src/tools/gmx_saltbr.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38 #include <math.h>
  39 #include <string.h>
  40
  41 #include "macros.h"
  42 #include "vec.h"
  43 #include "sysstuff.h"
  44 #include "typedefs.h"
  45 #include "filenm.h"
  46 #include "statutil.h"
  47 #include "copyrite.h"
  48 #include "futil.h"
  49 #include "gmx_fatal.h"
  50 #include "smalloc.h"
  51 #include "pbc.h"
  52 #include "xvgr.h"
  53 #include "gmx_ana.h"
  54
  55
  56 typedef struct {
  57   char *label;
  58   int  cg;
  59   real q;
  60 } t_charge;
  61
  62 static t_charge *mk_charge(t_atoms *atoms,t_block *cgs,int *nncg)
  63 {
  64   t_charge *cg=NULL;
  65   char     buf[32];
  66   int      i,j,ncg,resnr,anr;
  67   real     qq;
  68
  69   /* Find the charged groups */
  70   ncg=0;
  71   for(i=0; (i<cgs->nr); i++) {
  72     qq=0.0;
  73     for(j=cgs->index[i]; (j<cgs->index[i+1]); j++) {
  74       qq+=atoms->atom[j].q;
  75     }
  76     if (fabs(qq) > 1.0e-5) {
  77       srenew(cg,ncg+1);
  78       cg[ncg].q=qq;
  79       cg[ncg].cg=i;
  80       anr=cgs->index[i];
  81       resnr=atoms->atom[anr].resind;
  82       sprintf(buf,"%s%d",
  83               *(atoms->resinfo[resnr].name),
  84               atoms->resinfo[resnr].nr);
  85       cg[ncg].label=strdup(buf);
  86       ncg++;
  87     }
  88   }
  89   *nncg=ncg;
  90
  91   for(i=0; (i<ncg); i++) {
  92     printf("CG: %10s Q: %6g  Atoms:",
  93            cg[i].label,cg[i].q);
  94     for(j=cgs->index[cg[i].cg]; (j<cgs->index[cg[i].cg+1]); j++)
  95       printf(" %4u",j);
  96     printf("\n");
  97   }
  98
  99   return cg;
 100 }
 101
 102 static real calc_dist(t_pbc *pbc,rvec x[],t_block *cgs,int icg,int jcg)
 103 {
 104   int  i,j;
 105   rvec dx;
 106   real d2,mindist2=1000;
 107
 108   for(i=cgs->index[icg]; (i<cgs->index[icg+1]); i++) {
 109     for(j=cgs->index[jcg]; (j<cgs->index[jcg+1]); j++) {
 110       pbc_dx(pbc,x[i],x[j],dx);
 111       d2 = norm2(dx);
 112       if (d2 < mindist2)
 113         mindist2 = d2;
 114     }
 115   }
 116   return sqrt(mindist2);
 117 }
 118
 119 int gmx_saltbr(int argc,char *argv[])
 120 {
 121   const char *desc[] = {
 122     "g_saltbr plots the distance between all combination of charged groups",
 123     "as a function of time. The groups are combined in different ways."
 124     "A minimum distance can be given, (eg. the cut-off), then groups",
 125     "that are never closer than that distance will not be plotted.[BR]",
 126     "Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg",
 127     "and plus-plus.xvg, or files for every individual ion-pair if selected"
 128   };
 129   static bool bSep=FALSE;
 130   static real truncate=1000.0;
 131   t_pargs pa[] = {
 132     { "-t",   FALSE, etREAL, {&truncate},
 133       "trunc distance" },
 134     { "-sep", FALSE, etBOOL, {&bSep},
 135       "Use separate files for each interaction (may be MANY)" }
 136   };
 137   t_filenm   fnm[] = {
 138     { efTRX, "-f",  NULL, ffREAD },
 139     { efTPX, NULL,  NULL, ffREAD },
 140   };
 141 #define NFILE asize(fnm)
 142
 143   FILE       *out[3],*fp;
 144   static const char *title[3] = {
 145     "Distance between positively charged groups",
 146     "Distance between negatively charged groups",
 147     "Distance between oppositely charged groups"
 148   };
 149   static const char *fn[3] = {
 150     "plus-plus.xvg",
 151     "min-min.xvg",
 152     "plus-min.xvg"
 153   };
 154   int        nset[3]={0,0,0};
 155
 156   t_topology *top;
 157   int        ePBC;
 158   char       *buf;
 159   int        status,i,j,k,m,nnn,teller,ncg,n1,n2,n3,natoms;
 160   real       t,*time,qi,qj;
 161   t_charge   *cg;
 162   real       ***cgdist;
 163   int        **nWithin;
 164
 165   double     t0,dt;
 166   char       label[234];
 167   t_pbc      pbc;
 168   rvec       *x;
 169   matrix     box;
 170   output_env_t oenv;
 171
 172   CopyRight(stderr,argv[0]);
 173
 174   parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
 175                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 176
 177   top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
 178   cg=mk_charge(&top->atoms,&(top->cgs),&ncg);
 179   snew(cgdist,ncg);
 180   snew(nWithin,ncg);
 181   for(i=0; (i<ncg); i++) {
 182     snew(cgdist[i],ncg);
 183     snew(nWithin[i],ncg);
 184   }
 185
 186   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 187
 188   teller=0;
 189   time=NULL;
 190   do {
 191     srenew(time,teller+1);
 192     time[teller]=t;
 193
 194     set_pbc(&pbc,ePBC,box);
 195
 196     for(i=0; (i<ncg); i++) {
 197       for(j=i+1; (j<ncg); j++) {
 198         srenew(cgdist[i][j],teller+1);
 199         cgdist[i][j][teller]=
 200           calc_dist(&pbc,x,&(top->cgs),cg[i].cg,cg[j].cg);
 201         if (cgdist[i][j][teller] < truncate)
 202           nWithin[i][j]=1;
 203       }
 204     }
 205
 206     teller++;
 207   } while (read_next_x(oenv,status,&t,natoms,x,box));
 208   fprintf(stderr,"\n");
 209   close_trj(status);
 210
 211   if (bSep) {
 212     snew(buf,256);
 213     for(i=0; (i<ncg); i++)
 214       for(j=i+1; (j<ncg); j++) {
 215         if (nWithin[i][j]) {
 216           sprintf(buf,"sb-%s:%s.xvg",cg[i].label,cg[j].label);
 217           fp=xvgropen(buf,buf,"Time (ps)","Distance (nm)",oenv);
 218           for(k=0; (k<teller); k++)
 219             fprintf(fp,"%10g  %10g\n",time[k],cgdist[i][j][k]);
 220           ffclose(fp);
 221         }
 222       }
 223     sfree(buf);
 224   }
 225   else {
 226
 227     for(m=0; (m<3); m++)
 228       out[m]=xvgropen(fn[m],title[m],"Time (ps)","Distance (nm)",oenv);
 229
 230     snew(buf,256);
 231     for(i=0; (i<ncg); i++) {
 232       qi=cg[i].q;
 233       for(j=i+1; (j<ncg); j++) {
 234         qj=cg[j].q;
 235         if (nWithin[i][j]) {
 236           sprintf(buf,"%s:%s",cg[i].label,cg[j].label);
 237           if (qi*qj < 0)
 238             nnn=2;
 239           else if (qi+qj > 0)
 240             nnn=0;
 241           else
 242             nnn=1;
 243
 244           if (nset[nnn] == 0)
 245             xvgr_legend(out[nnn],1,&buf,oenv);
 246           else {
 247             if (output_env_get_xvg_format(oenv) == exvgXMGR) {
 248               fprintf(out[nnn],"@ legend string %d \"%s\"\n",nset[nnn],buf);
 249             } else if (output_env_get_xvg_format(oenv) == exvgXMGRACE) {
 250               fprintf(out[nnn],"@ s%d legend \"%s\"\n",nset[nnn],buf);
 251             }
 252           }
 253           nset[nnn]++;
 254           nWithin[i][j]=nnn+1;
 255         }
 256       }
 257     }
 258     for(k=0; (k<teller); k++) {
 259       for(m=0; (m<3); m++)
 260         fprintf(out[m],"%10g",time[k]);
 261
 262       for(i=0; (i<ncg); i++) {
 263         for(j=i+1; (j<ncg); j++) {
 264           nnn=nWithin[i][j];
 265           if (nnn >0)
 266             fprintf(out[nnn-1],"  %10g",cgdist[i][j][k]);
 267         }
 268       }
 269       for(m=0; (m<3); m++)
 270         fprintf(out[m],"\n");
 271     }
 272     for(m=0; (m<3); m++) {
 273       ffclose(out[m]);
 274       if (nset[m] == 0)
 275         remove(fn[m]);
 276     }
 277   }
 278   thanx(stderr);
 279
 280   return 0;
 281 }