Posts made by fbodo

undefined

Hi QMQDCHEM ,
Could you share your BAND.DAT file so that I can do some quick test?
Thanks

undefined

Dear Alexander,
We runned a few tests, and, indeed, we found the same behavior. This, though, is not due to an error in the definition in the basis set, but rather to some formatting issue, since the Cs goes up to P4 the code expects that also the Iodine pseudo goes up to P4 and fills the missing coefficients and exponents with zeros.

Luckily there is an easy workaround to this, it is sufficient to flip Cs and I definition in the geometry and the results are the same as the one you obtained by defining the basis set in the input as you can see from my test.

I will leave you here two output snippets hoping that they help clarifying the issue:

Cs defined before I in the geometry section

 INPUT COORDINATES

 ATOM AT. N.              COORDINATES
   1  38     5.000000000000E-01  5.000000000000E-01  5.000000000000E-01
   2  55     0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
   3  53     0.000000000000E+00  5.000000000000E-01  5.000000000000E-01
[...]

 *******************************************************************************
 *** PSEUDOPOTENTIAL INFORMATION ***
 *******************************************************************************

 ATOMIC NUMBER  38, NUCLEAR CHARGE 10.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS     6.9334610  135.2710429   0     4.1140038   17.9440714   0
  P1 TMS     7.2168166   29.4380813   0     7.1736962   58.8806749   0
             3.0227988    4.9362827   0     2.8656990    9.7233521   0
  P2 TMS     6.3215146   11.9072392   0     6.3914995   17.8595514   0
             1.7697266    2.1991802   0     1.6367717    2.8935709   0
  P3 TMS     4.2441984   -5.5093333   0     4.2291645   -7.3046417   0

 ATOMIC NUMBER  55, NUCLEAR CHARGE  9.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS     4.0811192   84.5477223   0     2.4215224   16.6540350   0
  P1 TMS     5.5339726   52.3496307   0     5.5067944  104.6994132   0
             2.2809616    8.8065577   0     2.1034905   17.6166111   0
  P2 TMS     1.8131494    5.2689855   0     1.8077217    7.9036419   0
             0.8729040    1.3364313   0     0.8587203    2.0056513   0
  P3 TMS     5.2170839  -16.4976543   0     5.1481965  -23.3081313   0
             1.5805995   -2.2368273   0     1.3478959   -2.2269420   0
  P4 TMS     1.8077398   -2.5041987   0     1.8050613   -3.1382445   0

 ATOMIC NUMBER  53, NUCLEAR CHARGE 25.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS    40.0333760   49.9896490   0    17.3005760  281.0065560   0
             8.8517200   61.4167390   0
  P1 TMS    15.7201410   67.4162390   0    15.2082220  134.8076960   0
             8.2941860   14.5665480   0     7.7539490   28.9684220   0
  P2 TMS    13.8177510   35.5387560   0    13.5878050   53.3397590   0
             6.9476300    9.7164660   0     6.9600990   14.9775000   0
  P3 TMS    18.5229500  -20.1766180   0    18.2510350  -26.0880770   0
             7.5579010   -0.2204340   0     7.5974040   -0.2216460   0
  P4 TMS     0.0000000    0.0000000   0     0.0000000    0.0000000   0

I defined before Cs in the geometry section

 INPUT COORDINATES

 ATOM AT. N.              COORDINATES
   1  38     5.000000000000E-01  5.000000000000E-01  5.000000000000E-01
   2  53     0.000000000000E+00  5.000000000000E-01  5.000000000000E-01
   3  55     0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
[...]
 *******************************************************************************
 *** PSEUDOPOTENTIAL INFORMATION ***
 *******************************************************************************

 ATOMIC NUMBER  38, NUCLEAR CHARGE 10.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS     6.9334610  135.2710429   0     4.1140038   17.9440714   0
  P1 TMS     7.2168166   29.4380813   0     7.1736962   58.8806749   0
             3.0227988    4.9362827   0     2.8656990    9.7233521   0
  P2 TMS     6.3215146   11.9072392   0     6.3914995   17.8595514   0
             1.7697266    2.1991802   0     1.6367717    2.8935709   0
  P3 TMS     4.2441984   -5.5093333   0     4.2291645   -7.3046417   0

 ATOMIC NUMBER  53, NUCLEAR CHARGE 25.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS    40.0333760   49.9896490   0    17.3005760  281.0065560   0
             8.8517200   61.4167390   0
  P1 TMS    15.7201410   67.4162390   0    15.2082220  134.8076960   0
             8.2941860   14.5665480   0     7.7539490   28.9684220   0
  P2 TMS    13.8177510   35.5387560   0    13.5878050   53.3397590   0
             6.9476300    9.7164660   0     6.9600990   14.9775000   0
  P3 TMS    18.5229500  -20.1766180   0    18.2510350  -26.0880770   0
             7.5579010   -0.2204340   0     7.5974040   -0.2216460   0

 ATOMIC NUMBER  55, NUCLEAR CHARGE  9.000,                      PSEUDOPOTENTIAL
   TYPE       EXPONENT      COEFF.    N      EXPONENT      COEFF.    N
  P0 TMS     4.0811192   84.5477223   0     2.4215224   16.6540350   0
  P1 TMS     5.5339726   52.3496307   0     5.5067944  104.6994132   0
             2.2809616    8.8065577   0     2.1034905   17.6166111   0
  P2 TMS     1.8131494    5.2689855   0     1.8077217    7.9036419   0
             0.8729040    1.3364313   0     0.8587203    2.0056513   0
  P3 TMS     5.2170839  -16.4976543   0     5.1481965  -23.3081313   0
             1.5805995   -2.2368273   0     1.3478959   -2.2269420   0
  P4 TMS     1.8077398   -2.5041987   0     1.8050613   -3.1382445   0

I hope this helps

undefined

Dear esmuigors
esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

Should I only take the atoms labelled by "T" if the lattice is tetragonal, and which ones are to be taken in case of an orthorombic one? Or does "T"'and "F" stand just for "TRUE"'and "FALSE"?

You are correct T and F stand for 'TRUE' and 'FALSE'.

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

I am actually talking about the standard runPcry23 script. Perhaps it should not be like that? Or should I modify this script?

That script already contain the few line of codes I suggested you, if not feel free to modify it and add those lines.

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

Actually, I have now tried using only the "T"-labeled atoms and got this error:

ERROR **** geometry **** FORMAT ERROR IN INPUT DECK

I checked the input on top of the CS2_B1WC.pob_tzvp_rev2_gamma_onlyT.out file it seems like you are defining six atoms in the asymmetric unit, but only two atomic positions are specified in the input.

CRYSTAL
0 0 0
64
6.34350113
5.54788046
9.71085545
6.      ! Definitions of the number of atoms in the asymmetric unit 
   6	 0.000000000000e+00	 0.000000000000e+00	-5.000000000000e-01 
  16	 2.303037287581e-17	 3.119080311720e-01	 1.207617820468e-01
ATOMSYMM
...

The number of atoms in the asymmetric unit and the position specified should always match.

I hope this helps you,

Best,

undefined

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

About the manual extraction – do I understand correctly that I should take the primitive and not crystallographic cell parameters?! The input in the .d12 file is in crystallographic cell, isn't it?

Hi esmuigors,
If you want to proceed with the manual extraction of the geometry you should copy the Crystallographic cell lattice parameters required by the space group you are working with (e.g. Monoclinic will require you a, b, c and β, while a cubic only the a lattice vector), the only exception to this are P lattices where the primitive and crystallographic coincide. Accordingly, also the fractionary coordinate you will copy should be the one of the Crystallographic cell, but you should copy only the atoms present in the asymmetric unit of your system identified by a T in the FINAL OPTIMIZED GEOMETRY print in the .out file, I will include here below an example to better clarify.

 FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM      3
 (NON PERIODIC DIRECTION: LATTICE PARAMETER FORMALLY SET TO 500)
 *******************************************************************************
 LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
 PRIMITIVE CELL - CENTRING CODE 6/0 VOLUME=    62.890767 - DENSITY 13.512 g/cm^3
         A              B              C           ALPHA      BETA       GAMMA 
     6.02167869     6.02167869     6.02167869   147.475653 147.475653  46.660012
 *******************************************************************************
 ATOMS IN THE ASYMMETRIC UNIT    2 - ATOMS IN THE UNIT CELL:    4
     ATOM                 X/A                 Y/B                 Z/C    
 *******************************************************************************
      1 T 273 TA   -2.420755613827E-03 -2.420755613827E-03  4.983867094700E-20
      2 F 273 TA   -2.524207556138E-01  2.475792443862E-01 -5.000000000000E-01
      3 T 233 AS    4.184207556138E-01  4.184207556138E-01 -2.220446049250E-16
      4 F 233 AS    1.684207556138E-01 -3.315792443862E-01 -5.000000000000E-01

 TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL
  0.0000  1.0000  1.0000  1.0000  0.0000  1.0000  1.0000  1.0000  0.0000

 *******************************************************************************
 CRYSTALLOGRAPHIC CELL (VOLUME=        125.78153367)
         A              B              C           ALPHA      BETA       GAMMA 
     3.37253732     3.37253732    11.05868170    90.000000  90.000000  90.000000

 COORDINATES IN THE CRYSTALLOGRAPHIC CELL
     ATOM                 X/A                 Y/B                 Z/C    
 *******************************************************************************
      1 T 273 TA   -1.956455588613E-19  2.296201495291E-19 -2.420755613827E-03
      2 F 273 TA   -5.000000000000E-01  2.084229456032E-17 -2.524207556138E-01
      3 T 233 AS    5.000000000000E-01  5.000000000000E-01 -8.157924438617E-02
      4 F 233 AS   -5.117515658395E-17 -5.000000000000E-01 -3.315792443862E-01

In this example you'll have to extract from the second geometry print (i.e. Crystallographic cell) the a and c lattice parameters, given the Tetragonal lattice, alongside the fractionary coordinate of atoms 1 and 3.

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

Are there any workarounds to persuade the script to actually copy the fort.34 file?

In this regards, I don't have your script, but it should be sufficient to add to your script something along these lines in the section where all the files are copied back to your working folder:

if [ -e fort.34 ] then
    cp fort.34 $HERE/$INPUTFILE.f34
fi

in this case $HERE=$PWD, while $INPUTFILE is the variable corresponding to your input name.

I hope this helps.

undefined

Hi job314,
I have tried to run the input file and geometry you provided us as you can see in the enclosed output file it runned without any hickups for us. Please let us know if you were to encounter this issue once more

undefined

Hi job314,
I gave a quick look at the files you have uploaded, and I don't seem to find the RESTART option in the INPUT file. Could you please check if this is, indeed, the input associated with your issue?

undefined

CRYSTALClear is an open source project that provides an easy Python interface with CRYSTAL. The package allows you to quickly extract information from the CRYSTAL output files and to easily generate customizable plots of computed quantities. In particular, the package supports plotting functionalities for:

Band Structures and DOSS	Mechanical Properties	IR and Raman Spectra

QTAIM	Transport Properties	Density Maps

For a more comprehensive review of the package capabilities we refer you to the Documentation Website.

How to Install

Prerequisites:

Python: Ensure you have Python installed on your system.
conda (Optional but Recommended): conda is a powerful package and environment manager that simplifies the process of managing Python dependencies. If you don't have conda, install it from the official Anaconda distribution: https://www.anaconda.com/

Installation Steps:

Create a Dedicated Environment (Recommended):
Creating a separate conda environment for CRYSTALClear helps isolate its dependencies from other projects and avoid potential conflicts.

conda create -n env_name python=3.9  # Replace 3.9 with your desired Python version

Activate the Environment (Reccommended):

conda activate env_name

Install CRYSTALClear using pip:

pip install CRYSTALClear

This command will install the CRYSTALClear library and its dependencies.

Verification:

Check Installation:
After installation, you can verify the installation by importing the library in a Python script or interactive session:

import CRYSTALClear

If the import is successful without any errors, the installation was successful.

Additional Notes:

Dependencies: The CRYSTALClear library might have dependencies on other libraries. pip will automatically install these dependencies during the installation process.
Updating: To update the CRYSTALClear library to the latest version:

pip install --upgrade CRYSTALClear

Troubleshooting:

If you encounter any issues during installation:
- Check for any error messages and try to resolve them based on the error descriptions.
- Ensure you have an active internet connection.
- Try updating pip to the latest version: pip install --upgrade pip
- If the issue persists, consider creating a new conda environment and reinstalling the library.

If you the issues persist please feel free to comment here below we will try our best to help you.

How to Use it

In order to use any of the feature available in the package the user need to generate
a CRYSTAL object through the crystal_io module. Three classes are available to the user
for different use cases:

Crystal_output: To extract informations and generate the object required to plot
from any .out file of the CRYSTAL package.
Properties_output: To generate the objects required to plot any of quantities
stored in the .DAT and .f25 files generated by the PROPERTIES module.
External_unit: To generate the objects required to plot any of the quantites stored
in .DAT and .f25 file generated by CRYSTAL.

Once the object is generated the user can generate the desired plot using the functions
in the plot module

Example

   # Example Band Structure plot
   from CRYSTALClear.crystal_io import Properties_output
   import CRYSTALClear.plot as CCplt
   import matplotlib.pyplot as plt

   data = Properties_output().read_electron_band()
   CCplt.plot_electron_band(data, **kwargs) # see the documentation for the available **kwargs 

   # The plotting function returns a matplotlib object that can be visualized as follows
   plt.show()

The plotting function will return one (or a list of) matplotlib object(s) that the user can easily modify as any other plot produced with the library.

For a more comprehensive set of example we refer you to the following jupyter notebook repository.

How to Contribute

Any contribution to the project is more than welcome and greatly appreciated, given the open source nature of the project. If you'd like to do so, please check our guidelines on GitHub

How to Cite

If you use this package in any of your work we kindly ask you to cite the following pubblication:

Camino, Bruno, Huanyu Zhou, Eleonora Ascrizzi, Alberto Boccuni, Filippo Bodo, Alessandro Cossard, Davide Mitoli, Anna Maria Ferrari, Alessandro Erba, and Nicholas M. Harrison, Comput. Phys. Commun. 292, 108853 (2023).

@article{camino2023crystalpytools,
  title={CRYSTALpytools: A Python infrastructure for the CRYSTAL code},
  author={Camino, Bruno and Zhou, Huanyu and Ascrizzi, Eleonora and Boccuni, Alberto and Bodo, Filippo and Cossard, Alessandro and Mitoli, Davide and Ferrari, Anna Maria and Erba, Alessandro and Harrison, Nicholas M},
  journal={Computer Physics Communications},
  volume={292},
  pages={108853},
  year={2023},
  publisher={Elsevier}
}