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-%d",
  83               *(atoms->resinfo[resnr].name),
  84               atoms->resinfo[resnr].nr,
  85               anr+1);
  86       cg[ncg].label=strdup(buf);
  87       ncg++;
  88     }
  89   }
  90   *nncg=ncg;
  91
  92   for(i=0; (i<ncg); i++) {
  93     printf("CG: %10s Q: %6g  Atoms:",
  94            cg[i].label,cg[i].q);
  95     for(j=cgs->index[cg[i].cg]; (j<cgs->index[cg[i].cg+1]); j++)
  96       printf(" %4u",j);
  97     printf("\n");
  98   }
  99
 100   return cg;
 101 }
 102
 103 static real calc_dist(t_pbc *pbc,rvec x[],t_block *cgs,int icg,int jcg)
 104 {
 105   int  i,j;
 106   rvec dx;
 107   real d2,mindist2=1000;
 108
 109   for(i=cgs->index[icg]; (i<cgs->index[icg+1]); i++) {
 110     for(j=cgs->index[jcg]; (j<cgs->index[jcg+1]); j++) {
 111       pbc_dx(pbc,x[i],x[j],dx);
 112       d2 = norm2(dx);
 113       if (d2 < mindist2)
 114         mindist2 = d2;
 115     }
 116   }
 117   return sqrt(mindist2);
 118 }
 119
 120 int gmx_saltbr(int argc,char *argv[])
 121 {
 122   const char *desc[] = {
 123     "g_saltbr plots the distance between all combination of charged groups",
 124     "as a function of time. The groups are combined in different ways.",
 125     "A truncation/cut-off distance can be supplied with -t, ",
 126     "such that only groups interacting within this distance will be plotted in the ",
 127     "output.[BR]",
 128     "Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg",
 129     "and plus-plus.xvg, or files for every individual ion-pair if the [TT]-sep[tt]",
 130     "option is selected. In this case files are named as [TT]sb-ResnameResnr-Atomnr[tt].",
 131     "There may be many such files."
 132   };
 133   static gmx_bool bSep=FALSE;
 134   static real truncate=1000.0;
 135   t_pargs pa[] = {
 136     { "-t",   FALSE, etREAL, {&truncate},
 137       "trunc distance" },
 138     { "-sep", FALSE, etBOOL, {&bSep},
 139       "Use separate files for each interaction (may be MANY)" }
 140   };
 141   t_filenm   fnm[] = {
 142     { efTRX, "-f",  NULL, ffREAD },
 143     { efTPX, NULL,  NULL, ffREAD },
 144   };
 145 #define NFILE asize(fnm)
 146
 147   FILE       *out[3],*fp;
 148   static const char *title[3] = {
 149     "Distance between positively charged groups",
 150     "Distance between negatively charged groups",
 151     "Distance between oppositely charged groups"
 152   };
 153   static const char *fn[3] = {
 154     "plus-plus.xvg",
 155     "min-min.xvg",
 156     "plus-min.xvg"
 157   };
 158   int        nset[3]={0,0,0};
 159
 160   t_topology *top;
 161   int        ePBC;
 162   char       *buf;
 163   t_trxstatus *status;
 164   int        i,j,k,m,nnn,teller,ncg,n1,n2,n3,natoms;
 165   real       t,*time,qi,qj;
 166   t_charge   *cg;
 167   real       ***cgdist;
 168   int        **nWithin;
 169
 170   double     t0,dt;
 171   char       label[234];
 172   t_pbc      pbc;
 173   rvec       *x;
 174   matrix     box;
 175   output_env_t oenv;
 176
 177   CopyRight(stderr,argv[0]);
 178
 179   parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
 180                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 181
 182   top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
 183   cg=mk_charge(&top->atoms,&(top->cgs),&ncg);
 184   snew(cgdist,ncg);
 185   snew(nWithin,ncg);
 186   for(i=0; (i<ncg); i++) {
 187     snew(cgdist[i],ncg);
 188     snew(nWithin[i],ncg);
 189   }
 190
 191   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 192
 193   teller=0;
 194   time=NULL;
 195   do {
 196     srenew(time,teller+1);
 197     time[teller]=t;
 198
 199     set_pbc(&pbc,ePBC,box);
 200
 201     for(i=0; (i<ncg); i++) {
 202       for(j=i+1; (j<ncg); j++) {
 203         srenew(cgdist[i][j],teller+1);
 204         cgdist[i][j][teller]=
 205           calc_dist(&pbc,x,&(top->cgs),cg[i].cg,cg[j].cg);
 206         if (cgdist[i][j][teller] < truncate)
 207           nWithin[i][j]=1;
 208       }
 209     }
 210
 211     teller++;
 212   } while (read_next_x(oenv,status,&t,natoms,x,box));
 213   fprintf(stderr,"\n");
 214   close_trj(status);
 215
 216   if (bSep) {
 217     snew(buf,256);
 218     for(i=0; (i<ncg); i++)
 219       for(j=i+1; (j<ncg); j++) {
 220         if (nWithin[i][j]) {
 221           sprintf(buf,"sb-%s:%s.xvg",cg[i].label,cg[j].label);
 222           fp=xvgropen(buf,buf,"Time (ps)","Distance (nm)",oenv);
 223           for(k=0; (k<teller); k++)
 224             fprintf(fp,"%10g  %10g\n",time[k],cgdist[i][j][k]);
 225           ffclose(fp);
 226         }
 227       }
 228     sfree(buf);
 229   }
 230   else {
 231
 232     for(m=0; (m<3); m++)
 233       out[m]=xvgropen(fn[m],title[m],"Time (ps)","Distance (nm)",oenv);
 234
 235     snew(buf,256);
 236     for(i=0; (i<ncg); i++) {
 237       qi=cg[i].q;
 238       for(j=i+1; (j<ncg); j++) {
 239         qj=cg[j].q;
 240         if (nWithin[i][j]) {
 241           sprintf(buf,"%s:%s",cg[i].label,cg[j].label);
 242           if (qi*qj < 0)
 243             nnn=2;
 244           else if (qi+qj > 0)
 245             nnn=0;
 246           else
 247             nnn=1;
 248
 249           if (nset[nnn] == 0)
 250             xvgr_legend(out[nnn],1,(const char**)&buf,oenv);
 251           else {
 252             if (output_env_get_xvg_format(oenv) == exvgXMGR) {
 253               fprintf(out[nnn],"@ legend string %d \"%s\"\n",nset[nnn],buf);
 254             } else if (output_env_get_xvg_format(oenv) == exvgXMGRACE) {
 255               fprintf(out[nnn],"@ s%d legend \"%s\"\n",nset[nnn],buf);
 256             }
 257           }
 258           nset[nnn]++;
 259           nWithin[i][j]=nnn+1;
 260         }
 261       }
 262     }
 263     for(k=0; (k<teller); k++) {
 264       for(m=0; (m<3); m++)
 265         fprintf(out[m],"%10g",time[k]);
 266
 267       for(i=0; (i<ncg); i++) {
 268         for(j=i+1; (j<ncg); j++) {
 269           nnn=nWithin[i][j];
 270           if (nnn >0)
 271             fprintf(out[nnn-1],"  %10g",cgdist[i][j][k]);
 272         }
 273       }
 274       for(m=0; (m<3); m++)
 275         fprintf(out[m],"\n");
 276     }
 277     for(m=0; (m<3); m++) {
 278       ffclose(out[m]);
 279       if (nset[m] == 0)
 280         remove(fn[m]);
 281     }
 282   }
 283   thanx(stderr);
 284
 285   return 0;
 286 }