[ase-users] ase-users Digest, Vol 114, Issue 11
Ask Hjorth Larsen
asklarsen at gmail.com
Tue Jan 2 14:17:18 CET 2018
Hi Fabian,
(Please send to the list; re-added list to recipients)
2017-12-21 12:56 GMT+01:00 fabian <Fabian.T89 at web.de>:
> Hi,
>
> I just use the TTT and FFF flags for the VASP format to indicate which atoms
> should be relaxed.
>
> I want to create specific input files for additional calculations were no
> relaxation should be performed.
> If i set the NSW tag to 0 in the INCAR file it is not necessary to keep them
> i guess but if i want to do additional stuff later
> it would be handy to still have them.
>
> Is it somehow possible to reread them from the original CONTCAR/POSCAR file
> and make a pair wise
> comparison based on the atomic positions in an additional step to add them
> to the new file?
Could you attach the file in question? I cannot guess what is happening.
Best regards
Ask
>
>
> All the best and thank you for your awesome support
>
> fabian
>
>
> Am 21.12.2017 um 02:09 schrieb Ask Hjorth Larsen:
>
> Hi,
>
> El 19 dic. 2017 22:14, "fabian" <Fabian.T89 at web.de> escribió:
>
> Dear Eric,
>
> Unfortunately when i try to use your code like this:
>
>
>
> from ase.io import read, write
> from ase import Atom
> from ase.atoms import Atoms
> from ase.constraints import FixAtoms
> import numpy as np
> n_atom=2
>
> Filename='CONTCAR'
> atoms = read(Filename)
> indices = np.arange(len(atoms))
>
> indices[n_atom] = 0
> indices[0] = n_atom
> atoms = atoms[indices]
> write('POSCAR', atoms, vasp5=True, sort=False,
> direct=True,long_format=True,format='vasp')
>
>
> i get the following error:
>
>
> File "...\make_newposcar.py", line 13, in <module>
> atoms = atoms[indices]
> File "C:\Program Files (x86)\Python27\lib\site-packages\ase\atoms.py",
> line 877, in __getitem__
> con.index_shuffle(self, i)
> File "C:\Program Files
> (x86)\Python27\lib\site-packages\ase\constraints.py", line 133, in
> index_shuffle
>
>
> Right. It appears the atoms have a constraint which does not know how to
> act when the atoms are reordered. Unfortunately you will need to remove the
> constraint (e.g. atoms.set_constraint(None)) in order to reorder the atoms
> object. Probably you can simply set the constraint again once you need to
> do a calculation.
>
> It looks like the error message should be better though. I will try to have
> a look at this if I can find time.
>
> Which constraint is it, by the way?
>
> Best regards
> Ask
>
>
>
> for new, old in slice2enlist(ind, len(atoms)):
> File "C:\Program Files
> (x86)\Python27\lib\site-packages\ase\constraints.py", line 22, in
> slice2enlist
> return enumerate(range(*s.indices(n)))
> AttributeError: 'numpy.ndarray' object has no attribute 'indices'
>
>
> Would you be willing to give me another tip? I feel like i should be able to
> solve this by myself, but somehow i can´t find a
> solution.
>
>
> All the best
>
> fabian
>
>
>
> Am 10.12.2017 um 12:58 schrieb Ask Hjorth Larsen:
>>
>> 2017-12-10 12:00 GMT+01:00 fabian <Fabian.T89 at web.de>:
>>>
>>> Dear Eric,
>>>
>>> Thanks once again for your help.
>>>
>>> Now i am left with the problem that the cell information and the
>>> constraints
>>> are not written, wich i would
>>> like to keep.
>>
>> Oh right, oops.
>>
>> Actually:
>>
>> import numpy as np
>> indices = np.arange(len(atoms))
>> indices[n_atom] = 0
>> indices[0] = n_atom
>> atoms = atoms[indices]
>>
>> This is the most general way to reorder atoms objects: Creating an
>> array of indices and slicing the atoms object with the array.
>>
>> This will preserve the maximum amount of info on the atoms object,
>> including FixAtoms constraints.
>>
>> Best regards
>> Ask
>>
>>> It is easy to just rewrite the cell parameter, but to reflect the
>>> constraints correctly they have to be
>>> shifted in the list of constraints depending on whether the poped atom
>>> had
>>> constraints or not.
>>>
>>> Unfortunately my code posted below gives me the error:
>>>
>>> TypeError: unsupported operand type(s) for +: 'instance' and 'int'
>>>
>>> Is it somehow possible to access the list of constaints directly with the
>>> FixAtoms method and later rewrite them via:
>>>
>>> indices = shifted_list
>>> constraint = FixAtoms(indices=indices)
>>> atoms.set_constraint(constraints)
>>>
>>> or
>>>
>>> atoms.set_constraint([FixAtoms(indices=shifted_list)]+new_position)
>>>
>>>
>>> Here is the code that doesnt work:
>>>
>>> from ase.io import read, write
>>> from ase import Atom
>>> from ase.atoms import Atoms
>>> from ase.constraints import FixAtoms
>>>
>>> n_atom=390
>>> Filename='CONTCAR'
>>> atoms = read(Filename)
>>> cell = atoms.get_cell()
>>> atoms.resort = None
>>> constraints=atoms.constraints
>>> #indices=FixAtoms(constraints).indicies
>>>
>>>
>>> print(constraints)
>>> print (type(constraints))
>>> if n_atom not in constraints:
>>> print ("yes")
>>> #shift_constraints=[x+1 for x in constraints]
>>> map(lambda x:x+1, constraints)
>>> elif n_atom in constraints:
>>> pass # n_atom has to be deleted from constraints. And constraints
>>> have
>>> to be shifted by +1.
>>> # 0 has to be added to list of constraints
>>> atoms = Atoms([atoms.pop(n_atom)]) + atoms
>>>
>>>
>>> atoms.set_cell(cell)
>>> atoms.set_constraint(constraints)
>>> write('POSCAR', atoms, vasp5=True, sort=False,
>>> direct=True,long_format=True,format='vasp')
>>>
>>>
>>> Thanks in advance
>>>
>>> fabian
>>>
>>>
>>>
>>> Am 09.12.2017 um 20:34 schrieb 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
>>>
>>>
>
>
>
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