[CP2K-user] [CP2K:13720] Re: Running CP2K calc with ASE

[Aniruddha Dive]

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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>>>>>> Groups "cp2k" group.
>>>>>>
>>>>> To unsubscribe from this group and stop receiving emails from it, send 
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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 
>>>>>> <https://groups.google.com/d/msgid/cp2k/df050a2d-1161-4e2c-98c9-0463adcb4c3do%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>>
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