[CP2K-user] [CP2K:14544] Re: Running CP2K calc with ASE
Sun Geng
gengs... at gmail.com
Thu Jan 14 19:06:56 UTC 2021
Hi Kane,
Sorry, I did not check it out for cp2k-v8.1.
I have been mostly using CP2K-v6.1 with ase.
Maybe someone who is more familiar with code knows which subroutine
does the job reading positions from standard input,
then It will be easier to adopt the code.
Best,
Geng
Kane Shenton <jksh... at gmail.com> 于2021年1月14日周四 上午7:56写道：
>
> Hi!
>
> I've just run into the same issue. Thanks, Geng, for shedding some light and providing the hack to fix it!
>
> It's unclear to me how to adapt your fortran code to newer versions of cp2k since, as you say, there have been lots of changes.
>
> Have you, by any chance, subsequently written a similar hack for newer versions of cp2k (e.g. v8.1)?
>
> Best,
> Kane
>
>
> On Wednesday, August 19, 2020 at 11:33:38 PM UTC+2 ani... at gmail.com wrote:
>>
>> Thanks a lot!!
>>
>>
>> On Tuesday, August 18, 2020 at 9:05:44 AM UTC-7, Sun Geng wrote:
>>>
>>> Hi Aniruddha M Dive,
>>> Below is the code that I changed a few lines in cp2k_shell.F and ase-cp2k calculator. ( You will see the lines I commented out)
>>> Please note that the code is only tested wit cp2k-v6.1 (I found the most recent cp2k code revised cp2k_shell.F significantly).
>>> The idea is that the python code will write a file " CP2K_POSITIONS" with coordinates instead of writing them into PIPE,
>>> and cp2k_shell will read the positions from the file instead of the PIPE.
>>> Best,
>>> Geng
>>>
>>>
>>> IF (para_env%mepos==para_env%source) THEN
>>> !READ (*,*,iostat=iostat) n_atom2
>>> !IF (iostat/=0) CPABORT('setpos read n_atom')
>>> !IF (n_atom2/=SIZE(pos)) THEN
>>> ! CALL my_assert(.FALSE.,'setpos invalid number of atoms',failure)
>>> ! DO i=1,n_atom
>>> ! READ(*,'(a)',iostat=iostat) cmdStr
>>> ! CALL compress(cmdStr,full=.TRUE.)
>>> ! CALL uppercase(cmdStr)
>>> ! IF (cmdStr=='*END') EXIT
>>> ! END DO
>>> ! GOTO 10
>>> !END IF
>>> !READ (*,*,iostat=iostat) pos
>>> !IF (iostat/=0) CPABORT('setpos read coord')
>>> inquire(unit=201,opened=unitalive)
>>> if (unitalive) CPABORT('UNIT 201 is being used')
>>> inquire(file="CP2K_POSITIONS",exist=filepresence)
>>> if (.not. filepresence) CPABORT('FILE CP2K_POSITIONS NOT EXIST')
>>> open(201,action='READ',file="CP2K_POSITIONS",iostat=iostat,status='OLD',form='FORMATTED',ACCESS='SEQUENTIAL')
>>> if (iostat/=0) CPABORT('read CP2K_POSITIONS')
>>> READ(201,*,iostat=iostat) n_atom2
>>> IF (iostat/=0) CPABORT('setpos read n_atom2')
>>> IF (n_atom2/=SIZE(pos)) THEN
>>> CALL my_assert(.FALSE.,'setpos invalid number of atoms',failure)
>>> DO i=1,n_atom
>>> READ(201,'(a)',iostat=iostat) cmdStr
>>> CALL compress(cmdStr,full=.TRUE.)
>>> CALL uppercase(cmdStr)
>>> IF (cmdStr=='*END') EXIT
>>> END DO
>>> GOTO 10
>>> END IF
>>> READ (201,*,iostat=iostat) pos
>>> CLOSE(201)
>>> IF (iostat/=0) CPABORT('setpos read coord')
>>> pos(:) = pos(:)/pos_fact
>>> READ(*,'(a)',iostat=iostat) cmdStr
>>> CALL compress(cmdStr,full=.TRUE.)
>>> CALL uppercase(cmdStr)
>>> CALL my_assert(cmdStr=='*END',' missing *END',failure)
>>> END IF
>>>
>>>
>>> ---changes in ase cp2k calcualtor -----
>>> if 'positions' in system_changes:
>>> with open("CP2K_POSITIONS","w") as fp:
>>> fp.write("%d\n" % (3*n_atoms))
>>> for pos in self.atoms.get_positions():
>>> fp.write('%.18e %.18e %.18e\n' % tuple(pos))
>>> self._shell.send('SET_POS %d' % self._force_env_id)
>>> #self._shell.send('%d' % (3 * n_atoms))
>>> #for pos in self.atoms.get_positions():
>>> # self._shell.send('%.18e %.18e %.18e' % tuple(pos))
>>> self._shell.send('*END')
>>> max_change = float(self._shell.recv())
>>> assert max_change >= 0 # sanity check
>>> self._shell.expect('* READY')
>>> if os.path.isfile("CP2K_POSITIONS"):
>>> os.remove("CP2K_POSITIONS")
>>>
>>> 在2020年8月17日星期一 UTC-7 下午4:42:29<ani... at gmail.com> 写道：
>>>>
>>>> Thanks Geng,
>>>>
>>>> I went through your earlier post regarding the same issue. Can you send me the respective cp2k_shell.F file that works for you. I would like to incorporate it and check.
>>>>
>>>> Also can you send me the python script you used as well.
>>>>
>>>> Best Regards,
>>>> Aniruddha M Dive
>>>>
>>>>
>>>> On Monday, August 17, 2020 at 7:44:08 AM UTC-7, Sun Geng wrote:
>>>>>
>>>>> Dear Aniruddha,
>>>>>
>>>>> Sometimes ago, I have encountered a similar problem,
>>>>> I think the reason is that the python code communicates positions/forces with the mpi cp2k_shell.popt.
>>>>> There is a problem when MPI code read the pipe: the MPI code will only read truncated data (such as positions) from the pipe, not all of them.
>>>>> So CP2K_shell.popt is still waiting for more coordinates and gets stuck.
>>>>>
>>>>> Best,
>>>>> Geng
>>>>>
>>>>>
>>>>>
>>>>> 在2020年8月13日星期四 UTC-7 下午1:20:17<ani... at gmail.com> 写道：
>>>>>>
>>>>>> Thanks Hasan,
>>>>>>
>>>>>> I was able to get the Cp2K working. However I face another issue. The simulation runs well for few steps and after that I cannot see my output file being updated. The simulation shows running however I am not able to see any output being updated in the cp2k output file as well as the slurm output file. I have attached my job submission script, python script as well as the out files for reference. Could this be a memory issue?
>>>>>>
>>>>>> Best,
>>>>>> Aniruddha M Dive
>>>>>>
>>>>>>
>>>>>> On Tuesday, August 4, 2020 at 10:12:17 AM UTC-7, Hasan Al-Mahayni wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I had similar problems starting CP2K with ASE earlier this summer. I will attach an example of geometric optimization for a slab, I hope it helps. You need to copy paste a large portion of your cp2k input file in your python script, because ASE does not provide all the input parameters you will need to perform geo_opt. Please find an example attached below.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Hasan.
>>>>>>>
>>>>>>> On Tue, Aug 4, 2020 at 1:16 AM Maxime Van den Bossche <maxi... at gmail.com> wrote:
>>>>>>>>
>>>>>>>> Dear Aniruddha,
>>>>>>>>
>>>>>>>> Since you haven't provided a minimal example, nor the error message you're getting
>>>>>>>> from ASE or CP2K, I haven't looked into debugging the (bulky) example you sent.
>>>>>>>>
>>>>>>>> But I don't think you can do the geometry optimization in this way. ASE uses the cp2k_shell binary,
>>>>>>>> which seems to only perform single-point calculations but not e.g. geometry optimizations.
>>>>>>>>
>>>>>>>> The idea behind cp2k_shell is that the 'driver' (in this case ASE) is the one moving the atoms
>>>>>>>> around, and what CP2K does is e.g. calculating the energy and the gradients for a given geometry.
>>>>>>>>
>>>>>>>> Here is a minimal example of a geometry optimization, and you can work your way up
>>>>>>>> from there:
>>>>>>>>
>>>>>>>> from ase.build import molecule
>>>>>>>> from ase.calculators.cp2k import CP2K
>>>>>>>> from ase.optimize import BFGS
>>>>>>>>
>>>>>>>> atoms = molecule('H2O')
>>>>>>>> atoms.center(vacuum=2.0)
>>>>>>>>
>>>>>>>> calc = CP2K(command='cp2k_shell.sopt')
>>>>>>>> atoms.set_calculator(calc)
>>>>>>>>
>>>>>>>> dyn = BFGS(atoms)
>>>>>>>> dyn.run(fmax=0.05)
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Maxime
>>>>>>>>
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>>>>>>>>
>>>>>>>> To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/df050a2d-1161-4e2c-98c9-0463adcb4c3do%40googlegroups.com.
>
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