[ase-users] ase-users Digest, Vol 114, Issue 11

[fabian]

Dear Eric,

Thank you for the clarification!


Unfortunately if i try to use your solution like this:

from ase.io import read, write
from ase import Atom
from ase.atoms import Atoms
from ase.constraints import FixAtoms
n_atom=379
Filename='CONTCAR'
atoms = read(Filename)
atoms = atoms.pop(n_atom) + atoms
write('POSCAR', atoms, vasp5=True, sort=False, 
direct=True,long_format=True, format='vasp')


i get the following error:


TypeError: unsupported operand type(s) for +: 'Atom' and 'Atoms'


Do you have any suggestion how to resolve this issue?

All the best and thank you for your reply


fabian



Am 08.12.2017 um 23:26 schrieb ase-users-request at listserv.fysik.dtu.dk:
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> Today's Topics:
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>     1. Re: From CIF files to XYZ (Eric Hermes)
>     2. Re: Resort atoms object by atom number (Eric Hermes)
>     3. Re: Thermochemistry (Eric Hermes)
>     4. saxis in vasp calculator (Protik Das)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 8 Dec 2017 19:08:01 +0000
> From: Eric Hermes <ehermes at chem.wisc.edu>
> To: "ase-users at listserv.fysik.dtu.dk"
> 	<ase-users at listserv.fysik.dtu.dk>
> Subject: Re: [ase-users] From CIF files to XYZ
> Message-ID: <1512760079.4568.1.camel at wisc.edu>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, 2017-12-08 at 18:48 +0000, Landi, Alessandro via ase-users
> wrote:
>> Hello.
>>
>> Obviously, I typed it wrong.
>>
>> Here the right command lines I use:
>>
>> atoms_ase=ase.io.read('filename.cif')
>> ase.io.write('filename.xyz', atoms_ase)
>>
>> Anyway, I have the problem that the xyz file is wrong as I explained
>> in my first e-mail: the molecules need to be reconnected (see files
>> attached).
> I don't understand what you mean by "reconnected". Neither xyz file
> that you uploaded contains any information regarding connectivity, and
> ASE doesn't have any conception of connectivity anyway (aside from a
> distance-based metric used in the ASE GUI to draw sticks between nearby
> atoms). The atom ordering produced by ASE is more consistent than the
> "realstructure.xyz" file as compared to the original cif ordering. It
> might be that whatever program you are using with the xyz files expects
> connected atoms to be contiguous; to the best of my knowledge this is
> not typical. If you want to ensure this ordering within ASE, you will
> need to manually rearrange the Atoms object.
>
> Eric
>
>> "pentacene.cif" is the cif file that I give as input to ASE;
>> "pentacene.xyz" is the xyz file written by ASE;
>> "realstructure.xyz" is the structure of the reconnected molecules
>> (obtained using CCDC Mercury)
>>
>> Any suggestions?
>>
>> Best regards,
>> Alessandro
>>
>> Da: Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>
>> Inviato: venerd? 8 dicembre 2017 18:36:10
>> A: Landi, Alessandro
>> Cc: ase-users at listserv.fysik.dtu.dk
>> Oggetto: Re: [ase-users] From CIF files to XYZ
>> ?
>> Hello,
>>
>> When you read the structure an Atoms object is created. You need to
>> store that object on a variable and then you can write that one. As
>> so:
>>
>> First read the data:
>> from ase.io import read, write
>> atoms = read('filename.cif')
>> Then write:
>> write('filename.xyz', atoms)
>> or you can use:
>> atoms.write('filename.xyz')
>>
>>
>>
>>
>> 2017-12-08 12:19 GMT+00:00 Landi, Alessandro via ase-users <ase-users
>> @listserv.fysik.dtu.dk>:
>>> Hello everyone.
>>>
>>> I am using ASE to read some CIF files and (among other things) to
>>> convert the structure in xyz format.
>>>
>>> However using the following commands:
>>>
>>> ase.io.read('filename.cif', atoms_ase)
>>> ase.io.write('filename.xyz', atoms_ase)
>>>
>>> I obtain a wrong structure, since the molecules need to be
>>> reconnected. This happens for all the molecules I have tested
>>> (about 20).
>>>
>>> Could you please explain me what I am doing wrong?
>>>
>>> If could be of any help, I attached an example:
>>> "pentacene.cif" is the cif file that I give as input to ASE;
>>> "pentacene.xyz" is the xyz file written by ASE;
>>> "realstructure.xyz" is the structure of the reconnected molecules
>>> (obtained using CCDC Mercury)
>>>
>>> Best regards,
>>> Alessandro
>>>
>>>
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 8 Dec 2017 19:15:01 +0000
> From: Eric Hermes <ehermes at chem.wisc.edu>
> To: "ase-users at listserv.fysik.dtu.dk"
> 	<ase-users at listserv.fysik.dtu.dk>
> Subject: Re: [ase-users] Resort atoms object by atom number
> Message-ID: <1512760499.4568.3.camel at wisc.edu>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, 2017-12-08 at 19:47 +0100, fabian via ase-users wrote:
>> Dear all,
>> I read a POSCAR file into an atoms object via
>> atoms = read("POSCAR")
>> now i want to resort the atoms object such that the atom with the
>> Number n_atom is moved from its postion to the index 0?
>> (1 if not counted the pythonic way), such that it is later writen as
>> the first entry? into the atoms object.?
>> later i want to write the object via:
>> write('POSCAR', atoms, vasp5=True, sort=False,
>> direct=True,long_format=True, format='vasp')
>> and have the entry corresponding to n_atom as the first Atom in the
>> POSCAR file. I found a dirty workaround with temp files but
>> this means i have to convert each initial structure to the right
>> format . Else i create wrong files.
>> Is this possible within ASE?
>> On a side not if i pop an atom via:
>> atoms.pop( n_atom)
>>
>> is n_atom defined the pythonic way and starting at 0?
> To start by answering your last question: yes, everything in ASE is 0-
> indexed. Note that this is not only the Pythonic way, it is a common
> standard used by most languages with some notable exceptions (Fortran,
> Julia, and R probably being the most relevant).
>
> In fact, you should be able to use Atoms.pop() to do exactly what you
> want. Try the following:
>
> atoms = atoms.pop(n_atom) + atoms
>
> One other thing is that when ASE sorts VASP POSCAR files, the first
> atom will never change place, so sort=False is not completely necessary
> (you can still use it if you want to though).
>
> Eric
>
>> Al the best
>> fabian
>> ?_______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
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>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 8 Dec 2017 19:25:11 +0000
> From: Eric Hermes <ehermes at chem.wisc.edu>
> To: "ase-users at listserv.fysik.dtu.dk"
> 	<ase-users at listserv.fysik.dtu.dk>
> Subject: Re: [ase-users] Thermochemistry
> Message-ID: <1512761110.4568.5.camel at wisc.edu>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, 2017-12-08 at 14:53 +0300, Alexander Romanov via ase-users
> wrote:
>> Hello,
>>
>> I investigate diffusion of atoms on metal surfaces and want to use
>> thermochemistry module for energy estimation of transition states.
>> What can I do with imaginary frequencies?? If I understand properly,
>> Gaussian simply subtract them from calculation, but ase module can't
>> do this automatically.? Can I do the same manually??
> Which frequencies you pass to the Thermo classes is up to you. You are
> free to exclude any imaginary frequencies returned by the Vibrations
> class from the list you pass to the Thermo class if you want.
>
> However, be aware of what you are doing by excluding certain
> frequencies from the Thermo classes. You need to ensure that you are
> considering all 3N degrees of freedom of your system.
>
> For an ideal gas, 5 or 6 of those are translations/rotations, so 5 or 6
> of your vibrational frequencies should be small and potentially
> imaginary (since you will capture the effects of those modes with a
> rigid rotor/particle in a box model separately).
>
> In the context of transition state theory, you actually are removing a
> degree of freedom from your system, so the imaginary mode of a
> transition state corresponding to the reaction coordinate should be
> removed from the thermodynamic analysis.
>
> In most other cases, simply removing a vibrational frequency will
> result in significant errors in the system entropy, which is very
> important if you are trying to compare the free energy of two system
> configurations.
>
> Eric
>
>> Best regards,
>> Alex
>> _______________________________________________
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>> ase-users at listserv.fysik.dtu.dk
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>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 8 Dec 2017 14:25:43 -0800
> From: Protik Das <protik77 at gmail.com>
> To: Eric Hermes via ase-users <ase-users at listserv.fysik.dtu.dk>
> Subject: [ase-users] saxis in vasp calculator
> Message-ID:
> 	<CADFNK8Urug3oj5h342dv2JAhLAjbMkVJa-rUYSCX6aoz2Ysxfw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I am trying to set saxis keyword using the vasp calculator of ase. But
> unfortunately the INCAR file does not have the keyword. I tried giving a
> numpy array and a list as input but no luck.
>
> With the saxis in the calculator object, there is an empty line in the
> INCAR file which is not there without the keyword. I am using ASE 3.15.0
> with python 3.6.3.
>
> Any help regarding this will be really appreciated.
>