int gmx_sigeps(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_sigeps[tt] is a simple utility that converts C6/C12 or C6/Cn combinations",
"to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential",
"in file. In addition, it makes an approximation of a Buckingham potential",
"to a Lennard-Jones potential."
};
static real c6 = 1.0e-3, cn = 1.0e-6, qi = 0, qj = 0, sig = 0.3, eps = 1, sigfac = 0.7;
static real Abh = 1e5, Bbh = 32, Cbh = 1e-3;
static int npow = 12;
t_pargs pa[] = {
{ "-c6", FALSE, etREAL, {&c6}, "C6" },
{ "-cn", FALSE, etREAL, {&cn}, "Constant for repulsion" },
{ "-pow", FALSE, etINT, {&npow}, "Power of the repulsion term" },
{ "-sig", FALSE, etREAL, {&sig}, "[GRK]sigma[grk]" },
{ "-eps", FALSE, etREAL, {&eps}, "[GRK]epsilon[grk]" },
{ "-A", FALSE, etREAL, {&Abh}, "Buckingham A" },
{ "-B", FALSE, etREAL, {&Bbh}, "Buckingham B" },
{ "-C", FALSE, etREAL, {&Cbh}, "Buckingham C" },
{ "-qi", FALSE, etREAL, {&qi}, "qi" },
{ "-qj", FALSE, etREAL, {&qj}, "qj" },
{ "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of [GRK]sigma[grk] for starting the plot" }
};
t_filenm fnm[] = {
{ efXVG, "-o", "potje", ffWRITE }
};
output_env_t oenv;
#define NFILE asize(fnm)
const char *legend[] = { "Lennard-Jones", "Buckingham" };
FILE *fp;
int i;
gmx_bool bBham;
real qq, x, oldx, minimum, mval, dp[2], pp[2];
int cur = 0;
#define next (1-cur)
parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc),
desc, 0, NULL, &oenv);
bBham = (opt2parg_bSet("-A", asize(pa), pa) ||
opt2parg_bSet("-B", asize(pa), pa) ||
opt2parg_bSet("-C", asize(pa), pa));
if (bBham)
{
c6 = Cbh;
sig = pow((6.0/npow)*pow(npow/Bbh, npow-6.0), 1.0/(npow-6.0));
eps = c6/(4*pow(sig, 6.0));
cn = 4*eps*pow(sig, npow);
}
else
{
if (opt2parg_bSet("-sig", asize(pa), pa) ||
opt2parg_bSet("-eps", asize(pa), pa))
{
c6 = 4*eps*pow(sig, 6);
cn = 4*eps*pow(sig, npow);
}
else if (opt2parg_bSet("-c6", asize(pa), pa) ||
opt2parg_bSet("-cn", asize(pa), pa) ||
opt2parg_bSet("-pow", asize(pa), pa))
{
sig = pow(cn/c6, 1.0/(npow-6.0));
eps = 0.25*c6*pow(sig, -6.0);
}
else
{
sig = eps = 0;
}
printf("c6 = %12.5e, c%d = %12.5e\n", c6, npow, cn);
printf("sigma = %12.5f, epsilon = %12.5f\n", sig, eps);
minimum = pow(npow/6.0*pow(sig, npow-6.0), 1.0/(npow-6));
printf("Van der Waals minimum at %g, V = %g\n\n",
minimum, pot(minimum, 0, c6, cn, npow));
printf("Fit of Lennard Jones (%d-6) to Buckingham:\n", npow);
Bbh = npow/minimum;
Cbh = c6;
Abh = 4*eps*pow(sig/minimum, npow)*exp(npow);
printf("A = %g, B = %g, C = %g\n", Abh, Bbh, Cbh);
}
qq = qi*qj;
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Potential", "r (nm)", "E (kJ/mol)",
oenv);
xvgr_legend(fp, asize(legend), legend,
oenv);
if (sig == 0)
{
sig = 0.25;
}
minimum = -1;
mval = 0;
oldx = 0;
for (i = 0; (i < 100); i++)
{
x = sigfac*sig+sig*i*0.02;
dp[next] = dpot(x, qq, c6, cn, npow);
fprintf(fp, "%10g %10g %10g\n", x, pot(x, qq, c6, cn, npow),
bhpot(x, Abh, Bbh, Cbh));
if (qq != 0)
{
if ((i > 0) && (dp[cur]*dp[next] < 0))
{
minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
mval = pot(minimum, qq, c6, cn, npow);
printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
minimum, mval);
}
}
cur = next;
oldx = x;
}
ffclose(fp);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"Plot the potential"
};
static real c6=1.0e-3,c12=1.0e-6,qi=1,qj=2,sig=0.3,eps=1,sigfac=0.7;
t_pargs pa[] = {
{ "-c6", FALSE, etREAL, {&c6}, "c6" },
{ "-c12", FALSE, etREAL, {&c12}, "c12" },
{ "-sig", FALSE, etREAL, {&sig}, "sig" },
{ "-eps", FALSE, etREAL, {&eps}, "eps" },
{ "-qi", FALSE, etREAL, {&qi}, "qi" },
{ "-qj", FALSE, etREAL, {&qj}, "qj" },
{ "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of sigma for starting the plot" }
};
t_filenm fnm[] = {
{ efXVG, "-o", "potje", ffWRITE }
};
#define NFILE asize(fnm)
FILE *fp;
int i;
real qq,x,oldx,minimum,mval,dp[2],pp[2];
int cur=0;
#define next (1-cur)
/* CopyRight(stdout,argv[0]);*/
parse_common_args(&argc,argv,PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),
desc,0,NULL);
if (opt2parg_bSet("-sig",asize(pa),pa) ||
opt2parg_bSet("-eps",asize(pa),pa)) {
c6 = 4*eps*pow(sig,6);
c12 = 4*eps*pow(sig,12);
}
else if ((c6 != 0) && (c12 != 0)) {
sig = pow(c12/c6,1.0/6.0);
eps = c6*c6/(4*c12);
}
else {
sig = eps = 0;
}
printf("c6 = %12.5e, c12 = %12.5e\n",c6,c12);
printf("sigma = %12.5f, epsilon = %12.5f\n",sig,eps);
qq = qi*qj;
fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"Potential","r (nm)","E (kJ/mol)");
if (sig == 0)
sig=0.25;
minimum = -1;
mval = 0;
oldx = 0;
for(i=0; (i<100); i++) {
x = sigfac*sig+sig*i*0.02;
dp[next] = dpot(x,qq,c6,c12);
fprintf(fp,"%10g %10g %10g\n",x,pot(x,qq,c6,c12),
dp[next]);
if ((i > 0) && (dp[cur]*dp[next] < 0)) {
minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
mval = pot(minimum,qq,c6,c12);
/*fprintf(stdout,"dp[cur] = %g, dp[next] = %g oldx = %g, dx = %g\n",
dp[cur],dp[next],oldx,x-oldx);*/
printf("Minimum at r = %g (nm). Value = %g (kJ/mol)\n",
minimum,mval);
}
cur = next;
oldx = x;
}
ffclose(fp);
do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
thanx(stderr);
return 0;
}
