Analyse is a set of programs able to extract data of interest
from the results of an MCTDH calculation. In essence, there is a
library of modules providing an interface to the MCTDH program
output. These modules can be then built into programs as
required. The documentation is in two parts: Firstly the various
programs for computing observable quantities are described, and
secondly the various shell-scripts for plotting the results using
the Gnuplot program are detailed.
The programs can be compiled using the shell script
$MCTDH_DIR/bin/compile. Type:
to produce the executable $MCTDH_DIR/bin/$MCTDH_PLATFORM/ progname<ver>, where progname is the name of one of the analysis programs (e.g. overlap or autospec). Typing
compile progname
will compile all the analysis programs.
compile analyse
The compile script has various options (type compile -h for a list). For example, to produce the exectuable $MCTDH_DIR/bin/$MCTDH_PLATFORM/overlap<ver> d (e.g. overlap83d) with debug information, type
compile -d overlap
For more information on the compile script, see Compiling the programs.
NB: All programs are usually compiled when the package is
installed.
All program names have the version number apended to them, e.g. the overlap program from version 8 release 3 is called overlap83. The following programs exist:
Below the options of each analyse program are described. This information can also be obtained by using the -h option, e.g.
The information given there is a little bit more reliable since the on-line documentation might not be up to date in some cases.
aoverlap83 -h
Purpose: Calculates the diabatic and adiabatic population. And also one or two dimensional adiabatic densities. Usage: adpop83 [-i -f -d -p -o -r -n -skip -w -ver -h -?] [Degrees of Freedom] Options : -i DIR : data is stored in directory DIR -f FILE : the PSI is read from FILE rather than from ./psi The string FILE may be a relative or a full path-name. -d FILE : the DVR is read from FILE rather than from ./dvr The string FILE may be a relative or a full path-name. -p FILE : the PES is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -o FILE : The ouput is written to file FILE rather than to ./adp The string FILE may be a relative or a full path-name. If FILE=no, i.e. -o no, no output file will be written. -r : The PSI is read from restart file rather than from ./psi -n num : only the first num WFs are read from psi-file. -skip m : the first m WFs are skipped. -step step : Compute the overlap only every step-th output. -w : Overwrite the output-file adp. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The arguments "dof*" have to be replaced by the names of the degree of freedom. To calculate 2-dim densities separate the two DOF with a comma. EXAMPLES: adpop83 dof1 adpop83 dof3,dof4 adpop83 dof1 dof2 dof3,dof4 ------------------------------------------------------------------------------
The adpop83 program is used to calculate the
populations of the electronic states. This is done for the
diabatic and for the adiabatic wavefunction. The results are
stored in the file adp for each time step. The data can
be plotted with plgen. Also one and two dimensional densities can
be calculated with adpop83. The densities are stored in
the adp_dof* and
adp_dof*_dof* files where
dof* is replaced by the name of the corresponding degree
of freedom. The densities are calculated with and without
weights.
NB: adpop works only for multi-set calculations.
NB: As the calculation runs over the primitive grid, the
calculation is slow. Analysing one WF takes about
[grid-dimension]*[A-vector length]*1.5*10-8 s on a 3
GHz P4.
NB: The adpop population file can be easyly plotted with
plgen.
NB: For the adpop density files the script pladpop exists. This
script plots the adiabatic densities of the different electronic
states with or without weights.
Purpose: Calculates the adiabatic potential and the adiabatic projector. Usage: adproj83 [Options] Options : -i DIR : data is stored in directory DIR -p FILE : the PES is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -w : Overwrite the output files. -nopot : Adiabatic PES are not calculated. -s s : Only adiabatic PES and Projector Matrix Elements for state s will be calculated. -me i j : Only Projector Matrix Elements P_i_j will be calcualted. -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------
The adproj83 program is used to calculate the
adiabatic potential matrix elements and the adiabatic projector
matrix elements for each electronic state. The results are
written into several vpot files that can be fitted with the
potfit program. To do this the keyword "pes = none" has to be set
in the potfit input file. With a MCTDH-run the projection
operator file can be created. To receive the adiabatic
populations run expect with the projection operator file
and the corresponding psi file.
NB: The vpot files for the adiabatic potential are:
apr_vs, where s is the electronic state.
NB: The vpot files for the projection matrices are:
apr_ps_ij, where s is the electronic state and ij
denotes the matrix element. Please note that the projection
matrices are symmetric, this means that each off-diagonal matrix
element is only given once.
Purpose: Calculates the difference between two A-vectors. See review Eqs.(159-163) for a definition of the output Usage : aoverlap83 [-f -i -o -n -w -ver -h -?] [psi2] . Options : -f FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : Same as -f FILE. -o FILE : The difference is written to file FILE.pl rather than to ./aovl_XXX The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no aovl-file will be opened. -abs : Take the absolute value of A, when computing the overlap. -n step : Compute the A-overlap only every step-th output. -w : An existing aoverlap file is overwritten. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The argument psi2 is the name of the file containing the comparison wavefunction. If no argument is given, the user is prompted for the missing argument. ----------------------------------------------------------------------------
The aoverlap83 program is very similar to the overlap83 program, except that it considers the A-vectors exclusively, i.e. it implicitly assumes that the spf's of the two calculations are identical. aoverlap83 is useful when the two calculations to be compared use different DVR's but identical numbers of spf's. When the overlap between two calculations is OK but the aoverlap is not then the two calculations use different spf's, e.g. a different position of the projector. See also overlap83 below.
Purpose: Computation of the spectrum by fourier-transforming the autocorrelation function. Three spectra are generated acording to the weight functions cos^n(pi*t/(2*T)) (n=0,1,2). Additionally there is the weight function exp(-(t/tau)^iexp). Usage : autospec83 [-f -i -o -e -n -r -ph -p -q -g -t -FT -EP -Mb -ver -h] [emin emax unit tau iexp] Options : -f FILE : The autocorrelation is read from file FILE rather than from ./auto The string FILE may be a relative or full path-name. -i DIR : Take DIR as input directory. -o FILE : The spectrum is written to file FILE.pl rather than to ./spectrum.pl The string FILE may be a relative or full path-name. -e R Unit: the offset energy is set to R in units Unit; e.g. 0.3 ev -n : The maxima of the three spectra are normalised to 1. -r : Plot the resolution rather than the spectrum -ph ph : Use phase correction exp(i*ph*1.d-6*t^2) -p I : The no. of plot-points is I rather than 500 Use "-p 1200" for final plots -q I : Same as -p. -g ncos : GNUplot command lines are written to the output file. ncos is the exponent of the cosine damping function. -t tcut : The autocorrelation function is read only up to t=tcut -FT : No multiplication with the energy prefactor. Fourier transform only. (default!) -EP : Multiplication with the energy prefactor. -Mb norm : Absorption spectrum in Mb. norm is ||D*Psi|| (in au) where D is the Dipole moment. -Mb sets -EP. -ver : Version information about the program -h : Print this help text. -? : Print this help text. Following the options one may provide the arguments (separated by blank): Emin, Emax, Unit, tau, iexp If not enough arguments are given, the user is prompted for the missing arguments. Use the Unit 'no' if the propagation is run with the keywords: 'time-not-fs','energy-not-ev'. When using the options -EP or -Mb one must make sure that the zero point of the energy is set appropriately. Use the option -e if the total energy differs from photon energy. 1 Mb = 10^-18 cm^2. The norm ||D*Psi|| can be found in the log file of the operate run. ----------------------------------------------------------------------------
The program computes the spectrum by Fourier transform of the
autocorrelation function which is multiplied with the weight
function
exp(-(t/tau)iexp)*cosn(pi*t/2T), (n =
0, 1, 2). (In the output file there is one column for each
n). The variables tau (real [fs]) and
iexp (integer) are input arguments.
More precisely:
sigma(omega,n) = prefac*Integral (0, T) Re[ c(t) *
exp(i*(omega -Eoffset)*t)] *
exp(-(t/tau)iexp)* cosn(pi*t/2T)
dt
is the formula which is evaluated. Here c(t) is the
autocorrelation function and T denotes the largest time
for which c(t) is known. (T may be reduced by
the option -t). The variable omega runs between
Emin and Emax. The
pre-factor prefac is 1/pi if -FT is set
(default), or is omega/pi if -EP is set, or is
0.4279828*dipolemoment**2 if -Mb is set. In the latter
case, dipolemoment is the norm of the D*Psi, where D denotes the
dipole operator. This norm is printed in the MCTDH log file, when
the operation D*Psi is performed by operate. The
-Mb option allows to plot the absorption spectrum on
absolute scale in mega barns (Mb). 1 Mb = 10-18
cm2
When one of the options -EP or -Mb is set, one must ensure, that the energy is the photon energy. It may hence be necessary to shift the energies from total ones to photon energies by using the -e option.
If the option -r is set, the program computes the resolution, i.e. the spectrum of a single line. The time points are taken from the auto file. If there is no auto file and if the option -t is given, a time step of 1 fs is assumed.
The pre-factor omega is omitted by default, or when the option
-FT is given. In this case (and only in this case) the
energy Emin (and eventually
Emax) may be negative. NB: When the
pre-factor is omitted (default), the spectrum is normalized to 1
au.
Example: autospec83 -e 13.4071 ev 13 17 ev 50 2
Purpose : Interpolation of natpot terms to another grid. Usage : chnpot83 [-D -d -rd -w -mnd -n -nd -ver-h -?] input Options : -D PATH : The output is directed to PATH. This option overwrites name in the run-section of the input file. -d DIR : The dvr is read from file DIR/dvr. This option overwrites dvrdir in the run-section of the input file. -rd FILE : The new dvr is read from file FILE. This option overwrites readdvr in the run-section of the input file. -w : Overwrite an existing "natpot" file. -mnd : Make Name Directory. Creates the name directory, if not existent. -nf FILE : The natpot is read from file FILE. This option overwrites natpotfile in the run-section of the input file. -nd DIR : The natpot is read from file DIR/natpot. This option overwrites natpotdir in the run-section of the input file. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The argument "input" is the file containing the Run-Section, the new Primitive-Basis-Section written in MCTDH form and the Fit-Section. ----------------------------------------------------------------------------
The program interpolates natural potential terms calculated by program Potfit (written in "natpot" file) from one grid to another. Normally one runs Potfit on an initial coarse grid, then interpolates the natpot terms to a finer grid. At present, the program can interpolate only one or two dimensional natpot terms. The program reads the old grid from "dvr" file. The input file consist of three sections, a Run-Section, a Primitive-Basis-Section and a Fit-Section (see below) and the final keyword "end-input".
In Run-Section following keywords are possible:
Keywords of chnpot RUN-SECTION | |||
---|---|---|---|
Keyword | compulsory / optional | Description | equivalent option |
name = S | C | The name of the calculation. A directory with path S is required in which files will be written. | -D |
dvrdir = S | C | The old DVR file is located in directory S. | -d |
natpotdir = S | O | The old natpot file is located in directory S. If this keyword is not given, natpotdir=dvrdir is assumed. | -nd |
natpotfile = S | O | The path of the old natpot file is S. If this keyword is not given, natpotfile=natpotdir/natpot, or natpotfile=dvrdir/natpot is assumed. | -nf |
readdvr = S | O | The new DVR should be read from directory S. Without argument, S = name is assumed. Without this keyword the dvr file is created in the name directory. | -rd |
overwrite | O | Files in name directory will be overwritten. | -w |
The Primitive-Basis-Section is as in MCTDH.
In the Fit-Section the parameters for interpolation are given. For translational degrees of freedom one can use cubic (bicubic) spline interpolation or ENO (Essentially Non Oscillatory) interpolation. For angular degrees of freedom (in the case of periodicity) one can select between cosine, sine or fourier interpolation. Note, that the interpolation method should be defined for each degree of freedom, and not for each mode. If grid points for some degree of freedom have not changed, it can be omitted. The keyword "spline" ("spl") is used for spline interpolation. ENO interpolation is currently implemented for non-combined modes. It consists basically on a polynomial interpolation where the points from the original data set used to obtain the interpolant function are automatically selected to fulfill some smooth criterium. The algorithm will provide a continuous non-oscillatory interpolation near regions with sudden changes in slope, as encountered for example when an energy cut is found in the original data. The formulation of the algorithm can be found in J. Comput. Phys. 71, (1987), 231-303. ENO interpolation is requested using the keyword eno, which can optionally be followed by the keywords rmax=integer, maximum degree of interpolation (default 3), rmin=integer, minimum degree of interpolation (default 1) and dfac=real, weight factor controling how preferential is the symmetric interpolation with respect to the asymmetric one (default 50.0). The ENO implementation is a new feature and by now is rather experimental. Use it with care. The defaults should provide a reasonable behaviour of the interpolator, specifically, setting a higher maximum order or lowering dfac too much may result in a noisy potential energy function at the end. Increasing too much dfac (say, above 200) will tight the interpolator always to a symmetric interpolation, thus not being able to avoid discontinuities. A good idea would be to compare it for a given case to the corresponding spline interpolation and pick up the most satisfactory result. The keywords "cosine" ("cos"), "sine" ("sin") and "fourier" ("ft") are used for the Fourier-interpolation of angular degrees of freedom. (NB: "ft" or (equivalently) "fourier" means that sine and cosine functions are used). The keyword "sym" after "sin", "cos" and "ft" can be used, indicating that only even functions (i.e. Cos2x, Cos4x, ...) should be used. The angular fit procedure is described in JCP 104,(1996) 7974. The parameter M (default is max(50,2*gdim)) can be given as a keyword following the sin, cos, or ft keyword (see Eq.(37) in JCP 104,(1996) 7974). Finally, the keyword "period=xx" defines the period of the potential curve, for which xx="2pi/N" or "P" format can be used, where N is an integer and P is a real number. If the keyword period is missing, period=2pi is taken as default.
Here is an example of Fit-Section:
Fit-Section
R spline
r spline
q eno rmax=3 dfac=60
Q eno dfac=70 rmin=1
theta cosine 60 period=2pi/2
phi fourier sym period=2pi
end-fit-section
Note, that the interpolation method for the degrees of freedom in combined mode should be the same (for angular modes cosine, sine and fourier can be mixed). Some parameters of the calculation are written to the "chnpot.log" file. The program writes the new natural potentials file "natpot" and the "dvr" file (if the option -rd or keyword readdvr in Run-Section are not used) to the name directory. For over-writing of the natpot file use "-w" option. For an example input file see chnpot.inp
Example: chnpot83 -w -rd input
Note that chnpot may be used to change the modelabels. Chnpot maps the n-th old DOF onto the n-th new DOF, the modelabels are not used. If you just want to change the modelabels without re-fitting the potential, simply set up the PRIMITIVE-BASIS-SECTION of the chnpot input file using the new modelabels but otherwise the old basis definitions. A FIT-SECTION is not needed in this case.
Is used by the elk_test program to compare different sets of results.
Converts a multi-packet wavefunction to the corresponding single-packet ones, i.e. extracts the pth packet from the multi-packet wavefunction dir/psi and writes it to the file dir/psip (or dir/psi0p if p < 10). For p = 0 all packets contained in psi are extracted and written to the files dir/psi01, dir/psi02, etc.
Purpose: Calculates the cross-correlation function c(t) c(t) = <psi_ref(0)|psi(t)> Usage : crosscorr83 [-f -i -o -n -r -R -t -el -ig -ver -h -?] [psi_ref] . Options : -f FILE : The wavefunction (density operator) is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -o FILE : The difference is written to file FILE rather than to ./cross_XXX The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no cross-file will be opened and the output will be directed to screen. -r : Take the restart rather than the psi file as reference WF. -R : Take the restart rather than the psi file as time-dep. WF. In general, this makes sense only when also -r is set. -O oper : Apply operator "oper" before evaluating the overlap. -t tfin : Compute the overlap only up to tfin. -n step : Compute the overlap only every step-th output. -i init : Compute the overlap using the init-th (rather than the first) reference WF. (-i is ignored when -r is set). -el nst : Compute the cross-correlation for state nst only. -ig : Ignore "different bases" error-msg. -spf : Print information on overlap of the two orbital sets. dim - trace(dover^+ * dover) for all m,s. -diag : Print diagonal elements of overlap matrix of the two orbital sets. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The argument psi_ref is the name of the file containing the (time-independent) comparison wavefunction (density operator). With the aid of the option -O, crosscorr can compute matrix elements <psi_ref|oper|psi>. This, however, requires that psi_ref and psi are MCTDH-WFs with identical numbers of SPFs. If no argument is given, the user is prompted for the missing argument. Note: The option "-o no" directs output to screen. Note: If the argument ends with a slash "/", the string "psi" or "restart" is appended. If the argument ends with "restart", -r is set. -----------------------------------------------------------------------------The two wavefunctions (density operators) must, of course, have the same primitive grids, but they may have different combination schemes and may differ in numbers of SPF's. A reference wavefunction can conveniently be generated by running MCTDH with the -t option.
Purpose: Computation of the spectrum by fourier-transforming the cross-correlation function. Output is: Energy, Re(FT), Im(FT), Abs(FT), where FT denotes the Fourier-transform (prefactor Pi^-1) of the cross-correlation function. Usage : crosspec83 [-o -e -p -q -a -g -all -reim -re -im -sin -cos -dc -t -ph -r -old -h ] [emin emax unit file]. Options : -o FILE : The spectrum is written to file FILE.pl rather than to ./cspec.pl The string FILE may be a relative or full path-name. -e R Unit : the offset energy is set to R in units Unit; e.g. 0.3 ev -p I : The no. of plot-points is I rather than 500 Use "-p 1200" for final plots -q I : Same as -p I -g : GNUplot command lines are written to the output file. -a : GNUplot is called automatically. (sets "-g"). -all : Re, Im and Abs parts (rather than Abs) are plotted. (ignored if neither -g or -a are set). -reim : Real and Imaginary parts (rather than Abs) are plotted. (ignored if neither -g or -a are set). -re : Real part (rather than Abs) is plotted. (ignored if neither -g or -a are set). -im : Imag. part (rather than Abs) is plotted. (ignored if neither -g or -a are set). -sin : The crosscorrelation function is multiplied with sin(pi*t/T). -cos : The crosscorrelation function is multiplied with sin(pi*t/2T). -dc : A DC component is subtracted from the cross-corr before FT. -r : Plot the resolution rather than the spectrum -ph ph : Use phase correction exp(i*ph*1.d-6*t^2) -t tcut : The crosscorrelation function is read only up to t=tcut -old : The old output format is used. (Different order of colums, output times Pi.) -ver : Version information about the program -h : Print this help text. -? : Print this help text. Following the options one may provide the arguments (separated by blank): Emin, Emax, Unit If not enough arguments are given, the user is prompted for the missing arguments. Use the Unit 'no' if the propagation is run with the keywords: 'time-not-fs','energy-not-ev'. ------------------------------------------------------------------------------This routine simply performs the Fourier integral pi^-1 * Int[0,T] exp(i*(E-E_offset)*t)*c(t) dt without invoking damping functions (except possibly for sin(pi*t/T) and cos(pi*t/2T)). The option -dc subtracts the average of the cross-correlation function from this function before FT. E_offset is zero, if not set by option -e. The option -old removes the prefactor pi^-1 and interchanges the columns. (Now: Energy, Re, Im, Abs; with -old: Energy, Abs, Re, Im). The new output format is chosen to make crosspec compatible with autospec. The output file cspec.pl may be read by flux, using the -ed option of flux83. In this case neither -g nor -a must be given, such that no GNUplot command lines appear in the output file.
If the option -r is set, the program computes the resolution, i.e. the spectrum of a single line. The time points are taken from the crosscorr file. If there is no crosscorr file and if the option -t is given, a time step of 1 fs is assumed.
Purpose: Generates 2D-densities from the wavefunction. Usage: dengen83 [-i -f -n -skip -step -o -rst -pop2 -nw -ver -h -?] f1 f2 Options : -i DIR : data is stored in directory DIR -f FILE : the wavefunction is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -o FILE : The output is written to file FILE rather than to ./dens2d The string FILE may be a relative or a full path-name. -n num : only num WFs are processed. -skip m : the first m WFs are skipped. -step step : only every step's WF will be processed. -rst : the restart file is read, rather than the psi file. -nw : No weights are employed. Plot the "naked" DVR populations. -pop2 : the basis set occupations are plotted rather than grid populations. For FFT this implies momentum space representation. -w : Overwrite the output file. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The arguments f1 and f2 denote the DOFs for which a 2D-density is generated. The arguments f1 and f2 may be integers or modelabels. If there are more WFs on psi file than you want to inspect, use the options -n, -skip, or -step. Example: "dengen83 -skip 10 -n 2 rd rv" will generate densities of the WFs no. 11 and 12 (i.e. t=10 and 11 if tpsi=1fs), and "dengen83 -step 10 -n 2 rd rv" will generate densities of the WFs no. 1 and 11 (i.e. t=0 and 10 if tpsi=1fs). NB: The option -pop2 is ignored for phifbr,sphfbr,k,external bases. --------------------------------------------------------------------------------dengen83 computes 2D-densities similar as does showsys83. However, in contrast to showsys83, dengen83 computes only 2D-densities, is not menu driven, is not interactive and does not plot. It merely writes the data to an output file, which may then visualized by GNUPLOT. If the computation of the 2D-densities takes a large amount of computer time, the use of dengen83 is of advantage, because dengen83 may run in the background, overnight or on a batch system.
Purpose: Converts a diabatic wavefunction to adiabatic. Usage: di2ad83 [-i -f -p -o -w -ver -h -?] Options : -i DIR : data is stored in directory DIR -f FILE : the wavefunction is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -p FILE : the PES is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -o FILE : The ouput is written to file FILE rather than to ./psi.ad The string FILE may be a relative or a full path-name. -w : An existing output file is overwritten. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The wavefunction and the pes-file must be in "exact" format. One may use psi2ex83 to transform the WF. --------------------------------------------------------------This program reads the wavefunction in a psi file, and uses the PES information in a pes file to transform it to the adiabatic representation. The waveunction and pes file must be in a full-grid representation. If the psi file was created using an MCTDH wavefunction, this can first be converted using the psi2ex program. The pes file can be created using mctdh83 -pes with an input file for a numerically exact calculation.
Output is in a full grid representation to the file psi.ad, unless otherwise given using -o FILE.
Program solves the generalized eigenvalue problem H1 B = H0 B E by a singular value decomposition, where H0 and H1 are overlap and Hamiltonian matrices calculated by Fmat program. The output of the program are the eigenvalues and intensities. The matrix elements are calculated using the hermitian or symmetric scalar product. The widths, in the case of symmetric scalar product, are calculated as -2*Im(E) .
Purpose : Diagonalizes the Hamiltonian matrix calculated by fmat. Usage : diag83 [-d -o -lo -hi -n -t -es -e -u -w -ver -h -?] mtt_ovl mtt_ham [[mtt_ovl_2] [mtt_ham_2]]. Options : -d PATH : The output is directed to PATH rather than to the current directory. The string PATH may be a relative or a full path-name. If PATH=no, i.e. "-d no", no output files will be opened. -o NAME : Change the name of output file from "diag" to NAME. -lo klo : Take matrix elements in Mtt files only from the klo-th index. -hi khi : Take matrix elements in Mtt files only up to the khi-th index. -n step : Take only every n-th step of the Mtt matrix elements. -t : Expand the nXn mtt-matrix to (2n-1)X(2n-1) one including negative times. In this case the second set of overlap and Hamiltonian matrices are needed. -es eps : Set cut-off parameter for eigenvalues. Default is eps=1.e-10 -e E unit: The offset energy is set to E unit. Note: "-e lsth" is equivalent to "-e 4.74746 ev". "-e co2" is equivalent to "-e -2534.5298 cm-1". -u UNIT : Set the output energy unit to UNIT. Default is au. -w : Overwrite an existing "diag" file. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The arguments "mtt_ovl" and "mtt_ham" are the Overlap- and Hamiltonian matrix files calculated by "fmat83" program. If "-t" option is used, the second set of Overlap- and Hamiltonian matrices with different scalar product is needed. Examples : diag83 -es 1.d-8 -hi 60 mtt_h mtt_H1_h : diag83 -hi 40 -n 2 -t mtt_h mtt_H1_h mtt_s mtt_H1_s Important note: Both overlap and Hamiltonian-matrices should be calculated either as hermitian or as symmetric scalar products. ------------------------------------------------------------------------------
Notes:
The arguments with options -lo,-hi and -n i.e. klo, hki and step are related to the calculated "mtt"-files, and not to the MCTDH calculation. For example, if "mtt"-files were calculated with step=2, then using step=3 in Diag program will be equivalent to step=6 with respect to the MCTDH calculation.
If "-t" option is used, the matrix elements are extended to negative times according to the rule: Psi(-t)=conj(Psi(t)). So, here the second set of overlap- and Hamiltonian matrices needed, calculated using the symmetric scalar product, if the first is hermitian, or hermitian scalar product if the first is symmetric. Note, that each set of overlap and Hamiltonian matrices should be calculated using the same scalar product (hermitian or symmetric).
The option "-u UNIT" changes the output energy unit to UNIT. The available units in program can be seen by shell-command "mhelp -s unit".
The following examples show the steps performing the diagonalization after completing the MCTDH calculation. The first concerns the reactive system (to calculate resonances and widths), the second - the bound system.
1. fmat83 -sym ! calculates mtt_s fmat83 -sym -O H1 ! calculates mtt_H1_s diag83 -u ev -es 1.d-9 mtt_s mtt_H1_s 2. fmat83 ! calculates mtt_h fmat83 -O H1 ! calculates mtt_H1_h fmat83 -sym ! calculates mtt_s fmat83 -sym -O H1 ! calculates mtt_H1_s diag83 -u cm-1 -es 1.d-8 -n 2 -t mtt_h mtt_H1_h mtt_s mtt_H1_s
Purpose: Calculates the electric field for optimal control Usage : efield83 [-b -t -A -T -O -F -p -i -ver -h -?] Options: -b : Compute the electric field during a backward propagation. -t : Compute overlap with target during a forward propagation. -A : Align phases of overlaps of multiple initial and target states i.e. optimize |sum_i|^2 instead of sum_i | |^2 -T oper : Maximise matrix element of operator oper. -O oper : Use oper as dipole operator to compute the field. -F pnlty : Parameter to penalize the field strength. -p : Do not read old psi file. Instaed propagate 2 WFs simultaneously. -i iter : Number of current iteration. -h or -? : Prints this help text. -ver : Prints version information. The matrix element of the dipole operator (-O option) formed with the initial and target state is calculated and the E-field is evaluated. This routine MUST be started in the background before the invocation of MCTDH. It exchanges information with the running propagation via FIFOs. Note: This routine is usually started by the script optcntrl. ------------------------------------------------------------------------------
Purpose: Calculates the time evolution of an expectation value. Usage : expect [-f -i -o -g -a -r -t -p -u -n -w -ver -h -?] [operator]. Options : -f FILE : The operator is read from file FILE rather than from ./oper The string FILE may be a relative or a full path-name. -i FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -o FILE : The output is written to file FILE.pl rather than to ./expect.pl The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no output file will be opened, and the output is directed to screen. -g : GNUplot comand lines are written to the output file(s). -a : GNUplot is called automatically. (sets -g and -w). -p : Print GNUplot to lpr (sets -g). -r : Do not divide the expectation values by norm^2. -rst : Use restart rather than psi file. -t tfin : The expectation values are computed only up to time=tfin. -u UNIT : The unit used is UNITs (Default is a.u.). -n step : Compute the property only every step-th output. -w : An existing property file is overwritten. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The argument operator is the name of the operator, as specified in an HAMILTONIAN-SECTION_xxx, for which the expectation value is required. If no argument is given, the user is prompted for the missing argument. ------------------------------------------------------------------------------The operator must first have been process by the MCTDH program. This means that it must first be set up in a .op file. If it is known before a propagation is made, this operator can be included with the system operator in the main oper file (by using a named HAMILTONIAN-SECTION_XXX). Alternatively, e.g. if a propagation has already been made, the file oper_name can be generated using the genoper=name keyword.
Start the program in the directory containing the propagated wavefunction in a psi file. If no arguments are given, the program looks in the oper file to see which operators are there and asks which is to be evaluated. The -o option can use a file other than this. The expectation value of this operator is then calculated for each time, and output to the file expect.pl, unless otherwise instructed. The -a option enables the automatic plotting of the results.
Purpose: Checks whether a state has been found in all comparison calculations and computes the internal error. Usage : fdcheck83 k exact datasets k = number of datasets. exact = 0 if if there is no exact comaprison data set, =1 else. datasets = data as created by fdmatch83. Example: fdcheck83 4 0 < list where list contains the output of fdmatch83, or: fdmatch83 f1.eig f2.eig f3.eig | sort -n | fdcheck83 3 0 ---------------------------------------------------------------------------
fdcheck analyses the output of fdmatch. It computes the mean value and the variance of eigenvalues and intensities which are grouped together by fdmatch. If there is an exact data set, fdcheck computes the errors of eigenvalues and intensities with respect to the exact data.
Purpose: Finds the optimal matches between a number of lists of eigenvalues obtained with the (real) filter program. Usage : fdmatch83 file_1 ... file_k | sort -n | less where file_j (j=1...k) is typically a *.eig file generated by the filter program. There may be up to 10 files. -----------------------------------------------------------------------
fdmatch orders the eigenvalues computed by different filter runs such that optimal matches are obtained. The output of fdmatch may be piped to fdcheck.
Purpose: Computes the quantum flux. See review Eqs.(197-201) for a definition of the output Usage : flux83 [-f -i -o -ed -dvr -t -n -lo -hi -p -P -O -e -x -v -w -r -c -u -sm -es -wtt -ver -h -?] [emin emax unit CAP-dof CAP-type] [.inp-file]. Options : -f FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : The operator is read from file FILE rather than from ./oper The string FILE may be a relative or a full path-name. -dvr FL : The DVR information is read from file FL rather than from ./dvr The string FL may be a relative or a full path-name. -ed FL : The energy distribution is read from file FL rather than from ./adwkb The string FL may be a relative or a full path-name. One may use a flux-file as energy-distribution file. In this case, the flux-column will be taken as edstr. If a "d" follows the file-name, the DELTA(E) column will be taken. If a "+" follows the file-name, the present flux will be added to the edstr input. Alternatively, one may use a spectrum.pl (autospec83) or a cspec.pl (crosspec83) file as energy distribution. The options "d" and "+" work here as well. With "d" the third (rather than the second) column of the ed-file is used, and with "+" the data is added to DELTA(E) rather than overwriting it. -o PATH : The output is directed to PATH rather than to the current directory. The string PATH may be a relative or a full path-name. If PATH=no, i.e. "-o no", no output-files will be opened. -n step : Compute Wtt' only every step-th psi-output. -es nst : Compute the flux for the electronic state nst only. -lo klo : Compute Wtt' only from the klo-th psi-output onwards. -hi khi : Compute Wtt' only up to the khi-th psi-output. -p I : The no. of energy-points is I rather than 500. -e R U : The offset energy is set to R in units U; e.g. "-e 0.3 ev". Note: "-e lsth" is equivalent to "-e 4.74746 ev". -s strt : Set the starting point of the flux evaluation to strt. Default is the grid-point where the cap starts. -t : Test run. Check of the data sets. No output files opened. -P : Use projectors. -P is follwed by the mode number, the projector name and up to 8 parameters. The input is closed by a "%". There may be several projectors. Example: -P 3 KLeg 2 1 % -P 2 eigenf vib 6 % -O oper : Apply operator "oper" before measuring the flux. -u unit : Transform flux to unit "unit". (useful when a operator is applied). Note: Rather than a unit one may give a number. -w : The gtau file may be overwritten. Without -w option gtau is read from the gtau file (if it exist). -r : Enforce reading the gtau file. Stop if gtau does not exist. -v : Re-compute only the theta part of gtau. (useful in combination with the -s option). -x : Evaluate flux only for the theta part of gtau. (useful for tests in combination with the -s -v options). -c icos : Cosine**icos damping of gtau. -sm : smooth Delta(E) by averaging the adwkb data over 5 points. -wtt : Only Wtt is computed. Note: The arguments "Emin, Emax, unit" must not be given when -wtt is set. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The arguments specify the energy interval and the degree of freedom of the CAP. The CAP-dof may be a number or a modelabel. The CAP-type may "right", "left" or "both". "right" is the default. If the number given as CAP-dof is larger than the number of DoFs, this number is interpreted as the H-term, h, of the CAP. Example: flux83 -lo 25 -w 0.3 2.5 ev rd flux83 1000 3000 cm-1 x left If no argument is given, the user is prompted for the missing argument(s). The path of an input file may be given as the very last argument. Options will overwrite the input-file. ------------------------------------------------------------------------------
The flux83 analyse routine has currently two
restrictions:
flux83 can work with operators and/or projectors,
however, they must not operate on the CAP-mode. The operators are
to be defined in an HAMILTONIAN-SECTION_xxx, where
xxx is the name of the operator to which flux83
refers. Presently there are projectors onto eigenfunctions of
one-mode operators (also to be defined in an HAMILTONIAN-SECTION_xxx ) and
projectors onto diffractive states (plane-waves) and onto
rotational states. For a full list of projectors available, see
the table below. New projectors may be coded and added to the
file analyse/flxprj.F. The arguments needed by flux83 are
the energy-range ( including its unit) and the CAP-mode, i.e.:
Emin, Emax, unit, CAP-mode .
Often options are necessary to steer the performance of
flux83. Rather than options and arguments one may provide
an input-file (for an example see below). Note: options will
overwrite the statements of the input-file.
The option -t (Test run) is very useful for checking how many
data sets are on the psi file, which CAP's have been used, what
are the mode labels, etc. The most time consuming part is the
generation of the function gtau, as it requires the computation
of the matrix elements Wtt' of the CAP. If a gtau file exist,
flux83 will try to read this file (provided the -w option is not
given). Thus the computation of the flux for an other energy
interval or a different flux-unit (-u) is fast, as the gtau file
already exist. When the gtau file is corrupted, use -w to
overwrite it. The options -n, -hi and -lo may be used to reduce
the number of time-points when computing Wtt' and gtau. This is
useful for convergence checks. The option -lo must be used when
the mctdh calculation was run with auto-cap (ACAP).
The option -s start determines
the grid-point from where on the flux is evaluated. To be more
precise, start is the grid-point at which the g_theta evaluation
is switched on. If the option -s
is not given, start is set to the
grid-point where the CAP is switched on. When start is larger than gdim(fcap) (i.e.
grid length of the CAP-DOF), then the evaluation of the g_theta
part is suppressed. See Appendix B of J.Chem.Phys 116
(2002), 10641, or the MCTDH-feature article (Theor. Chem. Acc.
109, 251 (2003)) for more details. It often improves the
speed of convergence, in particular with respect to the total
propagation time, if the start of the flux evaluation is moved
closer towards the scattering center. Only for testing purposes
one may chose a start value,
which is further away from the scattering center as the default
value, i.e. a start value which lies inside the CAP region.
The CAP may be left (i.e. located at small coordinate
values, or right (i.e. located at large coordinate values,
this is the default), or both (i.e. the CAP may be
anywhere, no checking of areas where the CAP vanishes).
Lines like the following are output by flux83 to screen (see also the flux.log file)
------------------------------------------------------------------------------ 2000*Integral(W_tt) = 996.1052 (total outgoing flux) 1000*Integral(flux) = 995.6810 (total outgoing flux) 1000*Integral(DELTA) = 998.8516 (total incomming flux) ------------------------------------------------------------------------------The first and second lines gives the total flux going into the specified CAP. The total flux is obtained by (first line) analytically integrating the flux over all energies (see Eq.(118) of Theor. Chem. Acc. 109, 251 (2003)), or by numerically integrating the energy resolved flux over the specified energy interval. The third line is the numerical integral of DELTA(E) over the specified energy interval. Here:
Example (H+D2 reactive scattering) :
flux83 -e lsth -lo 7 0.25 2.75 ev rv
or
flux83 flx.inp
where flx.inp is an input file. The extension .inp may be dropped. The input-file is organised similar to the MCTDH input-file, however, there are no sections. The last line of the input-file must read: end-input. Below an example input file is shown.
------------------------------------------------------------- # flux input file. Surface scattering. # Average rotational energy for a specific diffraction state. outdir = flux_rot low = 26 flux-unit = mev operator = rot
projector 3 diff2 2 1 # mode ,name, parameters energy = 0.05, 0.30, ev cap = z end-input -------------------------------------------------------------
Keywords of flux input-file | ||
---|---|---|
Keyword | Description | equivalent option |
overwrite | overwrites gtau file. gtau will be re-computed completely. | -w |
test | performs a test run | -t |
psi = S | read psi file form path S | -f |
outdir = S | write output to directory S | -o |
dvr = S | read dvr file form path S | -dvr |
edstr = S | read the energy-distribution from file S | -ed |
flux-unit= S | The computed flux is converted to unit S. If a number is given, the flux will be multiplied with that number. I.e. flux-unit=ev and flux-unit=27.2114 will produce the same output. This option is useful when an operator is applied. | -u |
operfile = S | read oper file form path S | -i |
high = I | Compute the flux (i.e. gtau) only up to the I-th psi-output | -hi |
low = I | Compute the flux (i.e. gtau) only from the I-th psi-output onwards. | -lo |
el-state = I | Compute the flux for the I-th electronic state only. | -es |
step = I | Compute the flux (i.e. gtau) only every I-th psi-output. | -n |
epoints = I | The number of output energy-points is I rather than 500. | -p |
cos = I | Cosine**I damping of gtau | -c |
smooth | Smooth the Delta(E) data read from adwkb file by averaging over 5 energy points. | -sm |
start = I | Evaluate the flux at the grid-point start. The default value for start is the start of the CAP (i.e. the last grid-point with vanishing CAP). | -s |
theta-only | Uses only the theta-part of gtau when computing the flux. This is useful for investigating the importance of the theta-region. Note: The W-part only of gtau will be taken when start is set to a number larger than the number of grid-points of the CAP-mode. | -x |
gtau-only | Compute only the theta-part of gtau. This option requires that a gtau file exist. The time-consuming evaluation of the W-part of gtau is suppressed, but gtau_theta is re-evaluated. This option is useful to test different start points (see keyword start). Note: the keywords low and high will be ignored. There values are taken from the previous run. | -v |
wtt-only | Compute only the diagonal terms Wtt.This rather fast calculation is useful to determine the optimal value for low (-lo). | -wtt |
eoffset = R, S | The offset energy is set to R in units S; e.g. "eoffset = 0.3, ev". Note: "eoffset = lsth" is equivalent to "-e 4.74746 ev". | -e |
operator = S | Apply operator S before evaluating the flux. | -O |
projector I S (S1) I1 I2 .. | Apply the projector S with(label S1 and) parameters I1 I2 ... to mode I before evaluating the flux. projector has to be the first keyword on a line. There are no equal-sign and no commas. There may be several projectors. One line for each projector. No additional keywords in a projector-line. | -P |
energy = R1, R2, S | Evaluate the flux between Emin=R1 and Emax=R2 where Emin and Emax are given in unit S. | (arguments) |
cap = S or I | The cap is on mode I. Rather than giving the number of the mode, I, one may give the modelabel S. | (arguments) |
captype = S | The cap-type is S=both,right,left. | (arguments) |
Projectors | |||
---|---|---|---|
projector name | label | parameters | Description |
eigenf | name of an operator | pop | An eigenfunction of a 1D operator is taken as projector. The 1D operator is to be defined in a HAMILTONIAN-SECTION_ XX when the operator-file is build. The operator XX must be of usediag type. A 1D spf is assumed, i.e a combined mode is incompatible with eigenf. The parameter pop defines which eigenfunction is taken. pop=1 refers to the ground-state. |
read | path of restart directory | pop state | The pop-th SPF of a "foreign" restart file is taken as projector. This "foreign" restart file may be build by an geninwf run. The primitive grids and the combination scheme of the "foreign" restart file and the present calculation must be identical, but the numbers of SPF's and the number of electronic states may differ. If the parameters pop and state are not given, they are set to 1. |
sph | (none) | j m | projects on the (j,mj) rotational state. A sphFBR (see Primitive Basis Section) is required, the two modes of which must not be further combined. I.e a 2D spf is assumed. |
diff | (none) | n | projects on the n-th diffraction channel. (i.e. onto a plane wave). A 1D spf is assumed. |
diff2 | (none) | n m | projects on the (n,m)-th diffraction channel. (i.e. onto a 2D plane wave). A 2D spf is assumed. |
pop2 | (none) | n | projects on the n-th basis function of an underlying DVR. This projector thus can only be used if the (uncombined) DOF is described by an simple DVR. |
Leg | (none) | j | projects on the j-th rotational state. A Leg or Leg/R DVR is required as primitive basis and the DOF should be uncombined. |
KLeg | (none) | j m | projects on the (j,mj) rotational state. A KLeg-DVR combined with a K-DVR, i.e. a 2D spf, is required. |
PLeg | (none) | j m | projects on the (j,mj) rotational state. A PLeg-DVR combined with an exp-DVR, i.e. a 2D spf, is required. |
KLeg2 | (none) | j1 m1 j2 m2 sym | projects on the
(j1,m1;j2,m2)
rotational state of two coupled angular DOFs. The mode must
be of the type KLeg/K/KLeg/K, i.e. a 4D mode. If sym>0
(sym<0), the projection is on the symmetrized
(antisymmetrized) state, i.e. {|j1,m1,j2,m2> ± |j2,m2,j1,m1>} / √2 . |
Purpose: Computes the overlap- or the Hamiltonian-matrix. Usage : fmat83 [-f -i -d -o -dvr -n -lo -hi -O -w -sym -es -ver -h -?] . Options : -f FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : The operator is read from file FILE rather than from ./oper The string FILE may be a relative or a full path-name. -dvr FL : The DVR information is read from file FL rather than from ./dvr The string FL may be a relative or a full path-name. -d PATH : The output is directed to PATH directory rather than to the current directory. The string PATH may be a relative or a full path-name. If PATH=no, i.e. "-d no", no output-files will be opened. -o NAME : Change the name of the output file from "mtt_h"("mtt_s") to NAME. -n step : Compute Mtt' only every step-th tpsi. -es nst : Compute Mtt' for the electronic state nst only. -lo klo : Compute Mtt' only from the klo-th tpsi onwards. -hi khi : Compute Mtt' only up to the khi-th tpsi. -O oper : Apply operator "oper" before evaluating the overlap. -w : Overwrite an existing Mtt file. -sym : Use the symmetric scalar product rather than the hermitian one. -ver : Version information about the program -h : Print this help text. -? : Print this help text. Example : fmat83 -hi 65 -O ham Important note: The used operator must be build with the "nodiag" flag! ------------------------------------------------------------------------------
N.B. The outputfile is called "mtt_h" or "mtt_s" if no operator is used (i.e. if the overlap matrix is calculated) and is called "mtt_h_oper" or "mtt_s_oper" if the operator oper is employed. The flags "h" and "s" are for the case of hermitian and symmetric scalar products. The operator oper must be defined in a HAMILTONIAN-SECTION_oper and must carry the nodiag flag. The generated matrices may be diagonalised (generalised eigenvalue problem) to obtain the eigenvalues of the operator oper. This should be done with the program diag. Resonances may be calculated as well by using the symmetric scalar product (-sym option).
Purpose: Calculates the initial guess field for optimal control The pulse is a Gaussian times sin(omega_field*t) Usage : guessfld83 tfinal tout omega_rabi omega_f [frequency unit] The times tfinal, tout, are in fs. The field-strength, omega_rabi, and the field-frequency, omega_f, are in eV, au or cm-1. The frequency unit can be given with an additional optional string. The default unit is au. ------------------------------------------------------------------------------The field is defined by: E(t) = omega_rabi*cos(omega_f*(t-tfinal/2.d0)) + *sin( PI*t/tfinal )**2 The field will be written in ASCII to the file fieldf.0 for every tout over the interval -2*tout ... tfinal + 2*tout.
Purpose: Checks the hermiticity of the A-vector. Only available for density type II. Usage: herma<ver> [-f -i -n -r -ver -h -?] . Options : -f FILE : The density matrix is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : Same as -f FILE. -n step : Compute the error only every step-th output. -r : Take the restart file rather than the psi file. -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------
Purpose : J-interpolation of flux data. Usage : jinpol83 [-d -f -o -j -j1 -j2 -m -r0 -rf -e1 -e2 -ed -es -em -mp -A -B -C -p -ver -h]. Options : -id IDIR: The probabilities files are read from directory IDIR. -od ODIR: The probabilities files are written to directory ODIR. -f FILE : The probabilities are read from file IDIR/FILEext where ext denote the extension jKJ (e.g. 205). -o FILE : The interpolated probabilities are written to ODIR/FILEext where ext denote the extension jKJ (e.g. 205). -j j : Search for files with j-value j. j is the first number in extension. -j1 J1 : First J value of interpolation range. -j2 J2 : Last J value of interpolation range. -k K : Search for files with K-value K. K is the second number in extension. -r0 R0 : R0 is the estimated value of the transition-state coordinate. -rf Rf : Rf is the fixed value of the transition-state coordinate. (No optimization). -m mass : Reduced mass in AMU (default mass = 1.0). -e1 E1 : First energy of fit-interval. -e2 E2 : Last energy of fit-interval. -ed edim: Number of energy points used to compute the integrals. (def.= 500). -es shft: The energies read from the probability files are shifted by shft. -em Emin: The input probabilities are set to zero for E<Emin. -mp maxp: The input probabilities are set to maxp if prob>maxp. -A : Minimize F = SQRT(A*B) - C -B : Minimize F/C (default) -C : Minimize -C -p : Print every iteration step. -ver : Version information about the program -h : Print this help text. The defaults settings are: IDIR=., ODIR=., j=0, k=0, r0=3.0, Edim=500, Eshift=0.0, Emin=-1.d9, maxp=1.d9, mass=1.0 (i.e. 1837.15 au). Example: jinpol83 -f flux -o mflux -j 2 -j1 1 -j2 4 -e1 0.0 -e2 1.2 This will read the files flux201 and flux204 from and write the files mflux201, mflux202, mflux203, and mflux204 to current directory. NB: The energy interval [E1,E2] is used for determining r0 only. The energy interval of output is the one of the first flux file. ------------------------------------------------------------------------------jinpol83 interpolates the (reaction) probabilities for different total J. As input it needs two sets of probabilities (e.g. flux files) for J1 and J2. It then creates probabilities for all J with J1 < J < J2. The algorithm has some similarity with J-shifting, but is much more accurate. This J-interpolation algorithm is described in an appendix of J.Chem.Phys. 116 (2002) 10641.
Purpose : Join psi files have been calculated with different number of SPFs. Usage : joinpsi83 [-w -D -o -l -f -p -ver -h -?] file1 file2 ... Options : -w : Overwrite existing output file. -D PATH : The output is directed to PATH. The string PATH may be a relative or a full path-name. -o NAME : Change the name of output file from "psi" to NAME. -l LIST : The list if psi files is read from file LIST, rather from the input line. -f n1 n2 ... : Force the number of SPFs to be equal to n1,n2,... . Otherwise the maximum number from psi files will be chosen. -p : Print information to the screen. -ver : Version information about the program -h : Print this help text. -? : Print this help text. Examples : joinpsi83 ../dir1/psi ../dir2/psi ../dir3/psi joinpsi83 -w -f 30 40 20 -l list_psi ------------------------------------------------------------------------------The program is useful, if the maximum number of SPFs is not needed for all propagation times (for example in the scattering problem). One may perform several calculations with varying numbers of SPFs (usually with smaller numbers of SPFs at the beginning and at the end of the propagation, if it is a scattering process), and then joins the psi-files with the aid of this program for the further analysis (e.g. flux analysis, etc.). The number of SPFs for the resultant psi-file equals the maximum from all psi-files. The artificially augmented SPFs are filled with zeros. The program is working only with psi=single or psi=double formats.
Purpose : Calculates the minimum and maximum value of a PES Usage : maxpe83 [-h -ver ] path-to-name-directory First generate an oper file for an exact calculation and then run maxpe83 with the path to that directory as argument. -ver : Version information about the program -h : Print this help text NB: The routine vminmax is a more powerful alternative which does not require an operator in exact, but in pes format -------------------------------------------------------------Calculates the maximum and minimum value of a PES. This is useful to check for the presence of large eigenvalues, which affect the efficiency of a numerically exact propagation.
Note that vminmax83 is a more powerful alternative which does not require the operator in exact, but in pes format.
Purpose : Checks, how much memory can be allocated. Usage : mmemtest83 [-h ] Options : -h Print this help text. Run mmemtest83 on the computer, on which you want to run a program of the MCTDH package. Note, that only mctdh83 and potfit83 can use up to 8 GB (on 64 bit architectures with sufficient memory). All other MCTDH-programs are limited to a allocate at most 2 GB. ------------------------------------------------------------------
Purpose: Calculates the norm and A-norm of a wavefunction. or density operator of type II. Usage: norm [-f -i -n -r -ver -h -?] . Options : -f FILE : The wavefunction (density operator) is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i DIR : data is stored in directory DIR -n step : Compute the norm only every step-th output. -r : Take the restart file rather than the psi file. -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------
Purpose: Checks the orthonormality of the spf's (spdo's). For density operators it checks also the hermiticity of the one-particle density operators. Usage: ortho<ver> [-f -i -n -r -ver -h -?] . Options : -f FILE : The wavefunction (density operator) is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : Same as -f FILE. -n step : Compute the orthonormality error only every step-th output. -r : Take the restart file rather than the psi file. -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------The output is to the screen and shows the square root of the sum of the squares of the matrix-elements of (ov-1) where ov denotes the overlap-matrix of the spf's.
overlapver
[-f -i -o -n -w -h -?] comp_file
Purpose: Calculates the difference between two wavefunctions or density operators. See review Eqs.(159-163) for a definition of the output. Usage : overlap83 [-f -i -o -a -b -c -t -n -w -ig -ver -h -?] [Psi] . Options : -f FILE : The wavefunction (density operator) is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : Same as -f FILE. -o FILE : The overlaps are written to file FILE.pl rather than to ./ovl_XXX The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no ovl-file will be opened. -a : Compute the overlaps according to their position on psi-file, i.e. times (tpsi) are ignored. -b : Compute the overlaps <Psi(t_final-t)|Psi1(t)>, i.e. the bra-state runs backwards in time. -c : Compute the overlaps <dconjg(Psi(t))|Psi1(t)>, i.e. the complex-symmetric scalar product is used. -s s s1 : Compute the overlaps <Psi(t)_s|Psi1(t)_s1>, s and s1 denote the electronic states of bra- and ket-WF. -t tend : Compute the overlap only up to t=tend. -n step : Compute the overlap only every step-th output. -w : An existing overlap file is overwritten. -ig : Ignore "different bases" error-msg. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The argument Psi (bra-states) is the name of the file containing the comparison wavefunction or density operator. The ket-states are read from ./psi or from the file given by the -f option. If no argument is given, the user is prompted for the missing argument. If one calculates the overlap between density operators of different types, [Psi] has to be the one of type II. NB: The overlap is written to the file ./ovl_XXX, the screen-output shows error=||Psi-Psi1||. ------------------------------------------------------------------------------Calculates the error (overlap) between the wavefunctions (density operators) in ./psi (or FILE) and comp_file . The results are written to the screen and a file, the name of which depends on the input file names, or the argument of the -o option. E.g.
overlap83 ../dir/psi
calculates the error between the wavefunctions (density
operators) in ./psi and ../dir/psi, and the results is stored in
./ovl_dir (unless the -o option was used). The WFs on ../dir/psi
are taken as bra-states and the WFs of the psi-file of the
current directory are the ket-states.
In contrast
overlap83 -i psi1 psi2
would calculate the error between the wavefunctions (density
operators) in ./psi1 and ./psi2, storing the results in
./ovl_psi2.
The output (on screen) is as described in the review
Eqs.(159-163). In particular: Error = ||psi1-psi2|| = Eq.(159);
Hilbert = arccos( |<psi1|psi2>|/(||psi1||*||psi2||)) =
Eq.(163); Phase = arctan( Im(<psi1|psi2>|)/
Re(<psi1|psi2>|) = Eq.(161); Ph. corr = Eq.(162).
The overlaps <psi1|psi2> <psi1|psi1> and
<psi2|psi2> are written to the file ovl_dir, where
dir denotes the name-directory of the second calculation.
If this file exist and when the option -w is not given, overlap83
will read the file ovl_dir rather than re-do the
calculation.
Purpose: Calculates the time evolution of an expectation value. Usage : pexpect [-f -i -o -g -a -r -t -p -u -n -w -ver -h -?] [mode operator]. Options : -f FILE : The operator is read from file FILE rather than from ./oper The string FILE may be a relative or a full path-name. -i FILE : The one particle density is read from file FILE rather than from ./pdensity The string FILE may be a relative or a full path-name. -o FILE : The output is written to file FILE.pl rather than to ./pexpect.pl The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no output file will be opened. -g : GNUplot comand lines are written to the output file(s). -a : GNUplot is called automatically. (sets -g and -w). -p : Print GNUplot to lpr (sets -g). -r : Do not divide the expectation values by norm^2. -t tfin : The expectation values are computed only up to time=tfin. -u UNIT : The unit used is UNITs (Default is a.u.). -n step : Compute the property only every step-th output. -w : An existing property file is overwritten. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The first argument "mode" is the (combined) mode for which the expectation value is calculated. The second argument "operator" is the name of the operator, as specified in an HAMILTONIAN-SECTION_xxx, for which the expectation value is required. If "system" is chosen as operator the uncorrelated energy of the specified mode is computed. If no argument is given, the user is prompted for the missing argument(s). ------------------------------------------------------------------------------The first argument "mode" is the (combined) mode for which the expectation value is calculated. The second argument "operator" is the name of the operator, as specified in an HAMILTONIAN-SECTION_xxx, for which the expectation value is required. If "system" is chosen as operator the uncorrelated energy of the specified mode is computed. If no argument is given, the user is prompted for the missing argument(s). The operator must first have been processed by the MCTDH program. This means that it must first be set up in a .op file. If it is known before a propagation is made, this operator can be included with the system operator in the main oper file (by using a named HAMILTONIAN-SECTION_XXX). Alternatively, e.g. if a propagation has already been made, the file oper_name can be generated using the genoper=name keyword.
Start the program in the directory containing the one-particle density in a pdensity file. If no operator is given, the program looks in the oper file to see which operators are there and asks which is to be evaluated. The -o option can use a file other than this. The expectation value of this operator is then calculated for each time, and output to the file pexpect.pl, unless otherwise instructed. The -a option enables the automatic plotting of the results. Note that pexpect computes expectation values of one-particle operators. (For combined modes this may include more than one degree of freedom). If the specified operator acts on several modes, pexpect uses only the uncorrelated part for the specified mode.
Purpose: Build and output reduced density from pdensity file. Usage : prhosub [-i -n -nw -k -q -ver -h -?] [mode [state]] Options : -i FILE : The one particle density is read from file FILE rather than from ./pdensity The string FILE may be a relative or a full path-name. -n step : Compute the density only every step-th output. -nw : No weights are employed. Write the "naked" DVR populations. -k min max: Write the momentum spectrum for the interval min<p<max. If "-k d" is given, default values for min and max will be taken. -q pts : Use the number of pts points for representing the momentum spectrum. Default: pts = 501 This option is ignored, when -k is not given. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The argument "mode" is the mode for which the reduced density is calculated. "state" is the electronic state. If an argument is not given, the the default value 1 will be taken. ------------------------------------------------------------------------------The pdensity file must have been produced with the line pdensity=I in the run-section. Here, I is the number of the degree of freedom of interest. pdensity=I will then contain the reduced density in natural orbital representation. prhosubver produces one file of output for each tout, with the reduced density represented on the primitive grid. The columns are then x, x', real part, imag. part, absolute value.
Start the program in the directory containing the one-particle density in a pdensity file.
Purpose: Computation of the quadratic entropy. sum p_i^2. Usage : probsq83 [-i -t -a -ver -h -?] Options : -i FILE : The autocorrelation is read from file FILE rather than from ./auto The string FILE may be a relative or full path-name. -a tstart: The autocorrelation function is read only from t=tstart on. -t tcut : The autocorrelation function is read only up to t=tcut -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------The program computes the integral (1/T)*Int[0,T] g(t)*|c(t)|**2 dt where T denotes the final time of the autocorrelation c(t) and g(t) is some weighting function. g(t) = 1, (pi/2)*sin(pi*t/T), (pi/2)*cos(pi*t/2T), 2*sin(pi*t/T)**2. For large T this converges to Sum pi , where pi denotes the occupation probability of the i-th eigenstate. This sum is related to the so called quadratic entropy. Output are the values Sum pi, 1/(Sum pi), and -Log2(Sum pi).
Purpose: Converts the wavefunction in a psi file from MCTDH to numerically exact form. Default is single precision. Usage : psi2ex83 [-f -i -o -stp -n -skip -pop2 -plot -abs -w -dp -ver -h -?] Options : -f FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i FILE : Same as -f FILE. -o FILE : The output is written to file FILE rather than to ./psi.ex The string FILE may be a relative or a full path-name. -stp step: Compute the exact WF only every step-th output. -n num : only the first num WFs are read from psi-file. -skip m : the first m WFs are skipped. -pop2 : exaxt WF is given in second population -plot : only meaningful if -pop2 is activated and some dof is of fft type. For each dof of fft type, swaps the x axis in a convenient way for further plotting. NB: the resulting WF cannot be used in a subsequent MCTDH calculation. -abs : The absolute value of the exact WF is written. In this case the (dummy) A-vector and psiinfo are not written, i.e. the file contains abs(WF) only. Note: -abs sets -plot. -dp : The file is written double precision. -w : An existing output file is overwritten. -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------The program reads the MCTDH wavefunction in a psi file and converts it to the numerically exact form, represented on the full grid. This is useful for other analyse routines. The output is by default single precision to the file psi.ex. The argument -dp forces double precision output, and -o FILE changes the output file name. The argument -pop2 gives the exact wavefunction in second population. In case some of the degrees of freedom is of fft type, the x axis (which in such a case is the momentum axis) can be swapped using the option -plot, so that it goes from negative to positive values and can nicely be plotted. In case -plot is set, the momentum grid ranges from -(gdim/2)*dp to (gdim/2-1)*dp in steps of dp, where dp=2*pi/(dx*gdim). The values for dx (grid spacing) and gdim (number of grid points) are listed in the log file. In case -plot is not set, the momentum grid runs form zero to (gdim/2-1)*dp and then from -(gdim/2)*dp to -dp.
The format of the psi file is explained in the MCTDH/Output
Documentation.
When the option -abs is given, the absolute value of the
wavefunction is written. In this case the file contains only the
wavefunction. The order of the elements is like in a Fortran
array: Psi(dof_1,dof_2,...,dof_f).
Purpose: Converts the wavefunction of a psi file to restart format. The argument "step" is the number of the WF to be converted. Usage : psi2rst83 [-f -i -o -w -ver -h -?] step Options : -f FILE: The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i DIR : The wavefunction is read from file DIR/psi rather than from ./psi -o DIR : The output is written to file DIR/restart rather than to ./restart -w : An existing output file is overwritten. -ver : Version information about the program -h : Print this help text. -? : Print this help text. NB: The output is written to the file restart in the current directory, or to DIR/restart, if the option -o is given. To receive some information on the WF file, run "psi2rst nn", where nn is zero or a large number (larger than the number of WFs on file). ------------------------------------------------------------------------------
rdautoever
[-f -i -o -d -t -h-?] ns nmd
Analyse program "rdautoe" (Read autoe-file) Purpose : Analyses the error measures of the autocorrelation. Usage : rdautoe83 [-f -i -o -d -t -ver -h -?] [ns mode]. Options : -f FILE : the error measures are read from file FILE rather than from ./autoe The string FILE may be a relative or full path-name. -i FILE : Same as -f FILE -o FILE : The error measures are written to file FILE.pl rather than to ./autoe.pl The string FILE may be a relative or full path-name. If FILE=no, i.e."-o no", no autoe.pl file will be opened. -t dt : Print the error measures every dt fs. -d : Write the difference of the autocorrelations to output file. -g : GNUplot command lines are written to the output file(s). -ver : Version information about the program -h : Print this help text. -? : Print this help text. There are two arguments: The first argument is ns, i.e. the number of electronic state to be considered. The second argument is nmd, i.e. the runing number of the mode to be considered. (nmd=0 -> All modes are decreased by one spf). If not enough arguments are given, the user is prompted for the missing arguments. ------------------------------------------------------------------------------The routine rdautoe reads the autoe-file and writes the modified autocorrelation function to the output file (e.g. autoe.pl) which has exactly the same format as the auto file and hence may be read be the routine autospec83. By modified autocorrelation function we denote the autocorrelation which is calculated by dropping the most weakly occupied spf of mode nmd and state ns. A spf in each mode (and state) is dropped, if nmd=0. If the option -d is given, the difference of the modified autocorrelation and the (original) autocorrelation is outputed.
rdcheckver
[-f -i -oc -on -g -gq -t -h -?] ns nmd
Analyse program "rdcheck" (Read check file) Purpose : Reads the check-file. Analyses the state population and natural weights. Usage : rdcheck83 [-f -i -oc -on -e -g -gq -t -n -ver -h -?] ns nmd. Options : -f FILE : The data is read from file FILE rather than from ./check The string FILE may be a relative or full path-name. -i DIR : Data is read from file DIR/check -oc FILE: The state populations are written to file FILE.pl rather than to ./chk.pl The string FILE may be a relative or full path-name. If FILE=no, i.e."-oc no", no chk.pl file will be opened. -on FILE: The natural populations are written to file FILE.pl rather than to ./nat.pl The string FILE may be a relative or full path-name. If FILE=no, i.e."-on no", no nat.pl file will be opened. -oq FILE: The expextation values <q> and <dq> are written to file FILE.pl rather than to ./qdq.pl The string FILE may be a relative or full path-name. If FILE=no, i.e."-oq no", no qdq.pl file will be opened. -e : State energies are written to screen. -g : GNUplot command lines are written to the output file(s). -gq n : Selects the n-th dof for th qdq-plot. Sets -g -r : Renormalise the natural weights via division by state population. -t dt : Print the natural weights every dt fs. -n : No units. Sets fs=1. Use, if 'time-not-fs' is set. -ver : Version information about the program -h : Print this help text. -? : Print this help text. There are two arguments: The first argument is ns, i.e. the state for which the natpops are written. (ns=0 -> no output files written). The second argument is nmd, i.e. the runing number of the mode for which the natpops are written. If not enough arguments are given, the user is prompted for the missing arguments. ------------------------------------------------------------------------------If one just wants to check the convergence of the natural weights, type: rdcheck83 0 , or, to see the development of the lowest natural weights in timesteps of 1.2 fs: rdcheck83 -t 1.2 0
Analyse program "rdgrid" (Read grid points) Purpose : Read the DVR grid from dvr file and print it. Usage : rdgrid [ -f -i -h -? ] dof . Options : -f FILE: the DVR file is read from file FILE rather than from ./dvr . The string FILE may be a relative or full path-name. -i DIR : dvr file is read from directory DIR. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The argument dof is the number of the degree of freedom for which the grid is printed. If no argument is given, the user is prompted for the missing argument. ------------------------------------------------------------------------------This program is useful to obtain a quick overview of the actual locations of the grid points. Note that the programs showsys and showpot can show cuts of multi-dimensional potential energy surfaces only along grid points. The input values for the cuts are hence changed by these programs to take the value of the nearest grid point.
Analyse program "rdgpop" (Read grid populations) Purpose : Analyses the grid population read from file gridpop. Usage : rdgpop83 [-f -i -g -o -t -n -ver -h -?] [nz dof]. Options : -f FILE : the grid populations (densities) are read from file FILE rather than from ./gridpop The string FILE may be a relative or full path-name. -i FILE : Same as -f FILE -o FILE : The grid populations are written to file FILE.pl rather than to ./gpop.pl The string FILE may be a relative or full path-name. If FILE=no, i.e."-o no", no gpop.pl file will be opened. -t dt : Print the maximal occupations every dt fs. -n : No units. To be used when 'time-not-fs' is set. -g : GNUplot command lines are written to the output file(s). -ver : Version information about the program -h : Print this help text. -? : Print this help text. There are two arguments: The first argument is nz, i.e. the number of grid points sumed over. The second argument is dof, i.e. the runing number of the degree of freedom to be considered. (dof=0 -> no output to file gpop.pl). If not enough arguments are given, the user is prompted for the missing arguments. ------------------------------------------------------------------------------The grid population is summed over the first nz and the last nz points of both the spatial (DVR) grid and the basis (FBR) occupations. By varying nz one may study how much the grid may be shortened. The integer dof specifies the degree of freedom to be investigated. Depending on the MCTDH input, the grid populations are summed over all electronic states or (if gridpop=el is given in the run-section) treated separately for each electronic state. For a simple check on the convergence with respect to the primitive grids simply type rdgpop83 1 0 while being in the name directory.
Purpose : Reads the step-file and evaluates statistic measures of the integrator steps. Usage : rdsteps83 [-f -i -ver -h -?]. Options : -f FILE : the data is read from file FILE rather than from ./steps The string FILE may be a relative or full path-name. -i DIR : data is stored in directory DIR -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------
Purpose : Reads the step-file and evaluates statistic measures of the integrator steps. Usage : rdsteps83 [-f -i -ver -h -?]. Options : -f FILE : the data is read from file FILE rather than from ./steps The string FILE may be a relative or full path-name. -i DIR : data is stored in directory DIR -ver : Version information about the program -h : Print this help text. -? : Print this help text. dieter@cantor:/worka/dieter/mctdh83.94$ rdupdate83 -h ld.so: Incorrectly built binary which accesses errno or h_errno directly. ld.so: See /usr/share/doc/libc6/FAQ.gz. Purpose : Reads the update steps from file "update" Usage : rdupdate [-f -i -inter -ver -h -?]. Options : -f FILE : the data is read from file FILE rather than from ./update The string FILE may be a relative or full path-name. -i DIR : data is stored in directory DIR -inter : enables interactive plotting -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------Reads the CMF step sizes from file, and removes repetition steps. The use of the -inter argument starts an menu to enable interactive plotting of the data. Without this argument, the data is written to the screen.
Purpose : Reads the autocorrelation from file "auto" Usage : rdauto [-f -i -inter -ver -h -?]. Options : -f FILE : the data is read from file FILE rather than from ./auto The string FILE may be a relative or full path-name. -i DIR : data is stored in directory DIR -inter : enables interactive plotting -ver : Version information about the program -h : Print this help text. -? : Print this help text. ----------------------------------------------------------------------------The use of the -inter argument starts an menu to enable interactive plotting of the data. Without this argument, the data is written to the screen.
Purpose : Reads the eigvalues from file "eigval" Usage : rdeigval [-f -i -inter -ver -h -?]. Options : -f FILE : the data is read from file FILE rather than from ./eigval The string FILE may be a relative or full path-name. -i DIR : data is stored in directory DIR -inter : enables interactive plotting -ver : Version information about the program -h : Print this help text. -? : Print this help text. ----------------------------------------------------------------------------The use of the -inter argument starts an menu to enable interactive plotting of the data. Without this argument, the data is written to the screen.
showd1dver
[-T|-S|-I|-P|-M|-Ma] [-f -i -o -a -g -p -x -y -fac -n -w -sm -nw
-pop2 -G -inter -ver -h -?] fx sx
Purpose: To selectively plot 1-dimensional densitites. Usage : showd1d83 [-T|-S|-I|-P|-M|-Ma] [-f -i -o -a -g -p -x -y -fac -n -no -t -nofs -l -sm -w -nw -pop2 -G -inter -ver -h -?] [fx sx]. Output Formats : -S : "Step through" by pressing RETURN. (default). -M : "Movie", one picture every second. -I id : "Index file", id=0 shows the first picture, id=1 the second, etc. -P pnt : "Point file", shows the population of the pnt-th grid-point over time. -T : "3D time file" (grid file). -Ma : Mathematica file (for dynamic plots). Options : -f FILE : The wavefunction is read from file FILE rather than from ./gridpop The string FILE may be a relative or a full path-name. -i DIR : Use DIR as name-directory. -o FILE : The output is written to file FILE_f* rather than to ./den1d_f* The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no output file will be opened. -pop2 : 2nd population plotted (i.e. basis set occupations). -g : GNUplot comand lines are written to the output file(s). -a : GNUplot is called automatically. (sets -g and -w). -p : Print GNUplot (sets -g). Allowed only with -I or -T. -sm : Smooth the plot-data by splines. (only for GNUplot, sets -g). -l : Use logarithmic scale. (Only for GNUplot). -n step : Show only every step-th picture. (Only useful for -S, -M). -t tfinal : Show densities only up to t=tfinal. -nw : No weights are employed. Plot the "naked" DVR populations. -no : No output file opened. -nofs : No transformation to fs. Use when 'time-not-fs' was set in mctdh. -x xmin xmax : Set the abszisse length (default: auto). Ignored for -T, -Ma. -y ymax : Set the ordinate length (default: auto). Ignored for -T, -Ma. -fac factor : Multiply the density values by factor. -G : Plot gridlines. -w : An existing output file is overwritten. -h : Print this help text. -? : Print this help text. -ver : Version information about the program The arguments fx and sx select the dof and state (x=integer). If no argument is given, the user is prompted for the missing argument. EXAMPLES: showd1d83 -a f1 showd1d83 -a -M -y 0.3 -n 2 f2 s1 showd1d83 -w -p -I 20 f1 showd1d83 -a -p -T f3 ------------------------------------------------------------------------------
For instance, showd1d83 -a f2 would plot the density for the 2nd degree of freedom by automatically calling GNUplot. If RETURN is pressed, the density for the next output-time is shown.
The output is to a file den1d_fx_sx or den1d_fx if no state is specified.
The state is by default taken as 1. Thus if sx is not specified as an argument the 1st state is selected. Note that there is normally only one (effective) electronic state as the densities of the different states are summed before they are written to the file gridpop. If you want to avoid this and investigate the different electronic states separately, you have to provide the keyword "gridpop=el" in the mctdh input file.
The options -T, -S, -I, and -M selects the format for the
output.
A Gnuplot index file writes a set of data for each time:
coordinate, Abs(spf), Re(spf), Im(spf)
with 2 blank lines between. Gnuplot can then select a set using
the "index" option of the "plot" command. If -I
id is specified only the plot number id
will be ploted. (This is particularly useful when the plot should
be printed. See the -p option). If -S is
specified (or, since this is the default, if no format option is
given) one can scroll through the pictures by pressing RETURN. If
-M is specified one sees a "movie", one picture
each second.
A Gnuplot grid file (option -T) writes a set of data for each
time:
coordinate, time, Abs(spf), Re(spf), Im(spf)
with 1 blank lines between. Gnuplot can then plot a 3D plot of
the spf evolution with time.
The mathematica option (-Ma) writes information to the screen to
be read by a mathematica script (plspf.m). This enables dynamic
pictures.
If one want to use showd1d to investigate the grid populations, one should use the option -nw (no weights) because the use of weights may lead to a wrong conclusion. The option -l (logarithmic plot) is also useful when checking grid populations.
showrstver
[-f -i -o -a -g -abs -abs2 -re -im -reim -sm -p -y -nw -w -ver -h
-?] fx sx
Purpose: Plot the single-particle functions of a restart file. Usage : showrst83 [-f -i -o -a -g -abs -abs2 -re -im -reim -sm -p -x -y -nw -w -G -ver -h -?] [fx sx] . Options : -f FILE : The wavefunction is read from file FILE rather than from ./restart The string FILE may be a relative or a full path-name. -i DIR : Use DIR as name directory. -o FILE : The plot data is written to file FILE_f* rather than to ./rst.pl_f* The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no output-file will be opened. -g : GNUplot comand lines are written to the output file(s). -a : GNUplot is called automatically. (sets -g and -w). -sm : Smooth the plot-data by splines. (only for GNUplot, sets -g). -p id : Print GNUplot (sets -g). The integer id is the number of the spf to be printed. -abs : Plot absolute values. (default). -abs2 : Plot absolute values squared. -re : Plot real part (only for GNUplot, sets -g). -im : Plot imaginary part (only for GNUplot, sets -g). -reim : Plot both imaginary and real parts (only for GNUplot, sets -g). -nw : No weights are employed. Plot the "naked" DVR values. -x xmin xmax : Set the abszisse length. -y ymax : Set the ordinate length (default: auto). -G : Plot gridlines. -w : An existing output file is overwritten. -ver : Version information about the program -h : Print this help text. -? : Print this help text. The arguments select the dof (fx) and state (sx) Replace x by appropriate number, any order is allowed. If no argument is given, the user is prompted for the missing argument. ------------------------------------------------------------------------------The state is by default taken as 1. Thus if sx is not specified as an argument the 1st state is selected.
E.g. showrst83 -a -re f2 would plot the real-part of the single-particle functions for the 2nd degree of freedom. GNUplot will be called automatically (-a option). The output is to the file rst.pl_f2.
showspfver
[-spf -nat -f -i -o -a -g -p -x -y -sm -abs -abs2 -re -im -reim
-n -w -h -?] fx sx x
Purpose: To selectively plot (uncombined) natorbs or spf's. Usage : showspf83 [-T|-S|-I|-M|-Ma] [-f -i -o -a -g -p -x -y -sm -abs -abs2 -re -im -reim -n -w -nwi -nofs -spf -nat -G -ver -h -?] [fx sx x] . Output Formats : -S : "Step through" by pressing RETURN. (default). -M : "Movie", one picture every second. -I id : "Index file", id=0 shows the first picture, id=1 the second, etc. -T : "3D time file" (grid file). -Ma : Mathematica file (for dynamic plots). Options : -f FILE : The wavefunction is read from file FILE rather than from ./psi The string FILE may be a relative or a full path-name. -i DIR : Use DIR as name directory. -o FILE : The output is written to file FILE*_f* rather than to ./natorb*_f* The string FILE may be a relative or a full path-name. If FILE=no, i.e. "-o no", no output-file will be opened. -g : GNUplot comand lines are written to the output file(s). -a : GNUplot is called automatically. (sets -g and -w). -p : Print GNUplot (sets -g). Allowed only with -I or -T. -sm : Smooth the plot-data by splines. (only for GNUplot, sets -g). -abs : Plot absolute values. (default). -abs2 : Plot absolute values squared. -re : Plot real part (only for GNUplot, sets -g). -im : Plot imaginary part (only for GNUplot, sets -g). -reim : Plot both imaginary and real parts (only for GNUplot, sets -g). -spf : Plot the of the single-particle functions rather than natorbs. -nat : Plot the of the natural orbitals rather than spf's (default). Note x=1 -> highest occupied natorb. -nofs : No transformation to fs. Use when 'time-not-fs' was set in mctdh. -nw : No weights are employed. Plot the "naked" DVR values. -n step : Show only every step-th picture. (Only useful for -S, -M). -x xmin xmax : Set the abszisse length. -y ymax : Set the ordinate length (default: auto). Ignored for -T and -Ma. -G : Plot gridlines. -w : An existing output file is overwritten. -h : Print this help text. -? : Print this help text. -ver : Version information about the program The arguments select the spf (x), dof (fx) and state (sx) Replace x by appropriate number, any order is allowed. If no argument is given, the user is prompted for the missing argument. ------------------------------------------------------------------------------E.g. showspf83 -a -spf f2 4 would plot the absolute value of the 4th single-particle function for the 2nd degree of freedom.
By default natural orbitals are output to a file natorbx_fx_sx. If the -spf flag is used, the single-particle functions are output to a file spfx_fx_sx.
The state is by default taken as 1. Thus if sx is not specified as an argument the 1st state is selected.
The options -T, -S, -I, and -M selects the format for the
output.
A Gnuplot index file writes a set of data for each time:
coordinate, Abs(spf), Re(spf), Im(spf)
with 2 blank lines between. Gnuplot can then select a set using
the "index" option of the "plot" command. If -I id is
specified only the plot number id will be ploted. (This
is particularly useful when the plot should be printed. See the
-p option): If -S is specified (or, since this is the
default, no format option is given) one can scroll through the
pictures by pressing RETURN. If -M is specified one sees
a "movie", one picture each second.
A Gnuplot grid file (option -T) writes a set of data for each
time:
coordinate, time, Abs(spf), Re(spf), Im(spf)
with 1 blank lines between. Gnuplot can then plot a 3D plot of
the spf evolution with time.
The mathematica option (-Ma) writes information to the screen to
be read by a mathematica script (plspf.m). This enables dynamic
pictures.
showsysver
[-i -f -n -o -pes -rst -pop2 -ver -h -?]
Purpose: Enables 2D plotting of the wavefunction or PES. Usage: showsys83 [-i -f -p -o -pes -nopes -n -skip -step -rst -nw -pop2 -ver -h -?] Options : -i DIR : data is stored in directory DIR -f FILE : the wavefunction is read from FILE rather than from ./psi The string FILE may be a relative or a full path-name. -p FILE : the PES is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -o FILE : The ouput is written to file FILE.pl rather than to ./surface.pl The string FILE may be a relative or a full path-name. -pes : only the PES file is read, i.e. no wavefunction plotting. -nopes : the PES file is not read, no potential plotting, no dia->ad trafo. -rst : the restart file is read, rather than the psi file. -n num : only num WFs are processed. -skip m : the first m WFs are skipped. -step step : only every step's WF will be processed. -nw : No weights are employed. Plot the "naked" DVR populations. (WF only). -pop2 : the basis set occupations are plotted rather than grid populations. For FFT this implies momentum space representation. -ver : Version information about the program. -h : Print this help text. -? : Print this help text. The program is menu driven. Just type "showsys83" or "showsys83 -pop2" or "showsys83 -pes" or "showsys83 -rst" and then follow the menu. If there are more WFs on psi file than you want to inspect, use the options -n, -skip, or -step. Example: "showsys83 -skip 10 -n 2" will plot the WFs no. 11 and 12 (i.e. t=10 and 11 if tpsi=1fs), and "showsys83 -step 10 -n 2" will plot the WFs no. 1 and 11. If one wants to plot a potential one should use "shwsys83 -pes", because otherwise the WF is read, which consumes a large amount of memory. NB1: The option -step may also be set by the menu-point 285. The WFs to be processed may also be selected by setting time bounds (menu-point 30). NB2: The option -pop2 is ignored for phifbr,sphfbr,k,external bases. --------------------------------------------------------------------------------Cuts of a potential energy surface (PES) can be generated from an pes file, and cuts and (1D or 2D) densities of the wavefunction can be generated from a psi file.
If the (1D or 2D) densities of the wavefunction are to be displayed in the second representation, i.e. as basis set occupation, momentum representation or angular momentum representation, use the option -pop2 . (This switch is not available through the menu).
After starting the program a menu is presented with the help of which one can select a plot via an interactive process. The menu offers the following choices:
If the psi file contains a number of snapshots these will be displayed a shot at a time. In the default "step through" mode, press enter to change the frame. Using option 280 it is possible to change to "movie" mode, when the frames are shown at 1 second intervals. It may be useful to turn of the key (option 240) as the key (labelling contours) can cause the frames to have different sizes.
Using the "overlay" option it is possible to display a PES under the evolving wavepacket. First plot and save the PES to an xyz file (option 5). Change to plotting a wavepacket (using 10). Then turn on the overlay plots option with 400. Now with 410 the file name should be given containing the PES. The selected file name is shown. Unless the replot options are toggled (9 for the plot, 420 for the overlay) "plot to screen" (1) will now prompt for contours for both plots before plotting.
Warning: Plotting densities may take a large amount of
computer time, if the dimension is large (f>3). Because of
this it may be useful to reduce the number of plots by shortening
the time-interval. Use menu point 30 to set the time-bounds
appropriately. Alternatively (and simpler) one may use the
options -n and/or -skip and/or -step to limit the number of
wavefunctions read in and processed. E.g. showsys83 -n
11 will plot only the densities for the first 11 time-steps.
If tout=1 this means from 0 to 10 fs. showsys83 -skip 50 -n
1 will plot the density no. 51 only, and showsys83 -skip
5 -n 2 -step 10 will plot the densities no. 6, 16 and
26.
Note that there is the routine dengen83 which generates
2D densities similar as showsys does.
showpotver [-i -d -v -n -u -vfit -vpot -diff -abs -ver -h -?]
Purpose : plots potential and/or potential fit interactively Usage : showpot83 [-i -d -v -n -u -vfit -vpot -diff -abs -ver -h -?] Options : -i NAME : The files are stored in the directory NAME -d FILE : The dvr is read from file FILE/dvr rather than from ./dvr or NAME/dvr -v FILE : The potential is read from file FILE If FILE is not given, FILE=vpot is assumed. If FILE=no, i.e -v no, vpot file is not read. -n FILE : The potential fit is read from file FILE If FILE is not given, FILE=natpot is assumed. -u UNIT : The energy unit UNIT is applied. -vfit : Set plottask to vfit. -vpot : Set plottask to vpot. -diff : Set plottask to vfit-vpot. -abs : Set plottask to abs(vfit-vpot). -ver : Version information about the program -h : Print this help text. -? : Print this help text. ------------------------------------------------------------------------------ NOTE - If the -n option is not used, the program assumes that a natpot file exists in the working directory (or in the NAME directory if specified). If the -v option is not used, the program looks in the same place for a vpot file. If one is present, it can be used as a comparison for the fit. - If you specify both input files, they MUST be based on the same dvr and they SHOULD be based on the same PES parameters. If the latter condition is not met a warning is issued. In this case the user should have a look at the log file showpot.log where the potfit input files of the vpot and the natpot file are stored. - If you specify -v notice that showpot loads the complete vpot file into a single precision vector held in memory. Hence, if one is dealing with a huge product grid, the loading may take a while and showpot may consume quite a bit of memory. Actually its memory consumption is of the same order as potfit's memory consumption in the direct=1_sp mode.Cuts of a potential energy surface (PES) can be generated from a vpot and a natpot file. Both files are generated by the potfit program. The first one contains the exact potential on the complete product grid, the latter a corresponding fit.
After starting the program a menu is presented by the help of which one can select a cut via an interactive process. The menu offers the following choices:
To define a cut, one must attribute x to one coordinate, and one may attribute y to another coordinate (the latter choice generates a 2D plot). The remaining coordinates must be assigned numbers (coordinate values), but at most one of these coordinates may be assigned with the label min or max. If min or max is given, the program sets this coordinate such that the potential is minimal (maximal)with respect to variations of this particular coordinate. max is useful for the plottask abs(Vfit-Vpot).
Description of the logarithmic spacing if Gnuplot commands are included into the output file:
Purpose : Sums spectral components (output from autospec) Usage : sumspec83 [options] file1 fac1 file2 fac2 [file3 fac3 ...] Options : -i DIR : paths are relative to directory DIR -o FILE : write to file FILE. The default is: sumspec.pl -w : overwrite enabled. -g ncos : GNUplot command lines are written to the output file. ncos = 0,1,2 is the exponent of the cosine damping function. NB: This sets "using 1:(ncos+2)" -a : GNUplot is called automatically. (sets "-g 1"). -x xmin xmax : The energy range is set to [xmin,xmax]. (ignored if neither -g nor -a is set). -y ymin ymax : The ordinate scale is set to [ymin,ymax]. (ignored if neither -g nor -a is set). -s shift: Shift the energy scale by -shift (ignored if neither -g nor -a is set). -S shift: Shift the energy scale by -shift Similar to -s, but this time the output file is modified. -ver : Version information about the program -h : Print this help text. -? : Print this help text. Example: sumspec83 -a -G b2u/spectrum.pl 1.0 b2g/spectrum.pl 1.0 Following the options there follow the names of the files containing the spectral data. For all components a factor, giving the weight, has to follow the file-name. ------------------------------------------------------------------------------The spectral component files are assumed to be generated by the autospec program, but sumspec will add the columns 2,3, and 4 of any sets of files. Hence, one may use sumspec to add flux files. In this case use the option "-g 2" to plot the probabilities.
Purpose: calculate reaction probability with the Tannor-Weeks method (see e.g. JCP 110 (1999) 2761, Section IIB.) Usage: twprob83 [ -o -F -e -p -t -h -? ] emin emax unit file edstr1 edstr2 Options: -o FILE: filename for output -F x : multiply output with a factor x -e R U : shift energy scale in output by value R in units U -p I : number of energy points is I (default: 500) -t tcut: read crosscorrelation function only up to t=tcut -[h?] : print this help text "emin" and "emax" together with "unit" determine the energy range of the output. "file" contains the time-dependent overlap of the propagated WF with a reference WF (output of crosscorrver). "edstr[12]" are files that contain the energy distributions of the two WFs. This can be an adwkb file, or any other file, in which case the distribution is determined by columns 1 and 2 (useful for autospec/cspec/flux files). ------------------------------------------------------------------------
This utility calculates state-resolved reaction probabilities according to the formula
from the correlation function , where denotes the initial state of the propagated wavefunction, and denotes a reference wavefunction. and are the energy distributions of these two wavefunctions, respectively.
The reference wavefunction must be a direct product of a (narrow) Gaussian in the translational DOF and an internal state of the products. This internal state is chosen according to the channel you are interested in.
The energy distributions are best obtained from adwkb-files. However, for the propagated wavefunction it is also possible to calculate from the autocorrelation function (using crosspecver).
The usage of twprobver is usually as follows:
In practice, you will probably be interested in a lot of channels (note that with twprob there is no implicit summing like in flux), so you will want to write a script that generates the GENINWF input file, runs mctdh, crosscorr and twprob for each channel. It's advisable to make use of the readoper/readdvr options to speed up these calculations (the geninwf part of mctdh as well as crosscorr and twprob take virtually no time to complete).
The output file consists of two columns: energy E and probability P(E). E runs between the given EMIN and EMAX. Note that P(E) is set to zero for values of E that lie outside either of the two energy distributions.
Note: The distribution Δ(E) in the above formulas is called |Δ(E)|2 in section 8.6.3 of the MCTDH review.
Purpose: Finds the "num" lowest and largest points on a PES. Usage: vminmax83 [ -i -p -o -n -s -d -ham -u -w -ver -h -?] Options : -i DIR : DIR is taken as name-directory rather than ./ -p FILE : the PES is read from FILE rather than from ./pes The string FILE may be a relative or a full path-name. -o FILE : The ouput is written to file FILE rather than to name/vmm The string FILE may be a relative or a full path-name. If FILE=no, i.e. -o no, no output file will be written. -n num : Print num maximal and minimal values. The default is num = 100 . Maximum is 250. -s s : Print maximal and minimal values for adiabatic state s. (Def: s=1). -d s1 s2: Print maximal and minimal values for diabatic state (s1,s2). -ham nhm: Use the Hamiltonian nhm. Default is nhm=1 (system). -u UNIT : Use energy unit UNIT. (Default: eV). -w : Overwrite the output-file vmm. -ver : Version information about the program -h : Print this help text. -? : Print this help text. For a multi-state PES file the lowest adiabatic surface is analysed by default. To analyse diabatic diagonal or off-diagonal surfaces use the option -d. ------------------------------------------------------------------------------This program is very useful for checking if the potential of the implemented operator assumes unexpectedly large positive or negative values. The pes-file is most conveniently generated by using the MCTDH option -pes.
Purpose : Computation of the XFROG trace of a 1-dim function, using a rectrangular gate function with Gaussian shoulders. Usage : xfrog [-o -n -rf -rt -fd -td -g -ver -h -?] infile Options : -o FILE : The output is written to file FILE rather than to infile.xfg The string FILE can be a relative or a full path-name. -n nfield : Number of points to be read from infile (default: all) -rf nres : Sampling of outpot in frequency domain (default: nfield+1) -rt nres : Sampling of outpot in time domain (default: nfield) -fd min max : Frequency range of the outtput (default: 0 to nfield/T) -td min max : Time range of the outtput (default: 0 to T) -g w1 w2 : Width of the gatefunction in time domain (default: w1=w2=1): w1 width of rectangular part, w2 width of Gaussian shoulders. -ver : Version info of this program. -h, -? : Print this help text. The argument infile is the file containing the electric field. The gate function is rectangular pulse of unity height and width w1 with Gaussian shoulders of the form exp(-t**2/(2*w2**2)) The user will be prompted for missing arguments. All input is in au. ------------------------------------------------------------------------------
There are a number of shell scripts located on $MCTDH_DIR/bin, which enable a convenient plotting of some results of an MCTDH calculation. In general, these scripts call one of the above analyse routines, write the output to a temporary file and plot it using GNUPLOT. (A GNUPLOT of version 3.7 or higher should be used). The default version of the called analyse routines is ver=83. This may be changed by setting the environment variable $MCTDH_VERSION or by using the option -v. The name directory mustbe the current directory when executing the pl-scripts. The pl-scripts allow for options and some scripts need arguments. A help text is always generated by executing plxxx -h .
The different scripts support different options. If appropriate, however, the scripts commonly support the following options:
-h : print a help text. -a val : set lower range of x to val. -x val : set upper range of x to val. -y val : set upper range of y to val. -z val : set lower range of y to val. -G : draw grid lines. -l : use logarithmic scale for y. -s : suppress messages of the called analyse program. -v val : set the version number of the analyse program to be called to val.
-p : prompt for printing the plot at default printer lpr. -P printer : specify alternative printer (e.g. -P "| lpr -Pps2"), or print to a file (e.g. -P plot.ps).
compile : See Installation and Compilation
cdm : A very convenient cd for the MCTDH directory. E.g
cdm linear will cd to $MCTDH_DIR/source/lib/linear. The
destination directory may be abbreviated, as long as the
abbreviation is unique. I.e. cdm lin is sufficient. The
source dirs come before all others. I.e. cdm m cd-es to
source/mctdh. To cd to doc/mctdh one types cdm doc/m. The
cdm script is part of .mctdhrc and is available only, when
working under bash.
elk_test : See Automatic Program Test
elk_test_gen : See Automatic Program Test
ddiff : compares files of current directory with those
of another directory. (not recursive).
mkGpatch : makes a GNU-patch. See Applying
Patches
mkMpatch : makes a M-patch. See Applying
Patches
mdistribute : Copies the files collected by
mkMpatch or mfind to the MCTDH directory.
mdircp : Copies a MCTDH directory to a new location,
excluding all those files which are not on the original package
before installation (e.g. object, binary, *~, and *.dvi files).
mdircp can also create tar files and may send them
to a remote host.
mfind : Finds all files of the MCTDH directory that are
newer than a specified date (default 1 day).
mcb : MCTDH Code Browser
mcg : MCTDH Code Grep
mcl : MCTDH Code List
menv : MCTDH Environment
mhelp : MCTDH short help for input
minstall : Sets environment variables and makes another
MCTDH directory active. This script is part of .mctdhrc and is
available only, when working under bash. Typing "
minstall path-of-second-MCTDH-directory " makes
the second-MCTDH-directory active.
mbackup : A simple but convenient backup script for
MCTDH developers. This backup system uses mdircp and
mdiff as well. The command lb lists the backup
directory. See MCTDH
Backup
mdiff : Compares two MCTDH directories and lists files
which differ. It can show the differences using diff or
mgdiff.
mklinks : Creates links from
$MCTDH_DIR/source/surfaces/ to addsurf
phelp : Programmers help. Gives a description of MCTDH
variables.
vddiff : Version doc diff. Compares the
documentation of two MCTDH directories.
vrdiff : Version rest diff. Compares the 'rest'
of two MCTDH directories.
vsdiff : Version source diff. Compares the source
of two MCTDH directories.