From ab89567c7be59f4903db668943e34260143d9975 Mon Sep 17 00:00:00 2001 From: Trovemaster Date: Tue, 9 May 2017 18:09:52 +0100 Subject: [PATCH] wiki commit 1st wiki commit --- TROVE.wiki/36281301.html | 128 ++++++++ TROVE.wiki/55183997.html | 57 ++++ TROVE.wiki/55902415.html | 53 +++ TROVE.wiki/66759538.html | 58 ++++ TROVE.wiki/C20_55183971.html | 79 +++++ TROVE.wiki/Exo-cross_56495757.html | 55 ++++ TROVE.wiki/Import-ucapsyu_55902413.html | 55 ++++ TROVE.wiki/TROVE-Input-structure.asciidoc | 372 ++++++++++++++++++++++ TROVE.wiki/TROVE-pipeline.md | 14 + TROVE.wiki/TROVE.md | 1 + TROVE.wiki/TROVE_66759535.html | 55 ++++ 11 files changed, 927 insertions(+) create mode 100644 TROVE.wiki/36281301.html create mode 100644 TROVE.wiki/55183997.html create mode 100644 TROVE.wiki/55902415.html create mode 100644 TROVE.wiki/66759538.html create mode 100644 TROVE.wiki/C20_55183971.html create mode 100644 TROVE.wiki/Exo-cross_56495757.html create mode 100644 TROVE.wiki/Import-ucapsyu_55902413.html create mode 100644 TROVE.wiki/TROVE-Input-structure.asciidoc create mode 100644 TROVE.wiki/TROVE-pipeline.md create mode 100644 TROVE.wiki/TROVE.md create mode 100644 TROVE.wiki/TROVE_66759535.html diff --git a/TROVE.wiki/36281301.html b/TROVE.wiki/36281301.html new file mode 100644 index 0000000..80e2992 --- /dev/null +++ b/TROVE.wiki/36281301.html @@ -0,0 +1,128 @@ + + + + Sergey Yurchenko : Solving the rovibronic Schrödinger equation for the nuclear motion + + + + + +
+
+
+ +

+ + Sergey Yurchenko : Solving the rovibronic Schrödinger equation for the nuclear motion + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko, last modified on Oct 31, 2013 +
+
+

Duo is a general program for solving a coupled rovibronic problem for diatomics.

+ +

Within the Born-Oppenheimer approximation the spin-orbit (SO) free
+Hamiltonian of the diatomic problem in the absence of the hyperfine splitting
+ is given by 2:

+ +

where is the electronic part, is the rotational part and is the vibrational part.
+The rotational angular momentum is perpendicular to the internuclear axis. Considering Hund's case a and representing the rotational angular momentum as

+ +

in terms of the total , electronic , and spin angular momenta and choosing the body-fixed axis along the internuclear axis the rotational part is given by

+ +

where , and are the corresponding momentum ladder operators.

+ + +

The duo basis set functions are chosen as the product

+ +

where is the electronic function, is the rotational function, is the vibrational function; 'state' is the label identifying the electronic state; , , and are the axis projections of the electronic, spin and total angular momenta, respectively, and ; is the projection of the total angular momentum along the laboratory axis ; is the vibrational quantum number.

+ +

For the rotational basis set the rigid rotor functions are used, with the following matrix elements:

+ +

where is omitted for the simplicity.

+ +

The electronic basis functions appear in the solution only implicitly as matrix elements of different components of the operator as well as of the spin-orbit contributions. We choose these basis functions to satisfy the following conditions^2^:

+ +

where is a reflection through the molecular-fixed -plane (parity operator) and for states and for all other states. The following non-vanishing matrix elements of the spin operators are valid:

+ +

where the label 'states' is omitted for the simplicity.

+ +

For example, the non-vanishing and symmetrically unique matrix elements of the ladder angular momentum operators as well as of the SO-matrix elements on this basis functions for the three lowest states of AlO , and are obtained using MOLPRO and can be summarized as follows:

+ +

where is omitted for the simplicity.
+All other non-vanishing matrix elements can be obtained by applying the symmetric properties upon the reflection (see above).

+ +

It should be noted for the MOLPRO functions are not eigenfunctions of as required by the equation above. For example, the electronic state gives rise to two degenerate solutions labelled in MOLPRO as and . The corresponding matrix representation of the operator is not diagonal as computed by MOLPRO with the matrix elements is usually given by

+ +

Besides the matrix elements of and as well as the spin-orbit matrix elements are complex numbers in the MOLPRO representation.
+The transformation from and (MOLPRO) to our representation (duo) is then given by

+ +

In this representation the matrix representations of all couplings are real including that of which is diagonal.
+For example, the and operators couple the and states of AlO via the following matrix elements in the MOLPRO representation:

+ +

where is a real number.

+ +

For we obtain

+ +

Similarly, for the diagonal SO component coupling two components of the of AlO state, MOLPRO gives the following non-vanishing matrix elements:

+ +

where is a real number. These couplings in the duo representation become real:

+ +

The (non-vanishing) non-diagonal SO-matrix elements in the MOLPRO representation

+ +

( is a real number) in our representations (only non-vanishing and symmetrically unique) read

+ +

The same relations can be obtained for the $B-A$ pair.

+ +

The term of the Hamiltonian matrix depends only on the internuclear distance and thus can be included into the functional forms of the potential energy functions (diagonal and ) or of the SO coupling terms (non-diagonal ) and thus can be excluded from our analysis.

+ +

The vibrational basis functions are prepared as solutions of the pure vibrational uncoupled eigen-problems for a given adiabatic electronic 'state'

+ +

using the DVR method in the equidistant grid representation. Here is the corresponding potential energy function. For each electronic state once elects vmax lowest eigenfunctions as contracted basis functions for the rovibronic problem.
+The vibrational matrix elements for all -dependent terms appearing in the rovibronic Hamiltonian are evaluated numerically using the Simpson rule.

+ +

Finally, the spin-rovibronic functions are symmetrized to be eigenfunctions of the parity operator .
+A Hamiltonian matrix is generated and then diagonalized using the LAPACK routines DSYEV or DSYEVR as provided by the intel MKL libraries.

+ + + +

1 R. J. Le Roy, LEVEL 8.0 A Computer Program for Solving the Radial Schrodinger Equation
+for Bound and Quasibound Levels, University of Waterloo Chemical Physics Research Report
+CP-663, http://leroy.uwaterloo.ca/programs/ (2007).
+2 H. Kato, Bull. Chem. Soc. Japan 66, 3203 (1993).

+
+ + + +
+ +
+ diff --git a/TROVE.wiki/55183997.html b/TROVE.wiki/55183997.html new file mode 100644 index 0000000..8af5ea3 --- /dev/null +++ b/TROVE.wiki/55183997.html @@ -0,0 +1,57 @@ + + + + Sergey Yurchenko : Duo+add-ons + + + + + +
+
+
+ +

+ + Sergey Yurchenko : Duo+add-ons + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on May 18, 2015 +
+
+

Duo add-ons

+

Intensity
+Fitting

+
+ + + +
+ +
+ diff --git a/TROVE.wiki/55902415.html b/TROVE.wiki/55902415.html new file mode 100644 index 0000000..8a45461 --- /dev/null +++ b/TROVE.wiki/55902415.html @@ -0,0 +1,53 @@ + + + + Sergey Yurchenko : Sergey Yurchenko’s Home + + + + + +
+
+
+ +

+ Home Page + + Sergey Yurchenko : Sergey Yurchenko’s Home + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko, last modified on May 09, 2017 +
+
+

This is the home page for Sergey Yurchenko's personal space.

 

Exo-cross

 

TROVE

+
+ + + +
+ +
+ diff --git a/TROVE.wiki/66759538.html b/TROVE.wiki/66759538.html new file mode 100644 index 0000000..65e911a --- /dev/null +++ b/TROVE.wiki/66759538.html @@ -0,0 +1,58 @@ + + + + Sergey Yurchenko : Checkpoint Files (.chk) + + + + + +
+
+
+ +

+ + Sergey Yurchenko : Checkpoint Files (.chk) + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on May 09, 2017 +
+
+

[Under construction]

Checkpoint files are the storage files used by TROVE in assisting with computation and storing results. They are an extremely useful component to TROVE as they effectively reduce computation time by storing any important results and using them in later stages. In essence, it tries to not repeat itself. The usage of checkpoints is determined by the CHECK_POINT header in the input file and this dictates whether certain checkpoint files are generated, read or not involved in a computation. It should be noted that each checkpoint has a signature in its header that should hopefully prevent mixing of different checkpoint files from different projects.

Standard (contracted) representation:

hamiltonian.chk

This contains the expansion of the kinetic energy and potential energy terms and (if stated using the EXTERNAL save keyword) the dipole moment function in terms of the internal co-ordinates

Notes:

  • The most important checkpoint file as every other computation follows from it. 99% of the time this should be generated in the very first step using the HAMILTONIAN save keyword.
  • This checkpoint can also be generated by using the combination of the KINETIC save and POTENTIAL save keywords instead (They must be used together though).
  • Every other computation after generating this will almost certainly use this checkpoint file and can be read using HAMILTONIAN read keyword
numerov_bset.chk

This contains the Numerov-basis functions and used in the proceeding contraction process.

Notes:

  • Depending on whether you use the scheme, this is automatically generated if the HAMILTONIAN save keyword is used.
  • If you opted to use the KINETIC save and POTENTIAL save keywords instead, then you'll need to specify the BASIS_SET save keyword in order for this to be generated.
prim_bset.chk

This contains the description of the primitive basis set functions and is used in the proceeding contraction process.
Notes:

  • Same notes as numerov_bset.chk
contr_vectors.chk

This contains the contracted basis functions.

Notes:

  • Will only be generated if the CONTRACT save keyword is used. This is recommended as it greatly reduces the size of the matrices generated.
  • Can be read using the CONTRACT read keyword.
contr_descr.chk

Contains a human readable description of the contracted basis functions.

Notes:

  • Generated with contr_vectors.chk
  • Not used by TROVE
contr_quanta.chk

Contains a human readable list of the energies corresponding to the contracted basis functions.

Notes:

  • Generated with contr_vectors.chk
  • Not used by TROVE
contr_matelem.chk

This contains the vibrational elements of the Hamiltonian in the contracted basis representation.

Notes:

  • This is required for all J>0 calculations
  • Is generated using the MATELEM save keyword ensuring you've previously generated the contracted basis functions.
  • Can also be generated using Checkpoint file splitting
eigen_vectors[J].chk

This contains the eigenvectors for a specific J computation. The [J] part is replaced with the value used. (e.g a J =0 computation will generate eigen_vectors0.chk, J=1 to eigen_vectors1.chk etc.)

Notes:

  • Is generated using the EIGENFUNC save keyword.
  • The J=0 checkpoint file eigen_vectors0.chk is especially important as it is used in the producing the J=0 representation
eigen_descr[J].chk

Contains a human readable form of the eigenvalues and corresponding quantum numbers

Notes:

  • Generated alongside eigen_vector[J].chk with a similar naming convention
  • The very first eigenvalue in the eigen_descr0.chk is the Zero-point energy.
eigen_quanta[J].chk

Contains a human readable description of eigenvectors

Notes:

  • Generated alongside eigen_vector[J].chk with a similar naming convention.
contr_extfield.chk

Contains the vibrational matrix elements of the dipole moment function in the contracted representation.

Notes:

  • Generated with the EXTMATELM save keyword
  • Useful if you require intensities and transition moments calculations.
+
+ + + +
+ +
+ diff --git a/TROVE.wiki/C20_55183971.html b/TROVE.wiki/C20_55183971.html new file mode 100644 index 0000000..ba79a90 --- /dev/null +++ b/TROVE.wiki/C20_55183971.html @@ -0,0 +1,79 @@ + + + + Sergey Yurchenko : C20 + + + + + +
+
+
+ +

+ + Sergey Yurchenko : C20 + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on May 18, 2015 +
+
+

C2

+

C2 project: towards the production of a hot line list 

+
+ + + + + + + + + + +

 

 

 

 

 

+
+ +
+
+

Attachments:

+
+ +
+ + worddav1289fcf52e105e432454683e58dbb792.png (image/png) +
+
+
+ + +
+ +
+ diff --git a/TROVE.wiki/Exo-cross_56495757.html b/TROVE.wiki/Exo-cross_56495757.html new file mode 100644 index 0000000..19afc8f --- /dev/null +++ b/TROVE.wiki/Exo-cross_56495757.html @@ -0,0 +1,55 @@ + + + + Sergey Yurchenko : Exo-cross + + + + + +
+
+
+ +

+ + Sergey Yurchenko : Exo-cross + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on Jul 07, 2015 +
+
+

Manual

ExoCross is  a Fortran 95 code for generating spectra (emission. absorption) and thermodynamic properties (partition function, specific heat etc) from molecular line lists in the ExoMol format.

 

  1. Keywords
  2. Computing partition functions for a set of temperatures 
  3. Computing cross-sections
  4. Applying filters
  5. Structure of output files
  6. Examples of batch jobs
+
+ + + +
+ +
+ diff --git a/TROVE.wiki/Import-ucapsyu_55902413.html b/TROVE.wiki/Import-ucapsyu_55902413.html new file mode 100644 index 0000000..e9e970c --- /dev/null +++ b/TROVE.wiki/Import-ucapsyu_55902413.html @@ -0,0 +1,55 @@ + + + + Sergey Yurchenko : Import ucapsyu + + + + + +
+
+
+ +

+ + Sergey Yurchenko : Import ucapsyu + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on May 19, 2015 +
+
+ +
+ + + +
+ +
+ diff --git a/TROVE.wiki/TROVE-Input-structure.asciidoc b/TROVE.wiki/TROVE-Input-structure.asciidoc new file mode 100644 index 0000000..3e5e653 --- /dev/null +++ b/TROVE.wiki/TROVE-Input-structure.asciidoc @@ -0,0 +1,372 @@ +Example of the TROVE input file + + + ( CALCULATION OF VIBRATION ENERGIES FOR XY2 MOLECULE ) + ( H2S from Per Jensen-Polyansky paper ) + ( 2006, Morbid type PES ) + + KinOrder 4 (Max order in the kinetic energy expansion) + PotOrder 8 (Max order in the potential energy expansion) + + Natoms 3 (Number of atoms) + Nmodes 3 (Number of modes = 3*Natoms-6) + + (ACTIVE SPACE CUTOFFS:) + PRIMITIVES + Npolyads 12 (how many polyads we calculate) + END + + CONTRACTION + Npolyads 12 (how many polyads contract to) + enercut 50000.0 (energy cut in the primitive matrix for the diagonalization) + END + + SYMGROUP C2v(M) + + DIAGONALIZER + SYEV + end + + verbose 5 + + + dstep 1.0e-02 (finite difference element for each mode ) + COORDS linear (type of the internal coordinates: linear or local) + TRANSFORM r-rho (transformation type, from Z-matrix to user-defined) + MOLTYPE XY2 (Identifying type of the Molecule (e.g. XY3)) + REFER-CONF RIGID (Reference configuarion: RIGID or NON-RIGID) + + (ZMAT-type coordinates and atomic masses) + ZMAT + S 0 0 0 0 31.97207070 + H 1 0 0 0 1.00782505 + H 1 2 0 0 1.00782505 + end + + (description of the basis set) + BASIS + 0,'JKtau', Jrot 0 + 1,'numerov','linear', 'morse', range 0, 1, r 2, resc 2.0, points 2000,borders -0.8,1.40 + 1,'numerov','linear', 'morse', range 0, 1, r 2, resc 2.0, points 2000,borders -0.8,1.40 + 2,'numerov','linear', 'linear', range 0, 2, r 2, resc 1.0, points 800,borders 4.0,150.0 deg + END + + + CHECK_POINT + hamiltonian save ascii + external save (used for dipole) + potential save + kinetic save + basis_set save + CONTRACT save + matelem save split + extmatelem save split + EIGENFUNC save + END + + sparse + + EQUILIBRIUM + re13 1 1.335946936 + re13 1 1.335946936 + alphae 0 92.23305449 DEG + end + + + SPECPARAM + aa 0 1.80000000d0 + aa 0 1.80000000d0 + END + + + + POTEN + NPARAM 99 + POT_TYPE poten_xy2_tyuterev + COEFF list (powers or list) + B1 0 0.50000000000000E+06 + B2 0 0.50000000000000E+05 + G1 0 0.15000000000000E+02 + G2 0 0.10000000000000E+02 + F_0_0_0 0 0.00000000000000E+00 + F_0_0_1 1 0.66558757946989E+02 + F_1_0_0 1 -0.13835270702230E+02 + F_0_0_2 1 0.19241706419359E+05 + F_1_0_1 1 -0.39085933055337E+04 + F_1_1_0 1 -0.31149355752404E+03 + F_2_0_0 1 0.33290745334086E+05 + F_0_0_3 1 0.10343666713265E+04 + F_1_0_2 1 -0.48165782117836E+04 + F_1_1_1 1 0.41354718940233E+04 + F_2_0_1 1 -0.72043145530624E+03 + F_2_1_0 1 0.48511933758098E+02 + F_3_0_0 1 0.12117283124837E+04 + F_0_0_4 1 0.44464671636921E+04 + F_1_0_3 1 0.33571659849809E+04 + F_1_1_2 1 0.31029051718113E+04 + F_2_0_2 1 -0.58338973338342E+04 + F_2_1_1 1 -0.44328192731276E+04 + F_2_2_0 1 -0.24878275859011E+03 + F_3_0_1 1 0.14947055312873E+05 + F_3_1_0 1 -0.55841271688198E+03 + F_4_0_0 1 0.21296945363004E+04 + F_0_0_5 1 -0.50508896424493E+03 + F_1_0_4 1 -0.26093552185759E+02 + F_1_1_3 1 -0.25329228512041E+04 + F_2_0_3 1 -0.51902737935966E+03 + F_2_1_2 1 0.21617069817315E+04 + F_2_2_1 1 -0.31115676847174E+04 + F_3_0_2 1 -0.50618744688911E+04 + F_3_1_1 1 -0.41693530983475E+04 + F_3_2_0 1 -0.42939103081242E+03 + F_4_0_1 1 -0.17784572512185E+04 + F_4_1_0 1 -0.13725963435798E+04 + F_5_0_0 1 0.91502663553729E+03 + F_0_0_6 1 0.20597478671198E+04 + F_1_0_5 1 -0.38110893723882E+04 + F_1_1_4 1 -0.40149855742427E+04 + F_2_0_4 1 0.35684903849649E+03 + F_2_1_3 1 0.76380134684412E+04 + F_2_2_2 1 0.13282205301593E+04 + F_3_0_3 1 -0.22296302452430E+05 + F_3_1_2 1 0.19829621606016E+03 + F_3_2_1 1 0.14523940021696E+05 + F_3_3_0 1 -0.34239718850476E+04 + F_4_0_2 1 0.20380116378782E+04 + F_4_1_1 1 0.27065962177979E+05 + F_4_2_0 1 0.27067823765539E+04 + F_5_0_1 1 -0.17892025481676E+05 + F_5_1_0 1 0.44073077022432E+04 + F_6_0_0 1 0.33088079351590E+03 + F_0_0_7 1 -0.34693044353783E+02 + F_1_0_6 1 0.57311789852071E+01 + F_1_1_5 1 0.61709400787943E+03 + F_2_0_5 1 -0.16909937092592E+03 + F_2_1_4 1 -0.10976812366289E+04 + F_2_2_3 1 0.10266084327629E+04 + F_3_0_4 1 0.41150065363337E+03 + F_3_1_3 1 -0.99777814797890E+02 + F_3_2_2 1 -0.15537361203941E+04 + F_3_3_1 1 -0.88242728757078E+04 + F_4_0_3 1 -0.69333622980059E+03 + F_4_1_2 1 -0.70187546546645E+03 + F_4_2_1 1 -0.71361655720700E+04 + F_4_3_0 1 -0.33704787735331E+04 + F_5_0_2 1 -0.22850354518147E+03 + F_5_1_1 1 -0.89773184878870E+04 + F_5_2_0 1 0.37396979760858E+03 + F_6_0_1 1 -0.24308008877128E+04 + F_6_1_0 1 0.14637756586301E+04 + F_7_0_0 1 -0.17972145991843E+03 + F_0_0_8 1 -0.93650429181993E+02 + F_1_0_7 1 0.36713925059079E+02 + F_1_1_6 1 0.36968585044722E+02 + F_2_0_6 1 0.68482654708134E+03 + F_2_1_5 1 -0.50322851565079E+03 + F_2_2_4 1 0.22143906652684E+04 + F_3_0_5 1 -0.92367919806888E+03 + F_3_1_4 1 0.89951389954746E+03 + F_3_2_3 1 -0.40263060504651E+03 + F_3_3_2 1 -0.16132961209683E+04 + F_4_0_4 1 0.10323760435564E+04 + F_4_1_3 1 -0.17087943370917E+03 + F_4_2_2 1 0.46314280115681E+02 + F_4_3_1 1 0.12241105997100E+04 + F_4_4_0 1 -0.75868613299014E+04 + F_5_0_3 1 0.24245831723843E+03 + F_5_1_2 1 0.98584834963982E+03 + F_5_2_1 1 0.15449893868580E+04 + F_5_3_0 1 -0.34420115465232E+04 + F_6_0_2 1 -0.20826405470290E+03 + F_6_1_1 1 0.40446498074108E+04 + F_6_2_0 1 -0.37419323099604E+04 + F_7_0_1 1 0.99617055424284E+03 + F_7_1_0 1 -0.55293683662689E+03 + F_8_0_0 1 0.89266911359335E+02 + end + + + + DIPOLE (DMS3:f12-pVQZ) + rank 3 + NPARAM 72 99 0 + TYPE xy2_pq_coeff + COEFF list (powers or list) + COORDS linear linear cosrho + Orders 4 4 4 + Parameters + re 0 0.133600000000E+01 + alphae 0 0.922000000000E+02 + f03y1y0y0 7 -0.00816381812308d0 + f04y1y0y1 7 0.780098952603d0 + f05y2y0y0 6 0.223371981342d0 + f06y1y0y2 6 -0.241381576171d0 + f07y2y0y1 6 -0.370227208108d0 + f08y2y1y0 6 0.199704784368d0 + f09y3y0y0 6 0.166434873525d0 + f10y1y0y3 5 0.158378246956d0 + f11y2y0y2 5 0.194858473441d0 + f12y2y1y1 5 0.629949309998d0 + f13y3y0y1 5 -0.704911805546d0 + f14y3y1y0 5 -0.0712847872614d0 + f15y4y0y0 4 -0.0501322107482d0 + f16y1y0y4 4 -0.152249298434d0 + f17y2y0y3 4 -0.00242743550871d0 + f18y2y1y2 4 -0.301888853888d0 + f19y3y0y2 4 0.673123470301d0 + f20y3y1y1 4 0.288684058924d0 + f21y3y2y0 4 -0.0228984996042d0 + f22y4y0y1 4 0.0871286102004d0 + f23y4y1y0 4 -0.0575600087011d0 + f24y5y0y0 3 -0.146622711335d0 + f25y1y0y5 3 0.0891365657224d0 + f26y2y0y4 3 0.0482836421047d0 + f27y2y1y3 3 -0.943039955974d0 + f28y3y0y3 3 -0.294627411659d0 + f29y3y1y2 3 -0.370889326942d0 + f30y3y2y1 3 3.26835911709d0 + f31y4y0y2 3 -0.0735779194474d0 + f33y4y1y1 3 -1.66975815804d0 + f33y4y2y0 3 0.107241666365d0 + f34y5y0y1 3 1.004421768d0 + f35y5y1y0 3 0.0822674467561d0 + f36y6y0y0 3 0.182870627043d0 + f37y1y0y6 2 -0.627495693052d0 + f38y2y0y5 2 -0.223562407218d0 + f39y2y1y4 2 -1.95629458106d0 + f40y3y0y4 2 1.26935380052d0 + f41y3y1y3 2 1.09389125021d0 + f42y3y2y2 2 -0.800929145701d0 + f43y4y0y3 2 -0.288364781648d0 + f44y4y1y2 2 0.614002392111d0 + f45y4y2y1 2 -3.09834160735d0 + f46y4y3y0 2 -0.542615466462d0 + f47y5y0y2 2 -0.615952806276d0 + f48y5y1y1 2 1.79639486168d0 + f49y5y2y0 2 0.235244276554d0 + f50y6y0y1 2 -0.950869498909d0 + f51y6y1y0 2 -0.21185736393d0 + f52y7y0y0 2 -0.0780672199457d0 + f53y1y0y7 0 0.000000000000E+00 + f54y2y0y6 0 0.000000000000E+00 + f55y2y1y5 0 0.000000000000E+00 + f56y3y0y5 0 0.000000000000E+00 + f57y3y1y4 0 0.000000000000E+00 + f58y3y2y3 0 0.000000000000E+00 + f59y4y0y4 0 0.000000000000E+00 + f60y4y1y3 0 0.000000000000E+00 + f61y4y2y2 0 0.000000000000E+00 + f62y4y3y1 0 0.000000000000E+00 + f63y5y0y3 0 0.000000000000E+00 + f64y5y1y2 0 0.000000000000E+00 + f65y5y2y1 0 0.000000000000E+00 + f66y5y3y0 0 0.000000000000E+00 + f67y6y0y2 0 0.000000000000E+00 + f68y6y1y1 0 0.000000000000E+00 + f69y6y2y0 0 0.000000000000E+00 + f70y7y0y1 0 0.000000000000E+00 + f71y7y1y0 0 0.000000000000E+00 + f72y8y0y0 0 0.000000000000E+00 + re 0 0.133600000000E+01 + alphae 0 0.922000000000E+02 + dummy 0 0.000000000000E+00 + dummy 0 0.000000000000E+00 + xp(1) 8 1.00996190700d0 + x0x0x1 7 -0.173356277075d0 + x1x0x0 7 0.0059742437393d0 + x0x0x2 7 0.672338876056d0 + x0x2x0 7 0.462146895631d0 + x1x0x1 7 -0.20452439174d0 + x2x0x0 7 -0.154954172888d0 + x0x0x3 6 0.185735303832d0 + x0x2x1 6 -0.172338104721d0 + x1x0x2 6 0.248342629081d0 + x1x2x0 6 0.0670735523747d0 + x2x0x1 6 0.0846311303319d0 + x3x0x0 6 -0.202698907223d0 + x0x0x4 6 0.456480654844d0 + x0x2x2 6 0.07133374706d0 + x0x4x0 6 -0.133797273911d0 + x1x0x3 6 -0.407425843925d0 + x1x2x1 6 -0.096920241122d0 + x2x0x2 6 0.130237629582d0 + x2x2x0 6 -0.0504041976858d0 + x3x0x1 6 0.0376709697578d0 + x4x0x0 6 0.0637143876101d0 + x0x0x5 5 0.100504536942d0 + x0x2x3 5 -0.152880543902d0 + x0x4x1 5 0.606288827658d0 + x1x0x4 5 -0.189047600793d0 + x1x2x2 5 0.298243079636d0 + x1x4x0 5 -0.027904106836d0 + x2x0x3 5 -0.411869441202d0 + x2x2x1 5 -0.422271146693d0 + x3x0x2 5 0.0123954052637d0 + x3x2x0 5 0.0835107634672d0 + x4x0x1 5 0.0241562871019d0 + x5x0x0 5 0.111087821513d0 + x0x0x6 4 0.998023860129d0 + x0x2x4 4 0.0777177456402d0 + x0x4x2 4 -0.358021318356d0 + x0x6x0 4 -0.620347481097d0 + x1x0x5 4 0.486243591888d0 + x1x2x3 4 1.19822245827d0 + x1x4x1 4 -0.114071699815d0 + x2x0x4 4 0.187484630455d0 + x2x2x2 4 0.00666547878418d0 + x2x4x0 4 0.108138311514d0 + x3x0x3 4 0.252224252799d0 + x3x2x1 4 -0.539899157318d0 + x4x0x2 4 0.154995033122d0 + x4x2x0 4 -0.244759754761d0 + x5x0x1 4 -0.00496709390485d + x6x0x0 4 -0.107549134147d0 + x0x0x7 3 0.625647747735d0 + x0x2x5 3 0.221452879902d0 + x0x4x3 3 0.972670486374d0 + x0x6x1 3 0.0751751906524d0 + x1x0x6 3 0.617645166582d0 + x1x2x4 3 0.415280582145d0 + x1x4x2 3 -0.630646309761d0 + x1x6x0 3 -1.99242116173d0 + x2x0x5 3 -0.409523411574d0 + x2x2x3 3 -0.67195522245d0 + x2x4x1 3 0.387883787338d0 + x3x0x4 3 -0.337418273335d0 + x3x2x2 3 1.03474232451d0 + x3x4x0 3 -0.436958601672d0 + x4x0x3 3 0.518048465221d0 + x4x2x1 3 0.75422058878d0 + x5x0x2 3 -0.529691798627d0 + x5x2x0 3 0.252476017527d0 + x6x0x1 3 0.00538208702223d0 + x7x0x0 3 0.0435636010183d0 + x0x0x8 0 0d0 + x0x2x6 0 0d0 + x0x4x4 0 0d0 + x0x6x2 0 0.000000000000E+00 + x0x8x0 0 0.000000000000E+00 + x1x0x7 0 0.000000000000E+00 + x1x2x5 0 0.000000000000E+00 + x1x4x3 0 0.000000000000E+00 + x1x6x1 0 0.000000000000E+00 + x2x0x6 0 0.000000000000E+00 + x2x2x4 0 0.000000000000E+00 + x2x4x2 0 0.000000000000E+00 + x2x6x0 0 0.000000000000E+00 + x3x0x5 0 0.000000000000E+00 + x3x2x3 0 0.000000000000E+00 + x3x4x1 0 0.000000000000E+00 + x4x0x4 0 0.000000000000E+00 + x4x2x2 0 0.000000000000E+00 + x4x4x0 0 0.000000000000E+00 + x5x0x3 0 0.000000000000E+00 + x5x2x1 0 0.000000000000E+00 + x6x0x2 0 0.000000000000E+00 + x6x2x0 0 0.000000000000E+00 + x7x0x1 0 0.000000000000E+00 + x8x0x0 0 0.000000000000E+00 + end + + + diff --git a/TROVE.wiki/TROVE-pipeline.md b/TROVE.wiki/TROVE-pipeline.md new file mode 100644 index 0000000..573b53f --- /dev/null +++ b/TROVE.wiki/TROVE-pipeline.md @@ -0,0 +1,14 @@ + + ## The typical TROVE intensity project consists of the following steps: + +1. Expansion of the Hamiltonian operator (generating kinetic and potential energy expansion coefficients numerically on-the-fly) as well as of any “external” function (e.g., dipole moment, polarizability, spin–spin coupling, or any other property; PES correction used in the refinement process); +2. Numerov–Cooley solution of the 1D Schrodinger equations; +3. Eigen-solutions of the reduced Hamiltonian problems; +4. Symmetrization of the contracted eigenfunctions from Step 3 and construction of the symmetry-adapted vibrational basis set; +5. Calculation of the vibrational matrix of the Hamiltonian operator as well as external functions (e.g., dipole) when required; +6. Diagonalizaitons of the J=0 Hamiltonian matrices for each irreducible representation in question; +7. Conversion of the primitive basis set representation (vibrational matrix elements from Step 5) to the J=0 representation; +8. Construction of the symmetry-adapted ro-vibrational basis set as a direct product of the J=0 eigenfunctions and rigid rotor wavefunctions; +9. Construction of the ro-vibrational Hamiltonian matrices for each J>0 and irreducible representation Gamma; +10. Diagonalization of the Hamiltonian matrices and storing eigenvectors for the postprocessing (e.g., intensity calculations) if necessary; +11. For the intensity calculations (line list production), all pairs of the ro-vibrational eigenvectors (bra and ket) from Step 10 (subject to the selection rules as well as to the energy, frequency and J thresholds) are cross-correlated with the dipole moment XYZ components in the laboratory-fixed frame via a vector-matrix-vector product, where the body-fixed xyz components of the dipole moment from Step 5 are transformed to the XYZ-frame using the Wigner-matrices. diff --git a/TROVE.wiki/TROVE.md b/TROVE.wiki/TROVE.md new file mode 100644 index 0000000..8fbc072 --- /dev/null +++ b/TROVE.wiki/TROVE.md @@ -0,0 +1 @@ +TROVE is a FORTRAN 2003 variational nuclear motion solver for general polyatomic molecules of arbitrary structure (Yurchenko, Jensen, Thiel, J. Molec. Spectrosc. 245, 126 (2007)]). \ No newline at end of file diff --git a/TROVE.wiki/TROVE_66759535.html b/TROVE.wiki/TROVE_66759535.html new file mode 100644 index 0000000..cc1e86e --- /dev/null +++ b/TROVE.wiki/TROVE_66759535.html @@ -0,0 +1,55 @@ + + + + Sergey Yurchenko : TROVE + + + + + +
+
+
+ +

+ + Sergey Yurchenko : TROVE + +

+
+ +
+
+ + + + + + + + Created by Sergey Yurchenko on May 09, 2017 +
+
+ +
+ + + +
+ +
+