[Pw_forum] Help in using xcrysden for making structures

[Neel Singh]

hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that how can i draw my unit cell with giving positions of all the atoms without using the symmetries by xcrysden??. Means like if i specifiy,
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A? 0? 4.5 0

now if we visualise this type of structure with Xcrysden, we found a number of atoms genrated due to symmetry. If i make a file like
?& system

ibrav=2, celldm(1)=9.00, nat=18,......

ATOMIC POSITIONS{angstrom}

A? 0? 4.5 0
/
18 times we have specified the co-ordinates
/
/
A? 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.
Sir i want to know is there any way so that i can make my PWSCF input file with angstrom/bohr postions such that with one atomic postion Xcrysden will show only one atom??
Means i will give 18 atomic postions and xcrysden will produce 18 atom unit cell without using symmatries.

Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India



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[Duy Le]

If
1. you know there are 18 atoms in a unit cell
2. AND if you know their Cartesian coordinates
3. AND if you don't want to use the Bravais-lattice index,

you could use
1. ibrav=0
2. AND define your unit cell (using CELL_PARAMETERS): nothing more than the
3 "primitive" lattice vectors
3. AND ATOMIC_POSITIONS: I suggest that you should use crystal coordinates
instead of using Cartesian coordinates.

You can find description in
http://www.quantum-espresso.org/input-syntax/INPUT_PW.html

:)

Post by Neel Singh
hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us take
the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i
have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z}
of each atom in angstrom/bhor. I want to know that how can i draw my unit
cell with giving positions of all the atoms without using the symmetries by
xcrysden??. Means like if i specifiy,
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
now if we visualise this type of structure with Xcrysden, we found a number
of atoms genrated due to symmetry. If i make a file like
& system
ibrav=2, celldm(1)=9.00, nat=18,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
/
18 times we have specified the co-ordinates
/
/
A 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.
Sir i want to know is there any way so that i can make my PWSCF input file
with angstrom/bohr postions such that with one atomic postion Xcrysden will
show only one atom??
Means i will give 18 atomic postions and xcrysden will produce 18 atom unit
cell without using symmatries.
Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India
------------------------------
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[Gabriele Sclauzero]

Dear Neel,

Post by Neel Singh
hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us
take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i
know that i have 18 atoms in my unit cell and i know the Cartesian
co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that
how can i draw my unit cell with giving positions of all the atoms
without using the symmetries by xcrysden??. Means like if i specifiy,

I think that Xcrysden does not use rotational symmetries to visualize atoms (Tone, correct
me if I'm wrong). What it can do is to repeat periodically the atomic basis (i.e. the
minimal set of atoms which, repeat periodically with translations by lattice vectors, give
you the full infinite crystal) to show a nicely cut unit cell, which sometimes includes
translationally equivalent atoms.
In the ATOMIC_POSITIONS list you should include ONLY non-equivalent atoms.

Post by Neel Singh
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
now if we visualise this type of structure with Xcrysden, we found a
number of atoms genrated due to symmetry. If i make a file like
& system
ibrav=2, celldm(1)=9.00, nat=18,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
/
18 times we have specified the co-ordinates
/
/
A 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.

It means that either you specified wrong positions for one or more atoms, or maybe you
included translationally equivalent atoms in the list (i.e. at least a couple of atoms
which have positions which differ by a lattice vector).
BTW, you said that you have 18 atoms, not 90...

Post by Neel Singh
Sir i want to know is there any way so that i can make my PWSCF input
file with angstrom/bohr postions such that with one atomic postion
Xcrysden will show only one atom??

You have to specify the correct list of atomic positions. That's up to you, XCrysden
cannot be used to build input files at the moment. When you have the correct atomic
positions, you can switch between the 2 visualizations modes (atomic basis only, or
"nicely cut unit cell" with some replicas of the atoms in the basis) using the menu bar on
the bottom.

If you want more help, please post a complete input file, otherwise we cannot understand
what mistakes you made in building it.

Regards,

GS

Post by Neel Singh
Means i will give 18 atomic postions and xcrysden will produce 18 atom
unit cell without using symmatries.
Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India
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[Neel Singh]

hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that how can i draw my unit cell with giving positions of all the atoms without using the symmetries by xcrysden??. Means like if i specifiy,
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A? 0? 4.5 0

now if we visualise this type of structure with Xcrysden, we found a number of atoms genrated due to symmetry. If i make a file like
?& system

ibrav=2, celldm(1)=9.00, nat=18,......

ATOMIC POSITIONS{angstrom}

A? 0? 4.5 0
/
18 times we have specified the co-ordinates
/
/
A? 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.
Sir i want to know is there any way so that i can make my PWSCF input file with angstrom/bohr postions such that with one atomic postion Xcrysden will show only one atom??
Means i will give 18 atomic postions and xcrysden will produce 18 atom unit cell without using symmatries.

Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India



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[Duy Le]

If
1. you know there are 18 atoms in a unit cell
2. AND if you know their Cartesian coordinates
3. AND if you don't want to use the Bravais-lattice index,

you could use
1. ibrav=0
2. AND define your unit cell (using CELL_PARAMETERS): nothing more than the
3 "primitive" lattice vectors
3. AND ATOMIC_POSITIONS: I suggest that you should use crystal coordinates
instead of using Cartesian coordinates.

You can find description in
http://www.quantum-espresso.org/input-syntax/INPUT_PW.html

:)

Post by Neel Singh
hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us take
the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i
have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z}
of each atom in angstrom/bhor. I want to know that how can i draw my unit
cell with giving positions of all the atoms without using the symmetries by
xcrysden??. Means like if i specifiy,
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
now if we visualise this type of structure with Xcrysden, we found a number
of atoms genrated due to symmetry. If i make a file like
& system
ibrav=2, celldm(1)=9.00, nat=18,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
/
18 times we have specified the co-ordinates
/
/
A 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.
Sir i want to know is there any way so that i can make my PWSCF input file
with angstrom/bohr postions such that with one atomic postion Xcrysden will
show only one atom??
Means i will give 18 atomic postions and xcrysden will produce 18 atom unit
cell without using symmatries.
Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India
------------------------------
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Buzz <http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/>.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[Gabriele Sclauzero]

Dear Neel,

Post by Neel Singh
hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us
take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i
know that i have 18 atoms in my unit cell and i know the Cartesian
co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that
how can i draw my unit cell with giving positions of all the atoms
without using the symmetries by xcrysden??. Means like if i specifiy,

I think that Xcrysden does not use rotational symmetries to visualize atoms (Tone, correct
me if I'm wrong). What it can do is to repeat periodically the atomic basis (i.e. the
minimal set of atoms which, repeat periodically with translations by lattice vectors, give
you the full infinite crystal) to show a nicely cut unit cell, which sometimes includes
translationally equivalent atoms.
In the ATOMIC_POSITIONS list you should include ONLY non-equivalent atoms.

Post by Neel Singh
& system
ibrav=2, celldm(1)=9.00, nat=1,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
now if we visualise this type of structure with Xcrysden, we found a
number of atoms genrated due to symmetry. If i make a file like
& system
ibrav=2, celldm(1)=9.00, nat=18,......
ATOMIC POSITIONS{angstrom}
A 0 4.5 0
/
18 times we have specified the co-ordinates
/
/
A 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.

It means that either you specified wrong positions for one or more atoms, or maybe you
included translationally equivalent atoms in the list (i.e. at least a couple of atoms
which have positions which differ by a lattice vector).
BTW, you said that you have 18 atoms, not 90...

Post by Neel Singh
Sir i want to know is there any way so that i can make my PWSCF input
file with angstrom/bohr postions such that with one atomic postion
Xcrysden will show only one atom??

You have to specify the correct list of atomic positions. That's up to you, XCrysden
cannot be used to build input files at the moment. When you have the correct atomic
positions, you can switch between the 2 visualizations modes (atomic basis only, or
"nicely cut unit cell" with some replicas of the atoms in the basis) using the menu bar on
the bottom.

If you want more help, please post a complete input file, otherwise we cannot understand
what mistakes you made in building it.

Regards,

GS

Post by Neel Singh
Means i will give 18 atomic postions and xcrysden will produce 18 atom
unit cell without using symmatries.
Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India
------------------------------------------------------------------------
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Yahoo! Buzz
<http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/>.
------------------------------------------------------------------------
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http://www.democritos.it/mailman/listinfo/pw_forum