Developer group

dmitoli

Dear CRYSTAL community,

We would like to introduce the beta release of CRYSTALLine, a new desktop app to display and edit structures for CRYSTAL, to animate phonon modes, and to plot the properties a calculation returns. It's cross-platform: it runs on Linux, macOS and Windows. It is built on CRYSTALClear, and is free software under the GNU GPL v3.

CRYSTALLine follows in the tradition of MOLDRAW, written by Prof. Piero Ugliengo, which served this community for over twenty years: a program on your own machine for looking at a structure and editing it.

What it does

Handling of CRYSTAL outputs, .gui/.f34 and CIF files, each in a tab of its own, with crystallographic and calculation data beside it.
Automated live detection of symmetry (through spglib).
Easy structure editing through drag-and-drop: add, move, delete or change atoms, build supercells, switch between primitive and crystallographic settings.
Animation of vibrational modes of a frequency calculation, including out-of-Γ phonons with several exporting options.
Input builder for CRYSTAL (.d12) and PROPERTIES (.d3) from the structure on screen.
First Brillouin Zone visualiser and k-path selection.
Advanced plotting tools (from CRYSTALClear): electronic and phonon band structure, densities of states, IR and Raman spectra (harmonic and anharmonic), elastic surfaces and sections, equations of state, and simulated XRD patterns. Most plots have their options beside them and are redrawn as these are changed.
Visualisation of crystalline orbitals, charge density and electrostatic potential over the structure as isosurfaces or as slices along a lattice plane.

Installing

It needs Python 3.11 or newer, best in an environment of its own:

conda create --name crystal python=3.12
conda activate crystal
pip install CRYSTALLine
crystalline

The documentation has a small MgO example to try it, with a band structure and a phonon dispersion.

This is a beta

Accidents may take place. We would be grateful for reports of anything that fails or looks wrong, either in reply to this post or at github.com/crystaldevs/CRYSTALLine/issues. Suggestions for what to add next are more than welcome too.

Links

Documentation: crystaldevs.github.io/CRYSTALLine
Source code: github.com/crystaldevs/CRYSTALLine
PyPI: pypi.org/project/CRYSTALLine

Give it a try!

aerba

A possible "work-around" just came to my mind. As far as I understand, your job successfully completed the first deformation (STRAIN 1) to later fail during the next deformation (STRAIN 3) with the following error:

ERROR **** SCF **** SG_IRR ALLOCATION ERROR: ALREADY ALLOCATED

It looks like some arrays are not properly deallocated when moving from one deformation to the next. A possible work-around would be to compute each deformation in an independent calculation. You can use the DEFORM option to specify what deformations should be active. For instance with:

ELASTCON
PRINT
DEFORM
0 0 1 0 0 0
END

you would be asking to consider just the third deformation as active. With PRINT you ask for extended printing options. You will find the computed elastic constants for the third row of the elastic tensor printed in the output.

As for your calculation there are only three symmetry-independent deformations:

LIST OF ACTIVE DEFORMATIONS:
1
3
4

you could have all the elastic constants by running three calculations. One with:

ELASTCON
PRINT
DEFORM
1 0 0 0 0 0
END

a second one with

ELASTCON
PRINT
DEFORM
0 0 1 0 0 0
END

and a third with

ELASTCON
PRINT
DEFORM
0 0 0 1 0 0
END

Let me know if this helps.

aerba

Hi,

We have run your input files with CRYSTAL23 and the calculation was successful (see attached output file). Are you by any chance running an older version of the program?

aerba

Let me run some tests

aerba

Hi,

While there is no option to estimate the necessary memory, there are a couple of advanced printing options to monitor the memory used step-by-step throughout the calculation. Please, refer to the MEMOPRT and MEMOPRT2 keywords in the User's Manual.

Let me know if this helps,

aerba

Hi,

The input/output files you uploaded look fine. It is difficult for me to understand what happened.

aerba

Hi Jonas,

I see from your input that you are scanning along mode number 12 (with positive harmonic frequency of ~66 inverse centimeters). Have you tried scanning along mode 1 (with "negative" harmonic frequency of ~-14 inverse centimeters)?

aerba

Of course, in no case an isolated molecule would have access to neighboring functions. But in the crystal it does. If its own basis is not complete, a molecule in the crystal can get extra-stabilized by the neighboring functions not because of a "physical" or "chemical" interaction with neighboring molecules but because of an artifact due to the incompleteness of its basis. So if you were to compute the cohesive energy just as energy of the crystal - energy of the bare molecule, you would get an extra unphysical interaction. To make sure you get the right cohesive energy you could do one of two things: i) remove the extra interaction from the calculation on the crystal; ii) add it also to the molecular calculation so that it cancels when taking the difference (this is the MOLEBSSE strategy, also known as Boys-Bernardi counterpoise correction).

aerba

Hi Jonas,

As you correctly point out, in this case the molecular calculations are not affected by BSSE as you are extracting a single molecule (i.e. with no neighbors).

The calculation that is affected by BSSE is the one on the crystal, where each molecule within the molecular crystal could potentially "benefit" from the basis functions of the neighboring molecules if its own basis is not complete. So we use MOLEBSSE for this, to make sure we compare apples with apples (i.e. the energy of a molecule in the crystal that has access to the basis functions from neighboring molecules, with the energy of an isolated molecule that also has access to the same neighboring basis functions).

Hope this helps clarifying things a little,

SilviaCasassa

Dear Prof. Piquini,
I am sorry but I never received your files. Could you please try again?

Developer

Posts

What it does

Installing

This is a beta

Links

Member List