| |
| gmolpro_graphical_user_interface [2025/02/17 06:25] – [gmolpro graphical user interface] doll | gmolpro_graphical_user_interface [2025/04/03 08:43] (current) – external edit 127.0.0.1 |
|---|
| |
| |
| gmolpro (present release: version 2.6.0) is bundled with Molpro version 2024.3.0 . By calling "gmolpro", this bundled version is used. Note that on macOS, gmolpro starts without visiting shell initialisation scripts if you start it by clicking on the icon in the Mac Dock. | gmolpro (present release: version 2.7.0) should be used together with Molpro2025.1. On Mac, the package you download is already bundled with this Molpro version. On Linux, gmolpro does not come bundled with Molpro, and you need a separate installation of Molpro. Note that on macOS, gmolpro starts without visiting shell initialisation scripts if you start it by clicking on the icon in the Mac Dock. |
| |
| It requires | It requires |
| - a macOS (12.X i.e. Monterey or later) or Linux (Ubuntu 18.04 or later, Debian 11 or later, Fedora 40 or later, or openSUSE 15.5 or later) workstation; other macOS or Linux versions **//may (and often will)//** work | - a macOS (12.X i.e. Monterey or later) or Linux (Ubuntu 18.04 or later, Debian 11 or later, Fedora 40 or later, or openSUSE 15.6 or later) workstation; other macOS or Linux versions **//may (and often will)//** work |
| - a licence token which is valid for molpro and gmolpro. It may be installed in '' $HOME/.molpro/token'' . Alternatively (useful for group licences) on Linux, it may be installed in '' /usr/share/gmolpro/molpro/lib/.token '' (if gmolpro is installed in the default place /usr/bin/gmolpro), and on Mac in '' /Applications/gmolpro.app/Contents/Resources/molpro/lib/.token '' (the gmolpro app should always be installed in the default place ''/Applications/gmolpro.app'' ) | - a licence token which is valid for molpro and gmolpro. It may be installed in '' $HOME/.molpro/token'' . Alternatively (useful for group licences) on Linux, it may be installed in the place as described in the [[installation_guide]], and on Mac in ''/Applications/gmolpro.app/Contents/Resources/molpro/lib/.token'' (the gmolpro app should always be installed in the default place ''/Applications/gmolpro.app'' ) |
| |
| |
| ^ gmolpro release versus ... ^ ... recommended Molpro version ^ remarks ^ | ^ gmolpro release versus ... ^ ... recommended Molpro version ^ remarks ^ |
| | 2.6.0 | bundled with 2024.3.0 | | | 2.7.0 |2025.1 (Linux: needs separate installation; Mac: bundled with 2025.1.0) | Molpro versions beyond 2025.1 need gmolpro version at least 2.7.0 because the xml file will be split in xml and xml-sidecar| |
| | 2.5.0 | bundled with 2024.2.0 | linux version of Molpro2024.2.0 needs glibc >= 2.27 | | | 2.6.0 |bundled with 2024.3.0 | |
| | 2.4.0 | bundled with 2024.1.0 | | | 2.5.0 |bundled with 2024.2.0 |linux version of Molpro2024.2.0 needs glibc >= 2.27 | |
| | 2.3.0 | bundled with 2024.1.0 | | | 2.4.0 |bundled with 2024.1.0 | |
| | 2.2.0 | bundled with 2023.2.0 | | | 2.3.0 |bundled with 2024.1.0 | |
| | 2.1.0 | bundled with 2022.2.3 | | | 2.2.0 |bundled with 2023.2.0 | |
| | 2.0.0 | bundled with 2022.2.2 | | | 2.1.0 |bundled with 2022.2.3 | |
| | 1.4.0 | 2022.1 | | | 2.0.0 |bundled with 2022.2.2 | |
| | 1.3.1 | 2021.3 | | | 1.4.0 |2022.1 | |
| | 1.1 | 2021.1 | | | 1.3.1 |2021.3 | |
| | | 1.1 |2021.1 | |
| |
| |
| ===== Projects ===== | ===== Projects ===== |
| |
| All files belonging to a particular calculation (input, output, geometry etc.), as well as additional data, are contained in a //project//, which is implemented as a filesystem directory (a bundle). gMolpro automatically creates and maintains these projects. Project directories have extension ''.molpro'', e.g. ''c2h2.molpro'', but they may be accessed by the name without the extension. In the following, ''c2h2'' is used as example project name. | All files belonging to a particular calculation (input, output, geometry etc.), as well as additional data, are contained in a //project//, which is implemented as a filesystem directory (a bundle). gMolpro automatically creates and maintains these projects. Project directories have extension ''.molpro'', e.g. ''c2h2.molpro''. |
| |
| ===== Starting gMolpro ===== | ===== Starting gMolpro ===== |
| |
| |
| |{{vimeo>778042061|input window}}|The window guides though the options for a calculation, constructing Molpro input for DFT and single-reference calculations. Generally, one should go through this window from top to bottom, since some settings depend on each other. Let's look at the possibilities. The geometry can be imported from an xyz file(''Import Geometry'') or generated using the ''Builder Window''. Imported xyz files are not modified in the project, but can change during the calculation due to orientation or geometry optimization, and the optimized geometries can be exported and reused in subsequent calculations. The next important decision is the overall type of calculation - single geometry or structure optimization, with our without harmonic frequencies. We should then choose the method; let's try a correlated-wavefunction CCSD(T) calculation. The default for the Hamiltonian model is to use pseudopotentials to represent core electrons where appropriate, but you can choose instead to include all electrons, either non-relativistically or with a scalar relativistic Hamiltonian. There is also the possibility to specify whether and how core orbitals are included in the correlation treatment. The final principal choice is the basis set. The guided proposals for this are dependent on the method, hamiltonian and core correlation. You should first choose the overall quality - double, triple,... zeta - and then select within that if desired. It's also possible to specify the basis set element by element. The remainder of the input is associated with further options to control the running of the calculation and what it produces.| | |{{vimeo>778042061|input window}}|The window guides though the options for a calculation, constructing Molpro input for DFT and single-reference calculations. Generally, one should go through this window from top to bottom, since some settings depend on each other. Let's look at the possibilities. The geometry can be imported from an xyz file(''Import Geometry'') or generated using the ''Builder Window''. Imported xyz files are not modified in the project, but can change during the calculation due to orientation or geometry optimization, and the optimized geometries can be exported and reused in subsequent calculations. The next important decision is the overall type of calculation - single geometry or structure optimization, with or without harmonic frequencies. We should then choose the method; let's try a correlated-wavefunction CCSD(T) calculation. The default for the Hamiltonian model is to use pseudopotentials to represent core electrons where appropriate, but you can choose instead to include all electrons, either non-relativistically or with a scalar relativistic Hamiltonian. There is also the possibility to specify whether and how core orbitals are included in the correlation treatment. The final principal choice is the basis set. The guided proposals for this are dependent on the method, Hamiltonian and core correlation. You should first choose the overall quality - double, triple,... zeta - and then select within that if desired. It's also possible to specify the basis set element by element. The remainder of the input is associated with further options to control the running of the calculation and what it produces.| |
| |
| **Further notes:** | **Further notes:** |
| * ''Core-correlation:'' ''mixed'' means to include outer core orbitals for elements left of the p-block in the periodic system. ''small'' means also to include (outer) core orbitals of other elements. Note that the basis sets depend on these settings. | * ''Core-correlation:'' ''mixed'' means to include outer core orbitals for elements left of the p-block in the periodic system. ''small'' means also to include (outer) core orbitals of other elements. Note that the basis sets depend on these settings. |
| * ''Basis sets:'' first choose the quality (e.g. TZ, QZ), and then the default basis set. The recommended basis sets depend on the method. If the default basis is not available for some atom(s), or the use of other basis sets is desired for some atoms, use the element specific basis pulldown menu. | * ''Basis sets:'' first choose the quality (e.g. TZ, QZ), and then the default basis set. The recommended basis sets depend on the method. If the default basis is not available for some atom(s), or the use of other basis sets is desired for some atoms, use the element specific basis pulldown menu. |
| * The right-hand pane showing the input is not directly editable when in "guided mode". However, one can leave guided mode by clicking on this pane, and then any valid Molpro input can be entered. It is not possible to return to guided mode once it has been left. Externally-created projects also will open in this freehand mode. Other ways to manage projects include the [[https://molpro.gitlab.io/sjef/master/md__builds_molpro_sjef_program_sjef-program.html|sjef]] program or the [[https://molpro.gitlab.io/pysjef_molpro|pysjef_molpro]] and [[https://molpro.gitlab.io/pysjef|pysjef]] Python frameworks. | * The right-hand pane showing the input is not directly editable when in "guided mode". However, one can leave guided mode by clicking on this pane, and then any valid Molpro input can be entered. It is not possible to return to guided mode once it has been left. Externally-created projects also will open in this freehand mode. |
| |
| |
| |
| ==== Output window (white) ==== | ==== Output window (white) ==== |
| |{{:output_window.jpg?1000|output window}}|This window displays, with continuous update, the raw output produced by Molpro once the job has started. A second tab is provided for inspecting the log file that is used, for example, in finite-displacement geometry gradient calculations.| | |{{:output_window.jpg?1000|output window}}|This window displays, with continuous update, the raw output produced by Molpro once the job has started. A second tab is provided for inspecting the log file that is used, for example, in geometry optimisations.| |
| |
| |
| ==== View window (brown) ==== | ==== View window (brown) ==== |
| |
| |{{vimeo>471041694|starting gmolpro}}|The view window shows the final structure, ie after any geometry optimisation. It can also be used to display properties such as vibrational modes and orbitals, as well as the history of the geometry optimisation. In this example, a geometry optimisation and frequency calculation has already been carried out for glycine, and localised orbitals have been obtained. Notice that, as in the build window, you can alter the view, rotating by dragging with the mouse, or zooming using the centre mouse button (Linux) or command-key and mouse (macOS). First, let's check what happened in the optimisation by clicking the ''Optimization History'' button. We can play a movie of the optimising structure, or pick a particular point and export its geometry. The ''Vibrational Frequencies'' button shows the spectrum, from which individual modes can be selected and visualised. The ''Orbitals'' buttons brings up an energy level diagram from which individual orbitals can be selected. If more than one type of orbital has been calculated, you can choose the active set. Choose further display options from the ''Display/Orbital'' menu.| | |{{vimeo>471041694|starting gmolpro}}|The view window shows the final structure, ie after any geometry optimisation. It can also be used to display properties such as vibrational modes and orbitals, as well as the history of the geometry optimisation. In this example, a geometry optimisation and frequency calculation has already been carried out for glycine, and localised orbitals have been obtained. Notice that, as in the build window, you can alter the view, rotating by dragging with the mouse, or zooming using the centre mouse button (Linux) or command-key and mouse (macOS). First, let's check what happened in the optimisation by clicking the ''Optimization History'' button. We can play a movie of the optimisation, or pick a particular point and export its geometry. The ''Vibrational Frequencies'' button shows the spectrum, from which individual modes can be selected and animated. The ''Orbitals'' buttons brings up an energy level diagram from which individual orbitals can be selected. If more than one type of orbital has been calculated, you can choose the active set. Choose further display options from the ''Display/Orbital'' menu.| |
| |
| ===== Running calculations on remote servers ===== | ===== Running calculations on remote servers ===== |
| |
| |{{vimeo>778043635|running on remote servers}}|When you click ''Run'' in the input window, by default, the calculation will be run on your local machine. gmolpro needs a local copy of Molpro (from gmolpro version 2.0.0 on, gmolpro is bundled with Molpro, so that this is taken care of). After installing gmolpro, it will use the bundled version on the local machine. For many purposes, that is all you need. But support for running the calculation on another machine, and/or with non-default options such as process number and memory, is provided. One or more //backends// are defined in a file ''~/.sjef/molpro/backends.xml''. A backend is simply a specification of commands to launch, check and kill a job, and patterns to interpret status checks. One can then select which backend is assigned to the project, and this selection is remembered in the project's registry. The run command defined in the backend can be simply ''molpro'', or might be the name of a custom script to present a job to a scheduler such as Slurm. The name of the command can be followed by parameters, which can also be specified in substitutable form, which lets you define per-project options to be used in the job submission and (optionally) their default values, e.g. for memory, number of parallel processes, job-scheduling parameters etc. These values can be modified in the "Run parameters" pulldown for a chosen backend. gmolpro will always do its best to render a project constructed with any version of Molpro, but for job submission, Molpro version 2020.1 or later is required on the backend.| | |{{vimeo>778043635|running on remote servers}}|When you click ''Run'' in the input window, by default, the calculation will be run on your local machine. gmolpro needs a local installation of Molpro. Support for running the calculation on another machine, with options such as process number and memory, is provided. One or more //backends// are defined in a file ''~/.sjef/molpro/backends.xml''. A backend is simply a specification of commands to launch, check and kill a job, and patterns to interpret status checks. One can then select which backend is assigned to the project, and this selection is remembered in the project's registry. The run command defined in the backend can be simply ''molpro'', or might be the name of a custom script to present a job to a scheduler such as Slurm. The name of the command can be followed by parameters, which can also be specified in substitutable form, which lets you define per-project options to be used in the job submission and (optionally) their default values, e.g. for memory, number of parallel processes, job-scheduling parameters etc. These values can be modified in the "Run parameters" pulldown for a chosen backend. |
| |
| Configuring a backend is straightforward, and requires usually just the hostname (which will be connected to with ssh, and which should be accessible without password; the shell on the remote machine is expected to be able to execute basic shell commands) and the name of the run command. The run command script may contain any specified options, followed by a single argument that is the name of the input to Molpro. The ''molpro'' command conforms to this; for more complex requirements, for example for constructing a batch job, a wrapper script will be needed. | Configuring a backend is requires usually just the hostname (which will be connected to with ssh, and which should be accessible without password; the shell on the remote machine is expected to be able to execute basic shell commands) and the name of the run command. The run command script may contain any specified options, followed by a single argument that is the name of the input to Molpro. The ''molpro'' command conforms to this; for more complex requirements, for example for constructing a batch job, a wrapper script will be needed. |
| Further help is available on [[https://molpro.gitlab.io/sjef/master/md__builds_molpro_sjef_lib_backends.html|the detailed syntax of the backend.xml file]]. | Further help is available on [[https://molpro.gitlab.io/sjef/master/md__builds_molpro_sjef_lib_backends.html|the detailed syntax of the backend.xml file]]. |
| |
| If you wish to launch jobs on remote systems: | If you wish to launch jobs on remote systems: |
| - a file ''~/.sjef/molpro/backends.xml'' is necessary on the local machine, which specifies the remote machine and how jobs are submitted | - a file ''~/.sjef/molpro/backends.xml'' is necessary on the local machine, which specifies the remote machine and how jobs are submitted |
| - Molpro 2022.2 is recommended to be installed on the remote machine. Jobs will fail if Molpro is not found on the remote machine; jobs **//may//** work with a different Molpro version. | - Molpro must be installed on the remote machine. Jobs will fail if Molpro is not found on the remote machine. |
| - If jobs are managed by a scheduler, an appropriate script that constructs and submits the job, with the name of the input file as its single argument, possibly preceded by options. | - If jobs are managed by a scheduler, an appropriate script that constructs and submits the job is needed, with the name of the input file as its single argument, possibly preceded by options. |
| |
| ===== Frequently asked questions ===== | ===== Frequently asked questions ===== |
| {{:retina2.png?300|}} | {{:retina2.png?300|}} |
| |
| Please use the switch Display/Retina screen | -> Please use the switch Display/Retina screen. |
| |
| This switches between factor 1 and 2. If you need a more general factor, please edit the line in $HOME/.pqsmol/gmolpro.conf | This switches between factor 1 and 2. If you need a more general factor, please edit the line in $HOME/.pqsmol/gmolpro.conf |
| ==== • For developers: Using a different Molpro version ==== | ==== • For developers: Using a different Molpro version ==== |
| |
| From gmolpro version 2.0.0 on, gmolpro is bundled with Molpro, and uses this version of Molpro. | From version 2.0.0 on (and from 2.7.0, only the Mac version), gmolpro is bundled with Molpro, and uses this version of Molpro. |
| If you do not want to use the Molpro version in the bundle, then this can be achieved in the following way. | If you do not want to use the Molpro version in the bundle, then this can be achieved in the following way. |
| Open a terminal, and: | Open a terminal, and: |