src/tools/gmx_spatial.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 3.0
  10  *
  11  * Copyright (c) 1991-2001
  12  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  13  * University of Groningen, The Netherlands
  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
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
  31  *
  32  * And Hey:
  33  * Gyas ROwers Mature At Cryogenic Speed
  34  */
  35
  36
  37 #include "statutil.h"
  38 #include "typedefs.h"
  39 #include "smalloc.h"
  40 #include "vec.h"
  41 #include "copyrite.h"
  42 #include "statutil.h"
  43 #include "tpxio.h"
  44 #include "math.h"
  45 #include "index.h"
  46 #include "pbc.h"
  47 #include "rmpbc.h"
  48 #include "gmx_ana.h"
  49
  50
  51 static const double bohr=0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */
  52
  53 static void mequit(void){
  54   printf("Memory allocation error\n");
  55   exit(1);
  56 }
  57
  58 int gmx_spatial(int argc,char *argv[])
  59 {
  60   const char *desc[] = {
  61     "g_spatial calculates the spatial distribution function and ",
  62     "outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
  63     "This was developed from template.c (gromacs-3.3). ",
  64     "For a system of 32K atoms and a 50ns trajectory, the SDF can be generated ",
  65     "in about 30 minutes, with most of the time dedicated to the two runs through ",
  66     "trjconv that are required to center everything properly. ",
  67     "This also takes a whole bunch of space (3 copies of the xtc file). ",
  68     "Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
  69     "3-4 atoms in a widely mobile group like a free amino acid in solution works ",
  70     "well, or select the protein backbone in a stable folded structure to get the SDF ",
  71     "of solvent and look at the time-averaged solvation shell. ",
  72     "It is also possible using this program to generate the SDF based on some arbitrarty ",
  73     "Cartesian coordinate. To do that, simply omit the preliminary trjconv steps. \n",
  74     "USAGE: \n",
  75     "1. Use make_ndx to create a group containing the atoms around which you want the SDF \n",
  76     "2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none \n",
  77     "3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans \n",
  78     "4. run g_spatial on the xtc output of step #3. \n",
  79     "5. Load grid.cube into VMD and view as an isosurface. \n",
  80     "*** Systems such as micelles will require trjconv -pbc cluster between steps 1 and 2\n",
  81     "WARNINGS: \n",
  82     "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
  83     "However, the preparatory -fit rot+trans option to trjconv implies that your system will be rotating ",
  84     "and translating in space (in order that the selected group does not). Therefore the values that are ",
  85     "returned will only be valid for some region around your central group/coordinate that has full overlap ",
  86     "with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
  87     "It is up to the user to ensure that this is the case. \n",
  88     "BUGS: \n",
  89     "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
  90     "and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab ",
  91     "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
  92     "with an increased -nab value. \n",
  93     "RISKY OPTIONS: \n",
  94     "To reduce the amount of space and time required, you can output only the coords ",
  95     "that are going to be used in the first and subsequent run through trjconv. ",
  96     "However, be sure to set the -nab option to a sufficiently high value since ",
  97     "memory is allocated for cube bins based on the initial coords and the -nab ",
  98     "(Number of Additional Bins) option value. \n"
  99   };
 100
 101   static bool bPBC=FALSE;
 102   static bool bSHIFT=FALSE;
 103   static int iIGNOREOUTER=-1; /*Positive values may help if the surface is spikey */
 104   static bool bCUTDOWN=TRUE;
 105   static real rBINWIDTH=0.05; /* nm */
 106   static bool bCALCDIV=TRUE;
 107   static int iNAB=4;
 108
 109   t_pargs pa[] = {
 110     { "-pbc",      FALSE, etBOOL, {&bPBC},
 111       "Use periodic boundary conditions for computing distances" },
 112     { "-div",      FALSE, etBOOL, {&bCALCDIV},
 113       "Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (-nodiv) to get accurate counts per frame" },
 114     { "-ign",      FALSE, etINT, {&iIGNOREOUTER},
 115       "Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)" },
 116     /*    { "-cut",      bCUTDOWN, etBOOL, {&bCUTDOWN},*/
 117     /*      "Display a total cube that is of minimal size" }, */
 118     { "-bin",      FALSE, etREAL, {&rBINWIDTH},
 119       "Width of the bins in nm" },
 120     { "-nab",      FALSE, etINT, {&iNAB},
 121       "Number of additional bins to ensure proper memory allocation" }
 122   };
 123
 124   double MINBIN[3];
 125   double MAXBIN[3];
 126   t_topology top;
 127   int        ePBC;
 128   char       title[STRLEN];
 129   t_trxframe fr;
 130   rvec       *xtop,*shx[26];
 131   matrix     box,box_pbc;
 132   int        status;
 133   int        flags = TRX_READ_X;
 134   t_pbc      pbc;
 135   t_atoms    *atoms;
 136   int        natoms;
 137   char        *grpnm,*grpnmp;
 138   atom_id     *index,*indexp;
 139   int         i,nidx,nidxp;
 140   int v;
 141   int j,k;
 142   long ***bin=(long ***)NULL;
 143   long nbin[3];
 144   FILE *flp;
 145   long x,y,z,minx,miny,minz,maxx,maxy,maxz;
 146   long numfr, numcu;
 147   long tot,max,min;
 148   double norm;
 149   output_env_t oenv;
 150
 151   t_filenm fnm[] = {
 152     { efTPS,  NULL,  NULL, ffREAD },   /* this is for the topology */
 153     { efTRX, "-f", NULL, ffREAD },      /* and this for the trajectory */
 154     { efNDX, NULL, NULL, ffOPTRD }
 155   };
 156
 157 #define NFILE asize(fnm)
 158
 159   CopyRight(stderr,argv[0]);
 160
 161   /* This is the routine responsible for adding default options,
 162    * calling the X/motif interface, etc. */
 163   parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
 164                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 165
 166   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
 167   sfree(xtop);
 168
 169   atoms=&(top.atoms);
 170   printf("Select group to generate SDF:\n");
 171   get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
 172   printf("Select group to output coords (e.g. solute):\n");
 173   get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidxp,&indexp,&grpnmp);
 174
 175   /* The first time we read data is a little special */
 176   natoms=read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,flags);
 177
 178   /* Memory Allocation */
 179   MINBIN[XX]=MAXBIN[XX]=fr.x[0][XX];
 180   MINBIN[YY]=MAXBIN[YY]=fr.x[0][YY];
 181   MINBIN[ZZ]=MAXBIN[ZZ]=fr.x[0][ZZ];
 182   for(i=1; i<top.atoms.nr; ++i) {
 183     if(fr.x[i][XX]<MINBIN[XX])MINBIN[XX]=fr.x[i][XX];
 184     if(fr.x[i][XX]>MAXBIN[XX])MAXBIN[XX]=fr.x[i][XX];
 185     if(fr.x[i][YY]<MINBIN[YY])MINBIN[YY]=fr.x[i][YY];
 186     if(fr.x[i][YY]>MAXBIN[YY])MAXBIN[YY]=fr.x[i][YY];
 187     if(fr.x[i][ZZ]<MINBIN[ZZ])MINBIN[ZZ]=fr.x[i][ZZ];
 188     if(fr.x[i][ZZ]>MAXBIN[ZZ])MAXBIN[ZZ]=fr.x[i][ZZ];
 189   }
 190   for (i=ZZ; i>=XX; --i){
 191     MAXBIN[i]=(ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+(double)iNAB)*rBINWIDTH+MINBIN[i];
 192     MINBIN[i]-=(double)iNAB*rBINWIDTH;
 193     nbin[i]=(long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
 194   }
 195   bin=(long ***)malloc(nbin[XX]*sizeof(long **));
 196   if(!bin)mequit();
 197   for(i=0; i<nbin[XX]; ++i){
 198     bin[i]=(long **)malloc(nbin[YY]*sizeof(long *));
 199     if(!bin[i])mequit();
 200     for(j=0; j<nbin[YY]; ++j){
 201       bin[i][j]=(long *)calloc(nbin[ZZ],sizeof(long));
 202       if(!bin[i][j])mequit();
 203     }
 204   }
 205   copy_mat(box,box_pbc);
 206   numfr=0;
 207   minx=miny=minz=999;
 208   maxx=maxy=maxz=0;
 209   /* This is the main loop over frames */
 210   do {
 211     /* Must init pbc every step because of pressure coupling */
 212
 213     copy_mat(box,box_pbc);
 214     if (bPBC) {
 215       rm_pbc(&top.idef,ePBC,natoms,box,fr.x,fr.x);
 216       set_pbc(&pbc,ePBC,box_pbc);
 217     }
 218
 219     for(i=0; i<nidx; i++) {
 220       if(fr.x[index[i]][XX]<MINBIN[XX]||fr.x[index[i]][XX]>MAXBIN[XX]||
 221          fr.x[index[i]][YY]<MINBIN[YY]||fr.x[index[i]][YY]>MAXBIN[YY]||
 222          fr.x[index[i]][ZZ]<MINBIN[ZZ]||fr.x[index[i]][ZZ]>MAXBIN[ZZ])
 223         {
 224           printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
 225           printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n",MINBIN[XX],MINBIN[YY],MINBIN[ZZ],MAXBIN[XX],MAXBIN[YY],MAXBIN[ZZ]);
 226           printf("Memory was required for [%f,%f,%f]\n",fr.x[index[i]][XX],fr.x[index[i]][YY],fr.x[index[i]][ZZ]);
 227           exit(1);
 228         }
 229       x=(long)ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH);
 230       y=(long)ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH);
 231       z=(long)ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH);
 232       ++bin[x][y][z];
 233       if(x<minx)minx=x;
 234       if(x>maxx)maxx=x;
 235       if(y<miny)miny=y;
 236       if(y>maxy)maxy=y;
 237       if(z<minz)minz=z;
 238       if(z>maxz)maxz=z;
 239     }
 240     numfr++;
 241     /* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */
 242
 243   } while(read_next_frame(oenv,status,&fr));
 244
 245   if(!bCUTDOWN){
 246     minx=miny=minz=0;
 247     maxx=nbin[XX];
 248     maxy=nbin[YY];
 249     maxz=nbin[ZZ];
 250   }
 251
 252   /* OUTPUT */
 253   flp=ffopen("grid.cube","w");
 254   fprintf(flp,"Spatial Distribution Function\n");
 255   fprintf(flp,"test\n");
 256   fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
 257   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxx-minx+1-(2*iIGNOREOUTER),rBINWIDTH*10./bohr,0.,0.);
 258   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxy-miny+1-(2*iIGNOREOUTER),0.,rBINWIDTH*10./bohr,0.);
 259   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxz-minz+1-(2*iIGNOREOUTER),0.,0.,rBINWIDTH*10./bohr);
 260   for(i=0; i<nidxp; i++){
 261     v=2;
 262     if(*(top.atoms.atomname[indexp[i]][0])=='C')v=6;
 263     if(*(top.atoms.atomname[indexp[i]][0])=='N')v=7;
 264     if(*(top.atoms.atomname[indexp[i]][0])=='O')v=8;
 265     if(*(top.atoms.atomname[indexp[i]][0])=='H')v=1;
 266     if(*(top.atoms.atomname[indexp[i]][0])=='S')v=16;
 267     fprintf(flp,"%5d%12.6f%12.6f%12.6f%12.6f\n",v,0.,(double)fr.x[indexp[i]][XX]*10./bohr,(double)fr.x[indexp[i]][YY]*10./bohr,(double)fr.x[indexp[i]][ZZ]*10./bohr);
 268   }
 269
 270   tot=0;
 271   for(k=0;k<nbin[XX];k++) {
 272     if(!(k<minx||k>maxx))continue;
 273     for(j=0;j<nbin[YY];j++) {
 274       if(!(j<miny||j>maxy))continue;
 275       for(i=0;i<nbin[ZZ];i++) {
 276         if(!(i<minz||i>maxz))continue;
 277         if(bin[k][j][i]!=0){
 278           printf("A bin was not empty when it should have been empty. Programming error.\n");
 279           printf("bin[%d][%d][%d] was = %ld\n",k,j,i,bin[k][j][i]);
 280           exit(1);
 281         }
 282       }
 283     }
 284   }
 285
 286   min=999;
 287   max=0;
 288   for(k=0;k<nbin[XX];k++) {
 289     if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
 290     for(j=0;j<nbin[YY];j++) {
 291       if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
 292       for(i=0;i<nbin[ZZ];i++) {
 293         if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
 294         tot+=bin[k][j][i];
 295         if(bin[k][j][i]>max)max=bin[k][j][i];
 296         if(bin[k][j][i]<min)min=bin[k][j][i];
 297       }
 298     }
 299   }
 300
 301   numcu=(maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
 302   if(bCALCDIV){
 303     norm=((double)numcu*(double)numfr) / (double)tot;
 304   }else{
 305     norm=1.0;
 306   }
 307
 308   for(k=0;k<nbin[XX];k++) {
 309     if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
 310     for(j=0;j<nbin[YY];j++) {
 311       if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
 312       for(i=0;i<nbin[ZZ];i++) {
 313         if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
 314         fprintf(flp,"%12.6f ",norm*(double)bin[k][j][i]/(double)numfr);
 315       }
 316       fprintf(flp,"\n");
 317     }
 318     fprintf(flp,"\n");
 319   }
 320   ffclose(flp);
 321
 322   /* printf("x=%d to %d\n",minx,maxx); */
 323   /* printf("y=%d to %d\n",miny,maxy); */
 324   /* printf("z=%d to %d\n",minz,maxz); */
 325
 326   if(bCALCDIV){
 327     printf("Counts per frame in all %ld cubes divided by %le\n",numcu,1.0/norm);
 328     printf("Normalized data: average %le, min %le, max %le\n",1.0,norm*(double)min/(double)numfr,norm*(double)max/(double)numfr);
 329   }else{
 330     printf("grid.cube contains counts per frame in all %ld cubes\n",numcu);
 331     printf("Raw data: average %le, min %le, max %le\n",1.0/norm,(double)min/(double)numfr,(double)max/(double)numfr);
 332   }
 333
 334   thanx(stderr);
 335
 336   return 0;
 337 }
 338