Q. How to create input file from cif files?
Ans. First of all, why cif files to be used to create input file for QE. Because bigger unit cells with more than 3 types atoms are difficult to write by hand and to verify the input (at least for me). Cif files consists of everything related to crystallography of the material of the interest but it is not yet ready for the in put for QE.
Lets take an example how to prepare input from cif file called EDI.cif (available from IZA website)
Step 1. copy the EDI.cif to ~(path to espresso)/espresso-xx.x/PW/tools
Step 2. type "./cif2qe.sh EDI > EDI.in" by typing this you will be invocking a script to convert cif files to QE input file (dont add cif extenction for EDI in put and give .in extenction for out put)
Step 3. You should see EDI.in QE input file in the folder and open this file, you can observe that the scpipt had printed many option for you which is required for QE calculation but this is not complete an exhaustive, but you can use this as templete.
Step 4. Open the EDI.cif file in one of the following program, GIDS or VESTA or any other program which can visualize the cif file. Convert the building units of cif file into complete lattice. Now save the complete lattice in XYZ format this will be in angstrom units.
Step 5. Open this EDI.xyz file in gedit & copy the coordinates and paste this in to the EDI.in file replacing existing atomic coordinates (if any) change the ATOMIC_POSITIONS ******* to ATOMIC_POSITIONS angstrom.
Step 6. Verify the input file by visualizing in prompt by xcrysden --pwi EDI.in if any error verify the input card nat = xx. Always nat should be equal to number of atoms in the unit cell, count the number of atoms in file in this case nat = 15. Now execute the same command and you should be able to visualize the input file properly.
Don't forget to mention bohr for CELL_PARAMETERS as it is converted to
Ans. First of all, why cif files to be used to create input file for QE. Because bigger unit cells with more than 3 types atoms are difficult to write by hand and to verify the input (at least for me). Cif files consists of everything related to crystallography of the material of the interest but it is not yet ready for the in put for QE.
Lets take an example how to prepare input from cif file called EDI.cif (available from IZA website)
Step 1. copy the EDI.cif to ~(path to espresso)/espresso-xx.x/PW/tools
Step 2. type "./cif2qe.sh EDI > EDI.in" by typing this you will be invocking a script to convert cif files to QE input file (dont add cif extenction for EDI in put and give .in extenction for out put)
Step 3. You should see EDI.in QE input file in the folder and open this file, you can observe that the scpipt had printed many option for you which is required for QE calculation but this is not complete an exhaustive, but you can use this as templete.
Step 4. Open the EDI.cif file in one of the following program, GIDS or VESTA or any other program which can visualize the cif file. Convert the building units of cif file into complete lattice. Now save the complete lattice in XYZ format this will be in angstrom units.
Step 5. Open this EDI.xyz file in gedit & copy the coordinates and paste this in to the EDI.in file replacing existing atomic coordinates (if any) change the ATOMIC_POSITIONS ******* to ATOMIC_POSITIONS angstrom.
Step 6. Verify the input file by visualizing in prompt by xcrysden --pwi EDI.in if any error verify the input card nat = xx. Always nat should be equal to number of atoms in the unit cell, count the number of atoms in file in this case nat = 15. Now execute the same command and you should be able to visualize the input file properly.
Don't forget to mention bohr for CELL_PARAMETERS as it is converted to
nice.. this is helpful
ReplyDeleteHi, can I have a chat with you regarding Pwscf calculations. I am stuck somewhere from where I am unable to move forward. Thanks in advance.
ReplyDeletesure, I can give a try to your problem.
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