General¶
Introduction¶
This document will provide background information for the Graphical User Interface, part of the AMS package.
The purpose of this document is to give more detailed background information on how the GUI operates. It will not explain how to use it in detail. For that reason, we strongly suggest that before reading this document, you first check the GUI tutorials.
Release 2024.1¶
This release no longer supports old style ReaxFF input and output (the non-AMS version with the .rxkf result files). This release only supports QE via AMS, the old QE interface has been removed.
In comparison to AMS-GUI 2023.1, the 2024.1 release offers many bug fixes and the following new changes or main functionality:
General:
Show Info: Axes And Planes menu in View menu (if present): show info about the vector defined by selecting 2 atoms:
length of vector
angle with x, y and z-axis
projection on x, y and z-axis
also angle and projection on user defined vector and user defined plane (user specifies normal vector)
for periodic systems, similar info for angles and projections on the lattice vectors
for periodic systems, also show result using shortest image convention
In Show Info view: pin information so more info can be seen at the same time.
The Show Info view will update in AMSmovie when playing a movie.
AMSjobs:
Command to copy paths for local or remote jobs, in the Jobs menu, so they can easily be used in a terminal.
AMSinput:
Export a job to a PLAMS Python script (only applicable to single AMS jobs, not more complicated tasks like COSMO-RS Compound or Conformers).
No longer supports opening old style ReaxFF input (the non-AMS version)
SCRF support removed (as ADF no longer supports it)
Support QE engine (instead of the old non-engine QE)
Improved selection of ReaxFF force fields (note double click in table is easiest to use)
Support reaxff.charges option to define charge per atom (edit in AtomDetails).
Support defining TS reaction coordinate using an initial and final system
Support Repulsion engine add-on
DFTB Single Point more button links to Fragment panel
Builder now puts new molecules in region Builder instead of the confusing Auto_Generated region
Import molecule(s) from file(s): use filename or formula as name of the imported molecule (if importing into an empty molecule space). Note the molecule name is visible only when multiple molecules are present (via Edit -> New Molecule for example, or when importing multiple files.).
Import molecules from files: now you can select multiple files to be imported at the same time, each in its own molecule space.
Import molecule using SMILES: import multiple SMILES (separated by spaces) as multiple molecule. And use SMILES or formula as name of the imported molecule (if importing into an empty molecule space). Note the molecule name is visible only when multiple molecules are present (via edit -> New Molecule for example, or when using multiple SMILESs).
Import molecule from a forcefield.rkf file: read forcefield types, charges and patch file as well
Use LoadSystem key via Coordinates panel
When showing multiple molecules in a grid, clicking in an empty grid space will create a new molecule
Powder X-Ray Diffraction (XRD) available from the View menu. This requires pymatgen which can be installed from SCM → Packages
Delete All Molecules: same as New, but only for the molecules (leaves the changed settings intact)
Add TSRC distance term using a dummy atom
BAND restart DOS and band structure support
Paste multiple values in Atom details fields: depending on number of pasted values update all atoms in atom selection (also make sure current field is in selection), all atoms, or only current field.
Improve reading of run scripts (especially picking up input options for non-unique keys)
Paste engine block only (starting with Engine and ending with EndEngine)
Import Engine Settings (similar to pasting the engine block only), from .run scripts, ams.rkf (the userinput variable is used), or engine.txt as made by params. Intended use is with MD Active Learning, to use the resulting engine after training in another job (just use Import Engine Settings and select the ams.rkf file from the active learning job). The command lives in the File menu.
When using LoadEngine, switch to a dummy LoadEngine module to make it clear for the user and to prevent engine settings to be changed. LoadEngine could be used when importing a run script that is using it.
Offer to try to read run script when pasting an AMS job script (recognized by something like ams << eor and matching eor at end of input, as in all example run scripts and run scripts made by AMSinput)
Support MD Reaction Boost
MD Active Learning module (which is Simple Active Learning), see also Import Engine Settings
Support pNMR
Perturb atoms randomly by 0.01 Angstrom via the Edit→Perturb option.
Undo/Redo work only on the molecule structure, and now also only when the focus is on that panel, thus while editing the molecule or after clicking in it, and NOT when editing input options.
AMSmovie:
PES Scans: improve labels below molecule
PES Scans: option to reorder all frames by PES points, useful if some PES points are redone at the end
No longer support .rxkf files
Analysis MSD supports properties, making it possible to compute ionic conductivity
Active learning trajectories: in File -> Related Files the trajectories of related trajectories are available (stepX_attempt_Y_simulation, and final simulation).
AMSview:
NCI diagram support for ADF results
Improve ease of positioning planes (contour planes and colored planes), via explicit setting of normal vectors and a point on the plane
Add visualization along a line: the values of the field, and these values integrated along the line. The resulting line graph may be saved as image or as XY values.
Add visualization along a line: now also the values integrated over a plane perpendicular to the line, and these may also be integrated over the line (thus integrating 3D space);
Add special Grid Cell that covers at least one cell spanned by the lattice vectors (offset to match the cell as shown by AMSview).
AMSspectra:
NMR: support visualization of pNMR results
AMSdos:
Support display of DOS info from QE using QE as AMS engine, older QE stuff no longer supported.
AMSbands:
Support display of DOS and BAND structure info from QE using QE as AMS engine, older QE stuff no longer supported.
ParAMS GUI:
Improved selection of ReaxFF force fields
Generate validation set now by JobID as an option
Option to load a paramter (interface) yaml file (it will replace any paramter data already loaded).
Support Machine Learning training, input and visualization
When opening a MD Active Learning job (simple active learning) the last training result will be shown.
Option to open AMSinput with an engine with training results (based on the engine.txt files)
Release 2023.1¶
In comparison to AMS-GUI 2022.1, the 2023.1 release offers many bug fixes and the following new main functionality:
General:
Two new periodic view options are added. The three available options are now:
(old) Repeat unit cells
(new) A layer of x (default = 2.0) Angstrom around the unit cell
(new) Complete the molecules that are partially inside the unit cell
The 2.0 Angstrom layer is the new periodic view default, and the periodic display threshold was increased.
New atom selection methods are added
Select atoms by index
Select atoms with an interactive box widget and box parameters
Select atoms by region
AMSjobs:
Apply to all check when doing something to multiple jobs
Report to tsv file now always includes filename from which results are collected
AMSinput:
Presets have been changed: check the documentation for details.
Builder supports explicit bonds from .in files
ACE Reaction Network support
ASE engine support
Improve import of job from run scripts
Show molecule formula per region on Regions panel
Sort coordinate table by coordinate or element type
PES scan per x/y/z coordinate supported
Multiple NEB intermediates
Dynamic factors in hybrid engine
MD reactor (Martinez nanoreactor)
GW for BAND
MP2, RPA and double hybrids for BAND
Conformers support, both generating conformers and using conformers with further calculations using the conformers.rkf file
MD analysis jobs supported as part of the main job
MD analysis: automatically run over all elements for RDF and ACF if requested
Save As: menu shortcut
Preoptimizer now optionally honors constraints
AMSmovie:
The graphs use now Time on the X-axis instead of Frame, if Time is available for plotting (as in MD results)
Analysis of MD trajectories now remember settings and shows last result, if present
Analysis: multiple calculations for one trajectory of same type (multiple RDF etc) now supported
Analysis: calculated the RDF/ACF/MSD/Histogram in a separate job, possibly on some remote system
ACE reaction support
ChemTraYzer2 support: handle the molecule population and event files, producing graphs in addition to the tables
AMSspectra:
Support Conformers via amsbatch.rkf
Support BAND GW
AMSbands:
Option to shift the Fermi energy to zero.
AMSdos:
Use stacked curves for the partial DOS (similar to the DOS in AMSbands).
Option to shift the Fermi energy to zero.
Option to mirror beta dos.
AMSkinetics:
Import PES Exploration binding sites result to obtain a complete Zacros system setup
AMSview:
Visualization of atom vector properties
Visualization of NBO natural charges
Visualization of RISM Guv RDF
AMSoutput:
Added some DFTB menu shortcuts
Added generic Header menu with shortcuts to all headers (any text between bars)
ParAMS GUI:
GLOMPO support
GUI to set up the job options (in the Settings tab)
Release 2022.1¶
In comparison to AMS-GUI 2021.1, the 2022.1 release offers many bug fixes and the following new main functionality:
General:
All GUI modules transfer job to ParAMS GUI via menu command (cmd/ctrl-T)
(Linux only) Better dependency handling. Incompatible libraries from $AMSBIN/lib no longer need to be removed.
(Windows only) Option to use a different method of GUI inter-communication. The default uses sockets that can be blocked by security software. Set the environment variable SCM_SCMD_PIPE to use the new alternative that uses named pipes.
AMSinput:
Open .run files (also importing many options)
Import system block from .run files
Open and export system block (as in run scripts) as .in files
AMS Lattice scan
GFNFF engine
Lennard-Jones engine
APPLE&P Force Field type
FCF support updated
GW support updated
DFTB fragments
QTAIM / IQA support updated
FQFMu forcefield for FQQM.
FQQM and FDE combination
Workflows target with OLED tasks
Region constraints
Constraint for all bonded pairs in selection
Constraints work with shortest PBC distance
Conceptual DFT / Fukui improvements by Laurent Joubert
Autografs update SBU database
Single Point option for COSMO-RS compound
Crystal slicer automatically converts to conventional cell and aligns axes
AMSjobs:
Better support for running PLAMS jobs
Improved queue settings interface
Option to test your remote queue settings
Better support for larger runscripts for queuing systems
AMSspectra:
Support for GW improved
Preferences:
Added region display radius setting
AMSlevels:
DFTB fragment orbitals
AMSview:
Visualization of OLED properties
Histograms of atom properties
DFTB fragment orbitals
AMSbands:
Support for spin-orbit coupling results
AMSmovie:
Bond source can be chosen. Choices are: auto (prefers stored bonds), guessed, initial, or no bonds.
PES Exploration/EON energy landscape. Addition of Arrhenius prefactors to info and Fragmented states.
Acerxn support
ChemTraYzer 2:
Input
setup input (based on json description and .def file
AMSinput style unit changes and revert to default (right click)
when opening the GUI, update the input fields with values as found in the chemtrayzer2/job file, if it exists
Running
run ChemTraYzer 2, job
output and results are in chemtrayzer2 folder next to the ams.rkf file
progress dialog while running, cancel button to interrupt
errors from run are reported
Output
automatically show the results in tables when available
right bottom of table: button with name of table, click it to open by the OS (on MacOS open the .csv file in Numbers for example)
tables can be sorted per column
tables can be searched, with some advanced search options. use help balloon to get info on search syntax
feedback on search in status line (number of items found, column searched)
click, shift-click, control (or right) click to adjust selection in tables
selection in upper table searches for matching evens in lower table
selection in lower table shows corresponding atoms (hiding other atoms) in corresponding (first) frame in the Movie window
left-right arrow keys to skip through movie frames
up-down arrow keys to move selection up or down (thus go through different events for example)
escape clears selection, or the search if it has focus
if no selection, escape clears the search
Mean Square Displacement (MSD) via analysis program
ParAMS GUI:
General
‘All’, ‘Jobs’, ‘Training Set’, ‘Validation Set’, ‘Engines’: table with training data
Molecule window: show system for selected entries
‘Info’: detailed info for any entry in job collection or training data
‘Parameters’: table with parameters, ranges and other details to be optimized
‘Params Configuration’: show and set up the ParAMS job details
‘Graphs’: results of optimization in graphs
‘Results’: text output files
import old style reaxff geo/params files
revert option to ditch changes due to editing or handling results
Running
run the ParAMS job via AMSjobs
opening a ParAMS job will automatically read the results if available
live update of the results
running and live update also work for running on remote machines (as all other jobs in AMSjobs)
restart a previous run when using the CMA optimizer
Training Data
different tabs to show all of these or just one subset (‘All’, ‘Jobs’, Training Set’, ‘Validation Set’, ‘Engines’)
filter by type of entries (Energies, Bonds, PES, Jobs, Engines, …)
when multiple systems are relevant for an entry, use arrow left-right to move through them
add jobs from inside the Params GUI, or via any other GUI module (cmd/ctrl - T)
use the ParAMS importers to generate training set entries when importing a job
select atoms to set the proper index when creating some expressions
menu commands to add most common expressions in the training set
edit all (non-output) items in all tables
editing via AMSinput for jobs and engines
smart editing of multiple items in many cases (expressions for multiple items like relative energies, or deactivate all selected parameters for example)
tab-completion to quickly enter Job IDs
energy expressions may be balanced automatically (as they correspond to a reaction typically)
set up training set and validation set (manual or random)
merge training sets / job collections
edit all JobIDs at once: prefix or change
when results are available the contribution to errors is shown with the matching item
results are live-updating
Parameters
ReaxFF, xTB and Lennard-Jones parameters supported
detailed information about meaning of parameter and optimization range etc
adjust parameter optimization range Min and Max
generate new ReaxFF blocks, initialize ReaxFF blocks
parameters are live-updating
ParAMS Configuration
set up the params.conf.py file to use for running
predefined common options via menus
fully editable by user if desired
Graphs
relevant graphs are shown automatically when running
graphs are live-updating
validation and training set graphs together, compare with first iteration
graphs of PES data (like energy vs distance or angle etc)
interaction in graphs (click on an item to select matching training set entries, and select relevant atoms in molecule display if applicable)
save graphs as image or xy from File menu
Results
show text output easily accessible via menus
text is live-updating
Tables
tables can be sorted per column
tables can be searched. use help balloon to get info on search syntax
feedback on search in status line (number of items found, column searched)
click, shift-click, control (or right) click to adjust selection in tables
up-down arrow keys to move selection up or down
escape clears selection, or the search if it has focus
if no selection, escape clears the search
AMSkinetics
Renamed module from Microkinetics
Added support for the Kinetic Monte-Carlo program Zacros.