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
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  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
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  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   t_trxstatus *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   gmx_rmpbc_t  gpbc=NULL;
 151
 152   t_filenm fnm[] = {
 153     { efTPS,  NULL,  NULL, ffREAD },   /* this is for the topology */
 154     { efTRX, "-f", NULL, ffREAD },      /* and this for the trajectory */
 155     { efNDX, NULL, NULL, ffOPTRD }
 156   };
 157
 158 #define NFILE asize(fnm)
 159
 160   CopyRight(stderr,argv[0]);
 161
 162   /* This is the routine responsible for adding default options,
 163    * calling the X/motif interface, etc. */
 164   parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
 165                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 166
 167   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
 168   sfree(xtop);
 169
 170   atoms=&(top.atoms);
 171   printf("Select group to generate SDF:\n");
 172   get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
 173   printf("Select group to output coords (e.g. solute):\n");
 174   get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidxp,&indexp,&grpnmp);
 175
 176   /* The first time we read data is a little special */
 177   natoms=read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,flags);
 178
 179   /* Memory Allocation */
 180   MINBIN[XX]=MAXBIN[XX]=fr.x[0][XX];
 181   MINBIN[YY]=MAXBIN[YY]=fr.x[0][YY];
 182   MINBIN[ZZ]=MAXBIN[ZZ]=fr.x[0][ZZ];
 183   for(i=1; i<top.atoms.nr; ++i) {
 184     if(fr.x[i][XX]<MINBIN[XX])MINBIN[XX]=fr.x[i][XX];
 185     if(fr.x[i][XX]>MAXBIN[XX])MAXBIN[XX]=fr.x[i][XX];
 186     if(fr.x[i][YY]<MINBIN[YY])MINBIN[YY]=fr.x[i][YY];
 187     if(fr.x[i][YY]>MAXBIN[YY])MAXBIN[YY]=fr.x[i][YY];
 188     if(fr.x[i][ZZ]<MINBIN[ZZ])MINBIN[ZZ]=fr.x[i][ZZ];
 189     if(fr.x[i][ZZ]>MAXBIN[ZZ])MAXBIN[ZZ]=fr.x[i][ZZ];
 190   }
 191   for (i=ZZ; i>=XX; --i){
 192     MAXBIN[i]=(ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+(double)iNAB)*rBINWIDTH+MINBIN[i];
 193     MINBIN[i]-=(double)iNAB*rBINWIDTH;
 194     nbin[i]=(long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
 195   }
 196   bin=(long ***)malloc(nbin[XX]*sizeof(long **));
 197   if(!bin)mequit();
 198   for(i=0; i<nbin[XX]; ++i){
 199     bin[i]=(long **)malloc(nbin[YY]*sizeof(long *));
 200     if(!bin[i])mequit();
 201     for(j=0; j<nbin[YY]; ++j){
 202       bin[i][j]=(long *)calloc(nbin[ZZ],sizeof(long));
 203       if(!bin[i][j])mequit();
 204     }
 205   }
 206   copy_mat(box,box_pbc);
 207   numfr=0;
 208   minx=miny=minz=999;
 209   maxx=maxy=maxz=0;
 210
 211   if (bPBC)
 212     gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
 213   /* This is the main loop over frames */
 214   do {
 215     /* Must init pbc every step because of pressure coupling */
 216
 217     copy_mat(box,box_pbc);
 218     if (bPBC) {
 219       gmx_rmpbc_trxfr(gpbc,&fr);
 220       set_pbc(&pbc,ePBC,box_pbc);
 221     }
 222
 223     for(i=0; i<nidx; i++) {
 224       if(fr.x[index[i]][XX]<MINBIN[XX]||fr.x[index[i]][XX]>MAXBIN[XX]||
 225          fr.x[index[i]][YY]<MINBIN[YY]||fr.x[index[i]][YY]>MAXBIN[YY]||
 226          fr.x[index[i]][ZZ]<MINBIN[ZZ]||fr.x[index[i]][ZZ]>MAXBIN[ZZ])
 227         {
 228           printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
 229           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]);
 230           printf("Memory was required for [%f,%f,%f]\n",fr.x[index[i]][XX],fr.x[index[i]][YY],fr.x[index[i]][ZZ]);
 231           exit(1);
 232         }
 233       x=(long)ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH);
 234       y=(long)ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH);
 235       z=(long)ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH);
 236       ++bin[x][y][z];
 237       if(x<minx)minx=x;
 238       if(x>maxx)maxx=x;
 239       if(y<miny)miny=y;
 240       if(y>maxy)maxy=y;
 241       if(z<minz)minz=z;
 242       if(z>maxz)maxz=z;
 243     }
 244     numfr++;
 245     /* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */
 246
 247   } while(read_next_frame(oenv,status,&fr));
 248
 249   if (bPBC)
 250     gmx_rmpbc_done(gpbc);
 251
 252   if(!bCUTDOWN){
 253     minx=miny=minz=0;
 254     maxx=nbin[XX];
 255     maxy=nbin[YY];
 256     maxz=nbin[ZZ];
 257   }
 258
 259   /* OUTPUT */
 260   flp=ffopen("grid.cube","w");
 261   fprintf(flp,"Spatial Distribution Function\n");
 262   fprintf(flp,"test\n");
 263   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);
 264   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxx-minx+1-(2*iIGNOREOUTER),rBINWIDTH*10./bohr,0.,0.);
 265   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxy-miny+1-(2*iIGNOREOUTER),0.,rBINWIDTH*10./bohr,0.);
 266   fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxz-minz+1-(2*iIGNOREOUTER),0.,0.,rBINWIDTH*10./bohr);
 267   for(i=0; i<nidxp; i++){
 268     v=2;
 269     if(*(top.atoms.atomname[indexp[i]][0])=='C')v=6;
 270     if(*(top.atoms.atomname[indexp[i]][0])=='N')v=7;
 271     if(*(top.atoms.atomname[indexp[i]][0])=='O')v=8;
 272     if(*(top.atoms.atomname[indexp[i]][0])=='H')v=1;
 273     if(*(top.atoms.atomname[indexp[i]][0])=='S')v=16;
 274     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);
 275   }
 276
 277   tot=0;
 278   for(k=0;k<nbin[XX];k++) {
 279     if(!(k<minx||k>maxx))continue;
 280     for(j=0;j<nbin[YY];j++) {
 281       if(!(j<miny||j>maxy))continue;
 282       for(i=0;i<nbin[ZZ];i++) {
 283         if(!(i<minz||i>maxz))continue;
 284         if(bin[k][j][i]!=0){
 285           printf("A bin was not empty when it should have been empty. Programming error.\n");
 286           printf("bin[%d][%d][%d] was = %ld\n",k,j,i,bin[k][j][i]);
 287           exit(1);
 288         }
 289       }
 290     }
 291   }
 292
 293   min=999;
 294   max=0;
 295   for(k=0;k<nbin[XX];k++) {
 296     if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
 297     for(j=0;j<nbin[YY];j++) {
 298       if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
 299       for(i=0;i<nbin[ZZ];i++) {
 300         if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
 301         tot+=bin[k][j][i];
 302         if(bin[k][j][i]>max)max=bin[k][j][i];
 303         if(bin[k][j][i]<min)min=bin[k][j][i];
 304       }
 305     }
 306   }
 307
 308   numcu=(maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
 309   if(bCALCDIV){
 310     norm=((double)numcu*(double)numfr) / (double)tot;
 311   }else{
 312     norm=1.0;
 313   }
 314
 315   for(k=0;k<nbin[XX];k++) {
 316     if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
 317     for(j=0;j<nbin[YY];j++) {
 318       if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
 319       for(i=0;i<nbin[ZZ];i++) {
 320         if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
 321         fprintf(flp,"%12.6f ",norm*(double)bin[k][j][i]/(double)numfr);
 322       }
 323       fprintf(flp,"\n");
 324     }
 325     fprintf(flp,"\n");
 326   }
 327   ffclose(flp);
 328
 329   /* printf("x=%d to %d\n",minx,maxx); */
 330   /* printf("y=%d to %d\n",miny,maxy); */
 331   /* printf("z=%d to %d\n",minz,maxz); */
 332
 333   if(bCALCDIV){
 334     printf("Counts per frame in all %ld cubes divided by %le\n",numcu,1.0/norm);
 335     printf("Normalized data: average %le, min %le, max %le\n",1.0,norm*(double)min/(double)numfr,norm*(double)max/(double)numfr);
 336   }else{
 337     printf("grid.cube contains counts per frame in all %ld cubes\n",numcu);
 338     printf("Raw data: average %le, min %le, max %le\n",1.0/norm,(double)min/(double)numfr,(double)max/(double)numfr);
 339   }
 340
 341   thanx(stderr);
 342
 343   return 0;
 344 }
 345