timecorr

Calculate auto/cross-correlation functions for given vector(s) using spherical harmonics.

timecorr vec1 <vecname1> [vec2 <vecname2>] out <filename> [order <order>] [tstep <tstep>] [tcorr <tcorr>][dplr] [norm] [drct] [dplrout <dplrfile>] [ptrajformat]

vec1 <vecname1> [vec2 <vecname2>] Vector(s) on which to operate. By default the auto-correlation function will be calculated if one vector is specified, and the cross-correlation function will be calculated if two vectors are specified.
out <filename> Name of file to write output to.
[order <order>] Order of Legendre polynomials to use; default 2.
[tstep <tstep>] Time between snapshots (default 1.0).
[tcorr <tcorr>] Maximum time to calculate correlation functions for (default 10000.0).
[dplr] Output correlation functions $C_l \equiv < P_l / (r(0)^3r(\tau)^3 >$ and $< 1/(r(0)^3r(\tau)^3>$ in addition to the $P_l$ correlation function.
[norm] Normalize all correlation functions, i.e., $C_l(t=0)= P_l(t=0)=1.0$ .
[drct] Use the direct method to calculate correlations instead of FFT; this will be much slower.
[dplrout] (dplr only) Write extra information for each vector related to dplr option to <dplrfile>.
[ptrajformat] Write output in ptraj style (prevents use of data formatting options).

DataSet Aspects:

[P] P<order> correlation function.
[C] C<order> correlation function (dplr only).
[R3R3] <1/(r(0)3r(t)3> correlation function (dplr only).
[R] (_TC_DIPOLAR_) Average magnitude (<R>).
[RRIG] (_TC_DIPOLAR_) Sqrt( <R^2> ).
[R3] (_TC_DIPOLAR_) <1/R^3>.
[R6] (_TC_DIPOLAR_) <1/R^6>.
[Name] (_TC_DIPOLAR_) Vector name.

Calculate time auto/cross-correlation functions for vectors using spherical harmonics theory. NOTE: To calculate direct correlation functions for vectors just use the corr analysis command. The norm keyword will normalize the resulting correlation functions. Note that if dplr is specified, a new global data set named _TC_DIPOLAR_ will be created, containing extra data for each vector analyzed with a ’timecorr dplr’ command.

Examples:
Vectors between atoms 5 and 6 as well as 7 and 8 are calculated below, for which auto and cross time correlation functions are obtained.

vector v0 @5 @6
 vector v1 @7 @8
 timecorr vec1 v0 tstep 1.0 tcorr 100.0 out v0.out order 2
 timecorr vec1 v1 tstep 1.0 tcorr 100.0 out v1.out order 2
 timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 100.0 out v0_v1.out order 2

Similarly, a vector perpendicular to the plane through atoms 18, 19, and 20 is obtained and further analyzed.

vector v2 @18,@19,@20 corrplane
 timecorr vec1 v3 tstep 1.0 tcorr 100.0 out v2.out order 2

Category: Analysis Commands, CPPTRAJ

Tags: analysis

timecorr

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