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

[Ask Hjorth Larsen]

Hi,

2017-12-09 12:16 GMT+01:00 fabian via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> 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'

Right, the first is an Atom and the second is an Atoms object.  They
both need to be Atoms.  Maybe the natural way is something like:

atoms = read(Filename)
atoms = Atoms([atoms.pop(n_atom)]) + atoms

Best regards
Ask



>
>
> 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:
>>
>> Send ase-users mailing list submissions to
>>         ase-users at listserv.fysik.dtu.dk
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>> or, via email, send a message with subject or body 'help' to
>>         ase-users-request at listserv.fysik.dtu.dk
>>
>> You can reach the person managing the list at
>>         ase-users-owner at listserv.fysik.dtu.dk
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of ase-users digest..."
>>
>>
>> Today's Topics:
>>
>>     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
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>>
>>
>> ------------------------------
>>
>> 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
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>>
>>
>> ------------------------------
>>
>> 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.
>>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users