int gmx_analyze(int argc,char *argv[])
{
static const char *desc[] = {
- "[TT]g_analyze[tt] reads an ascii file and analyzes data sets.",
+ "[TT]g_analyze[tt] reads an ASCII file and analyzes data sets.",
"A line in the input file may start with a time",
- "(see option [TT]-time[tt]) and any number of y values may follow.",
+ "(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
- "read when they are separated by & (option [TT]-n[tt]),",
- "in this case only one y value is read from each line.",
+ "read when they are separated by & (option [TT]-n[tt]);",
+ "in this case only one [IT]y[it]-value is read from each line.",
"All lines starting with # and @ are skipped.",
"All analyses can also be done for the derivative of a set",
"(option [TT]-d[tt]).[PAR]",
- "All options, except for [TT]-av[tt] and [TT]-power[tt] assume that the",
+ "All options, except for [TT]-av[tt] and [TT]-power[tt], assume that the",
"points are equidistant in time.[PAR]",
"[TT]g_analyze[tt] always shows the average and standard deviation of each",
- "set. For each set it also shows the relative deviation of the third",
+ "set, as well as the relative deviation of the third",
"and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
- "2 (int0-T y(t) cos(i pi t) dt)^2 / int0-T y(t) y(t) dt[BR]",
+ "2 (int0-T y(t) cos(i [GRK]pi[grk] t) dt)^2 / int0-T y(t) y(t) dt[BR]",
"This is useful for principal components obtained from covariance",
"analysis, since the principal components of random diffusion are",
"pure cosines.[PAR]",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The analytical curve for the block average is:[BR]",
- "f(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +[BR]",
- " (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),[BR]"
+ "f(t) = [GRK]sigma[grk][TT]*[tt]sqrt(2/T ( [GRK]alpha[grk] ([GRK]tau[grk]1 ((exp(-t/[GRK]tau[grk]1) - 1) [GRK]tau[grk]1/t + 1)) +[BR]",
+ " (1-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(-t/[GRK]tau[grk]2) - 1) [GRK]tau[grk]2/t + 1)))),[BR]"
"where T is the total time.",
- "a, tau1 and tau2 are obtained by fitting f^2(t) to error^2.",
+ "[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f^2(t) to error^2.",
"When the actual block average is very close to the analytical curve,",
- "the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).",
+ "the error is [GRK]sigma[grk][TT]*[tt]sqrt(2/T (a [GRK]tau[grk]1 + (1-a) [GRK]tau[grk]2)).",
"The complete derivation is given in",
"B. Hess, J. Chem. Phys. 116:209-217, 2002.[PAR]",
"Option [TT]-filter[tt] prints the RMS high-frequency fluctuation",
"of each set and over all sets with respect to a filtered average.",
- "The filter is proportional to cos(pi t/len) where t goes from -len/2",
+ "The filter is proportional to cos([GRK]pi[grk] t/len) where t goes from -len/2",
"to len/2. len is supplied with the option [TT]-filter[tt].",
"This filter reduces oscillations with period len/2 and len by a factor",
"of 0.79 and 0.33 respectively.[PAR]",
"Option [TT]-power[tt] fits the data to b t^a, which is accomplished",
"by fitting to a t + b on log-log scale. All points after the first",
- "zero or negative value are ignored.[PAR]"
+ "zero or with a negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
"on output from [TT]g_hbond[tt]. The input file can be taken directly",
{ "-xydy", FALSE, etBOOL, {&bXYdy},
"Interpret second data set as error in the y values for integrating" },
{ "-regression",FALSE,etBOOL,{&bRegression},
- "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option [TT]-time[tt]." },
+ "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [GRK]chi[grk]^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option [TT]-time[tt]." },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
"Do a Luzar and Chandler analysis on a correlation function and related as produced by [TT]g_hbond[tt]. When in addition the [TT]-xydy[tt] flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
{ "-fitend", FALSE, etREAL, {&fit_end},
"Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with [TT]-gem[tt]" },
{ "-smooth",FALSE, etREAL, {&smooth_tail_start},
- "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)" },
+ "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff