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33 * GROwing Monsters And Cloning Shrimps
44 #include "gmx_fatal.h"
54 /* All the possible (implemented) table functions */
79 /** Evaluates to true if the table type contains user data. */
80 #define ETAB_USER(e) ((e) == etabUSER || \
81 (e) == etabEwaldUser || (e) == etabEwaldUserSwitch)
88 /* This structure holds name and a flag that tells whether
89 this is a Coulomb type funtion */
90 static const t_tab_props tprops[etabNR] = {
93 { "LJ6Shift", FALSE },
94 { "LJ12Shift", FALSE },
100 { "Ewald-Switch", TRUE },
101 { "Ewald-User", TRUE },
102 { "Ewald-User-Switch", TRUE },
103 { "LJ6Switch", FALSE },
104 { "LJ12Switch", FALSE },
105 { "COULSwitch", TRUE },
106 { "LJ6-Encad shift", FALSE },
107 { "LJ12-Encad shift", FALSE },
108 { "COUL-Encad shift", TRUE },
113 /* Index in the table that says which function to use */
114 enum { etiCOUL, etiLJ6, etiLJ12, etiNR };
122 #define pow2(x) ((x)*(x))
123 #define pow3(x) ((x)*(x)*(x))
124 #define pow4(x) ((x)*(x)*(x)*(x))
125 #define pow5(x) ((x)*(x)*(x)*(x)*(x))
127 /* Calculate the potential and force for an r value
128 * in exactly the same way it is done in the inner loop.
129 * VFtab is a pointer to the table data, offset is
130 * the point where we should begin and stride is
131 * 4 if we have a buckingham table, 3 otherwise.
132 * If you want to evaluate table no N, set offset to 4*N.
134 * We use normal precision here, since that is what we
135 * will use in the inner loops.
137 static void evaluate_table(real VFtab[], int offset, int stride,
138 real tabscale, real r, real *y, real *yp)
142 real Y,F,Geps,Heps2,Fp;
151 Geps = eps*VFtab[n+2];
152 Heps2 = eps2*VFtab[n+3];
155 *yp = (Fp+Geps+2.0*Heps2)*tabscale;
158 static void copy2table(int n,int offset,int stride,
159 double x[],double Vtab[],double Ftab[],
162 /* Use double prec. for the intermediary variables
163 * and temporary x/vtab/vtab2 data to avoid unnecessary
170 for(i=0; (i<n); i++) {
174 G = 3*(Vtab[i+1] - Vtab[i]) + (Ftab[i+1] + 2*Ftab[i])*h;
175 H = -2*(Vtab[i+1] - Vtab[i]) - (Ftab[i+1] + Ftab[i])*h;
177 /* Fill the last entry with a linear potential,
178 * this is mainly for rounding issues with angle and dihedral potentials.
184 nn0 = offset + i*stride;
192 static void init_table(FILE *fp,int n,int nx0,
193 double tabscale,t_tabledata *td,gmx_bool bAlloc)
199 td->tabscale = tabscale;
205 for(i=0; (i<td->nx); i++)
206 td->x[i] = i/tabscale;
209 static void spline_forces(int nx,double h,double v[],gmx_bool bS3,gmx_bool bE3,
216 /* Formulas can be found in:
217 * H.J.C. Berendsen, Simulating the Physical World, Cambridge 2007
220 if (nx < 4 && (bS3 || bE3))
221 gmx_fatal(FARGS,"Can not generate splines with third derivative boundary conditions with less than 4 (%d) points",nx);
223 /* To make life easy we initially set the spacing to 1
224 * and correct for this at the end.
228 /* Fit V''' at the start */
229 v3 = v[3] - 3*v[2] + 3*v[1] - v[0];
231 fprintf(debug,"The left third derivative is %g\n",v3/(h*h*h));
232 b_s = 2*(v[1] - v[0]) + v3/6;
236 /* Fit V'' at the start */
239 v2 = -v[3] + 4*v[2] - 5*v[1] + 2*v[0];
240 /* v2 = v[2] - 2*v[1] + v[0]; */
242 fprintf(debug,"The left second derivative is %g\n",v2/(h*h));
243 b_s = 3*(v[1] - v[0]) - v2/2;
247 b_s = 3*(v[2] - v[0]) + f[0]*h;
251 /* Fit V''' at the end */
252 v3 = v[nx-1] - 3*v[nx-2] + 3*v[nx-3] - v[nx-4];
254 fprintf(debug,"The right third derivative is %g\n",v3/(h*h*h));
255 b_e = 2*(v[nx-1] - v[nx-2]) + v3/6;
258 /* V'=0 at the end */
259 b_e = 3*(v[nx-1] - v[nx-3]) + f[nx-1]*h;
264 beta = (bS3 ? 1 : 4);
266 /* For V'' fitting */
267 /* beta = (bS3 ? 2 : 4); */
270 for(i=start+1; i<end; i++) {
273 b = 3*(v[i+1] - v[i-1]);
274 f[i] = (b - f[i-1])/beta;
276 gamma[end-1] = 1/beta;
277 beta = (bE3 ? 1 : 4) - gamma[end-1];
278 f[end-1] = (b_e - f[end-2])/beta;
280 for(i=end-2; i>=start; i--)
281 f[i] -= gamma[i+1]*f[i+1];
284 /* Correct for the minus sign and the spacing */
285 for(i=start; i<end; i++)
289 static void set_forces(FILE *fp,int angle,
290 int nx,double h,double v[],double f[],
297 "Force generation for dihedral tables is not (yet) implemented");
300 while (v[start] == 0)
312 fprintf(fp,"Generating forces for table %d, boundary conditions: V''' at %g, %s at %g\n",
313 table+1,start*h,end==nx ? "V'''" : "V'=0",(end-1)*h);
314 spline_forces(end-start,h,v+start,TRUE,end==nx,f+start);
317 static void read_tables(FILE *fp,const char *fn,
318 int ntab,int angle,t_tabledata td[])
322 double **yy=NULL,start,end,dx0,dx1,ssd,vm,vp,f,numf;
323 int k,i,nx,nx0=0,ny,nny,ns;
324 gmx_bool bAllZero,bZeroV,bZeroF;
328 libfn = gmxlibfn(fn);
329 nx = read_xvg(libfn,&yy,&ny);
331 gmx_fatal(FARGS,"Trying to read file %s, but nr columns = %d, should be %d",
336 "The first distance in file %s is %f nm instead of %f nm",
344 if (yy[0][0] != start || yy[0][nx-1] != end)
345 gmx_fatal(FARGS,"The angles in file %s should go from %f to %f instead of %f to %f\n",
346 libfn,start,end,yy[0][0],yy[0][nx-1]);
349 tabscale = (nx-1)/(yy[0][nx-1] - yy[0][0]);
352 fprintf(fp,"Read user tables from %s with %d data points.\n",libfn,nx);
354 fprintf(fp,"Tabscale = %g points/nm\n",tabscale);
358 for(k=0; k<ntab; k++) {
361 for(i=0; (i < nx); i++) {
363 dx0 = yy[0][i-1] - yy[0][i-2];
364 dx1 = yy[0][i] - yy[0][i-1];
365 /* Check for 1% deviation in spacing */
366 if (fabs(dx1 - dx0) >= 0.005*(fabs(dx0) + fabs(dx1))) {
367 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]);
370 if (yy[1+k*2][i] != 0) {
376 if (yy[1+k*2][i] > 0.01*GMX_REAL_MAX ||
377 yy[1+k*2][i] < -0.01*GMX_REAL_MAX) {
378 gmx_fatal(FARGS,"Out of range potential value %g in file '%s'",
382 if (yy[1+k*2+1][i] != 0) {
388 if (yy[1+k*2+1][i] > 0.01*GMX_REAL_MAX ||
389 yy[1+k*2+1][i] < -0.01*GMX_REAL_MAX) {
390 gmx_fatal(FARGS,"Out of range force value %g in file '%s'",
396 if (!bZeroV && bZeroF) {
397 set_forces(fp,angle,nx,1/tabscale,yy[1+k*2],yy[1+k*2+1],k);
399 /* Check if the second column is close to minus the numerical
400 * derivative of the first column.
404 for(i=1; (i < nx-1); i++) {
408 if (vm != 0 && vp != 0 && f != 0) {
409 /* Take the centered difference */
410 numf = -(vp - vm)*0.5*tabscale;
411 ssd += fabs(2*(f - numf)/(f + numf));
417 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));
419 fprintf(debug,"%s",buf);
422 fprintf(fp,"\nWARNING: %s\n",buf);
423 fprintf(stderr,"\nWARNING: %s\n",buf);
428 if (bAllZero && fp) {
429 fprintf(fp,"\nNOTE: All elements in table %s are zero\n\n",libfn);
432 for(k=0; (k<ntab); k++) {
433 init_table(fp,nx,nx0,tabscale,&(td[k]),TRUE);
434 for(i=0; (i<nx); i++) {
435 td[k].x[i] = yy[0][i];
436 td[k].v[i] = yy[2*k+1][i];
437 td[k].f[i] = yy[2*k+2][i];
440 for(i=0; (i<ny); i++)
446 static void done_tabledata(t_tabledata *td)
458 static void fill_table(t_tabledata *td,int tp,const t_forcerec *fr)
460 /* Fill the table according to the formulas in the manual.
461 * In principle, we only need the potential and the second
462 * derivative, but then we would have to do lots of calculations
463 * in the inner loop. By precalculating some terms (see manual)
464 * we get better eventual performance, despite a larger table.
466 * Since some of these higher-order terms are very small,
467 * we always use double precision to calculate them here, in order
468 * to avoid unnecessary loss of precision.
475 double r1,rc,r12,r13;
477 double expr,Vtab,Ftab;
478 /* Parameters for David's function */
479 double A=0,B=0,C=0,A_3=0,B_4=0;
480 /* Parameters for the switching function */
482 /* Temporary parameters */
483 gmx_bool bSwitch,bShift;
484 double ewc=fr->ewaldcoeff;
485 double isp= 0.564189583547756;
487 bSwitch = ((tp == etabLJ6Switch) || (tp == etabLJ12Switch) ||
488 (tp == etabCOULSwitch) ||
489 (tp == etabEwaldSwitch) || (tp == etabEwaldUserSwitch));
490 bShift = ((tp == etabLJ6Shift) || (tp == etabLJ12Shift) ||
495 if (tprops[tp].bCoulomb) {
496 r1 = fr->rcoulomb_switch;
500 r1 = fr->rvdw_switch;
504 ksw = 1.0/(pow5(rc-r1));
510 else if (tp == etabLJ6Shift)
515 A = p * ((p+1)*r1-(p+4)*rc)/(pow(rc,p+2)*pow2(rc-r1));
516 B = -p * ((p+1)*r1-(p+3)*rc)/(pow(rc,p+2)*pow3(rc-r1));
517 C = 1.0/pow(rc,p)-A/3.0*pow3(rc-r1)-B/4.0*pow4(rc-r1);
518 if (tp == etabLJ6Shift) {
526 if (debug) { fprintf(debug,"Setting up tables\n"); fflush(debug); }
529 fp=xvgropen("switch.xvg","switch","r","s");
532 for(i=td->nx0; (i<td->nx); i++) {
536 if (gmx_within_tol(reppow,12.0,10*GMX_DOUBLE_EPS)) {
539 r12 = pow(r,-reppow);
544 /* swi is function, swi1 1st derivative and swi2 2nd derivative */
545 /* The switch function is 1 for r<r1, 0 for r>rc, and smooth for
546 * r1<=r<=rc. The 1st and 2nd derivatives are both zero at
548 * ksw is just the constant 1/(rc-r1)^5, to save some calculations...
557 swi = 1 - 10*pow3(r-r1)*ksw*pow2(rc-r1)
558 + 15*pow4(r-r1)*ksw*(rc-r1) - 6*pow5(r-r1)*ksw;
559 swi1 = -30*pow2(r-r1)*ksw*pow2(rc-r1)
560 + 60*pow3(r-r1)*ksw*(rc-r1) - 30*pow4(r-r1)*ksw;
563 else { /* not really needed, but avoids compiler warnings... */
568 fprintf(fp,"%10g %10g %10g %10g\n",r,swi,swi1,swi2);
591 Ftab = reppow*Vtab/r;
598 Ftab = reppow*Vtab/r;
603 Vtab = -(r6-6.0*(rc-r)*rc6/rc-rc6);
604 Ftab = -(6.0*r6/r-6.0*rc6/rc);
612 Vtab = r12-12.0*(rc-r)*rc6*rc6/rc-1.0*rc6*rc6;
613 Ftab = 12.0*r12/r-12.0*rc6*rc6/rc;
631 case etabEwaldSwitch:
632 Vtab = gmx_erfc(ewc*r)/r;
633 Ftab = gmx_erfc(ewc*r)/r2+2*exp(-(ewc*ewc*r2))*ewc*isp/r;
636 case etabEwaldUserSwitch:
637 /* Only calculate minus the reciprocal space contribution */
638 Vtab = -gmx_erf(ewc*r)/r;
639 Ftab = -gmx_erf(ewc*r)/r2+2*exp(-(ewc*ewc*r2))*ewc*isp/r;
643 Vtab = 1.0/r + fr->k_rf*r2 - fr->c_rf;
644 Ftab = 1.0/r2 - 2*fr->k_rf*r;
645 if (tp == etabRF_ZERO && r >= rc) {
657 Vtab = 1.0/r-(rc-r)/(rc*rc)-1.0/rc;
658 Ftab = 1.0/r2-1.0/(rc*rc);
665 gmx_fatal(FARGS,"Table type %d not implemented yet. (%s,%d)",
666 tp,__FILE__,__LINE__);
669 /* Normal coulomb with cut-off correction for potential */
672 /* If in Shifting range add something to it */
676 Vtab += - A_3*r13 - B_4*r12*r12;
677 Ftab += A*r12 + B*r13;
687 if ((r > r1) && bSwitch) {
688 Ftab = Ftab*swi - Vtab*swi1;
692 /* Convert to single precision when we store to mem */
697 /* Continue the table linearly from nx0 to 0.
698 * These values are only required for energy minimization with overlap or TPI.
700 for(i=td->nx0-1; i>=0; i--) {
701 td->v[i] = td->v[i+1] + td->f[i+1]*(td->x[i+1] - td->x[i]);
702 td->f[i] = td->f[i+1];
710 static void set_table_type(int tabsel[],const t_forcerec *fr,gmx_bool b14only)
714 /* Set the different table indices.
720 switch (fr->eeltype) {
726 case eelPMEUSERSWITCH:
733 eltype = fr->eeltype;
738 tabsel[etiCOUL] = etabCOUL;
741 tabsel[etiCOUL] = etabShift;
744 if (fr->rcoulomb > fr->rcoulomb_switch)
745 tabsel[etiCOUL] = etabShift;
747 tabsel[etiCOUL] = etabCOUL;
752 tabsel[etiCOUL] = etabEwald;
755 tabsel[etiCOUL] = etabEwaldSwitch;
758 tabsel[etiCOUL] = etabEwaldUser;
760 case eelPMEUSERSWITCH:
761 tabsel[etiCOUL] = etabEwaldUserSwitch;
766 tabsel[etiCOUL] = etabRF;
769 tabsel[etiCOUL] = etabRF_ZERO;
772 tabsel[etiCOUL] = etabCOULSwitch;
775 tabsel[etiCOUL] = etabUSER;
778 tabsel[etiCOUL] = etabCOULEncad;
781 gmx_fatal(FARGS,"Invalid eeltype %d",eltype);
784 /* Van der Waals time */
785 if (fr->bBHAM && !b14only) {
786 tabsel[etiLJ6] = etabLJ6;
787 tabsel[etiLJ12] = etabEXPMIN;
789 if (b14only && fr->vdwtype != evdwUSER)
792 vdwtype = fr->vdwtype;
796 tabsel[etiLJ6] = etabLJ6Switch;
797 tabsel[etiLJ12] = etabLJ12Switch;
800 tabsel[etiLJ6] = etabLJ6Shift;
801 tabsel[etiLJ12] = etabLJ12Shift;
804 tabsel[etiLJ6] = etabUSER;
805 tabsel[etiLJ12] = etabUSER;
808 tabsel[etiLJ6] = etabLJ6;
809 tabsel[etiLJ12] = etabLJ12;
812 tabsel[etiLJ6] = etabLJ6Encad;
813 tabsel[etiLJ12] = etabLJ12Encad;
816 gmx_fatal(FARGS,"Invalid vdwtype %d in %s line %d",vdwtype,
822 t_forcetable make_tables(FILE *out,const output_env_t oenv,
823 const t_forcerec *fr,
824 gmx_bool bVerbose,const char *fn,
827 const char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
828 const char *fns14[3] = { "ctab14.xvg", "dtab14.xvg", "rtab14.xvg" };
831 gmx_bool b14only,bReadTab,bGenTab;
833 int i,j,k,nx,nx0,tabsel[etiNR];
837 b14only = (flags & GMX_MAKETABLES_14ONLY);
839 if (flags & GMX_MAKETABLES_FORCEUSER) {
840 tabsel[etiCOUL] = etabUSER;
841 tabsel[etiLJ6] = etabUSER;
842 tabsel[etiLJ12] = etabUSER;
844 set_table_type(tabsel,fr,b14only);
854 /* Check whether we have to read or generate */
857 for(i=0; (i<etiNR); i++) {
858 if (ETAB_USER(tabsel[i]))
860 if (tabsel[i] != etabUSER)
864 read_tables(out,fn,etiNR,0,td);
865 if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY)) {
866 rtab = td[0].x[td[0].nx-1];
870 if (td[0].x[td[0].nx-1] < rtab)
871 gmx_fatal(FARGS,"Tables in file %s not long enough for cut-off:\n"
872 "\tshould be at least %f nm\n",fn,rtab);
873 nx = table.n = (int)(rtab*td[0].tabscale + 0.5);
875 table.scale = td[0].tabscale;
881 table.scale = 2000.0;
885 nx = table.n = rtab*table.scale;
889 if(fr->bham_b_max!=0)
890 table.scale_exp = table.scale/fr->bham_b_max;
892 table.scale_exp = table.scale;
895 /* Each table type (e.g. coul,lj6,lj12) requires four
896 * numbers per nx+1 data points. For performance reasons we want
897 * the table data to be aligned to 16-byte.
899 snew_aligned(table.tab, 12*(nx+1)*sizeof(real),16);
901 for(k=0; (k<etiNR); k++) {
902 if (tabsel[k] != etabUSER) {
903 init_table(out,nx,nx0,
904 (tabsel[k] == etabEXPMIN) ? table.scale_exp : table.scale,
906 fill_table(&(td[k]),tabsel[k],fr);
908 fprintf(out,"%s table with %d data points for %s%s.\n"
909 "Tabscale = %g points/nm\n",
910 ETAB_USER(tabsel[k]) ? "Modified" : "Generated",
911 td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
914 copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,table.tab);
916 if (bDebugMode() && bVerbose) {
918 fp=xvgropen(fns14[k],fns14[k],"r","V",oenv);
920 fp=xvgropen(fns[k],fns[k],"r","V",oenv);
921 /* plot the output 5 times denser than the table data */
922 for(i=5*((nx0+1)/2); i<5*table.n; i++) {
923 x0 = i*table.r/(5*(table.n-1));
924 evaluate_table(table.tab,4*k,12,table.scale,x0,&y0,&yp);
925 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
929 done_tabledata(&(td[k]));
936 t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
937 const t_forcerec *fr,
941 const char *fns[3] = { "gbctab.xvg", "gbdtab.xvg", "gbrtab.xvg" };
942 const char *fns14[3] = { "gbctab14.xvg", "gbdtab14.xvg", "gbrtab14.xvg" };
945 gmx_bool bReadTab,bGenTab;
947 int i,j,k,nx,nx0,tabsel[etiNR];
948 double r,r2,Vtab,Ftab,expterm;
952 double abs_error_r, abs_error_r2;
953 double rel_error_r, rel_error_r2;
954 double rel_error_r_old=0, rel_error_r2_old=0;
955 double x0_r_error, x0_r2_error;
958 /* Only set a Coulomb table for GB */
965 /* Set the table dimensions for GB, not really necessary to
966 * use etiNR (since we only have one table, but ...)
969 table.r = fr->gbtabr;
970 table.scale = fr->gbtabscale;
972 table.n = table.scale*table.r;
974 nx = table.scale*table.r;
976 /* Check whether we have to read or generate
977 * We will always generate a table, so remove the read code
978 * (Compare with original make_table function
983 /* Each table type (e.g. coul,lj6,lj12) requires four
984 * numbers per datapoint. For performance reasons we want
985 * the table data to be aligned to 16-byte. This is accomplished
986 * by allocating 16 bytes extra to a temporary pointer, and then
987 * calculating an aligned pointer. This new pointer must not be
988 * used in a free() call, but thankfully we're sloppy enough not
992 snew_aligned(table.tab,4*nx,16);
994 init_table(out,nx,nx0,table.scale,&(td[0]),!bReadTab);
996 /* Local implementation so we don't have to use the etabGB
997 * enum above, which will cause problems later when
998 * making the other tables (right now even though we are using
999 * GB, the normal Coulomb tables will be created, but this
1000 * will cause a problem since fr->eeltype==etabGB which will not
1001 * be defined in fill_table and set_table_type
1010 expterm = exp(-0.25*r2);
1012 Vtab = 1/sqrt(r2+expterm);
1013 Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1015 /* Convert to single precision when we store to mem */
1021 copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
1025 fp=xvgropen(fns[0],fns[0],"r","V",oenv);
1026 /* plot the output 5 times denser than the table data */
1027 /* for(i=5*nx0;i<5*table.n;i++) */
1028 for(i=nx0;i<table.n;i++)
1030 /* x0=i*table.r/(5*table.n); */
1031 x0=i*table.r/table.n;
1032 evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
1033 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
1040 for(i=100*nx0;i<99.81*table.n;i++)
1042 r = i*table.r/(100*table.n);
1044 expterm = exp(-0.25*r2);
1046 Vtab = 1/sqrt(r2+expterm);
1047 Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1050 evaluate_table(table.tab,0,4,table.scale,r,&y0,&yp);
1051 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);
1053 abs_error_r=fabs(y0-Vtab);
1054 abs_error_r2=fabs(yp-(-1)*Ftab);
1056 rel_error_r=abs_error_r/y0;
1057 rel_error_r2=fabs(abs_error_r2/yp);
1060 if(rel_error_r>rel_error_r_old)
1062 rel_error_r_old=rel_error_r;
1066 if(rel_error_r2>rel_error_r2_old)
1068 rel_error_r2_old=rel_error_r2;
1073 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);
1074 printf("gb: XO_R=%g, X0_R2=%g\n",x0_r_error, x0_r2_error);
1077 done_tabledata(&(td[0]));
1085 t_forcetable make_atf_table(FILE *out,const output_env_t oenv,
1086 const t_forcerec *fr,
1090 const char *fns[3] = { "tf_tab.xvg", "atfdtab.xvg", "atfrtab.xvg" };
1095 real rx, ry, rz, box_r;
1100 /* Set the table dimensions for ATF, not really necessary to
1101 * use etiNR (since we only have one table, but ...)
1105 if (fr->adress_type == eAdressSphere){
1106 /* take half box diagonal direction as tab range */
1107 rx = 0.5*box[0][0]+0.5*box[1][0]+0.5*box[2][0];
1108 ry = 0.5*box[0][1]+0.5*box[1][1]+0.5*box[2][1];
1109 rz = 0.5*box[0][2]+0.5*box[1][2]+0.5*box[2][2];
1110 box_r = sqrt(rx*rx+ry*ry+rz*rz);
1113 /* xsplit: take half box x direction as tab range */
1114 box_r = box[0][0]/2;
1119 table.scale_exp = 0;
1123 read_tables(out,fn,1,0,td);
1124 rtab = td[0].x[td[0].nx-1];
1126 if (fr->adress_type == eAdressXSplit && (rtab < box[0][0]/2)){
1127 gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
1128 "\tshould extend to at least half the length of the box in x-direction"
1129 "%f\n",fn,rtab, box[0][0]/2);
1132 gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
1133 "\tshould extend to at least for spherical adress"
1134 "%f (=distance from center to furthermost point in box \n",fn,rtab, box_r);
1140 table.scale = td[0].tabscale;
1143 /* Each table type (e.g. coul,lj6,lj12) requires four
1144 * numbers per datapoint. For performance reasons we want
1145 * the table data to be aligned to 16-byte. This is accomplished
1146 * by allocating 16 bytes extra to a temporary pointer, and then
1147 * calculating an aligned pointer. This new pointer must not be
1148 * used in a free() call, but thankfully we're sloppy enough not
1152 snew_aligned(table.tab,4*nx,16);
1154 copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
1158 fp=xvgropen(fns[0],fns[0],"r","V",oenv);
1159 /* plot the output 5 times denser than the table data */
1160 /* for(i=5*nx0;i<5*table.n;i++) */
1162 for(i=5*((nx0+1)/2); i<5*table.n; i++)
1164 /* x0=i*table.r/(5*table.n); */
1165 x0 = i*table.r/(5*(table.n-1));
1166 evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
1167 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
1173 done_tabledata(&(td[0]));
1179 bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle)
1190 read_tables(fplog,fn,1,angle,&td);
1192 /* Convert the table from degrees to radians */
1193 for(i=0; i<td.nx; i++) {
1197 td.tabscale *= RAD2DEG;
1200 tab.scale = td.tabscale;
1201 snew(tab.tab,tab.n*4);
1202 copy2table(tab.n,0,4,td.x,td.v,td.f,tab.tab);
1203 done_tabledata(&td);