ChemWiki - User contributions [en]

Resgrp:comp-photo-dyn

2009-01-06T17:16:06Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

The study of photochemical mechanisms using the DD-vMCG method can be approached in four stages.

1) The preliminary stage is a static description of the mechanism under study. This corresponds to a description of the main topological features of the potential energy surfaces of the coupled electronic states, as in any other study of the potential energy surfaces using CASSCF [link, see benzene tutorial]. In practice, this involves:

# Choice of the active space and basis set for the electronic wavefunction
# Characterisation of the relevant critical points (stationary points and conical intersection points)
# Characterisations of the main pathways (reaction paths and crossing seams)
# Definition – and possible selection – of the nuclear coordinates

Some comments:

- Choosing the active space may happen to be delicate when a full-valence description is too expensive (or just too large) to be used for frequency calculations, in particular if sigma and pi orbitals can mix. The user should keep in mind that the active space will be propagated along the trajectories followed by the centres of the Gaussian functions and may break in very distorted geometries.

- The main critical points involved in the mechanism must be identified, optimised and characterised. Stationary points are characterised by frequency calculations, and conical intersection points by examining the nature of the electronic states involved and the branching-space vectors that lifts the degeneracy. The important pathways can be characterised in the form of mimimum energy paths (intrinsic reaction coordinate) linking stationary points. In addition, a development version of GAUSSIAN implemented in our group [link, see documentation (Patrick's page)] can be used to characterise the curvatures of the intersection space (crossing seam). The same program can calculate minimum energy paths within the intersection space, linking conical intersection points characterised as seam minima or seam saddle points.

- For now, the nuclear coordinates are defined as the normal coordinates of the electronic ground-state minimum (magnitude of nuclear displacements along the directions of the normal modes) for convenience. Their number can be reduced to keep the most relevant ones and thus simplify the study of the system dynamics. A method based on the development version of GAUSSIAN mentioned above may be used in this context [[http://link.aip.org/link/?JCPSA6/128/124307/1 see reference]].

2) The second stage is the generation of the input files. This can be performed automatically by a utility program that asks the user questions in order to set the correct options, but two calculations have to be done first:

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculation itself. This part is managed by the MCTDH program and should finish normally if the input file were written correctly. However, this may fail for various reasons, often because converging the active space becomes difficult. Also, calculations may have to be redone several times, with conditions that can be improved, for example by increasing the number of Gaussian functions in the wavepacket expansion, or by changing the conical intersection point chosen for "regularization" scheme if this approach is to be followed.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Some comments:

- Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to further represent trajectories as movies using a utility program.

- The quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

- Stages 3 and 4, probably might have to be repeated several times before a satisfactory result is reached. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as the number of nuclear Gaussian functions, the final propagation time, the propagation time step, or the integrator may be required.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T17:15:23Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

The study of photochemical mechanisms using the DD-vMCG method can be approached in four stages.

1) The preliminary stage is a static description of the mechanism under study. This corresponds to a description of the main topological features of the potential energy surfaces of the coupled electronic states, as in any other study of the potential energy surfaces using CASSCF [link, see benzene tutorial]. In practice, this involves:

# Choice of the active space and basis set for the electronic wavefunction
# Characterisation of the relevant critical points (stationary points and conical intersection points)
# Characterisations of the main pathways (reaction paths and crossing seams)
# Definition – and possible selection – of the nuclear coordinates

Some comments:

- Choosing the active space may happen to be delicate when a full-valence description is too expensive (or just too large) to be used for frequency calculations, in particular if sigma and pi orbitals can mix. The user should keep in mind that the active space will be propagated along the trajectories followed by the centres of the Gaussian functions and may break in very distorted geometries.

- The main critical points involved in the mechanism must be identified, optimised and characterised. Stationary points are characterised by frequency calculations, and conical intersection points by examining the nature of the electronic states involved and the branching-space vectors that lifts the degeneracy. The important pathways can be characterised in the form of mimimum energy paths (intrinsic reaction coordinate) linking stationary points. In addition, a development version of GAUSSIAN implemented in our group [link, see documentation (Patrick's page)] can be used to characterise the curvatures of the intersection space (crossing seam). The same program can calculate minimum energy paths within the intersection space, linking conical intersection points characterised as seam minima or seam saddle points.

- For now, the nuclear coordinates are defined as the normal coordinates of the electronic ground-state minimum (magnitude of nuclear displacements along the directions of the normal modes) for convenience. Their number can be reduced to keep the most relevant ones and thus simplify the study of the system dynamics. A method based on the development version of GAUSSIAN mentioned above may be used in this context [[http://link.aip.org/link/?JCPSA6/128/124307/1 see reference]].

2) The second stage is the generation of the input files. This can be performed automatically by a utility program that asks the user questions in order to set the correct options, but two calculations have to be done first:

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculation itself. This part is managed by the MCTDH program and should finish normally if the input file were written correctly. However, this may fail for various reasons, often because converging the active space becomes difficult. Also, calculations may have to be redone several times, with conditions that can be improved, for example by increasing the number of Gaussian functions in the wavepacket expansion, or by changing the conical intersection point chosen for "regularization" scheme if this approach is to be followed.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Some comments:

- Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

- The quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

- Stages 3 and 4, probably might have to be repeated several times before a satisfactory result is reached. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as the number of nuclear Gaussian functions, the final propagation time, the propagation time step, or the integrator may be required.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T17:04:12Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

The study of photochemical mechanisms using the DD-vMCG method can be approached in four stages.

1) The preliminary stage is a static description of the mechanism under study. This corresponds to a description of the main topological features of the potential energy surfaces of the coupled electronic states, as in any other study of the potential energy surfaces using CASSCF [link, see benzene tutorial]. In practice, this involves:

# Choice of the active space
# Characterisation of the relevant critical points (stationary points and conical intersection points)
# Characterisations of the main pathways (reaction paths and crossing seams)
# Definition – and possible selection – of the nuclear coordinates

Some comments:
- Choosing the active space may happen to be delicate when a full-valence description is too expensive (or just too large) to be used for frequency calculations, in particular if sigma and pi orbitals can mix. The user should keep in mind that the active space will be propagated along the trajectories followed by the centres of the Gaussian functions and may break in very distorted geometries.
- The main critical points involved in the mechanism must be identified, optimised and characterised. Stationary points are characterised by frequency calculations, and conical intersection points by examining the nature of the electronic states involved and the branching-space vectors that lifts the degeneracy. The important pathways can be characterised in the form of mimimum energy paths (intrinsic reaction coordinate) linking stationary points. In addition, a development version of GAUSSIAN implemented in our group [link, see documentation (Patrick's page)] can be used to characterise the curvatures of the intersection space (crossing seam). The same program can calculate minimum energy paths within the intersection space, linking conical intersection points characterised as seam minima or seam saddle points.
- For now, the nuclear coordinates are defined as the normal coordinates of the electronic ground-state minimum (magnitude of nuclear displacements along the directions of the normal modes) for convenience. Their number can be reduced to keep the most relevant ones and thus simplify the study of the system dynamics. A method based on the development version of GAUSSIAN mentioned above may be used in this context [[http://link.aip.org/link/?JCPSA6/128/124307/1 see reference]].

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T17:03:53Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

The study of photochemical mechanisms using the DD-vMCG method can be approached in four stages.

1) The preliminary stage is a static description of the mechanism under study. This corresponds to a description of the main topological features of the potential energy surfaces of the coupled electronic states, as in any other study of the potential energy surfaces using CASSCF [link, see benzene tutorial]. In practice, this involves:

# Choice of the active space
# Characterisation of the relevant critical points (stationary points and conical intersection points)
# Characterisations of the main pathways (reaction paths and crossing seams)
# Definition – and possible selection – of the nuclear coordinates

Some comments:
- Choosing the active space may happen to be delicate when a full-valence description is too expensive (or just too large) to be used for frequency calculations, in particular if sigma and pi orbitals can mix. The user should keep in mind that the active space will be propagated along the trajectories followed by the centres of the Gaussian functions and may break in very distorted geometries.
- The main critical points involved in the mechanism must be identified, optimised and characterised. Stationary points are characterised by frequency calculations, and conical intersection points by examining the nature of the electronic states involved and the branching-space vectors that lifts the degeneracy. The important pathways can be characterised in the form of mimimum energy paths (intrinsic reaction coordinate) linking stationary points. In addition, a development version of GAUSSIAN implemented in our group [link, see documentation (Patrick's page)] can be used to characterise the curvatures of the intersection space (crossing seam). The same program can calculate minimum energy paths within the intersection space, linking conical intersection points characterised as seam minima or seam saddle points.
- For now, the nuclear coordinates are defined as the normal coordinates of the electronic ground-state minimum (magnitude of nuclear displacements along the directions of the normal modes) for convenience. Their number can be reduced to keep the most relevant ones and thus simplify the study of the system dynamics. A method based on the development version of GAUSSIAN mentioned above may be used in this context [[ see reference]].

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:33:08Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

The study of photochemical mechanisms using the DD-vMCG method can be approached in four stages.

1) The first stage is a static description of the mechanism under study. This corresponds to a description of the main topological features of the potential energy surfaces of the coupled electronic states. the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). In practice, this involves:

# Choice of the active space (needs some testing if the size is not obvious)
# Characterisation of the critical points
# Selection/definition of the nuclear coordinates

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:26:37Z

Blasorne: /* Current available versions */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularized" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:26:20Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called "regularization" scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:11:43Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Averages and widths of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:11:26Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

Normal coordinates can be transformed into Cartesian or internal coordinates. Cartesian coordinates can be used to represent trajectories as movies.

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:09:53Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
\ → can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:08:42Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
<tab> → can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:08:15Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
**→ can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:06:41Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
→ can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:06:21Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
→ can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T16:05:54Z

Blasorne: /* General overview */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= The direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators.

This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nuclear wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN around the centre of each Gaussian function in the expansion, for both electronic states involved in the photochemical process under study.

This approach provides a time-resolved simulation of the photochemical mechanism induced by the initial condition chosen by the user. Non-adiabatic effects and tunneling are better described than with semi-classical trajectory methods such as surface hopping [[http://www.informaworld.com/10.1080/00268970802172503 see recent review]].

== Current available versions ==

* mctdh90dev

This is the "old" and stable version of the code, which has been used by Marta Araujo and David Asturiol. This version relies on the multi-set formulation for DD-vMCG calculations (distinct Gaussian functions on different electronic states), which complicates the interpretation of results and often generates numerical problems. In addition, particular cases require particular versions of the source code to be recompiled.

* mctdh90.31dev

This version should be used from now on, but has not been tested extensively yet. It is more portable and more flexible in terms of options. The main new feature is the possibility of using the single-set formulation for DD-vMCG calculations (a unique set of Gaussian functions with varying occupancies on each electronic states).

''N.B.'': the potential energy surfaces are calculated in the adiabatic picture by GAUSSIAN and must be transformed to the diabatic picture for MCTDH. A simple scheme, based on the "regularised" diabatic states of Köppel ''et al.'' [[http://link.aip.org/link/?JCPSA6/115/2377/1 see reference]], has been used to date in which the gradient difference and non-adiabatic coupling at a point on the conical intersection seam can be used to estimate the transformation matrix. As a consequence, the user needs to provide the geometry and the branching-space vectors of a chosen conical intersection. This complicates the generation of the input files, as these three vectors are given in a Cartesian frame that must be re-orientated following some constraints discussed further in this manual. This also introduces a possible bias and also makes the interpretation of results quite delicate in terms of the assignment of the electronic populations in both representations. A work is in progress to implement a new scheme beyond these limitations.

== General overview ==

1) In general, the study of photochemical mechanisms using the DD-vMCG method can be approached in four stages. The first stage is the identification and characterisation of the main critical points involved in the mechanism (minima, transition states, and surface crossings), as in any other study of the potential energy surfaces using CASSCF (link, benzene). This first stage involves:

# Selection of the active space (needs some testing if the choice is not obvious)
# Characterisation of the critical points

* The stationary points can be characterised by frequency calculations, and the conical intersections by examining the electronic states involved and the branching space that lifts the degeneracy.

Reduction of dimensionality... Analysis of the energy difference...

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves looking at the time evolution of the:

* Normal coordinates at the centre of each Gaussian function ("trajectories")
→ can be transformed into Cartesian or internal coordinates and also represented as movies
* Average and width of the normal coordinates for the global wavepacket
* Adiabatic and diabatic energies at the centre of each Gaussian function ("trajectories")
* Electronic populations for the global wavepacket

''N.B.'': the quality of the calculation can be checked with various indicators. The simplest is the preservation of the mean total energy. If this increases too fast, the time step might have to be reduced.

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T15:52:34Z

Blasorne: /* General overview */

Resgrp:comp-photo-dyn

2009-01-06T15:43:31Z

Blasorne: /* Current available versions */

Resgrp:comp-photo-dyn

2009-01-06T15:37:19Z

Blasorne: /* Current available versions */

Resgrp:comp-photo-dyn

2009-01-06T15:30:42Z

Blasorne: /* Current available versions */

Resgrp:comp-photo-dyn

2009-01-06T15:28:55Z

Blasorne: /* Current available versions */

Resgrp:comp-photo-dyn

2009-01-06T15:13:58Z

Blasorne: /* Current available versions */

Resgrp:comp-photo-dyn

2009-01-06T15:10:04Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:59:40Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:59:11Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:58:32Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:56:03Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:51:37Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:50:33Z

Blasorne: /* The direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:48:38Z

Blasorne: /* Overview of the direct quantum dynamics package */

Resgrp:comp-photo-dyn

2009-01-06T14:48:24Z

Blasorne: /* Overview of the direct quantum dynamics Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of the direct quantum dynamics package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators. This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nucleqr wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:48:14Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of the direct quantum dynamics Package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators. This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nucleqr wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:47:07Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators. This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). The vMCG method is a particular case of MCTDH, where the nucleqr wavepacket is expanded in a time-dependent basis set of Gaussian functions. The direct dynamics implementation allows the electronic energy (potential energy for the nuclei) to be calculated on-the-fly by the quantum chemistry package GAUSSIAN.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:42:23Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The direct quantum dynamics method we use is based on the propagation of DD-vMCG (direct dynamics variational multi-configuration Gaussian) wavepackets. This has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]] and collaborators. This package consists of a set of programs for multidimensional quantum dynamics using the MCTDH algorithm (multi-configuration time- dependent Hartree). DD-vMCG is a particular case of MCTDH, where the wavepacket is expanded in a time-dependent basis set of Gaussian functions.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:31:06Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The quantum dynamics program we use has been implemented in a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]]. is a set of programs able to set up and propagate a wavepacket using the MCTDH method.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:29:37Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The quantum dynamics program we use is a development version of the Heidelberg MCTDH package [[http://www.pci.uni-heidelberg.de/cms/mctdh.html see web page]] supervised by Graham A. Worth [[http://www.stchem.bham.ac.uk/~worthgrp/ see web page]]. is a set of programs able to set up and propagate a wavepacket using the MCTDH method.

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:23:54Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The MCTDH package is a set of programs able to set up and propagate a wavepacket using the MCTDH method.
[[http://www.pci.uni-heidelberg.de/cms/mctdh.html see documentation here]]

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:23:14Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The MCTDH package is a set of programs able to set up and propagate a wavepacket using the MCTDH method.
[http://www.pci.uni-heidelberg.de/cms/mctdh.html Title]

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===

Resgrp:comp-photo-dyn

2009-01-06T14:22:00Z

Blasorne: /* Overview of Package */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...
MY COMMENTS IN UPPER CASE MAR

= Overview of Package =

The MCTDH package is a set of programs able to set up and propagate a wavepacket using the MCTDH method.
[[http://www.pci.uni-heidelberg.de/cms/mctdh.html]]

== Current available versions ==

* mctdh90dev

This is the "old" version of the code, which has been used by Marta Araujo and David Asturiol. This version works, but presents some technical hitches:

# The conical orientation before it can be converted to the mass weight normal vibrational coordinates has to be orientated: this has to be done with an Excel worksheet.
# Multi-basis set: this complicates the interpretation of results.

* mctdh90.31dev

Next version, it still be in development.

== General overview ==

1) In general, the study of photochemical mechanisms using the MCTDH package can be approached in four stages. The first stage is the optimization of the critical points: minima on the ground state and surface crossing as in any other study of the Potential Energy Surface (PES) using CASSCF (link, benzene). This first stage involves:

# Selection of the Active Space
# Characterization of the minima and conical intersection

* The minima can be characterized by frequency calculations, and the conical intersection by examining the electronic states involved and the branching space that lifts the degeneracy.

2) The second stage is the generation of the necessary files in order to construct a subspace of Normal Vibrational Coordinates in the state average space. The current code performs this automatically, but two calculations have to be given as input files.

# Frequency calculation at the ground-state minimum (log and chk or fchk files), used for (i) the initial geometry, (ii) the definition of the normal coordinates, and (iii) the initial active space.
# Optimised conical intersection (log file), used for the generation of diabatic electronic states from the adiabatic ones (when the so-called regularized diabatisation scheme is used).

3) The third stage corresponds to the dynamics calculations itself. This part is done automatically by the code, but may have to be done several times depending on the basis set, the size of the system and the active space.

4) Finally, the last step is the analysis of results. This involves:

* Conservation of the total energy.
* Normal Mode Coordinates
* Populations

Stages 3 and 4, probably might have to be repeated several times as well. Certainly, the spirit of this part is guided by the trial and error method. Playing with variables such as number of nuclear Gaussian functions, the final propagation time or the propagation time step is essential before a reasonable description is reached.

----

=== [[Resgrp:comp-photo-dyn/mctdh90dev|mctdh90dev]] ===