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45 #include "gmx_fatal.h"
57 /* All the possible (implemented) table functions */
82 /** Evaluates to true if the table type contains user data. */
83 #define ETAB_USER(e) ((e) == etabUSER || \
84 (e) == etabEwaldUser || (e) == etabEwaldUserSwitch)
91 /* This structure holds name and a flag that tells whether
92 this is a Coulomb type funtion */
93 static const t_tab_props tprops[etabNR] = {
96 { "LJ6Shift", FALSE },
97 { "LJ12Shift", FALSE },
103 { "Ewald-Switch", TRUE },
104 { "Ewald-User", TRUE },
105 { "Ewald-User-Switch", TRUE },
106 { "LJ6Switch", FALSE },
107 { "LJ12Switch", FALSE },
108 { "COULSwitch", TRUE },
109 { "LJ6-Encad shift", FALSE },
110 { "LJ12-Encad shift", FALSE },
111 { "COUL-Encad shift", TRUE },
116 /* Index in the table that says which function to use */
117 enum { etiCOUL, etiLJ6, etiLJ12, etiNR };
125 #define pow2(x) ((x)*(x))
126 #define pow3(x) ((x)*(x)*(x))
127 #define pow4(x) ((x)*(x)*(x)*(x))
128 #define pow5(x) ((x)*(x)*(x)*(x)*(x))
131 static double v_ewald_lr(double beta,double r)
135 return beta*2/sqrt(M_PI);
139 return gmx_erfd(beta*r)/r;
143 void table_spline3_fill_ewald_lr(real *table_f,
153 gmx_bool bOutOfRange;
154 double v_r0,v_r1,v_inrange,vi,a0,a1,a2dx;
159 gmx_fatal(FARGS,"Can not make a spline table with less than 2 points");
162 /* We need some margin to be able to divide table values by r
163 * in the kernel and also to do the integration arithmetics
164 * without going out of range. Furthemore, we divide by dx below.
166 tab_max = GMX_REAL_MAX*0.0001;
168 /* This function produces a table with:
169 * maximum energy error: V'''/(6*12*sqrt(3))*dx^3
170 * maximum force error: V'''/(6*4)*dx^2
171 * The rms force error is the max error times 1/sqrt(5)=0.45.
178 for(i=ntab-1; i>=0; i--)
182 v_r0 = v_ewald_lr(beta,x_r0);
193 /* Linear continuation for the last point in range */
194 vi = v_inrange - dc*(i - i_inrange)*dx;
207 /* Get the potential at table point i-1 */
208 v_r1 = v_ewald_lr(beta,(i-1)*dx);
210 if (v_r1 != v_r1 || v_r1 < -tab_max || v_r1 > tab_max)
217 /* Calculate the average second derivative times dx over interval i-1 to i.
218 * Using the function values at the end points and in the middle.
220 a2dx = (v_r0 + v_r1 - 2*v_ewald_lr(beta,x_r0-0.5*dx))/(0.25*dx);
221 /* Set the derivative of the spline to match the difference in potential
222 * over the interval plus the average effect of the quadratic term.
223 * This is the essential step for minimizing the error in the force.
225 dc = (v_r0 - v_r1)/dx + 0.5*a2dx;
230 /* Fill the table with the force, minus the derivative of the spline */
235 /* tab[i] will contain the average of the splines over the two intervals */
236 table_f[i] += -0.5*dc;
241 /* Make spline s(x) = a0 + a1*(x - xr) + 0.5*a2*(x - xr)^2
242 * matching the potential at the two end points
243 * and the derivative dc at the end point xr.
247 a2dx = (a1*dx + v_r1 - a0)*2/dx;
249 /* Set dc to the derivative at the next point */
252 if (dc_new != dc_new || dc_new < -tab_max || dc_new > tab_max)
262 table_f[(i-1)] = -0.5*dc;
264 /* Currently the last value only contains half the force: double it */
267 if(table_v!=NULL && table_fdv0!=NULL)
269 /* Copy to FDV0 table too. Allocation occurs in forcerec.c,
270 * init_ewald_f_table().
272 for(i=0;i<ntab-1;i++)
274 table_fdv0[4*i] = table_f[i];
275 table_fdv0[4*i+1] = table_f[i+1]-table_f[i];
276 table_fdv0[4*i+2] = table_v[i];
277 table_fdv0[4*i+3] = 0.0;
279 table_fdv0[4*(ntab-1)] = table_f[(ntab-1)];
280 table_fdv0[4*(ntab-1)+1] = -table_f[(ntab-1)];
281 table_fdv0[4*(ntab-1)+2] = table_v[(ntab-1)];
282 table_fdv0[4*(ntab-1)+3] = 0.0;
286 /* The scale (1/spacing) for third order spline interpolation
287 * of the Ewald mesh contribution which needs to be subtracted
288 * from the non-bonded interactions.
290 real ewald_spline3_table_scale(real ewaldcoeff,real rc)
292 double erf_x_d3=1.0522; /* max of (erf(x)/x)''' */
296 /* Force tolerance: single precision accuracy */
297 ftol = GMX_FLOAT_EPS;
298 sc_f = sqrt(erf_x_d3/(6*4*ftol*ewaldcoeff))*ewaldcoeff;
300 /* Energy tolerance: 10x more accurate than the cut-off jump */
301 etol = 0.1*gmx_erfc(ewaldcoeff*rc);
302 etol = max(etol,GMX_REAL_EPS);
303 sc_e = pow(erf_x_d3/(6*12*sqrt(3)*etol),1.0/3.0)*ewaldcoeff;
305 return max(sc_f,sc_e);
308 /* Calculate the potential and force for an r value
309 * in exactly the same way it is done in the inner loop.
310 * VFtab is a pointer to the table data, offset is
311 * the point where we should begin and stride is
312 * 4 if we have a buckingham table, 3 otherwise.
313 * If you want to evaluate table no N, set offset to 4*N.
315 * We use normal precision here, since that is what we
316 * will use in the inner loops.
318 static void evaluate_table(real VFtab[], int offset, int stride,
319 real tabscale, real r, real *y, real *yp)
323 real Y,F,Geps,Heps2,Fp;
332 Geps = eps*VFtab[n+2];
333 Heps2 = eps2*VFtab[n+3];
336 *yp = (Fp+Geps+2.0*Heps2)*tabscale;
339 static void copy2table(int n,int offset,int stride,
340 double x[],double Vtab[],double Ftab[],real scalefactor,
343 /* Use double prec. for the intermediary variables
344 * and temporary x/vtab/vtab2 data to avoid unnecessary
351 for(i=0; (i<n); i++) {
355 G = 3*(Vtab[i+1] - Vtab[i]) + (Ftab[i+1] + 2*Ftab[i])*h;
356 H = -2*(Vtab[i+1] - Vtab[i]) - (Ftab[i+1] + Ftab[i])*h;
358 /* Fill the last entry with a linear potential,
359 * this is mainly for rounding issues with angle and dihedral potentials.
365 nn0 = offset + i*stride;
366 dest[nn0] = scalefactor*Vtab[i];
367 dest[nn0+1] = scalefactor*F;
368 dest[nn0+2] = scalefactor*G;
369 dest[nn0+3] = scalefactor*H;
373 static void init_table(FILE *fp,int n,int nx0,
374 double tabscale,t_tabledata *td,gmx_bool bAlloc)
380 td->tabscale = tabscale;
386 for(i=0; (i<td->nx); i++)
387 td->x[i] = i/tabscale;
390 static void spline_forces(int nx,double h,double v[],gmx_bool bS3,gmx_bool bE3,
397 /* Formulas can be found in:
398 * H.J.C. Berendsen, Simulating the Physical World, Cambridge 2007
401 if (nx < 4 && (bS3 || bE3))
402 gmx_fatal(FARGS,"Can not generate splines with third derivative boundary conditions with less than 4 (%d) points",nx);
404 /* To make life easy we initially set the spacing to 1
405 * and correct for this at the end.
409 /* Fit V''' at the start */
410 v3 = v[3] - 3*v[2] + 3*v[1] - v[0];
412 fprintf(debug,"The left third derivative is %g\n",v3/(h*h*h));
413 b_s = 2*(v[1] - v[0]) + v3/6;
417 /* Fit V'' at the start */
420 v2 = -v[3] + 4*v[2] - 5*v[1] + 2*v[0];
421 /* v2 = v[2] - 2*v[1] + v[0]; */
423 fprintf(debug,"The left second derivative is %g\n",v2/(h*h));
424 b_s = 3*(v[1] - v[0]) - v2/2;
428 b_s = 3*(v[2] - v[0]) + f[0]*h;
432 /* Fit V''' at the end */
433 v3 = v[nx-1] - 3*v[nx-2] + 3*v[nx-3] - v[nx-4];
435 fprintf(debug,"The right third derivative is %g\n",v3/(h*h*h));
436 b_e = 2*(v[nx-1] - v[nx-2]) + v3/6;
439 /* V'=0 at the end */
440 b_e = 3*(v[nx-1] - v[nx-3]) + f[nx-1]*h;
445 beta = (bS3 ? 1 : 4);
447 /* For V'' fitting */
448 /* beta = (bS3 ? 2 : 4); */
451 for(i=start+1; i<end; i++) {
454 b = 3*(v[i+1] - v[i-1]);
455 f[i] = (b - f[i-1])/beta;
457 gamma[end-1] = 1/beta;
458 beta = (bE3 ? 1 : 4) - gamma[end-1];
459 f[end-1] = (b_e - f[end-2])/beta;
461 for(i=end-2; i>=start; i--)
462 f[i] -= gamma[i+1]*f[i+1];
465 /* Correct for the minus sign and the spacing */
466 for(i=start; i<end; i++)
470 static void set_forces(FILE *fp,int angle,
471 int nx,double h,double v[],double f[],
478 "Force generation for dihedral tables is not (yet) implemented");
481 while (v[start] == 0)
493 fprintf(fp,"Generating forces for table %d, boundary conditions: V''' at %g, %s at %g\n",
494 table+1,start*h,end==nx ? "V'''" : "V'=0",(end-1)*h);
495 spline_forces(end-start,h,v+start,TRUE,end==nx,f+start);
498 static void read_tables(FILE *fp,const char *fn,
499 int ntab,int angle,t_tabledata td[])
503 double **yy=NULL,start,end,dx0,dx1,ssd,vm,vp,f,numf;
504 int k,i,nx,nx0=0,ny,nny,ns;
505 gmx_bool bAllZero,bZeroV,bZeroF;
509 libfn = gmxlibfn(fn);
510 nx = read_xvg(libfn,&yy,&ny);
512 gmx_fatal(FARGS,"Trying to read file %s, but nr columns = %d, should be %d",
517 "The first distance in file %s is %f nm instead of %f nm",
525 if (yy[0][0] != start || yy[0][nx-1] != end)
526 gmx_fatal(FARGS,"The angles in file %s should go from %f to %f instead of %f to %f\n",
527 libfn,start,end,yy[0][0],yy[0][nx-1]);
530 tabscale = (nx-1)/(yy[0][nx-1] - yy[0][0]);
533 fprintf(fp,"Read user tables from %s with %d data points.\n",libfn,nx);
535 fprintf(fp,"Tabscale = %g points/nm\n",tabscale);
539 for(k=0; k<ntab; k++) {
542 for(i=0; (i < nx); i++) {
544 dx0 = yy[0][i-1] - yy[0][i-2];
545 dx1 = yy[0][i] - yy[0][i-1];
546 /* Check for 1% deviation in spacing */
547 if (fabs(dx1 - dx0) >= 0.005*(fabs(dx0) + fabs(dx1))) {
548 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]);
551 if (yy[1+k*2][i] != 0) {
557 if (yy[1+k*2][i] > 0.01*GMX_REAL_MAX ||
558 yy[1+k*2][i] < -0.01*GMX_REAL_MAX) {
559 gmx_fatal(FARGS,"Out of range potential value %g in file '%s'",
563 if (yy[1+k*2+1][i] != 0) {
569 if (yy[1+k*2+1][i] > 0.01*GMX_REAL_MAX ||
570 yy[1+k*2+1][i] < -0.01*GMX_REAL_MAX) {
571 gmx_fatal(FARGS,"Out of range force value %g in file '%s'",
577 if (!bZeroV && bZeroF) {
578 set_forces(fp,angle,nx,1/tabscale,yy[1+k*2],yy[1+k*2+1],k);
580 /* Check if the second column is close to minus the numerical
581 * derivative of the first column.
585 for(i=1; (i < nx-1); i++) {
589 if (vm != 0 && vp != 0 && f != 0) {
590 /* Take the centered difference */
591 numf = -(vp - vm)*0.5*tabscale;
592 ssd += fabs(2*(f - numf)/(f + numf));
598 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));
600 fprintf(debug,"%s",buf);
603 fprintf(fp,"\nWARNING: %s\n",buf);
604 fprintf(stderr,"\nWARNING: %s\n",buf);
609 if (bAllZero && fp) {
610 fprintf(fp,"\nNOTE: All elements in table %s are zero\n\n",libfn);
613 for(k=0; (k<ntab); k++) {
614 init_table(fp,nx,nx0,tabscale,&(td[k]),TRUE);
615 for(i=0; (i<nx); i++) {
616 td[k].x[i] = yy[0][i];
617 td[k].v[i] = yy[2*k+1][i];
618 td[k].f[i] = yy[2*k+2][i];
621 for(i=0; (i<ny); i++)
627 static void done_tabledata(t_tabledata *td)
639 static void fill_table(t_tabledata *td,int tp,const t_forcerec *fr)
641 /* Fill the table according to the formulas in the manual.
642 * In principle, we only need the potential and the second
643 * derivative, but then we would have to do lots of calculations
644 * in the inner loop. By precalculating some terms (see manual)
645 * we get better eventual performance, despite a larger table.
647 * Since some of these higher-order terms are very small,
648 * we always use double precision to calculate them here, in order
649 * to avoid unnecessary loss of precision.
656 double r1,rc,r12,r13;
658 double expr,Vtab,Ftab;
659 /* Parameters for David's function */
660 double A=0,B=0,C=0,A_3=0,B_4=0;
661 /* Parameters for the switching function */
663 /* Temporary parameters */
664 gmx_bool bSwitch,bShift;
665 double ewc=fr->ewaldcoeff;
667 bSwitch = ((tp == etabLJ6Switch) || (tp == etabLJ12Switch) ||
668 (tp == etabCOULSwitch) ||
669 (tp == etabEwaldSwitch) || (tp == etabEwaldUserSwitch));
670 bShift = ((tp == etabLJ6Shift) || (tp == etabLJ12Shift) ||
675 if (tprops[tp].bCoulomb) {
676 r1 = fr->rcoulomb_switch;
680 r1 = fr->rvdw_switch;
684 ksw = 1.0/(pow5(rc-r1));
690 else if (tp == etabLJ6Shift)
695 A = p * ((p+1)*r1-(p+4)*rc)/(pow(rc,p+2)*pow2(rc-r1));
696 B = -p * ((p+1)*r1-(p+3)*rc)/(pow(rc,p+2)*pow3(rc-r1));
697 C = 1.0/pow(rc,p)-A/3.0*pow3(rc-r1)-B/4.0*pow4(rc-r1);
698 if (tp == etabLJ6Shift) {
706 if (debug) { fprintf(debug,"Setting up tables\n"); fflush(debug); }
709 fp=xvgropen("switch.xvg","switch","r","s");
712 for(i=td->nx0; (i<td->nx); i++) {
716 if (gmx_within_tol(reppow,12.0,10*GMX_DOUBLE_EPS)) {
719 r12 = pow(r,-reppow);
724 /* swi is function, swi1 1st derivative and swi2 2nd derivative */
725 /* The switch function is 1 for r<r1, 0 for r>rc, and smooth for
726 * r1<=r<=rc. The 1st and 2nd derivatives are both zero at
728 * ksw is just the constant 1/(rc-r1)^5, to save some calculations...
737 swi = 1 - 10*pow3(r-r1)*ksw*pow2(rc-r1)
738 + 15*pow4(r-r1)*ksw*(rc-r1) - 6*pow5(r-r1)*ksw;
739 swi1 = -30*pow2(r-r1)*ksw*pow2(rc-r1)
740 + 60*pow3(r-r1)*ksw*(rc-r1) - 30*pow4(r-r1)*ksw;
743 else { /* not really needed, but avoids compiler warnings... */
748 fprintf(fp,"%10g %10g %10g %10g\n",r,swi,swi1,swi2);
772 Ftab = reppow*Vtab/r;
779 Ftab = reppow*Vtab/r;
784 Vtab = -(r6-6.0*(rc-r)*rc6/rc-rc6);
785 Ftab = -(6.0*r6/r-6.0*rc6/rc);
793 Vtab = -(r6-6.0*(rc-r)*rc6/rc-rc6);
794 Ftab = -(6.0*r6/r-6.0*rc6/rc);
812 case etabEwaldSwitch:
813 Vtab = gmx_erfc(ewc*r)/r;
814 Ftab = gmx_erfc(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
817 case etabEwaldUserSwitch:
818 /* Only calculate minus the reciprocal space contribution */
819 Vtab = -gmx_erf(ewc*r)/r;
820 Ftab = -gmx_erf(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
824 Vtab = 1.0/r + fr->k_rf*r2 - fr->c_rf;
825 Ftab = 1.0/r2 - 2*fr->k_rf*r;
826 if (tp == etabRF_ZERO && r >= rc) {
838 Vtab = 1.0/r-(rc-r)/(rc*rc)-1.0/rc;
839 Ftab = 1.0/r2-1.0/(rc*rc);
846 gmx_fatal(FARGS,"Table type %d not implemented yet. (%s,%d)",
847 tp,__FILE__,__LINE__);
850 /* Normal coulomb with cut-off correction for potential */
853 /* If in Shifting range add something to it */
857 Vtab += - A_3*r13 - B_4*r12*r12;
858 Ftab += A*r12 + B*r13;
868 if ((r > r1) && bSwitch) {
869 Ftab = Ftab*swi - Vtab*swi1;
873 /* Convert to single precision when we store to mem */
878 /* Continue the table linearly from nx0 to 0.
879 * These values are only required for energy minimization with overlap or TPI.
881 for(i=td->nx0-1; i>=0; i--) {
882 td->v[i] = td->v[i+1] + td->f[i+1]*(td->x[i+1] - td->x[i]);
883 td->f[i] = td->f[i+1];
891 static void set_table_type(int tabsel[],const t_forcerec *fr,gmx_bool b14only)
895 /* Set the different table indices.
901 switch (fr->eeltype) {
907 case eelPMEUSERSWITCH:
914 eltype = fr->eeltype;
919 tabsel[etiCOUL] = etabCOUL;
922 tabsel[etiCOUL] = etabShift;
925 if (fr->rcoulomb > fr->rcoulomb_switch)
926 tabsel[etiCOUL] = etabShift;
928 tabsel[etiCOUL] = etabCOUL;
933 tabsel[etiCOUL] = etabEwald;
936 tabsel[etiCOUL] = etabEwaldSwitch;
939 tabsel[etiCOUL] = etabEwaldUser;
941 case eelPMEUSERSWITCH:
942 tabsel[etiCOUL] = etabEwaldUserSwitch;
947 tabsel[etiCOUL] = etabRF;
950 tabsel[etiCOUL] = etabRF_ZERO;
953 tabsel[etiCOUL] = etabCOULSwitch;
956 tabsel[etiCOUL] = etabUSER;
959 tabsel[etiCOUL] = etabCOULEncad;
962 gmx_fatal(FARGS,"Invalid eeltype %d",eltype);
965 /* Van der Waals time */
966 if (fr->bBHAM && !b14only) {
967 tabsel[etiLJ6] = etabLJ6;
968 tabsel[etiLJ12] = etabEXPMIN;
970 if (b14only && fr->vdwtype != evdwUSER)
973 vdwtype = fr->vdwtype;
977 tabsel[etiLJ6] = etabLJ6Switch;
978 tabsel[etiLJ12] = etabLJ12Switch;
981 tabsel[etiLJ6] = etabLJ6Shift;
982 tabsel[etiLJ12] = etabLJ12Shift;
985 tabsel[etiLJ6] = etabUSER;
986 tabsel[etiLJ12] = etabUSER;
989 tabsel[etiLJ6] = etabLJ6;
990 tabsel[etiLJ12] = etabLJ12;
993 tabsel[etiLJ6] = etabLJ6Encad;
994 tabsel[etiLJ12] = etabLJ12Encad;
997 gmx_fatal(FARGS,"Invalid vdwtype %d in %s line %d",vdwtype,
1003 t_forcetable make_tables(FILE *out,const output_env_t oenv,
1004 const t_forcerec *fr,
1005 gmx_bool bVerbose,const char *fn,
1006 real rtab,int flags)
1008 const char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
1009 const char *fns14[3] = { "ctab14.xvg", "dtab14.xvg", "rtab14.xvg" };
1012 gmx_bool b14only,bReadTab,bGenTab;
1014 int i,j,k,nx,nx0,tabsel[etiNR];
1019 b14only = (flags & GMX_MAKETABLES_14ONLY);
1021 if (flags & GMX_MAKETABLES_FORCEUSER) {
1022 tabsel[etiCOUL] = etabUSER;
1023 tabsel[etiLJ6] = etabUSER;
1024 tabsel[etiLJ12] = etabUSER;
1026 set_table_type(tabsel,fr,b14only);
1032 table.scale_exp = 0;
1036 table.interaction = GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP;
1037 table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
1038 table.formatsize = 4;
1039 table.ninteractions = 3;
1040 table.stride = table.formatsize*table.ninteractions;
1042 /* Check whether we have to read or generate */
1045 for(i=0; (i<etiNR); i++) {
1046 if (ETAB_USER(tabsel[i]))
1048 if (tabsel[i] != etabUSER)
1052 read_tables(out,fn,etiNR,0,td);
1053 if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY)) {
1054 rtab = td[0].x[td[0].nx-1];
1058 if (td[0].x[td[0].nx-1] < rtab)
1059 gmx_fatal(FARGS,"Tables in file %s not long enough for cut-off:\n"
1060 "\tshould be at least %f nm\n",fn,rtab);
1061 nx = table.n = (int)(rtab*td[0].tabscale + 0.5);
1063 table.scale = td[0].tabscale;
1069 table.scale = 2000.0;
1071 table.scale = 500.0;
1073 nx = table.n = rtab*table.scale;
1077 if(fr->bham_b_max!=0)
1078 table.scale_exp = table.scale/fr->bham_b_max;
1080 table.scale_exp = table.scale;
1083 /* Each table type (e.g. coul,lj6,lj12) requires four
1084 * numbers per nx+1 data points. For performance reasons we want
1085 * the table data to be aligned to 16-byte.
1087 snew_aligned(table.data, 12*(nx+1)*sizeof(real),32);
1089 for(k=0; (k<etiNR); k++) {
1090 if (tabsel[k] != etabUSER) {
1091 init_table(out,nx,nx0,
1092 (tabsel[k] == etabEXPMIN) ? table.scale_exp : table.scale,
1093 &(td[k]),!bReadTab);
1094 fill_table(&(td[k]),tabsel[k],fr);
1096 fprintf(out,"%s table with %d data points for %s%s.\n"
1097 "Tabscale = %g points/nm\n",
1098 ETAB_USER(tabsel[k]) ? "Modified" : "Generated",
1099 td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
1103 /* Set scalefactor for c6/c12 tables. This is because we save flops in the non-table kernels
1104 * by including the derivative constants (6.0 or 12.0) in the parameters, since
1105 * we no longer calculate force in most steps. This means the c6/c12 parameters
1106 * have been scaled up, so we need to scale down the table interactions too.
1107 * It comes here since we need to scale user tables too.
1111 scalefactor = 1.0/6.0;
1113 else if(k==etiLJ12 && tabsel[k]!=etabEXPMIN)
1115 scalefactor = 1.0/12.0;
1122 copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,scalefactor,table.data);
1124 if (bDebugMode() && bVerbose) {
1126 fp=xvgropen(fns14[k],fns14[k],"r","V",oenv);
1128 fp=xvgropen(fns[k],fns[k],"r","V",oenv);
1129 /* plot the output 5 times denser than the table data */
1130 for(i=5*((nx0+1)/2); i<5*table.n; i++) {
1131 x0 = i*table.r/(5*(table.n-1));
1132 evaluate_table(table.data,4*k,12,table.scale,x0,&y0,&yp);
1133 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
1137 done_tabledata(&(td[k]));
1144 t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
1145 const t_forcerec *fr,
1149 const char *fns[3] = { "gbctab.xvg", "gbdtab.xvg", "gbrtab.xvg" };
1150 const char *fns14[3] = { "gbctab14.xvg", "gbdtab14.xvg", "gbrtab14.xvg" };
1153 gmx_bool bReadTab,bGenTab;
1155 int i,j,k,nx,nx0,tabsel[etiNR];
1156 double r,r2,Vtab,Ftab,expterm;
1160 double abs_error_r, abs_error_r2;
1161 double rel_error_r, rel_error_r2;
1162 double rel_error_r_old=0, rel_error_r2_old=0;
1163 double x0_r_error, x0_r2_error;
1166 /* Only set a Coulomb table for GB */
1173 /* Set the table dimensions for GB, not really necessary to
1174 * use etiNR (since we only have one table, but ...)
1177 table.interaction = GMX_TABLE_INTERACTION_ELEC;
1178 table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
1179 table.r = fr->gbtabr;
1180 table.scale = fr->gbtabscale;
1181 table.scale_exp = 0;
1182 table.n = table.scale*table.r;
1183 table.formatsize = 4;
1184 table.ninteractions = 1;
1185 table.stride = table.formatsize*table.ninteractions;
1187 nx = table.scale*table.r;
1189 /* Check whether we have to read or generate
1190 * We will always generate a table, so remove the read code
1191 * (Compare with original make_table function
1196 /* Each table type (e.g. coul,lj6,lj12) requires four
1197 * numbers per datapoint. For performance reasons we want
1198 * the table data to be aligned to 16-byte. This is accomplished
1199 * by allocating 16 bytes extra to a temporary pointer, and then
1200 * calculating an aligned pointer. This new pointer must not be
1201 * used in a free() call, but thankfully we're sloppy enough not
1205 snew_aligned(table.data,4*nx,32);
1207 init_table(out,nx,nx0,table.scale,&(td[0]),!bReadTab);
1209 /* Local implementation so we don't have to use the etabGB
1210 * enum above, which will cause problems later when
1211 * making the other tables (right now even though we are using
1212 * GB, the normal Coulomb tables will be created, but this
1213 * will cause a problem since fr->eeltype==etabGB which will not
1214 * be defined in fill_table and set_table_type
1223 expterm = exp(-0.25*r2);
1225 Vtab = 1/sqrt(r2+expterm);
1226 Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1228 /* Convert to single precision when we store to mem */
1234 copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,1.0,table.data);
1238 fp=xvgropen(fns[0],fns[0],"r","V",oenv);
1239 /* plot the output 5 times denser than the table data */
1240 /* for(i=5*nx0;i<5*table.n;i++) */
1241 for(i=nx0;i<table.n;i++)
1243 /* x0=i*table.r/(5*table.n); */
1244 x0=i*table.r/table.n;
1245 evaluate_table(table.data,0,4,table.scale,x0,&y0,&yp);
1246 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
1253 for(i=100*nx0;i<99.81*table.n;i++)
1255 r = i*table.r/(100*table.n);
1257 expterm = exp(-0.25*r2);
1259 Vtab = 1/sqrt(r2+expterm);
1260 Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1263 evaluate_table(table.data,0,4,table.scale,r,&y0,&yp);
1264 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);
1266 abs_error_r=fabs(y0-Vtab);
1267 abs_error_r2=fabs(yp-(-1)*Ftab);
1269 rel_error_r=abs_error_r/y0;
1270 rel_error_r2=fabs(abs_error_r2/yp);
1273 if(rel_error_r>rel_error_r_old)
1275 rel_error_r_old=rel_error_r;
1279 if(rel_error_r2>rel_error_r2_old)
1281 rel_error_r2_old=rel_error_r2;
1286 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);
1287 printf("gb: XO_R=%g, X0_R2=%g\n",x0_r_error, x0_r2_error);
1290 done_tabledata(&(td[0]));
1298 t_forcetable make_atf_table(FILE *out,const output_env_t oenv,
1299 const t_forcerec *fr,
1303 const char *fns[3] = { "tf_tab.xvg", "atfdtab.xvg", "atfrtab.xvg" };
1308 real rx, ry, rz, box_r;
1313 /* Set the table dimensions for ATF, not really necessary to
1314 * use etiNR (since we only have one table, but ...)
1318 if (fr->adress_type == eAdressSphere){
1319 /* take half box diagonal direction as tab range */
1320 rx = 0.5*box[0][0]+0.5*box[1][0]+0.5*box[2][0];
1321 ry = 0.5*box[0][1]+0.5*box[1][1]+0.5*box[2][1];
1322 rz = 0.5*box[0][2]+0.5*box[1][2]+0.5*box[2][2];
1323 box_r = sqrt(rx*rx+ry*ry+rz*rz);
1326 /* xsplit: take half box x direction as tab range */
1327 box_r = box[0][0]/2;
1332 table.scale_exp = 0;
1336 read_tables(out,fn,1,0,td);
1337 rtab = td[0].x[td[0].nx-1];
1339 if (fr->adress_type == eAdressXSplit && (rtab < box[0][0]/2)){
1340 gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
1341 "\tshould extend to at least half the length of the box in x-direction"
1342 "%f\n",fn,rtab, box[0][0]/2);
1345 gmx_fatal(FARGS,"AdResS full box therm force table in file %s extends to %f:\n"
1346 "\tshould extend to at least for spherical adress"
1347 "%f (=distance from center to furthermost point in box \n",fn,rtab, box_r);
1353 table.scale = td[0].tabscale;
1356 /* Each table type (e.g. coul,lj6,lj12) requires four
1357 * numbers per datapoint. For performance reasons we want
1358 * the table data to be aligned to 16-byte. This is accomplished
1359 * by allocating 16 bytes extra to a temporary pointer, and then
1360 * calculating an aligned pointer. This new pointer must not be
1361 * used in a free() call, but thankfully we're sloppy enough not
1365 snew_aligned(table.data,4*nx,32);
1367 copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,1.0,table.data);
1371 fp=xvgropen(fns[0],fns[0],"r","V",oenv);
1372 /* plot the output 5 times denser than the table data */
1373 /* for(i=5*nx0;i<5*table.n;i++) */
1375 for(i=5*((nx0+1)/2); i<5*table.n; i++)
1377 /* x0=i*table.r/(5*table.n); */
1378 x0 = i*table.r/(5*(table.n-1));
1379 evaluate_table(table.data,0,4,table.scale,x0,&y0,&yp);
1380 fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
1386 done_tabledata(&(td[0]));
1389 table.interaction = GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP;
1390 table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
1391 table.formatsize = 4;
1392 table.ninteractions = 3;
1393 table.stride = table.formatsize*table.ninteractions;
1399 bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle)
1410 read_tables(fplog,fn,1,angle,&td);
1412 /* Convert the table from degrees to radians */
1413 for(i=0; i<td.nx; i++) {
1417 td.tabscale *= RAD2DEG;
1420 tab.scale = td.tabscale;
1421 snew(tab.data,tab.n*4);
1422 copy2table(tab.n,0,4,td.x,td.v,td.f,1.0,tab.data);
1423 done_tabledata(&td);