src/tools/sigeps.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdio.h>
  40 #include <math.h>
  41 #include "typedefs.h"
  42 #include "statutil.h"
  43 #include "copyrite.h"
  44 #include "gmx_fatal.h"
  45 #include "xvgr.h"
  46 #include "pdbio.h"
  47 #include "macros.h"
  48 #include "smalloc.h"
  49 #include "vec.h"
  50 #include "pbc.h"
  51 #include "physics.h"
  52 #include "names.h"
  53 #include "txtdump.h"
  54 #include "trnio.h"
  55 #include "symtab.h"
  56 #include "confio.h"
  57
  58 real pot(real x,real qq,real c6,real cn,int npow)
  59 {
  60   return cn*pow(x,-npow)-c6*pow(x,-6)+qq*ONE_4PI_EPS0/x;
  61 }
  62
  63 real bhpot(real x,real qq,real A,real B,real C)
  64 {
  65   return A*exp(-B*x) - C*pow(x,-6.0);
  66 }
  67
  68 real dpot(real x,real qq,real c6,real cn,int npow)
  69 {
  70   return -(npow*cn*pow(x,-npow-1)-6*c6*pow(x,-7)+qq*ONE_4PI_EPS0/sqr(x));
  71 }
  72
  73 int main(int argc,char *argv[])
  74 {
  75   const char *desc[] = {
  76     "Sigeps is a simple utility that converts c6/c12 or c6/cn combinations",
  77     "to sigma and epsilon, or vice versa. It can also plot the potential",
  78     "in  file. In addition it makes an approximation of a Buckingham potential",
  79     "to a Lennard Jones potential."
  80   };
  81   static real c6=1.0e-3,cn=1.0e-6,qi=0,qj=0,sig=0.3,eps=1,sigfac=0.7;
  82   static real Abh=1e5,Bbh=32,Cbh=1e-3;
  83   static int  npow=12;
  84   t_pargs pa[] = {
  85     { "-c6",   FALSE,  etREAL,  {&c6},  "c6"   },
  86     { "-cn",   FALSE,  etREAL,  {&cn},  "constant for repulsion"   },
  87     { "-pow",  FALSE,  etINT,   {&npow},"power of the repulsion term" },
  88     { "-sig",  FALSE,  etREAL,  {&sig}, "sig"  },
  89     { "-eps",  FALSE,  etREAL,  {&eps}, "eps"  },
  90     { "-A",    FALSE,  etREAL,  {&Abh}, "Buckingham A" },
  91     { "-B",    FALSE,  etREAL,  {&Bbh}, "Buckingham B" },
  92     { "-C",    FALSE,  etREAL,  {&Cbh}, "Buckingham C" },
  93     { "-qi",   FALSE,  etREAL,  {&qi},  "qi"   },
  94     { "-qj",   FALSE,  etREAL,  {&qj},  "qj"   },
  95     { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of sigma for starting the plot" }
  96   };
  97   t_filenm fnm[] = {
  98     { efXVG, "-o", "potje", ffWRITE }
  99   };
 100   output_env_t oenv;
 101 #define NFILE asize(fnm)
 102   char *legend[] = { "Lennard-Jones", "Buckingham" };
 103   FILE      *fp;
 104   int       i;
 105   bool      bBham;
 106   real      qq,x,oldx,minimum,mval,dp[2],pp[2];
 107   int       cur=0;
 108 #define next (1-cur)
 109
 110   /* CopyRight(stdout,argv[0]);*/
 111   parse_common_args(&argc,argv,PCA_CAN_VIEW,
 112                     NFILE,fnm,asize(pa),pa,asize(desc),
 113                     desc,0,NULL,&oenv);
 114
 115   bBham = (opt2parg_bSet("-A",asize(pa),pa) ||
 116            opt2parg_bSet("-B",asize(pa),pa) ||
 117            opt2parg_bSet("-C",asize(pa),pa));
 118
 119   if (bBham) {
 120     c6  = Cbh;
 121     sig = pow((6.0/npow)*pow(npow/Bbh,npow-6.0),1.0/(npow-6.0));
 122     eps = c6/(4*pow(sig,6.0));
 123     cn  = 4*eps*pow(sig,npow);
 124   }
 125   else {
 126     if (opt2parg_bSet("-sig",asize(pa),pa) ||
 127         opt2parg_bSet("-eps",asize(pa),pa)) {
 128       c6  = 4*eps*pow(sig,6);
 129       cn  = 4*eps*pow(sig,npow);
 130     }
 131     else if (opt2parg_bSet("-c6",asize(pa),pa) ||
 132              opt2parg_bSet("-cn",asize(pa),pa) ||
 133              opt2parg_bSet("-pow",asize(pa),pa)) {
 134       sig = pow(cn/c6,1.0/(npow-6.0));
 135       eps = 0.25*c6*pow(sig,-6.0);
 136     }
 137     else {
 138       sig = eps = 0;
 139     }
 140     printf("c6    = %12.5e, c%d    = %12.5e\n",c6,npow,cn);
 141     printf("sigma = %12.5f, epsilon = %12.5f\n",sig,eps);
 142
 143     minimum = pow(npow/6.0*pow(sig,npow-6.0),1.0/(npow-6));
 144     printf("Van der Waals minimum at %g, V = %g\n\n",
 145            minimum,pot(minimum,0,c6,cn,npow));
 146     printf("Fit of Lennard Jones (%d-6) to Buckingham:\n",npow);
 147     Bbh = npow/minimum;
 148     Cbh = c6;
 149     Abh = 4*eps*pow(sig/minimum,npow)*exp(npow);
 150     printf("A = %g, B = %g, C = %g\n",Abh,Bbh,Cbh);
 151   }
 152   qq = qi*qj;
 153
 154   fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"Potential","r (nm)","E (kJ/mol)",
 155                 oenv);
 156   xvgr_legend(fp,asize(legend),legend,
 157                 oenv);
 158   if (sig == 0)
 159     sig=0.25;
 160   minimum = -1;
 161   mval    = 0;
 162   oldx    = 0;
 163   for(i=0; (i<100); i++) {
 164     x    = sigfac*sig+sig*i*0.02;
 165     dp[next] = dpot(x,qq,c6,cn,npow);
 166     fprintf(fp,"%10g  %10g  %10g\n",x,pot(x,qq,c6,cn,npow),
 167             bhpot(x,qq,Abh,Bbh,Cbh));
 168     if (qq != 0) {
 169       if ((i > 0) && (dp[cur]*dp[next] < 0)) {
 170         minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
 171         mval    = pot(minimum,qq,c6,cn,npow);
 172         printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
 173                minimum,mval);
 174       }
 175     }
 176     cur = next;
 177     oldx = x;
 178
 179   }
 180   ffclose(fp);
 181
 182   do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);
 183
 184   thanx(stderr);
 185
 186   return 0;
 187 }
 188
 189