+1)*sizeof(real)+16);
/* align it - size_t has the same same as a pointer */
table.tab = (real *) (((size_t) p_tmp + 16) & (~((size_t) 15)));
init_table(out,nx,nx0,table.scale,&(td[0]),!bReadTab);
/* Local implementation so we don't have to use the etabGB
* enum above, which will cause problems later when
* making the other tables (right now even though we are using
* GB, the normal Coulomb tables will be created, but this
* will cause a problem since fr->eeltype==etabGB which will not
* be defined in fill_table and set_table_type
*/
for(i=nx0;i<nx;i++)
{
Vtab = 0.0;
Ftab = 0.0;
r = td->x[i];
r2 = r*r;
expterm = exp(-0.25*r2);
Vtab = 1/sqrt(r2+expterm);
Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
/* Convert to single precision when we store to mem */
td->v[i] = Vtab;
td->f[i] = Ftab;
}
copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
if(bDebugMode())
{
fp=xvgropen(fns[0],fns[0],"r","V",oenv);
/* plot the output 5 times denser than the table data */
/* for(i=5*nx0;i<5*table.n;i++) */
for(i=nx0;i<table.n;i++)
{
/* x0=i*table.r/(5*table.n); */
x0=i*table.r/table.n;
evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
gmx_fio_fclose(fp);
}
/*
for(i=100*nx0;i<99.81*table.n;i++)
{
r = i*table.r/(100*table.n);
r2 = r*r;
expterm = exp(-0.25*r2);
Vtab = 1/sqrt(r2+expterm);
Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
evaluate_table(table.tab,0,4,table.scale,r,&y0,&yp);
printf("gb: i=%d, x0=%g, y0=%15.15f, Vtab=%15.15f, yp=%15.15f, Ftab=%15.15f\n",i,r, y0, Vtab, yp, Ftab);
abs_error_r=fabs(y0-Vtab);
abs_error_r2=fabs(yp-(-1)*Ftab);
rel_error_r=abs_error_r/y0;
rel_error_r2=fabs(abs_error_r2/yp);
if(rel_error_r>rel_error_r_old)
{
rel_error_r_old=rel_error_r;
x0_r_error=x0;
}
if(rel_error_r2>rel_error_r2_old)
{
rel_error_r2_old=rel_error_r2;
x0_r2_error=x0;
}
}
printf("gb: MAX REL ERROR IN R=%15.15f, MAX REL ERROR IN R2=%15.15f\n",rel_error_r_old, rel_error_r2_old);
printf("gb: XO_R=%g, X0_R2=%g\n",x0_r_error, x0_r2_error);
exit(1); */
done_tabledata(&(td[0]));
sfree(td);
return table;
}
t_forcetable make_tables(FILE *out,const output_env_t oenv,
const t_forcerec *fr,
gmx_bool bVerbose,const char *fn,
real rtab,int flags)
{
const char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
const char *fns14[3] = { "ctab14.xvg", "dtab14.xvg", "rtab14.xvg" };
FILE *fp;
t_tabledata *td;
gmx_bool b14only,bReadTab,bGenTab;
real x0,y0,yp;
int i,j,k,nx,nx0,tabsel[etiNR];
t_forcetable table;
b14only = (flags & GMX_MAKETABLES_14ONLY);
if (flags & GMX_MAKETABLES_FORCEUSER) {
tabsel[etiCOUL] = etabUSER;
tabsel[etiLJ6] = etabUSER;
tabsel[etiLJ12] = etabUSER;
} else {
set_table_type(tabsel,fr,b14only);
}
snew(td,etiNR);
table.r = rtab;
table.scale = 0;
table.n = 0;
table.scale_exp = 0;
nx0 = 10;
nx = 0;
/* Check whether we have to read or generate */
bReadTab = FALSE;
bGenTab = FALSE;
for(i=0; (i<etiNR); i++) {
if (ETAB_USER(tabsel[i]))
bReadTab = TRUE;
if (tabsel[i] != etabUSER)
bGenTab = TRUE;
}
if (bReadTab) {
read_tables(out,fn,etiNR,0,td);
if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY)) {
rtab = td[0].x[td[0].nx-1];
table.n = td[0].nx;
nx = table.n;
} else {
if (td[0].x[td[0].nx-1] < rtab)
gmx_fatal(FARGS,"Tables in file %s not long enough for cut-off:\n"
"\tshould be at least %f nm\n",fn,rtab);
nx = table.n = (int)(rtab*td[0].tabscale + 0.5);
}
table.scale = td[0].tabscale;
nx0 = td[0].nx0;
}
if (bGenTab) {
if (!bReadTab) {
#ifdef GMX_DOUBLE
table.scale = 2000.0;
#else
table.scale = 500.0;
#endif
nx = table.n = rtab*table.scale;
}
}
if (fr->bBHAM) {
if(fr->bham_b_max!=0)
table.scale_exp = table.scale/fr->bham_b_max;
else
table.scale_exp = table.scale;
}
/* Each table type (e.g. coul,lj6,lj12) requires four
* numbers per nx+1 data points. For performance reasons we want
* the table data to be aligned to 16-byte.
*/
snew_aligned(table.tab, 12*(nx+1)*sizeof(real),16);
for(k=0; (k<etiNR); k++) {
if (tabsel[k] != etabUSER) {
init_table(out,nx,nx0,
(tabsel[k] == etabEXPMIN) ? table.scale_exp : table.scale,
&(td[k]),!bReadTab);
fill_table(&(td[k]),tabsel[k],fr);
if (out)
fprintf(out,"%s table with %d data points for %s%s.\n"
"Tabscale = %g points/nm\n",
ETAB_USER(tabsel[k]) ? "Modified" : "Generated",
td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
td[k].tabscale);
}
copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,table.tab);
if (bDebugMode() && bVerbose) {
if (b14only)
fp=xvgropen(fns14[k],fns14[k],"r","V",oenv);
else
fp=xvgropen(fns[k],fns[k],"r","V",oenv);
/* plot the output 5 times denser than the table data */
for(i=5*((nx0+1)/2); i<5*table.n; i++) {
x0 = i*table.r/(5*(table.n-1));
evaluate_table(table.tab,4*k,12,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
gmx_fio_fclose(fp);
}
done_tabledata(&(td[k]));
}
sfree(td);
return table;
}
t_forcetable make_atf_table(FILE *out,const output_env_t oenv,
const t_forcerec *fr,
const char *fn,
matrix box)
{
const char *fns[3] = { "tf_tab.xvg", "atfdtab.xvg", "atfrtab.xvg" };
FILE *fp;
t_tabledata *td;
real x0,y0,yp,rtab;
int i,nx,nx0;
void * p_tmp;
real rx, ry, rz, box_r;
t_forcetable table;
/* Set the table dimensions for ATF, not really necessary to
* use etiNR (since we only have one table, but ...)
*/
snew(td,1);
if (fr->adress_type == eAdressSphere){
/* take half box diagonal direction as tab range */
rx = 0.5*box[0][0]+0.5*box[1][0]+0.5*box[2][0];
ry = 0.5*box[0][1]+0.5*box[1][1]+0.5*box[2][1];
rz = 0.5*box[0][2]+0.5*box[1][2]+0.5*box[2][2];
box_r = sqrt(rx*rx+ry*ry+rz*rz);
}else{
/* xsplit: take half box x direction as tab range */
box_r = box[0][0]/2;
}
table.r = box_r;
table.scale = 0;
table.n = 0;
table.scale_exp = 0;
nx0 = 10;
nx = 0;
read_tables(out,fn,1,0,td);
rtab = td[0].x[td[0].nx-1];
if (fr->adress_type == eAdressXSplit && (rtab < box[0][0]/2)){
gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
"\tshould extend to at least half the length of the box in x-direction"
"%f\n",fn,rtab, box[0][0]/2);
}
if (rtab < box_r){
gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
"\tshould extend to at least for spherical adress"
"%f (=distance from center to furthermost point in box \n",fn,rtab, box_r);
}
table.n = td[0].nx;
nx = table.n;
table.scale = td[0].tabscale;
nx0 = td[0].nx0;
/* Each table type (e.g. coul,lj6,lj12) requires four
* numbers per datapoint. For performance reasons we want
* the table data to be aligned to 16-byte. This is accomplished
* by allocating 16 bytes extra to a temporary pointer, and then
* calculating an aligned pointer. This new pointer must not be
* used in a free() call, but thankfully we're sloppy enough not
* to do this :-)
*/
/* 4 fp entries per table point, nx+1 points, and 16 bytes extra
to align it. */
p_tmp = malloc(4*(nx+1)*sizeof(real)+16);
/* align it - size_t has the same same as a pointer */
table.tab = (real *) (((size_t) p_tmp + 16) & (~((size_t) 15)));
copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
if(bDebugMode())
{
fp=xvgropen(fns[0],fns[0],"r","V",oenv);
/* plot the output 5 times denser than the table data */
/* for(i=5*nx0;i<5*table.n;i++) */
for(i=5*((nx0+1)/2); i<5*table.n; i++)
{
/* x0=i*table.r/(5*table.n); */
x0 = i*table.r/(5*(table.n-1));
evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
ffclose(fp);
}
done_tabledata(&(td[0]));
sfree(td);
return table;
}
t_forcetable make_tables(FILE *out,const output_env_t oenv,
const t_forcerec *fr,
gmx_bool bVerbose,const char *fn,
real rtab,int flags)
{
const char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
const char *fns14[3] = { "ctab14.xvg", "dtab14.xvg", "rtab14.xvg" };
FILE *fp;
t_tabledata *td;
gmx_bool b14only,bReadTab,bGenTab;
real x0,y0,yp;
int i,j,k,nx,nx0,tabsel[etiNR];
real scalefactor;
t_forcetable table;
b14only = (flags & GMX_MAKETABLES_14ONLY);
if (flags & GMX_MAKETABLES_FORCEUSER) {
tabsel[etiCOUL] = etabUSER;
tabsel[etiLJ6] = etabUSER;
tabsel[etiLJ12] = etabUSER;
} else {
set_table_type(tabsel,fr,b14only);
}
snew(td,etiNR);
table.r = rtab;
table.scale = 0;
table.n = 0;
table.scale_exp = 0;
nx0 = 10;
nx = 0;
table.interaction = GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP;
table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
table.formatsize = 4;
table.ninteractions = 3;
table.stride = table.formatsize*table.ninteractions;
/* Check whether we have to read or generate */
bReadTab = FALSE;
bGenTab = FALSE;
for(i=0; (i<etiNR); i++) {
if (ETAB_USER(tabsel[i]))
bReadTab = TRUE;
if (tabsel[i] != etabUSER)
bGenTab = TRUE;
}
if (bReadTab) {
read_tables(out,fn,etiNR,0,td);
if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY)) {
rtab = td[0].x[td[0].nx-1];
table.n = td[0].nx;
nx = table.n;
} else {
if (td[0].x[td[0].nx-1] < rtab)
gmx_fatal(FARGS,"Tables in file %s not long enough for cut-off:\n"
"\tshould be at least %f nm\n",fn,rtab);
nx = table.n = (int)(rtab*td[0].tabscale + 0.5);
}
table.scale = td[0].tabscale;
nx0 = td[0].nx0;
}
if (bGenTab) {
if (!bReadTab) {
#ifdef GMX_DOUBLE
table.scale = 2000.0;
#else
table.scale = 500.0;
#endif
nx = table.n = rtab*table.scale;
}
}
if (fr->bBHAM) {
if(fr->bham_b_max!=0)
table.scale_exp = table.scale/fr->bham_b_max;
else
table.scale_exp = table.scale;
}
/* Each table type (e.g. coul,lj6,lj12) requires four
* numbers per nx+1 data points. For performance reasons we want
* the table data to be aligned to 16-byte.
*/
snew_aligned(table.data, 12*(nx+1)*sizeof(real),16);
for(k=0; (k<etiNR); k++) {
if (tabsel[k] != etabUSER) {
init_table(out,nx,nx0,
(tabsel[k] == etabEXPMIN) ? table.scale_exp : table.scale,
&(td[k]),!bReadTab);
fill_table(&(td[k]),tabsel[k],fr);
if (out)
fprintf(out,"%s table with %d data points for %s%s.\n"
"Tabscale = %g points/nm\n",
ETAB_USER(tabsel[k]) ? "Modified" : "Generated",
td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
td[k].tabscale);
}
/* Set scalefactor for c6/c12 tables. This is because we save flops in the non-table kernels
* by including the derivative constants (6.0 or 12.0) in the parameters, since
* we no longer calculate force in most steps. This means the c6/c12 parameters
* have been scaled up, so we need to scale down the table interactions too.
* It comes here since we need to scale user tables too.
*/
if(k==etiLJ6)
{
scalefactor = 1.0/6.0;
}
else if(k==etiLJ12 && tabsel[k]!=etabEXPMIN)
{
scalefactor = 1.0/12.0;
}
else
{
scalefactor = 1.0;
}
copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,scalefactor,table.data);
if (bDebugMode() && bVerbose) {
if (b14only)
fp=xvgropen(fns14[k],fns14[k],"r","V",oenv);
else
fp=xvgropen(fns[k],fns[k],"r","V",oenv);
/* plot the output 5 times denser than the table data */
for(i=5*((nx0+1)/2); i<5*table.n; i++) {
x0 = i*table.r/(5*(table.n-1));
evaluate_table(table.data,4*k,12,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
gmx_fio_fclose(fp);
}
done_tabledata(&(td[k]));
}
sfree(td);
return table;
}
void make_tables(FILE *out,t_forcerec *fr,bool bVerbose,char *fn)
{
static char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
FILE *fp;
t_tabledata *td;
bool bReadTab,bGenTab;
real x0,y0,yp,rtab;
int i,j,k,nx,nx0,tabsel[etiNR];
set_table_type(tabsel,fr);
snew(td,etiNR);
fr->tabscale = 0;
rtab = fr->rtab;
nx0 = 10;
nx = 0;
/* Check whether we have to read or generate */
bReadTab = FALSE;
bGenTab = FALSE;
for(i=0; (i<etiNR); i++) {
if (tabsel[i] == etabUSER)
bReadTab = TRUE;
else
bGenTab = TRUE;
}
if (bReadTab) {
read_tables(out,fn,td);
fr->tabscale = td[0].tabscale;
fr->rtab = td[0].x[td[0].nx-1];
nx0 = td[0].nx0;
nx = fr->ntab = fr->rtab*fr->tabscale;
if (fr->rtab < rtab)
fatal_error(0,"Tables in file %s not long enough for cut-off:\n"
"\tshould be at least %f nm\n",fn,rtab);
}
if (bGenTab) {
if (!bReadTab) {
#ifdef DOUBLE
fr->tabscale = 2000.0;
#else
fr->tabscale = 500.0;
#endif
nx = fr->ntab = fr->rtab*fr->tabscale;
}
}
snew(fr->coulvdwtab,12*(nx+1)+1);
for(k=0; (k<etiNR); k++) {
if (tabsel[k] != etabUSER) {
init_table(out,nx,nx0,tabsel[k],
(tabsel[k] == etabEXPMIN) ? fr->tabscale_exp : fr->tabscale,
&(td[k]),!bReadTab);
fill_table(&(td[k]),tabsel[k],fr);
if (out)
fprintf(out,"Generated table with %d data points for %s.\n"
"Tabscale = %g points/nm\n",
td[k].nx,tabnm[tabsel[k]],td[k].tabscale);
}
copy2table(td[k].nx,k*4,12,td[k].x,td[k].v,td[k].v2,fr->coulvdwtab,-1);
if (bDebugMode() && bVerbose) {
fp=xvgropen(fns[k],fns[k],"r","V");
for(i=td[k].nx0+1; (i<td[k].nx-1); i++) {
for(j=0; (j<4); j++) {
x0=td[k].x[i]+0.25*j*(td[k].x[i+1]-td[k].x[i]);
splint(td[k].x,td[k].v,td[k].v2,nx-3,x0,&y0,&yp);
if(fp)
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
}
ffclose(fp);
}
done_tabledata(&(td[k]));
}
sfree(td);
}
