src/mdlib/tables.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
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  26  *
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40 #include "maths.h"
  41 #include "typedefs.h"
  42 #include "names.h"
  43 #include "smalloc.h"
  44 #include "gmx_fatal.h"
  45 #include "futil.h"
  46 #include "xvgr.h"
  47 #include "vec.h"
  48 #include "main.h"
  49 #include "network.h"
  50 #include "physics.h"
  51 #include "force.h"
  52 #include "gmxfio.h"
  53
  54 /* All the possible (implemented) table functions */
  55 enum {
  56   etabLJ6,
  57   etabLJ12,
  58   etabLJ6Shift,
  59   etabLJ12Shift,
  60   etabShift,
  61   etabRF,
  62   etabRF_ZERO,
  63   etabCOUL,
  64   etabEwald,
  65   etabEwaldSwitch,
  66   etabEwaldUser,
  67   etabEwaldUserSwitch,
  68   etabLJ6Switch,
  69   etabLJ12Switch,
  70   etabCOULSwitch,
  71   etabLJ6Encad,
  72   etabLJ12Encad,
  73   etabCOULEncad,
  74   etabEXPMIN,
  75   etabUSER,
  76   etabNR
  77 };
  78
  79 typedef struct {
  80   const char *name;
  81   bool bCoulomb;
  82 } t_tab_props;
  83
  84 /* This structure holds name and a flag that tells whether
  85    this is a Coulomb type funtion */
  86 static const t_tab_props tprops[etabNR] = {
  87   { "LJ6",  FALSE },
  88   { "LJ12", FALSE },
  89   { "LJ6Shift", FALSE },
  90   { "LJ12Shift", FALSE },
  91   { "Shift", TRUE },
  92   { "RF", TRUE },
  93   { "RF-zero", TRUE },
  94   { "COUL", TRUE },
  95   { "Ewald", TRUE },
  96   { "Ewald-Switch", TRUE },
  97   { "Ewald-User", TRUE },
  98   { "Ewald-User-Switch", TRUE },
  99   { "LJ6Switch", FALSE },
 100   { "LJ12Switch", FALSE },
 101   { "COULSwitch", TRUE },
 102   { "LJ6-Encad shift", FALSE },
 103   { "LJ12-Encad shift", FALSE },
 104   { "COUL-Encad shift",  TRUE },
 105   { "EXPMIN", FALSE },
 106   { "USER", FALSE }
 107 };
 108
 109 /* Index in the table that says which function to use */
 110 enum { etiCOUL, etiLJ6, etiLJ12, etiNR };
 111
 112 typedef struct {
 113   int  nx,nx0;
 114   double tabscale;
 115   double *x,*v,*f;
 116 } t_tabledata;
 117
 118 #define pow2(x) ((x)*(x))
 119 #define pow3(x) ((x)*(x)*(x))
 120 #define pow4(x) ((x)*(x)*(x)*(x))
 121 #define pow5(x) ((x)*(x)*(x)*(x)*(x))
 122
 123 /* Calculate the potential and force for an r value
 124  * in exactly the same way it is done in the inner loop.
 125  * VFtab is a pointer to the table data, offset is
 126  * the point where we should begin and stride is
 127  * 4 if we have a buckingham table, 3 otherwise.
 128  * If you want to evaluate table no N, set offset to 4*N.
 129  *
 130  * We use normal precision here, since that is what we
 131  * will use in the inner loops.
 132  */
 133 static void evaluate_table(real VFtab[], int offset, int stride,
 134                            real tabscale, real r, real *y, real *yp)
 135 {
 136   int n;
 137   real rt,eps,eps2;
 138   real Y,F,Geps,Heps2,Fp;
 139
 140   rt       =  r*tabscale;
 141   n        =  (int)rt;
 142   eps      =  rt - n;
 143   eps2     =  eps*eps;
 144   n        =  offset+stride*n;
 145   Y        =  VFtab[n];
 146   F        =  VFtab[n+1];
 147   Geps     =  eps*VFtab[n+2];
 148   Heps2    =  eps2*VFtab[n+3];
 149   Fp       =  F+Geps+Heps2;
 150   *y       =  Y+eps*Fp;
 151   *yp      =  (Fp+Geps+2.0*Heps2)*tabscale;
 152 }
 153
 154
 155 static void splint(real xa[],real ya[],real y2a[],
 156                    int n,real x,real *y,real *yp)
 157 {
 158   int  klo,khi,k;
 159   real h,b,a,eps;
 160   real F,G,H;
 161
 162   klo=1;
 163   khi=n;
 164
 165   while ((khi-klo) > 1) {
 166     k=(khi+klo) >> 1;
 167     if (xa[k] > x)
 168       khi=k;
 169     else
 170       klo=k;
 171   }
 172   h = xa[khi]-xa[klo];
 173   if (h == 0.0)
 174     gmx_fatal(FARGS,"Bad XA input to function splint");
 175   a   = (xa[khi]-x)/h;
 176   b   = (x-xa[klo])/h;
 177   *y  = a*ya[klo]+b*ya[khi]+((a*a*a-a)*y2a[klo]+(b*b*b-b)*y2a[khi])*(h*h)/6.0;
 178   *yp = (ya[khi]-ya[klo])/h+((3*a*a-1)*y2a[klo]-(3*b*b-1)*y2a[khi])*h/6.0;
 179
 180   eps = b;
 181   F   = (ya[khi]-ya[klo]-(h*h/6.0)*(2*y2a[klo]+y2a[khi]));
 182   G   = (h*h/2.0)*y2a[klo];
 183   H   = (h*h/6.0)*(y2a[khi]-y2a[klo]);
 184   *y  = ya[klo] + eps*F + eps*eps*G + eps*eps*eps*H;
 185   *yp = (F + 2*eps*G + 3*eps*eps*H)/h;
 186 }
 187
 188
 189 static void copy2table(int n,int offset,int stride,
 190                        double x[],double Vtab[],double Ftab[],
 191                        real dest[])
 192 {
 193 /* Use double prec. for the intermediary variables
 194  * and temporary x/vtab/vtab2 data to avoid unnecessary
 195  * loss of precision.
 196  */
 197   int  i,nn0;
 198   double F,G,H,h;
 199
 200   h = 0;
 201   for(i=0; (i<n); i++) {
 202     if (i < n-1) {
 203       h   = x[i+1] - x[i];
 204       F   = -Ftab[i]*h;
 205       G   =  3*(Vtab[i+1] - Vtab[i]) + (Ftab[i+1] + 2*Ftab[i])*h;
 206       H   = -2*(Vtab[i+1] - Vtab[i]) - (Ftab[i+1] +   Ftab[i])*h;
 207     } else {
 208       /* Fill the last entry with a linear potential,
 209        * this is mainly for rounding issues with angle and dihedral potentials.
 210        */
 211       F   = -Ftab[i]*h;
 212       G   = 0;
 213       H   = 0;
 214     }
 215     nn0 = offset + i*stride;
 216     dest[nn0]   = Vtab[i];
 217     dest[nn0+1] = F;
 218     dest[nn0+2] = G;
 219     dest[nn0+3] = H;
 220   }
 221 }
 222
 223 static void init_table(FILE *fp,int n,int nx0,
 224                        double tabscale,t_tabledata *td,bool bAlloc)
 225 {
 226   int i;
 227
 228   td->nx  = n;
 229   td->nx0 = nx0;
 230   td->tabscale = tabscale;
 231   if (bAlloc) {
 232     snew(td->x,td->nx);
 233     snew(td->v,td->nx);
 234     snew(td->f,td->nx);
 235   }
 236   for(i=td->nx0; (i<td->nx); i++)
 237     td->x[i] = i/tabscale;
 238 }
 239
 240 static void spline_forces(int nx,double h,double v[],bool bS3,bool bE3,
 241                           double f[])
 242 {
 243   int    start,end,i;
 244   double v3,b_s,b_e,b;
 245   double beta,*gamma;
 246
 247   /* Formulas can be found in:
 248    * H.J.C. Berendsen, Simulating the Physical World, Cambridge 2007
 249    */
 250
 251   if (nx < 4 && (bS3 || bE3))
 252     gmx_fatal(FARGS,"Can not generate splines with third derivative boundary conditions with less than 4 (%d) points",nx);
 253
 254   /* To make life easy we initially set the spacing to 1
 255    * and correct for this at the end.
 256    */
 257   beta = 2;
 258   if (bS3) {
 259     /* Fit V''' at the start */
 260     v3  = v[3] - 3*v[2] + 3*v[1] - v[0];
 261     if (debug)
 262       fprintf(debug,"The left third derivative is %g\n",v3/(h*h*h));
 263     b_s = 2*(v[1] - v[0]) + v3/6;
 264     start = 0;
 265
 266     if (FALSE) {
 267       /* Fit V'' at the start */
 268       real v2;
 269
 270       v2  = -v[3] + 4*v[2] - 5*v[1] + 2*v[0];
 271       /* v2  = v[2] - 2*v[1] + v[0]; */
 272       if (debug)
 273         fprintf(debug,"The left second derivative is %g\n",v2/(h*h));
 274       b_s = 3*(v[1] - v[0]) - v2/2;
 275       start = 0;
 276     }
 277   } else {
 278     b_s = 3*(v[2] - v[0]) + f[0]*h;
 279     start = 1;
 280   }
 281   if (bE3) {
 282     /* Fit V''' at the end */
 283     v3  = v[nx-1] - 3*v[nx-2] + 3*v[nx-3] - v[nx-4];
 284     if (debug)
 285       fprintf(debug,"The right third derivative is %g\n",v3/(h*h*h));
 286     b_e = 2*(v[nx-1] - v[nx-2]) + v3/6;
 287     end = nx;
 288   } else {
 289     /* V'=0 at the end */
 290     b_e = 3*(v[nx-1] - v[nx-3]) + f[nx-1]*h;
 291     end = nx - 1;
 292   }
 293
 294   snew(gamma,nx);
 295   beta = (bS3 ? 1 : 4);
 296
 297   /* For V'' fitting */
 298   /* beta = (bS3 ? 2 : 4); */
 299
 300   f[start] = b_s/beta;
 301   for(i=start+1; i<end; i++) {
 302     gamma[i] = 1/beta;
 303     beta = 4 - gamma[i];
 304     b    =  3*(v[i+1] - v[i-1]);
 305     f[i] = (b - f[i-1])/beta;
 306   }
 307   gamma[end-1] = 1/beta;
 308   beta = (bE3 ? 1 : 4) - gamma[end-1];
 309   f[end-1] = (b_e - f[end-2])/beta;
 310
 311   for(i=end-2; i>=start; i--)
 312     f[i] -= gamma[i+1]*f[i+1];
 313   sfree(gamma);
 314
 315   /* Correct for the minus sign and the spacing */
 316   for(i=start; i<end; i++)
 317     f[i] = -f[i]/h;
 318 }
 319
 320 static void set_forces(FILE *fp,int angle,
 321                        int nx,double h,double v[],double f[],
 322                        int table)
 323 {
 324   int start,end;
 325
 326   if (angle == 2)
 327     gmx_fatal(FARGS,
 328               "Force generation for dihedral tables is not (yet) implemented");
 329
 330   start = 0;
 331   while (v[start] == 0)
 332     start++;
 333
 334   end = nx;
 335   while(v[end-1] == 0)
 336     end--;
 337   if (end > nx - 2)
 338     end = nx;
 339   else
 340     end++;
 341
 342   if (fp)
 343     fprintf(fp,"Generating forces for table %d, boundary conditions: V''' at %g, %s at %g\n",
 344             table+1,start*h,end==nx ? "V'''" : "V'=0",(end-1)*h);
 345   spline_forces(end-start,h,v+start,TRUE,end==nx,f+start);
 346 }
 347
 348 static void read_tables(FILE *fp,const char *fn,
 349                         int ntab,int angle,t_tabledata td[])
 350 {
 351   char *libfn;
 352   char buf[STRLEN];
 353   double **yy=NULL,start,end,dx0,dx1,ssd,vm,vp,f,numf;
 354   int  k,i,nx,nx0=0,ny,nny,ns;
 355   bool bAllZero,bZeroV,bZeroF;
 356   double tabscale;
 357
 358   nny = 2*ntab+1;
 359   libfn = gmxlibfn(fn);
 360   nx  = read_xvg(libfn,&yy,&ny);
 361   if (ny != nny)
 362     gmx_fatal(FARGS,"Trying to read file %s, but nr columns = %d, should be %d",
 363                 libfn,ny,nny);
 364   if (angle == 0) {
 365     if (yy[0][0] != 0.0)
 366       gmx_fatal(FARGS,
 367                 "The first distance in file %s is %f nm instead of %f nm",
 368                 libfn,yy[0][0],0.0);
 369   } else {
 370     if (angle == 1)
 371       start = 0.0;
 372     else
 373       start = -180.0;
 374     end = 180.0;
 375     if (yy[0][0] != start || yy[0][nx-1] != end)
 376       gmx_fatal(FARGS,"The angles in file %s should go from %f to %f instead of %f to %f\n",
 377                 libfn,start,end,yy[0][0],yy[0][nx-1]);
 378   }
 379
 380   tabscale = (nx-1)/(yy[0][nx-1] - yy[0][0]);
 381
 382   if (fp) {
 383     fprintf(fp,"Read user tables from %s with %d data points.\n",libfn,nx);
 384     if (angle == 0)
 385       fprintf(fp,"Tabscale = %g points/nm\n",tabscale);
 386   }
 387
 388   bAllZero = TRUE;
 389   for(k=0; k<ntab; k++) {
 390     bZeroV = TRUE;
 391     bZeroF = TRUE;
 392     for(i=0; (i < nx); i++) {
 393       if (i >= 2) {
 394         dx0 = yy[0][i-1] - yy[0][i-2];
 395         dx1 = yy[0][i]   - yy[0][i-1];
 396         /* Check for 1% deviation in spacing */
 397         if (fabs(dx1 - dx0) >= 0.005*(fabs(dx0) + fabs(dx1))) {
 398           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]);
 399         }
 400       }
 401       if (yy[1+k*2][i] != 0) {
 402         bZeroV = FALSE;
 403         if (bAllZero) {
 404           bAllZero = FALSE;
 405           nx0 = i;
 406         }
 407         if (yy[1+k*2][i] >  0.01*GMX_REAL_MAX ||
 408             yy[1+k*2][i] < -0.01*GMX_REAL_MAX) {
 409           gmx_fatal(FARGS,"Out of range potential value %g in file '%s'",
 410                     yy[1+k*2][i],fn);
 411         }
 412       }
 413       if (yy[1+k*2+1][i] != 0) {
 414         bZeroF = FALSE;
 415         if (bAllZero) {
 416           bAllZero = FALSE;
 417           nx0 = i;
 418         }
 419         if (yy[1+k*2+1][i] >  0.01*GMX_REAL_MAX ||
 420             yy[1+k*2+1][i] < -0.01*GMX_REAL_MAX) {
 421           gmx_fatal(FARGS,"Out of range force value %g in file '%s'",
 422                     yy[1+k*2+1][i],fn);
 423         }
 424       }
 425     }
 426
 427     if (!bZeroV && bZeroF) {
 428       set_forces(fp,angle,nx,1/tabscale,yy[1+k*2],yy[1+k*2+1],k);
 429     } else {
 430       /* Check if the second column is close to minus the numerical
 431        * derivative of the first column.
 432        */
 433       ssd = 0;
 434       ns = 0;
 435       for(i=1; (i < nx-1); i++) {
 436         vm = yy[1+2*k][i-1];
 437         vp = yy[1+2*k][i+1];
 438         f  = yy[1+2*k+1][i];
 439         if (vm != 0 && vp != 0 && f != 0) {
 440           /* Take the centered difference */
 441           numf = -(vp - vm)*0.5*tabscale;
 442           ssd += fabs(2*(f - numf)/(f + numf));
 443           ns++;
 444         }
 445       }
 446       if (ns > 0) {
 447         ssd /= ns;
 448         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));
 449         if (debug)
 450           fprintf(debug,"%s",buf);
 451         if (ssd > 0.2) {
 452           if (fp)
 453             fprintf(fp,"\nWARNING: %s\n",buf);
 454           fprintf(stderr,"\nWARNING: %s\n",buf);
 455         }
 456       }
 457     }
 458   }
 459   if (bAllZero && fp) {
 460     fprintf(fp,"\nNOTE: All elements in table %s are zero\n\n",libfn);
 461   }
 462
 463   for(k=0; (k<ntab); k++) {
 464     init_table(fp,nx,nx0,tabscale,&(td[k]),TRUE);
 465     for(i=0; (i<nx); i++) {
 466       td[k].x[i] = yy[0][i];
 467       td[k].v[i] = yy[2*k+1][i];
 468       td[k].f[i] = yy[2*k+2][i];
 469     }
 470   }
 471   for(i=0; (i<ny); i++)
 472     sfree(yy[i]);
 473   sfree(yy);
 474   sfree(libfn);
 475 }
 476
 477 static void done_tabledata(t_tabledata *td)
 478 {
 479   int i;
 480
 481   if (!td)
 482     return;
 483
 484   sfree(td->x);
 485   sfree(td->v);
 486   sfree(td->f);
 487 }
 488
 489 static void fill_table(t_tabledata *td,int tp,const t_forcerec *fr)
 490 {
 491   /* Fill the table according to the formulas in the manual.
 492    * In principle, we only need the potential and the second
 493    * derivative, but then we would have to do lots of calculations
 494    * in the inner loop. By precalculating some terms (see manual)
 495    * we get better eventual performance, despite a larger table.
 496    *
 497    * Since some of these higher-order terms are very small,
 498    * we always use double precision to calculate them here, in order
 499    * to avoid unnecessary loss of precision.
 500    */
 501 #ifdef DEBUG_SWITCH
 502   FILE *fp;
 503 #endif
 504   int  i;
 505   double reppow,p;
 506   double r1,rc,r12,r13;
 507   double r,r2,r6,rc6;
 508   double expr,Vtab,Ftab;
 509   /* Parameters for David's function */
 510   double A=0,B=0,C=0,A_3=0,B_4=0;
 511   /* Parameters for the switching function */
 512   double ksw,swi,swi1;
 513   /* Temporary parameters */
 514   bool bSwitch,bShift;
 515   double ewc=fr->ewaldcoeff;
 516   double isp= 0.564189583547756;
 517
 518   bSwitch = ((tp == etabLJ6Switch) || (tp == etabLJ12Switch) ||
 519              (tp == etabCOULSwitch) ||
 520              (tp == etabEwaldSwitch) || (tp == etabEwaldUserSwitch));
 521   bShift  = ((tp == etabLJ6Shift) || (tp == etabLJ12Shift) ||
 522              (tp == etabShift));
 523
 524   reppow = fr->reppow;
 525
 526   if (tprops[tp].bCoulomb) {
 527     r1 = fr->rcoulomb_switch;
 528     rc = fr->rcoulomb;
 529   }
 530   else {
 531     r1 = fr->rvdw_switch;
 532     rc = fr->rvdw;
 533   }
 534   if (bSwitch)
 535     ksw  = 1.0/(pow5(rc-r1));
 536   else
 537     ksw  = 0.0;
 538   if (bShift) {
 539     if (tp == etabShift)
 540       p = 1;
 541     else if (tp == etabLJ6Shift)
 542       p = 6;
 543     else
 544       p = reppow;
 545
 546     A = p * ((p+1)*r1-(p+4)*rc)/(pow(rc,p+2)*pow2(rc-r1));
 547     B = -p * ((p+1)*r1-(p+3)*rc)/(pow(rc,p+2)*pow3(rc-r1));
 548     C = 1.0/pow(rc,p)-A/3.0*pow3(rc-r1)-B/4.0*pow4(rc-r1);
 549     if (tp == etabLJ6Shift) {
 550       A=-A;
 551       B=-B;
 552       C=-C;
 553     }
 554     A_3=A/3.0;
 555     B_4=B/4.0;
 556   }
 557   if (debug) { fprintf(debug,"Setting up tables\n"); fflush(debug); }
 558
 559 #ifdef DEBUG_SWITCH
 560   fp=xvgropen("switch.xvg","switch","r","s");
 561 #endif
 562
 563   for(i=td->nx0; (i<td->nx); i++) {
 564     r     = td->x[i];
 565     r2    = r*r;
 566     r6    = 1.0/(r2*r2*r2);
 567     r12   = r6*r6;
 568     Vtab  = 0.0;
 569     Ftab  = 0.0;
 570     if (bSwitch) {
 571       /* swi is function, swi1 1st derivative and swi2 2nd derivative */
 572       /* The switch function is 1 for r<r1, 0 for r>rc, and smooth for
 573        * r1<=r<=rc. The 1st and 2nd derivatives are both zero at
 574        * r1 and rc.
 575        * ksw is just the constant 1/(rc-r1)^5, to save some calculations...
 576        */
 577       if(r<=r1) {
 578         swi  = 1.0;
 579         swi1 = 0.0;
 580       } else if (r>=rc) {
 581         swi  = 0.0;
 582         swi1 = 0.0;
 583       } else {
 584         swi      = 1 - 10*pow3(r-r1)*ksw*pow2(rc-r1)
 585           + 15*pow4(r-r1)*ksw*(rc-r1) - 6*pow5(r-r1)*ksw;
 586         swi1     = -30*pow2(r-r1)*ksw*pow2(rc-r1)
 587           + 60*pow3(r-r1)*ksw*(rc-r1) - 30*pow4(r-r1)*ksw;
 588       }
 589     }
 590     else { /* not really needed, but avoids compiler warnings... */
 591       swi  = 1.0;
 592       swi1 = 0.0;
 593     }
 594 #ifdef DEBUG_SWITCH
 595     fprintf(fp,"%10g  %10g  %10g  %10g\n",r,swi,swi1,swi2);
 596 #endif
 597
 598     rc6 = rc*rc*rc;
 599         rc6 = 1.0/(rc6*rc6);
 600
 601     switch (tp) {
 602     case etabLJ6:
 603       /* Dispersion */
 604       Vtab  = -r6;
 605       Ftab  = 6.0*Vtab/r;
 606       break;
 607     case etabLJ6Switch:
 608     case etabLJ6Shift:
 609       /* Dispersion */
 610       if (r < rc) {
 611         Vtab  = -r6;
 612         Ftab  = 6.0*Vtab/r;
 613       }
 614       break;
 615     case etabLJ12:
 616       /* Repulsion */
 617       Vtab  = r12;
 618       Ftab  = reppow*Vtab/r;
 619       break;
 620     case etabLJ12Switch:
 621     case etabLJ12Shift:
 622       /* Repulsion */
 623       if (r < rc) {
 624         Vtab  = r12;
 625         Ftab  = reppow*Vtab/r;
 626       }
 627       break;
 628         case etabLJ6Encad:
 629         if(r < rc) {
 630             Vtab  = -(r6-6.0*(rc-r)*rc6/rc-rc6);
 631             Ftab  = -(6.0*r6/r-6.0*rc6/rc);
 632         } else { /* r>rc */
 633             Vtab  = 0;
 634             Ftab  = 0;
 635         }
 636         break;
 637     case etabLJ12Encad:
 638         if(r < rc) {
 639             Vtab  = r12-12.0*(rc-r)*rc6*rc6/rc-1.0*rc6*rc6;
 640             Ftab  = 12.0*r12/r-12.0*rc6*rc6/rc;
 641         } else { /* r>rc */
 642             Vtab  = 0;
 643             Ftab  = 0;
 644         }
 645         break;
 646     case etabCOUL:
 647       Vtab  = 1.0/r;
 648       Ftab  = 1.0/r2;
 649       break;
 650     case etabCOULSwitch:
 651     case etabShift:
 652       if (r < rc) {
 653         Vtab  = 1.0/r;
 654         Ftab  = 1.0/r2;
 655       }
 656       break;
 657     case etabEwald:
 658     case etabEwaldSwitch:
 659       Vtab  = gmx_erfc(ewc*r)/r;
 660       Ftab  = gmx_erfc(ewc*r)/r2+2*exp(-(ewc*ewc*r2))*ewc*isp/r;
 661       break;
 662     case etabEwaldUser:
 663     case etabEwaldUserSwitch:
 664       /* Only calculate minus the reciprocal space contribution */
 665       Vtab  = -gmx_erf(ewc*r)/r;
 666       Ftab  = -gmx_erf(ewc*r)/r2+2*exp(-(ewc*ewc*r2))*ewc*isp/r;
 667       break;
 668     case etabRF:
 669     case etabRF_ZERO:
 670       Vtab  = 1.0/r      +   fr->k_rf*r2 - fr->c_rf;
 671       Ftab  = 1.0/r2     - 2*fr->k_rf*r;
 672       if (tp == etabRF_ZERO && r >= rc) {
 673         Vtab = 0;
 674         Ftab = 0;
 675       }
 676       break;
 677     case etabEXPMIN:
 678       expr  = exp(-r);
 679       Vtab  = expr;
 680       Ftab  = expr;
 681       break;
 682     case etabCOULEncad:
 683         if(r < rc) {
 684             Vtab  = 1.0/r-(rc-r)/(rc*rc)-1.0/rc;
 685             Ftab  = 1.0/r2-1.0/(rc*rc);
 686         } else { /* r>rc */
 687             Vtab  = 0;
 688             Ftab  = 0;
 689         }
 690         break;
 691     default:
 692       gmx_fatal(FARGS,"Table type %d not implemented yet. (%s,%d)",
 693                   tp,__FILE__,__LINE__);
 694     }
 695     if (bShift) {
 696       /* Normal coulomb with cut-off correction for potential */
 697       if (r < rc) {
 698         Vtab -= C;
 699         /* If in Shifting range add something to it */
 700         if (r > r1) {
 701           r12 = (r-r1)*(r-r1);
 702           r13 = (r-r1)*r12;
 703           Vtab  += - A_3*r13 - B_4*r12*r12;
 704           Ftab  +=   A*r12 + B*r13;
 705         }
 706       }
 707     }
 708
 709     if (tp == etabEwaldUser) {
 710       Vtab += td->v[i];
 711       Ftab += td->f[i];
 712     }
 713
 714     if ((r > r1) && bSwitch) {
 715       Ftab = Ftab*swi - Vtab*swi1;
 716       Vtab = Vtab*swi;
 717     }
 718
 719     /* Convert to single precision when we store to mem */
 720     td->v[i]  = Vtab;
 721     td->f[i]  = Ftab;
 722   }
 723
 724 #ifdef DEBUG_SWITCH
 725   gmx_fio_fclose(fp);
 726 #endif
 727 }
 728
 729 static void set_table_type(int tabsel[],const t_forcerec *fr,bool b14only)
 730 {
 731   int eltype,vdwtype;
 732
 733   /* Set the different table indices.
 734    * Coulomb first.
 735    */
 736
 737
 738   if (b14only) {
 739     switch (fr->eeltype) {
 740     case eelRF_NEC:
 741       eltype = eelRF;
 742       break;
 743     case eelUSER:
 744     case eelPMEUSER:
 745       eltype = eelUSER;
 746       break;
 747     default:
 748       eltype = eelCUT;
 749     }
 750   } else {
 751     eltype = fr->eeltype;
 752   }
 753
 754   switch (eltype) {
 755   case eelCUT:
 756     tabsel[etiCOUL] = etabCOUL;
 757     break;
 758   case eelPPPM:
 759   case eelPOISSON:
 760     tabsel[etiCOUL] = etabShift;
 761     break;
 762   case eelSHIFT:
 763     if (fr->rcoulomb > fr->rcoulomb_switch)
 764       tabsel[etiCOUL] = etabShift;
 765     else
 766       tabsel[etiCOUL] = etabCOUL;
 767     break;
 768   case eelEWALD:
 769   case eelPME:
 770     tabsel[etiCOUL] = etabEwald;
 771     break;
 772   case eelPMESWITCH:
 773     tabsel[etiCOUL] = etabEwaldSwitch;
 774     break;
 775   case eelPMEUSER:
 776     tabsel[etiCOUL] = etabEwaldUser;
 777     break;
 778   case eelRF:
 779   case eelGRF:
 780   case eelRF_NEC:
 781     tabsel[etiCOUL] = etabRF;
 782     break;
 783   case eelRF_ZERO:
 784     tabsel[etiCOUL] = etabRF_ZERO;
 785     break;
 786   case eelSWITCH:
 787     tabsel[etiCOUL] = etabCOULSwitch;
 788     break;
 789   case eelUSER:
 790     tabsel[etiCOUL] = etabUSER;
 791     break;
 792   case eelENCADSHIFT:
 793     tabsel[etiCOUL] = etabCOULEncad;
 794     break;
 795   default:
 796     gmx_fatal(FARGS,"Invalid eeltype %d",eltype);
 797   }
 798
 799   /* Van der Waals time */
 800   if (fr->bBHAM && !b14only) {
 801     tabsel[etiLJ6]  = etabLJ6;
 802     tabsel[etiLJ12] = etabEXPMIN;
 803   } else {
 804     if (b14only && fr->vdwtype != evdwUSER)
 805       vdwtype = evdwCUT;
 806     else
 807       vdwtype = fr->vdwtype;
 808
 809     switch (vdwtype) {
 810     case evdwSWITCH:
 811       tabsel[etiLJ6]  = etabLJ6Switch;
 812       tabsel[etiLJ12] = etabLJ12Switch;
 813       break;
 814     case evdwSHIFT:
 815       tabsel[etiLJ6]  = etabLJ6Shift;
 816       tabsel[etiLJ12] = etabLJ12Shift;
 817       break;
 818     case evdwUSER:
 819       tabsel[etiLJ6]  = etabUSER;
 820       tabsel[etiLJ12] = etabUSER;
 821       break;
 822     case evdwCUT:
 823       tabsel[etiLJ6]  = etabLJ6;
 824       tabsel[etiLJ12] = etabLJ12;
 825       break;
 826     case evdwENCADSHIFT:
 827       tabsel[etiLJ6]  = etabLJ6Encad;
 828       tabsel[etiLJ12] = etabLJ12Encad;
 829       break;
 830     default:
 831       gmx_fatal(FARGS,"Invalid vdwtype %d in %s line %d",vdwtype,
 832                   __FILE__,__LINE__);
 833     }
 834   }
 835 }
 836
 837 t_forcetable make_tables(FILE *out,const output_env_t oenv,
 838                          const t_forcerec *fr,
 839                          bool bVerbose,const char *fn,
 840                          real rtab,int flags)
 841 {
 842   const char *fns[3] = { "ctab.xvg", "dtab.xvg", "rtab.xvg" };
 843   const char *fns14[3] = { "ctab14.xvg", "dtab14.xvg", "rtab14.xvg" };
 844   FILE        *fp;
 845   t_tabledata *td;
 846   bool        b14only,bReadTab,bGenTab;
 847   real        x0,y0,yp;
 848   int         i,j,k,nx,nx0,tabsel[etiNR];
 849   void *      p_tmp;
 850
 851   t_forcetable table;
 852
 853   b14only = (flags & GMX_MAKETABLES_14ONLY);
 854
 855   if (flags & GMX_MAKETABLES_FORCEUSER) {
 856     tabsel[etiCOUL] = etabUSER;
 857     tabsel[etiLJ6]  = etabUSER;
 858     tabsel[etiLJ12] = etabUSER;
 859   } else {
 860     set_table_type(tabsel,fr,b14only);
 861   }
 862   snew(td,etiNR);
 863   table.r         = rtab;
 864   table.scale     = 0;
 865   table.n         = 0;
 866   table.scale_exp = 0;
 867   nx0             = 10;
 868   nx              = 0;
 869
 870   /* Check whether we have to read or generate */
 871   bReadTab = FALSE;
 872   bGenTab  = FALSE;
 873   for(i=0; (i<etiNR); i++) {
 874     if (tabsel[i] == etabUSER || tabsel[i] == etabEwaldUser)
 875       bReadTab = TRUE;
 876     if (tabsel[i] != etabUSER)
 877       bGenTab  = TRUE;
 878   }
 879   if (bReadTab) {
 880     read_tables(out,fn,etiNR,0,td);
 881     if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY)) {
 882       rtab      = td[0].x[td[0].nx-1];
 883       table.n   = td[0].nx;
 884       nx        = table.n;
 885     } else {
 886       if (td[0].x[td[0].nx-1] < rtab)
 887         gmx_fatal(FARGS,"Tables in file %s not long enough for cut-off:\n"
 888                   "\tshould be at least %f nm\n",fn,rtab);
 889       nx        = table.n = (int)(rtab*td[0].tabscale + 0.5);
 890     }
 891     table.scale = td[0].tabscale;
 892     nx0         = td[0].nx0;
 893   }
 894   if (bGenTab) {
 895     if (!bReadTab) {
 896 #ifdef GMX_DOUBLE
 897       table.scale = 2000.0;
 898 #else
 899       table.scale = 500.0;
 900 #endif
 901       nx = table.n = rtab*table.scale;
 902     }
 903   }
 904   if (fr->bBHAM) {
 905     if(fr->bham_b_max!=0)
 906       table.scale_exp = table.scale/fr->bham_b_max;
 907     else
 908       table.scale_exp = table.scale;
 909   }
 910
 911   /* Each table type (e.g. coul,lj6,lj12) requires four
 912    * numbers per datapoint. For performance reasons we want
 913    * the table data to be aligned to 16-byte. This is accomplished
 914    * by allocating 16 bytes extra to a temporary pointer, and then
 915    * calculating an aligned pointer. This new pointer must not be
 916    * used in a free() call, but thankfully we're sloppy enough not
 917    * to do this :-)
 918    */
 919
 920   /* 12 fp entries per table point, nx+1 points, and 16 bytes extra to align it. */
 921   p_tmp = malloc(12*(nx+1)*sizeof(real)+16);
 922
 923   /* align it - size_t has the same same as a pointer */
 924   table.tab = (real *) (((size_t) p_tmp + 16) & (~((size_t) 15)));
 925
 926
 927   for(k=0; (k<etiNR); k++) {
 928     if (tabsel[k] != etabUSER) {
 929       init_table(out,nx,nx0,
 930                  (tabsel[k] == etabEXPMIN) ? table.scale_exp : table.scale,
 931                  &(td[k]),!bReadTab);
 932       fill_table(&(td[k]),tabsel[k],fr);
 933       if (out)
 934         fprintf(out,"%s table with %d data points for %s%s.\n"
 935                 "Tabscale = %g points/nm\n",
 936                 tabsel[k]==etabEwaldUser ? "Modified" : "Generated",
 937                 td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
 938                 td[k].tabscale);
 939     }
 940     copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,table.tab);
 941
 942     if (bDebugMode() && bVerbose) {
 943       if (b14only)
 944         fp=xvgropen(fns14[k],fns14[k],"r","V",oenv);
 945       else
 946         fp=xvgropen(fns[k],fns[k],"r","V",oenv);
 947       /* plot the output 5 times denser than the table data */
 948       for(i=5*((nx0+1)/2); i<5*table.n; i++) {
 949         x0 = i*table.r/(5*(table.n-1));
 950         evaluate_table(table.tab,4*k,12,table.scale,x0,&y0,&yp);
 951         fprintf(fp,"%15.10e  %15.10e  %15.10e\n",x0,y0,yp);
 952       }
 953       gmx_fio_fclose(fp);
 954     }
 955     done_tabledata(&(td[k]));
 956   }
 957   sfree(td);
 958
 959   return table;
 960 }
 961
 962 t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
 963                            const t_forcerec *fr,
 964                            const char *fn,
 965                            real rtab)
 966 {
 967         const char *fns[3] = { "gbctab.xvg", "gbdtab.xvg", "gbrtab.xvg" };
 968         const char *fns14[3] = { "gbctab14.xvg", "gbdtab14.xvg", "gbrtab14.xvg" };
 969         FILE        *fp;
 970         t_tabledata *td;
 971         bool        bReadTab,bGenTab;
 972         real        x0,y0,yp;
 973         int         i,j,k,nx,nx0,tabsel[etiNR];
 974         void *      p_tmp;
 975         double      r,r2,Vtab,Ftab,expterm;
 976
 977         t_forcetable table;
 978
 979         double abs_error_r, abs_error_r2;
 980         double rel_error_r, rel_error_r2;
 981         double rel_error_r_old=0, rel_error_r2_old=0;
 982         double x0_r_error, x0_r2_error;
 983
 984
 985         /* Only set a Coulomb table for GB */
 986         /*
 987          tabsel[0]=etabGB;
 988          tabsel[1]=-1;
 989          tabsel[2]=-1;
 990         */
 991
 992         /* Set the table dimensions for GB, not really necessary to
 993          * use etiNR (since we only have one table, but ...)
 994          */
 995         snew(td,1);
 996         table.r         = fr->gbtabr;
 997         table.scale     = fr->gbtabscale;
 998         table.scale_exp = 0;
 999         table.n         = table.scale*table.r;
1000         nx0             = 0;
1001         nx              = table.scale*table.r;
1002
1003         /* Check whether we have to read or generate
1004          * We will always generate a table, so remove the read code
1005          * (Compare with original make_table function
1006          */
1007         bReadTab = FALSE;
1008         bGenTab  = TRUE;
1009
1010         /* Each table type (e.g. coul,lj6,lj12) requires four
1011          * numbers per datapoint. For performance reasons we want
1012          * the table data to be aligned to 16-byte. This is accomplished
1013          * by allocating 16 bytes extra to a temporary pointer, and then
1014          * calculating an aligned pointer. This new pointer must not be
1015          * used in a free() call, but thankfully we're sloppy enough not
1016          * to do this :-)
1017          */
1018
1019         /* 4 fp entries per table point, nx+1 points, and 16 bytes extra
1020            to align it. */
1021         p_tmp = malloc(4*(nx+1)*sizeof(real)+16);
1022
1023         /* align it - size_t has the same same as a pointer */
1024         table.tab = (real *) (((size_t) p_tmp + 16) & (~((size_t) 15)));
1025
1026         init_table(out,nx,nx0,table.scale,&(td[0]),!bReadTab);
1027
1028         /* Local implementation so we don't have to use the etabGB
1029          * enum above, which will cause problems later when
1030          * making the other tables (right now even though we are using
1031          * GB, the normal Coulomb tables will be created, but this
1032          * will cause a problem since fr->eeltype==etabGB which will not
1033          * be defined in fill_table and set_table_type
1034          */
1035
1036         for(i=nx0;i<nx;i++)
1037     {
1038                 Vtab    = 0.0;
1039                 Ftab    = 0.0;
1040                 r       = td->x[i];
1041                 r2      = r*r;
1042                 expterm = exp(-0.25*r2);
1043
1044                 Vtab = 1/sqrt(r2+expterm);
1045                 Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1046
1047                 /* Convert to single precision when we store to mem */
1048                 td->v[i]  = Vtab;
1049                 td->f[i]  = Ftab;
1050
1051     }
1052
1053         copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
1054
1055         if(bDebugMode())
1056     {
1057                 fp=xvgropen(fns[0],fns[0],"r","V",oenv);
1058                 /* plot the output 5 times denser than the table data */
1059                 /* for(i=5*nx0;i<5*table.n;i++) */
1060                 for(i=nx0;i<table.n;i++)
1061                 {
1062                         /* x0=i*table.r/(5*table.n); */
1063                         x0=i*table.r/table.n;
1064                         evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
1065                         fprintf(fp,"%15.10e  %15.10e  %15.10e\n",x0,y0,yp);
1066
1067                 }
1068                 ffclose(fp);
1069     }
1070
1071         /*
1072          for(i=100*nx0;i<99.81*table.n;i++)
1073          {
1074          r = i*table.r/(100*table.n);
1075          r2      = r*r;
1076          expterm = exp(-0.25*r2);
1077
1078          Vtab = 1/sqrt(r2+expterm);
1079          Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
1080
1081
1082          evaluate_table(table.tab,0,4,table.scale,r,&y0,&yp);
1083          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);
1084
1085          abs_error_r=fabs(y0-Vtab);
1086          abs_error_r2=fabs(yp-(-1)*Ftab);
1087
1088          rel_error_r=abs_error_r/y0;
1089          rel_error_r2=fabs(abs_error_r2/yp);
1090
1091
1092          if(rel_error_r>rel_error_r_old)
1093          {
1094          rel_error_r_old=rel_error_r;
1095          x0_r_error=x0;
1096          }
1097
1098          if(rel_error_r2>rel_error_r2_old)
1099          {
1100          rel_error_r2_old=rel_error_r2;
1101          x0_r2_error=x0;
1102          }
1103          }
1104
1105          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);
1106          printf("gb: XO_R=%g, X0_R2=%g\n",x0_r_error, x0_r2_error);
1107
1108          exit(1); */
1109         done_tabledata(&(td[0]));
1110         sfree(td);
1111
1112         return table;
1113
1114
1115 }
1116
1117 bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle)
1118 {
1119   t_tabledata td;
1120   double start;
1121   int    i;
1122   bondedtable_t tab;
1123
1124   if (angle < 2)
1125     start = 0;
1126   else
1127     start = -180.0;
1128   read_tables(fplog,fn,1,angle,&td);
1129   if (angle > 0) {
1130     /* Convert the table from degrees to radians */
1131     for(i=0; i<td.nx; i++) {
1132       td.x[i] *= DEG2RAD;
1133       td.f[i] *= RAD2DEG;
1134     }
1135     td.tabscale *= RAD2DEG;
1136   }
1137   tab.n = td.nx;
1138   tab.scale = td.tabscale;
1139   snew(tab.tab,tab.n*4);
1140   copy2table(tab.n,0,4,td.x,td.v,td.f,tab.tab);
1141   done_tabledata(&td);
1142
1143   return tab;
1144 }
1145
1146