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| gmolpro_graphical_user_interface [2025/04/02 13:29] – simplify doll | gmolpro_graphical_user_interface [2025/08/28 14:13] (current) – version 2.9.0 doll |
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| 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. | gmolpro (present release: version 2.8.0) should be used together with Molpro2025.2. 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. |
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| 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 15.6 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 41 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 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'' ) | - 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'' ) |
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| ^ gmolpro release versus ... ^ ... recommended Molpro version ^ remarks ^ | ^ gmolpro release versus ... ^ ... recommended Molpro version ^ remarks ^ |
| | | 2.9.0 |2025.3 (Linux: needs separate installation; Mac: bundled with 2025.3.0) | |
| | | 2.8.0 |2025.2 (Linux: needs separate installation; Mac: bundled with 2025.2.0) | Molpro versions from 2025.2 on need gmolpro version at least 2.8.0 because the basis set library has been extended| |
| | 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| | | 2.7.0 |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| |
| | 2.6.0 |bundled with 2024.3.0 | | | 2.6.0 |bundled with 2024.3.0 | |
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| Hint: older versions (2.2.0 and before) may need to set the variable LIBGL_ALWAYS_SOFTWARE to TRUE (e.g. in bash ''export LIBGL_ALWAYS_SOFTWARE=1'') on some platforms such as openSUSE15.5, before starting gmolpro (bug in the Mesa library) | Hint: very old versions (2.2.0 and before) may need to set the variable LIBGL_ALWAYS_SOFTWARE to TRUE (e.g. in bash ''export LIBGL_ALWAYS_SOFTWARE=1'') on some platforms such as openSUSE15.5, before starting gmolpro (bug in the Mesa library) |
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| On fedora41, ''dnf install gdk-pixbuf2-xlib gdk-pixbuf2-modules-extra'' may be necessary. | On fedora, ''dnf install gdk-pixbuf2-xlib gdk-pixbuf2-modules-extra'' may be necessary. |
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| In general, packages may have to be installed if they were not shipped with the operating system, e.g. freeglut. | In general, packages may have to be installed if they were not shipped with the operating system, e.g. freeglut. |
| ==== View window (brown) ==== | ==== View window (brown) ==== |
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| |{{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.| |
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| ===== 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 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. | |{{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. |
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| 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]]. |
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| 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. |
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| ===== Frequently asked questions ===== | ===== Frequently asked questions ===== |
| {{:retina2.png?300|}} | {{:retina2.png?300|}} |
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| Please use the switch Display/Retina screen | -> Please use the switch Display/Retina screen. |
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| 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 |