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triat_u3
User's Guide
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triat_u3
User's Guide
triat_u3
?
The Fortran
and Perl
programs in the
triat_u3
suite perform calculations using the two-dimensional
limit of the Vibron Model. This approach is used to model the bending dynamics
of linear, quasilinear and bent molecules, using a model based on a bosonic
U(3) Lie algebra. This suite includes several programs, in particular it
includes a program to fit a fourteen parameter Hamiltonian to experimental
bending energy data. This Hamiltonian is the most general one-, two-, three-,
and four-body Hamiltonian operator in the model. The package, includes the
optimization program tri_min_T
, as well as other utilities to work
with the two-dimensional limit of the vibron model.
Copyright (2007-) Francisco Perez-Bernal
All Rights Reserved
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
The full text of the GPL is given in
/usr/share/common-licenses/GPL
or in the FSF website GPL license definition
.
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triat_u3
User's Guide
The program files can be found as a tgz file
(triat_U3_2.X.tgz
, where X stands for the
version number). The first step is to unpack the file:
$ tar xzf triat_U3_2.2.1.tgz $ ls triat_U3_2.2.1 triat_U3_2.2.1.tgz $ cd triat_U3_2.2.1/ triat_U3_2.2.1$ ls bin/ doc/ examples/ NEWS README src/
The directory structure is the following
bin: Executable files.
src: Fortran
source files and compilation
Makefile
.
doc: Program documentation (this file) in several formats.
examples: Different directories with examples of application of the programs.
XCNO: Program tri_min_T
, application to fitting the
large amplitude bending mode of fulminic acid.
HCP_A: Program tri_min_T
, application to fitting the
bending mode of the A excited electronic state of methinophosphide.
Eigenvalues: Program en_U3_gen_T
, input files and
examples of eigenvalues calculation.
Eigenstates: Program avec_U3_gen_T
, input files and
examples of eigenvalues and eigenstates calculation.
Observables: Input files and examples of calculations for several observables of interest.
The present section details the programs compilation procedure. There is also
a version of the program compiled statically in the bin directory
(files ending with the suffix stat
). If you run into trouble
during any program compilation you can move forward to Getting Started, Chapter 3 using the provided static
version of the programs.
The program compilation in Debian
systems should be quite smooth
if the libraries BLAS
and LAPACK
are installed.
These libraries are FORTRAN
libraries for numerical linear algebra
and can be found in most Linux Distributions. In the Debian (Lenny or
Squeeze)
distribution they are associated with packages
libblas-dev
and liblapack-dev
or other
(atlas
library). IMHO, the best option is to install the
atlas
package. More information about BLAS
and
LAPACK
can be found in the Netlib
website. <-- Compiled with
minuit subroutine
The third library (only needed for the minimization program) is part of the
CERN scientific routines, providing the Minuit
minimization tool
(See References, Chapter 4). This library in
Debian
can be installed with the packages
libpacklib1-dev
and libkernlib1-dev
, though it is
safer to install the cernlib-base-dev
package. -->
Once the libraries are installed the compilation is quite direct.
triat_U3_2.2.1$ cd src triat_U3_2.2.1/src$ ls assign_gen.f enrgy_modelH_U3_tri.o minuit-cern.f avalavec_gen_U3.f fcn_sub_gen.f minuit_u3.f avalavec_modelH_U3.f hbldu3_gen.f readenerg_gfort.f change_basis.f hbldu3_modelH.f scaleh_gen.f check_phase.f hbldu3_modelH_tri.f selectvl.f chisqre_u3_min_gen.f hbldu3_modelH_tri.o so3casimirW2.f cpexp.f intrac.f90 so3casimirW2WB2.f disdata.f ir_intensity.f90 so3casimirW4.f enrgy_gen_U3.f Makefile enrgy_modelH_U3_tri.f maxc.f
As can be seen in the directory Makefile
, if the compilation is
successful, the executable files are located under the
triat_U3_2.2.1/bin
directory.
List of executable files:
tri_min_T
: Optimization code. Look for the best fit to a set of
experimental data.
en_U3_gen_T
: Compute general Hamiltonian eigenvalues given a set
of parameters.
avec_U3_gen_T
: Compute general Hamiltonian eigenvalues and
eigenstates given a set of parameters.
en_U3_mh
: Compute simplified model Hamiltonian eigenvalues given a
set of parameters.
avec_U3_mh
: Compute simplified model Hamiltonian eigenvalues and
eigenstates given a set of parameters.
minuit_U3_genH
: Perl script to launch the minimization program.
Help on this script can be obtained executing minuit_U3_genH -h.
expected_val_n
: Perl script to compute the expectation value of
the number of tau boson. Help on this script can be obtained executing
expected_val_n -h.
intensity_IR
: Perl script to compute the squared expectation value
of the infrared transition operator. Help on this script can be obtained
executing intensity_IR -h.
There are also sections in the Makefile
(named
triat_min_Tstat, energenh_Tstat, and
avecgenh_Tstat, etc.), not included in the all label,
used to compile a static version of the programs. In case you want compile the
program statically, type, for example, make triat_min_Tstat.
Please, notice that in this case it is convenient to make a backup of the
provided statically linked programs (tri_min_Tstat
and
en_U3_gen_Tstat
) because you will delete them. If you need to
compile all the static versions available then run make stats.
If the programs works correctly in your system you can also, running as
root user, install them, by default under the directory
/usr/local/bin
. The associated Perl scripts will also be
installed in this directory. The programs are installed in this directory with
a suffix indicating the version installed and symbolic links to the original
name are also built. It is very convenient to add to the default
$PATH variable the /usr/local/bin
in case it is not
yet in it. This greatly facilitates the minimization program's execution
instructions explained in Program Execution, Section
3.1.1.4 and Examples, Section 3.1.2, because in
this case the explicit paths provided are not necessary. In order to install
it you should do it as superuser or using sudo
triat_U3_2.2.1/src$ sudo make install [sudo] password for sudouser: triat_U3_2.2.1/src$ ls /usr/local/bin/ ... avec_U3_gen_T avec_U3_gen_T_2.2.1 avec_U3_gen_Tstat avec_U3_gen_Tstat_2.2.1 avec_U3_mh avec_U3_mh_2.2.1 ...
If you want to remove these files you can also do it executing sudo make uninstall.
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triat_u3
User's Guide
tri_min_T
Given a set of experimental bending energies and assignments, the program
tri_min_T
and the Perl
launcher
minuit_U3_genH
optimize the Hamiltonian parameters to reproduce
the experimental information. The optimization is carried out using the
minuit-CERN
code (See References, Chapter
4).
Under the directory triat_U3_2.2.1/examples
two examples of use of
this program can be found, one for a linear molecule (fulminic acid fifth
normal vibrational degree of freedom) and one for a bent molecule (magnesium
hydroxide). We explain in detail the first case and chiefly highlight the
differences that arise in the second case.
We proceed now to explain the different input files and the way the provided programs are executed. There are three necessary input files. A file with the experimental energy files to be fit, a second file with general information for the program and a third file with the information on the Hamiltonian parameters needed by minuit to accomplish the minimization.
The experimental energies have to be included in a file. This file starts with a first line which is an integer equals to the number of available experimental levels. Thereafter the experimental information is given, using the following format:
energy error n_quanta l_value
The fields n_quanta and l_value indicate the number of quanta of vibration and the vibrational angular momentum that characterize the state. The number of quanta could correspond to the labeling for linear or bent molecules, as indicated later in the input file.
If the experimental error is fixed to zero, then the level in question is included in the display and compared to the calculated values but the result of this comparison is not included in the calculation of the chi-square and standard deviation, thus making no effect in the fitting procedure.
The general information not referring to Hamiltonian parameters is given in an
input file with a NAMELIST structure. It provides the information
needed to run the program apart from the information directly given to
Minuit
for the optimization.
We proceed to check the meaning of the variables are defined in this general input file. A template of it is as follows:
# ## GENERAL INPUT # &INP0 BENT=.F., DTFL='expdata.dat' / &INP1 N2=140, LMAX=5, VMAX=5, EMINL=.F. / # &INP2 IPRINT=0 /
Variables defined:
BENT: logical type. If .T.(.F.) the molecule is bent(linear) and experimental data are given accordingly.
DTFL: character type. Name of the file with experimental data.
N2: integer type. N value for the totally symmetric U(3) representation. As version 2.1 the maximum possible N value is 4000.
LMAX: integer type. Maximum value of the vibrational angular momentum (SO(2) quantum number) considered.
VMAX: integer type. Highest experimental overtone included in the fit.
EMINL: logical type. If this variable is .T. the spectrum energies are referred to the first eigenvalue for each vibrational angular momentum block. The default behavior is for EMINL=.F., that implies that all the eigenvalues are referred to the energy of the ground state for vibrational angular momentum zero.
IPRINT: integer type. Program output verbosity. Mainly for debugging purposes. Possible values in the interval 0-5.
The information provided to Minuit
for the algebraic spectroscopic
parameter optimization is given in a file. The structure of this file is a
three column list including the parameter labels, its initial values and
initial minimization steps for the fourteen possible Hamiltonian parameters.
This is followed by a statement using the Minuit
command
fix to indicate what parameter should be kept constant at the
initial value. The file ends with the Minuit
commands for the
optimization. More information can be found in the Fortran Minuit
Manual
and in the Minuit
homepage (See References, Chapter 4).
SET TITLE 'MINUIT MINIMIZATION. BENDING DYNAMICS' PARAMETERS 1 'P11 ' 6.129D+02 0.1D-02 2 'P21 ' 9.9D+00 0.1D-02 3 'P22 ' 0.30D+00 0.1D-02 4 'P23 ' -1.03D+00 0.1D-02 5 'P31 ' 0.0D+00 0.0D+00 6 'P32 ' 0.0D+00 0.0D+00 7 'P33 ' 0.0D+00 0.0D+00 8 'P41 ' 0.0D+00 0.0D+00 9 'P42 ' 0.0D+00 0.0D+00 10 'P43 ' 0.0D+00 0.0D+00 11 'P44 ' 0.0D+00 0.0D+00 12 'P45 ' 0.0D+00 0.0D+00 13 'P46 ' 0.0D+00 0.0D+00 14 'P47 ' 0.0D+00 0.0D+00 fix 5 7 8 9 10 11 12 13 14 #set err 1.0D-05 minimize 3000 call 3 exit
The parameters have labels Pnm, where n =
1,2,3,4 indicates that the operator is n-th body, and m
is an index to distinguish between the different operators of the same order.
From the Hamiltonian building subroutine hbldu3_gen.f
:
H = P11 n + P21 n^2 + P22 l^2 + P23 W^2 + P31 n^3 + P32 n·l^2 + P33 (n·W^2 + W^2·n) + P41 n^4 + P42 n^2·l^2 + P43 l^4 + P44 l^2·W^2 + P45 (n^2·W^2 + W^2·n^2) + P46 W^4 + P47 (W^2·Wbar^2 + Wbar^2·W^2)/2
where n is the U(2) number operator, l is the vibrational angular momentum, W^2 is the second order Casimir operator associated so SO(3), and Wbar^2 is the Casimir operator of the SObar(3) subalgebra.
The Perl
script minuit_U3_genH
, under the directory
triat_U3_2.2.1/bin
, is provided as a convenient interface to
launch the Fortran
optimization program. It creates a temporary
directory where the program runs and, in this way, several instances of the
program can be executed simultaneously.
In the following
If the script is executed with no argument it displays a brief help message.
triat_U3_2.2.1/examples/XCNO$ ../../bin/minuit_U3_genH Usage: minuit_U3_genH [-vtS] minpar_file input_file output_file minuit_U3_genH [-vt] [-e prgfile] minpar_file input_file output_file Options: t : do not remove temporary directory e : minimization program S : execute the statically linked program v : verbose output
The important options are -e and -t. The first one
implies that the user will provide the name (and path) of the executable
program file to be launched, while the second option indicates -mainly for
debugging purposes- that the temporary directory tmpdir_XXXX
is
not going to be removed once the program execution finishes. The
option,-s, implies the use of the statically linked program
tri_min_Tstat
. Finally, the option -v forces a
verbose output. If the option -e is absent, the script tries to
locate the program and execute it.
The script is invoked with three arguments. The first, minpar_file
is the file with the parameter input for Minuit
(see Minuit Parameter Input File, Section 3.1.1.3). The
second argument, input_file, is the general input (see General Input File, Section 3.1.1.2). The last
argument is output_file, the name of the file with the program
output. See Examples, Section 3.1.2 to check the
application of the program to two cases, one corresponding to a linear molecule
and the other to a bent molecule.
The files necessary to run this example are located under the directory
examples/XCNO
triat_U3_2.1$ cd examples/XCNO/ triat_U3_2.1/examples/XCNO$ ls exp_FulminicD_Feb03.dat minuit_genpar_FulminicD exp_FulminicH_Feb03.dat minuit_genpar_FulminicH input_U3_minuit_FulminicD output_FulminicD.orig input_U3_minuit_FulminicH output_FulminicH.orig
The files exp_FulminicH_Feb03.dat
and
exp_FulminicD_Feb03.dat
contain the available experimental
information for the large amplitude bending vibration of fulminic acid and its
deuterated isotopologue, and they conform to the standard described in Experimental Energy File, Section 3.1.1.1. The
general input file (see General Input File, Section
3.1.1.2) in this case is called input_U3_minuit_FulminicH
(and
input_U3_minuit_FulminicD
in the deuterated molecule case).
The information for the algebraic spectroscopic parameter optimization is provided in files minuit_par_FulminicH and minuit_par_FulminicD for HCNO and DCNO, respectively.
The program is executed invoking the Perl
script with the already
mentioned three arguments.
The verbose execution of the program for the fulminic acid case for both species is launched with the following commands:
triat_U3_2.2.1/examples/XCNO$ ../../bin/minuit_U3_genH -v \ > -e ~/triat_U3_2.2.1/bin/tri_min_T \ > minuit_genpar_FulminicD input_U3_minuit_FulminicD output_FulminicD Minuit CHISQRE minimization. U(3) General Hamiltonian. Executable program: ~/triat_U3_2.2.1/bin/tri_min_T Making temporary directory ... Done. Experimental energy file name is: exp_FulminicD_Feb03.dat Copying files to temporary directory ... Done. Running optimization program ... Done. Copying output file from temporary directory ... Done. Removing temporary directory ... Done. triat_U3_2.2.1/examples/XCNO$ triat_U3_2.2.1/examples/XCNO$ ../../bin/minuit_U3_genH -vS minuit_genpar_FulminicD \ > input_U3_minuit_FulminicH output_FulminicH Minuit CHISQRE minimization. U(3) General Hamiltonian. Executable program: ../../bin/tri_min_Tstat Making temporary directory ... Done. Experimental energy file name is: exp_FulminicH_Feb03.dat Copying files to temporary directory ... Done. Running optimization program ... Done. Copying output file from temporary directory ... Done. Removing temporary directory ... Done.
In the HCNO case the static version of the program is employed. The final part
of the output in these two cases, once convergence is reached, is included in
files output_Fulminic_HCNO.orig
and
output_Fulminic_DCNO.orig
.
Notice that the quality of the fit is given in terms of the standard deviation and not the rms. To compute the rms of the fit it is necessary to multiply the standard deviation by the square root of the total number of experimental data and divide it between the square root of the total number of experimental data minus the number of free parameters.
The files necessary to run this example are located under the directory
HCP_A
.
triat_U3_2.2.1$ cd examples/HCP_A/ triat_U3_2.2.1/examples/HCP_A$ ls exp_HCP_A_bending.dat minuit_genpar_HCP_A input_U3_minuit_HCP_A output_HCP_A_orig
The program is executed in the same way than in the linear case
triat_U3_2.2.1/examples/HCP_A$ ../../bin/minuit_U3_genH -v minuit_genpar_HCP_A \ > input_U3_minuit_HCP_A output_HCP_A Minuit CHISQRE minimization. U(3) General Hamiltonian. Executable program: ../../../bin/tri_min_T Making temporary directory ... Done. Experimental energy file name is: exp_HCP_A_bending.dat Copying files to temporary directory ... Done. Running optimization program ... Done. Copying output file from temporary directory ... Done. Removing temporary directory ... Done.
Last part of the output is saved on file output_HCP_A_orig
in
order that the use can compare the results.
There are three possible codes for the calculation of the Hamiltonian
eigenvalues. The first one, en_U3_gen_T
is valid for the general,
fourteen-parameter, Hamiltonian, while the other two, en_U3_mh
and
en_U3_mh_trid
, are valid for a simplified model Hamiltonian, with
only two parameters: the pairing and the number operator.
en_U3_gen_T
Under the directory triat_U3_2.2.1/examples/Eigenvalues
one
example of use of this program can be found.
The input file for this program is rather simple. An example input file with
all parameters equal to zero called input_file
is provided. A
possible input file is
10 # N INPUT FILE 0 # l 2 # iopts 0.0d0 # P11 0.0d0 # P21 0.0d0 # P22 -10.0d0 # P23 0.0d0 # P31 0.0d0 # P32 0.0d0 # P33 0.0d0 # P41 0.0d0 # P42 0.0d0 # P43 0.0d0 # P44 0.0d0 # P45 0.0d0 # P46 0.0d0 # P47
The parameter N is the value of the totally symmetric U(3) representation used to model the system. As version 2.1 the maximum possible N value is 6000. The vibrational angular momentum is given by the l value.
The parameter iopts controls the output of the eigenvalues. Possible values are
iopts = 0 the program displays only the ground state energy.
iopts = 1 the program displays all energies.
iopts = 2 the program displays all excitation energies (with g.s. (l=0) energy = 0)
For debugging purposes, in the source file enrgy_gen_U3.f
there is
a variable fixed at zero, called IPRINT. Nonzero positive values
increase the level of verbosity of the program.
This Fortran
program is directly launched, providing the described
input file as the standard input. If we execute the program with the input
file input_file_doc
given as an example the result is
triat_U3_2.2.1/examples/Eigenvalues$ ../../bin/en_U3_gen_T < input_file_doc 0.0000000000000000 380.00000000000011 680.00000000000023 900.00000000000023 1040.0000000000002 1100.0000000000002
The files necessary to run this example are located under the directory
examples/Eigenvalues
triat_U3_2.2.1/examples/Eigenvalues$ ls input_file input_file_doc input_file_HCP
The obtention of the eigenvalues that correspond to the parameters obtained in the fit to the HCP A state are, for zero vibrational angular momentum
triat_U3_2.2.1/examples/Eigenvalues$ ../../bin/en_U3_gen_T < input_file_HCP 0.0000000000000000 566.85562373229914 1028.5555120308779 1484.2632344381639 2046.9932672140753 2689.7360152596357 3382.0393187789541 4103.8525588498451 4838.4084093582642 5569.7433116564898 6281.1719539978449 6953.5491948507433 7562.3703503418556 8078.6701738697175 8529.0156142688957
en_U3_mh
Under the directory triat_U3_2.2.1/examples/Eigenvalues
one
example of use of this program can be found. The LAPACK
subroutine used for diagonalization is DSYEV.
The input file for this program is rather simple. An example input file with
all parameters equal to zero is provided (file input_file_mh
). A
possible input file is
10 # N INPUT FILE 0 # l 2 # iopts 1.0d0 # scale 0.5d0 # xi
The parameter N is the value of the totally symmetric U(3) representation used to model the system. As version 2.2.1 the maximum possible N value is 6000. The vibrational angular momentum is given by the l value.
The parameter iopts controls the output of the eigenvalues. Possible values are
iopts = 0 the program displays only the ground state energy.
iopts = 1 the program displays all energies.
iopts = 2 the program displays all excitation energies (with g.s. (l=0) energy = 0)
For debugging purposes, in the source file enrgy_modelH_U3_tri.f
there is a variable fixed at zero, called IPRINT. Nonzero
positive values increase the program verbosity.
The recommended way of computing eigenvalues is making use of the
Perl
script alg_U3_energy
described below in Model and General Hamiltonian Eigenvalues, Section
3.4.3. This Fortran
program can also be directly launched,
providing the described input file as the standard input. If we execute the
program with the provided input file input_file_mh_doc
, located in
the directory examples/Eigenvalues
, the result is
triat_U3_2.2.1/examples/Eigenvalues$ ../../bin/en_U3_mh < input_file_mh_doc 0.0000000000000000 2.0025471824580259 3.4348964743602903 4.7423306229038324 6.5330201878030874 8.7380263091129393
en_U3_mh_trid
Under the directory triat_U3_2.2.1/examples/Eigenvalues
one
example of use of this program can be found.
As in the previous case, the input file for this program is quite simple. An
example input file with all parameters equal to zero is provided (file
input_file_mh
). A possible input file is
10 # N INPUT FILE 0 # l 2 # iopts 1.0d0 # scale 0.5d0 # xi
Again, the parameter N is the value of the totally symmetric U(3)
representation used to model the system. The present program uses for the
matrix diagonalization a LAPACK
subroutine that takes advantage of
the fact that the matrix is tridiagonal and symmetric (subroutine
DSTEVX). The computing time is larger compared to the
en_U3_mh
program, but it is more stable numerically and it permits
to reach larger N values. It also allows for the calculation of a limited
subset of eigenvalues. As version 2.2.1 the maximum possible N
value in this case is 40000. The vibrational angular momentum is given by the
l value.
The parameter iopts controls the output of the eigenvalues. Possible values are
iopts = 0 the program displays only the ground state energy.
iopts = 1 the program displays all energies.
iopts = 2 the program displays all excitation energies (with g.s. (l=0) energy = 0)
iopts > 2 the program calculates and displays the first iopts excitation energies (with g.s. (l=0) energy = 0)
For debugging purposes, in the source file enrgy_modelH_U3_tri.f
there is a variable fixed at zero, called IPRINT. Nonzero
positive values increase the program verbosity.
This Fortran
program can be directly launched, providing the
described input file as the standard input. It is recommended to use the
Perl
script alg_U3_energy
, decribed in Model and General Hamiltonian Eigenvalues, Section
3.4.3, to compute system eigenvalues. If we execute the program with the
provided input file input_file_mh_doc
, located in the directory
examples/Eigenvalues
, the result is
triat_U3_2.2.1/examples/Eigenvalues$ ../../bin/en_U3_mh_trid < input_file_mh_doc 0.0000000000000000 2.0025471824580254 3.4348964743602899 4.7423306229038316 6.5330201878030865 8.7380263091129429
avec_U3_gen_T
Under the directory triat_U3_2.2.1/examples/Eigenstates
examples
of use of this program can be found.
The input file for this program is the same that for the previous program
en_U3_gen_T
. An example input file with all parameters equal to
zero is provided
10 # N INPUT FILE 0 # l 2 # iopts 0.0d0 # P11 0.0d0 # P21 0.0d0 # P22 0.0d0 # P23 0.0d0 # P31 0.0d0 # P32 0.0d0 # P33 0.0d0 # P41 0.0d0 # P42 0.0d0 # P43 0.0d0 # P44 0.0d0 # P45 0.0d0 # P46 0.0d0 # P47
See parameter explanation in Eigenvalue calculation code
en_U3_gen_T
, Section 3.2.1.
In the source file avalavec_gen_U3.f
a variable named
TOL, whose default value is TOL = 1.0D-05 that makes
equal to zero the square of the components whose absolute value is less than
TOL.
For debugging purposes, in the source file avec_gen_U3.f
there is
a variable fixed at zero, called IPRINT. Nonzero positive values
increase the level of verbosity of the program.
This Fortran
program is directly launched, providing the described
input file as the standard input. Each energy is followed by the corresponding
eigenstate expressed in the U(2) and SO(3) basis. The first column is the
component, and the second the component squared, followed by the basis state
quantum labels. If we execute the program with the input file found above the
result is
triat_U3_2.2.1/examples/Eigenstates$ ../../bin/avec_U3_gen_T \ > < input_file_doc N = 10 , l = 0 , DIM = 6 Energy = 0.0000 Component U(2) | n , l > Component SO(3) | v , K > 0.36932E-01 0.13640E-02 | 10 , 0 > 0.53532E-17 0.0000 | 5 , 0 > -0.26115 0.68198E-01 | 8 , 0 > 0.84737E-17 0.0000 | 4 , 0 > 0.60309 0.36372 | 6 , 0 > 0.76209E-16 0.0000 | 3 , 0 > -0.66066 0.43647 | 4 , 0 > 0.75201E-16 0.0000 | 2 , 0 > 0.35314 0.12471 | 2 , 0 > -0.65821E-15 0.0000 | 1 , 0 > -0.74448E-01 0.55424E-02 | 0 , 0 > -1.0000 1.0000 | 0 , 0 > Energy = 380.00 Component U(2) | n , l > Component SO(3) | v , K > 0.11964 0.14313E-01 | 10 , 0 > 0.30352E-15 0.0000 | 5 , 0 > -0.52450 0.27510 | 8 , 0 > -0.10342E-15 0.0000 | 4 , 0 > 0.46888 0.21985 | 6 , 0 > -0.13730E-15 0.0000 | 3 , 0 > 0.29962 0.89772E-01 | 4 , 0 > -0.25502E-15 0.0000 | 2 , 0 > -0.59486 0.35385 | 2 , 0 > -1.0000 1.0000 | 1 , 0 > 0.21705 0.47111E-01 | 0 , 0 > 0.32605E-15 0.0000 | 0 , 0 > ................................................................. Energy = 1100.0 Component U(2) | n , l > Component SO(3) | v , K > 0.60779 0.36941 | 10 , 0 > -1.0000 1.0000 | 5 , 0 > 0.42977 0.18470 | 8 , 0 > -0.12420E-15 0.0000 | 4 , 0 > 0.37219 0.13853 | 6 , 0 > 0.15755E-15 0.0000 | 3 , 0 > 0.33976 0.11544 | 4 , 0 > 0.35379E-16 0.0000 | 2 , 0 > 0.31782 0.10101 | 2 , 0 > 0.32559E-15 0.0000 | 1 , 0 > 0.30151 0.90909E-01 | 0 , 0 > 0.55052E-16 0.0000 | 0 , 0 > triat_U3_2.2.1/examples/Eigenstates$
The files necessary to run this example are located under the directory
examples/Eigenstates
triat_U3_2.2.1/examples/Eigenstates$ ls avec_HCP_A.dat input_file_doc input_file_HCP
The obtention of the eigenvalues and eigenstates that correspond to the
parameters obtained in the fit to the HCP A state are, for zero vibrational
angular momentum, included in the file avec_HCP_A.dat
. You can
reproduce this calculation as follows
triat_U3_2.2.1/examples/Eigenstates$ ../../bin/avec_U3_gen_T \ > < input_file_HCP > avec_HCP_A_new.dat
We now proceed to describe a set of Perl
scripts provided to
facilitate the calculation of different observables of interest. The sample
and input files provided for these scripts are located in the directory
triat_U3_2.2.1/examples/Observables
.
The Perl
script expected_val_n
computes the
expectation value of the tau boson number operator with different options. A
basic help can be obtained running the script with the -h option.
triat_U3_2.2.1/examples/Observables$ ../../bin/expected_val_n -h Perl script to calculate the normalized expected value of the U(2) Casimir n for a given eigenstate u (g.s. -> u = 1) and a xi value interval, for all the eigenstates given a xi value, or for the eigenstates of a general Hamiltonian. The expected value is normalized by the number of bosons N (<n>/N). by Currix TM Usage: expected_val_n [-vhS] [-e progpath] -N Nval lval scale xi expected_val_n [-vhS] [-e progpath] -E Nval lval scale xi expected_val_n [-vhS] [-e progpath] Nval lval scale u ximin ximax xistep expected_val_n [-vhS] [-e progpath] [-n] -g inputfile Options: N : expected value of n as a function of v (0, 1, 2, ... ) for all states E : expected value of n as a function of energy normalized by N for all states S : execute statically linked Fortran program v : verbose output h : help message g : general Hamiltonian (supply name of the parameter file) n : normalize energies by N in the general Hamiltonian case or or v by N if -N e : provide the executable triat files
The script allows the user to compute the expected value of the number operator for all the eigenstates for a given control parameter xi value [1] For example, to compute the expected value of the number operator in the eigenstates of the zero angular momentum, N = 10, and xi = 0.4 Hamiltonian
triat_U3_2.2.1/examples/Observables$ ../../bin/expected_val_n -E \ 10 0 1.0 0.4 0.227411444586968 0.282433724484853 0.375148937971884 0.209292031824226 0.489249830006017 0.275091429272299 0.63853518398931 0.506402309333926 0.831820286396651 0.740247061857603 1.06005653927139 0.986533443227093
If the dependence with the number of quanta, instead of the energy, is required, the -E option is replaced by -N.
The expected value for a particular eigenstate and evaluated in an interval of control parameter values can also be computed[2]. For example, to compute the expected value of n for the ground state of the zero angular momentum, N = 10, and 0.2 < xi < 0.4 Hamiltonian with a step of 0.05 in the control parameter
triat_U3_2.2.1/examples/Observables$ ../../bin/expected_val_n \ 10 0 1.0 1 0.2 0.4 0.05 0.2 0.0395832133992901 0.25 0.094015233850396 0.3 0.168639783188264 0.35 0.233906937667085 0.4 0.282433724484853
Finally, the last option is to compute the expectation value for the
eigenstates of a given general Hamiltonian. To do so, a file with the
parameter values of the Hamiltonian has to be provided. In the examples
directory you can find the file input_file_HCP
, with the
Hamiltonian parameters of the HCP molecule. To compute the expectation value
of n for these eigenstates
triat_U3_2.2.1/examples/Observables$ ../../bin/expected_val_n \ -ng input_file_HCP 0 0.252375640144704 19.5468965517241 0.214629419159648 35.4689655172414 0.175676105843901 51.1827586206897 0.223634301458906 70.5862068965517 0.293699978181552 92.748275862069 0.354259363279492 116.620689655172 0.411790067302586 141.513793103448 0.468494422286793 166.841379310345 0.525142319743586 192.058620689655 0.582222581646207 216.593103448276 0.640168981577777 239.775862068966 0.699641599554915 260.772413793103 0.761652148046633 278.575862068966 0.817777007616914 294.103448275862 0.820195218254436
These results can be checked against the contents of the file
expected_n_HCP.out
.
The Perl
script intensity_IR
computes the squared
expectation value of the infrared transition operator with different options[3]. A basic help can be obtained running the script
with the -h option.
triat_U3_2.2.1/examples/Observables$ ../../bin/intensity_IR -h Perl script to calculate the infrared intensity for a dipole transition between eigenstates {l_1}_{u_1} and {l_2}_{u_2} of the U(3) model Hamiltonian in a given xi or N value interval or for a given xi value. Note that {l}_{u} stands for u-th eigenvector with l angular momentum (g.s. u=1). The computed matrix element is |<{l_2}_{u_2}|T_+|{l_1}_{u_1}>|^2 + |<{l_2}_{u_2}|T_-|{l_1}_{u_1}>|^2 with the selection rule |l_1-l_2| = 1. by Currix TM Usage: intensity_IR [-Sv] Nval l1 u1 l2 u2 scale xi intensity_IR [-Sv] -s Nval l1 u1 l2 u2 scale ximin ximax xistep intensity_IR [-Sv] -n Nmin Nmax Nstep l1 u1 l2 u2 scale xi intensity_IR [-h] Options: S : execute statically linked Fortran program v : verbose output h : help message s : consider a series of control parameter values n : consider a series of N values
The script allows the user to compute the squared expectation value of the transition operator for a given pair of eigenstates of the model Hamiltonian for a given control parameter xi value [4] For example, to compute the transition intensity between the ground state (zero angular momentum) and the first eigenstate with angular momentum equal to one, in the N = 10, and xi = 0.4 Hamiltonian we will execute
triat_U3_2.2.1/examples/Observables$ ../../bin/intensity_IR \ > 10 0 1 1 1 1.0 0.4 0.4 9.6007861982152359788
The expectation value for a particular pair of eigenstates and evaluated in an interval of control parameter values can also be computed using the option -s. For example, to compute the transition intensity between the ground state (zero angular momentum) and the second eigenstate with angular momentum l=1, with N = 10, and 0.2 < xi < 0.4 Hamiltonian with a step of 0.05 in the control parameter
triat_U3_2.2.1/examples/Observables$ ../../bin/intensity_IR \ > -s 10 0 1 1 2 1.0 0.2 0.5 0.05 0.2 1.03195951590279317806E-0002 0.25 4.88985645132075223243E-0002 0.3 0.10416957597335169859 0.35 0.11597972613072936657 0.4 9.46745961688594321492E-0002 0.45 6.89270459035718042020E-0002 0.5 4.81758165286241743362E-0002
Finally, the last option is to compute the expectation value for two eigenstates varying the system's size, for different N values, using the option -n. For example, to compute the transition intensity between the ground state (zero angular momentum) and the second eigenstate with angular momentum l=1 in the critical value of the control parameter (xi = 0.2) with N taking values between 10 and 110 with a step of 20 bosons
triat_U3_2.2.1/examples/Observables$ ../../bin/intensity_IR \ > -n 10 110 20 0 1 1 2 1.0 0.2 10 1.03195951590279317806E-0002 30 1.76649230478514733430E-0002 50 2.11485562246530897512E-0002 70 2.35353506851742359296E-0002 90 2.53900792349369549193E-0002 110 2.69266373464041480800E-0002
The Perl
script alg_U3_energy
computes the
Hamiltonian eigenvalues for the model and the general algebraic Hamiltonian.
[5]. A basic help can be obtained running the
script with the -h option.
triat_U3_2.2.1/examples/Observables$ ../../bin/alg_U3_energy -h Perl script to calculate the either the ground state energy or the full spectrum of a U(3) model or general Hamiltonian. In the model Hamiltonian case, the calculation can be limited to only a subset of the eigenvalues (first nstates), and a program taking advantage of the tridiagonal character of the matrix is provided (and default for N > 5000). The output can be adapted to the drawing of Birge-Sponer plots. by Currix TM Usage: alg_U3_energy [-STvbB] Nval lval scale xi alg_U3_energy [-STvbB] [-I nstates] Nval lval scale xi alg_U3_energy [-STvG] Nval lval scale xi alg_U3_energy [-SvbB] [-n] -g inputfile alg_U3_energy -h Options: b : Birge Sponer plot output. B : Birge Sponer plot output with energy dependence. v : verbose output. I : compute the energies for the first nstates (nstates > 2) T : use the program version with tridiagonal matrix diagonalization G : compute only the ground state energy g : general Hamiltonian (supply name of the parameter file). S : execute the statically linked program. n : normalize energies or quantum number by N in the general Hamiltonian case. h : help message.
For example, to compute the energy spectrum for the first three excited states with angular momentum l = 2, N = 1000, and scale and control parameter equal to 1.0 and 0.555, respectively.
triat_U3_2.2.1/examples/Observables$ ../../bin/alg_U3_energy -I 4 1000 2 1.0 0.555 0 200.08946405931044 1 202.26535936605771 2 204.43652907169133 3 206.60297075985744
To compute the ground state energy for N = 10000, l = 0, and scale and control parameter equal to 1.0 and 0.75, respectively.
triat_U3_2.2.1/examples/Observables$ ../../bin/alg_U3_energy -G 10000 0 1.0 0.75 0 1197.8541544435745
Finally, to compute the full energy spectrum for l = 2, N = 1000, and scale and control parameter equal to 1.0 and 0.555
triat_U3_2.2.1/examples/Observables$ ../../bin/alg_U3_energy -I 1 1000 2 1.0 0.555 0 200.08946405931044 1 202.26535936605774 2 204.43652907169133 3 206.60297075985744 4 208.76468198691873 5 210.92166028156083 .... 495 992.09574571198141 496 994.26349601727406 497 996.43459207588285 498 998.60902996360642 499 1000.7868057766277
When the general Hamiltonian spectrum is computed it is necessary to provide
the program with an input file, as the provided example input file
input_file_HCP
triat_U3_2.2.1/examples/Observables$ ../../bin/alg_U3_energy -g input_file_HCP 0 0.0000000000000000 1 566.85562373229914 2 1028.5555120308779 3 1484.2632344381639 4 2046.9932672140753 5 2689.7360152596357 6 3382.0393187789541 7 4103.8525588498442 8 4838.4084093582642 9 5569.7433116564898 10 6281.1719539978449 11 6953.5491948507442 12 7562.3703503418556 13 8078.6701738697193 14 8529.0156142688975
The Perl
script exc_energ_diag_U3_mh
computes the
excitation energies necessary to plot correlation energy diagrams for given
control parameter values with different options[6]. A basic help can be obtained running the script with the
-h option.
triat_U3_2.2.1/examples/Observables$ ../../bin/exc_energ_diag_U3_mh -h Perl script to calculate the u first eigenvalues (g.s. -> u = 1) of the algebraic U(3) model Hamiltonian in a given xi value interval. If u = 0 all anergies are included. The energy values are normalized by the number of bosons N (E/N). by Currix TM Usage: exc_energ_diag_U3_mh [-vhS] [-e progpath] Nval lval scale u ximin ximax xistep Options: S : execute statically linked Fortran program v : verbose output h : help message e : provide the executable triat files
For example, to compute the excitation energy for the first three excited states with zero angular momentum, with N = 10, and in the interval of xi starting at 0.1 and ending at 0.4 with a step of 0.05 we execute
triat_U3_2.2.1/examples/Observables$ ../../bin/exc_energ_diag_U3_mh \ 10 0 1.0 4 0.1 0.4 0.05 0.1 0.0969591084744126 0.24303900731891 0.410527294642692 0.595860630601058 0.15 0.141605046653722 0.261843236909951 0.416273614122525 0.596349388138778 0.2 0.180891112017846 0.279990992516115 0.423496605540945 0.599080754985964 0.25 0.210586829109494 0.300331396846074 0.433272340537003 0.604387056209837 0.3 0.226957621450917 0.325171141950419 0.446759291603703 0.612551514295007 0.35 0.2312738839248 0.351753480722973 0.465174292657181 0.623837735817851 0.4 0.227411444586968 0.375148937971884 0.489249830006017 0.63853518398931
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triat_u3
User's Guide
Minuit minimization
package
: Comput. Phys. Commun. 10 (1975) 343-367.
J. Chem. Phys. 104 (1996) 6956.
Chem. Phys. Lett. 365 (2002) 57-68.
Chem. Phys. Lett. 375 (2003) 309-320.
Phys. Rev. A77 (2008) 032115.
triat_u3
User's Guide
This makes reference to the model Hamiltonian H = scale[(1-xi) n + xi/(N-1) P].
This makes reference to the model Hamiltonian H = scale[(1-xi) n + xi/(N-1) P].
The transition operator is defined as T = D+/sqrt(N) + D-/sqrt(N).
This makes reference to the model Hamiltonian H = scale[(1-xi) n + xi/(N-1) P].
This makes reference to the model Hamiltonian H = scale[(1-xi) n + xi/(N-1) P].
This makes reference to the model Hamiltonian H = scale[(1-xi) n + xi/(N-1) P].
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triat_u3
User's Guide
francisco.perez@dfaie.uhu.es