src/contrib/sigeps.c

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