The energy of the whole system in a QMMM simulation

jts2t... at gmail.com jts2t... at gmail.com
Sun Sep 10 15:24:40 UTC 2017

Hi, Matt, bother you again.

The real problem I want to figure out is, when I set 1-layer QM atoms, the
energy is
Total FORCE_EVAL ( QMMM ) energy (a.u.):           -351.508815087281562

While I set 2-layer QM-atoms, the energy is
Total FORCE_EVAL ( QMMM ) energy (a.u.):           -696.366434340290539

What bother me is that the energy should be almost the same, but the fact
is that they differ nearly twice.
So I want to know if there is some mistake in my understanding, or is there
some mistake in my setting ?

>
> The line I suggested _is_ the total energy QM + MM + QM-MM
>
> If you set print level medium you should see something like
>
>  QMMM| Evaluating forces on MM atoms due to the:
>  QMMM| - QM/MM Coupling computed collocating the Gaussian Potential
> Functions.
>  QMMM| QM/MM Nuclear Electrostatic Potential :
>  -0.210189515
>  QMMM| QMMM Total Energy (QM + QMMM electronic + QMMM nuclear):
> -694.056114328
>  QMMM| MM energy NOT included in the above term! Check for:  FORCE_EVAL (
> QMMM )
>  QMMM| that includes both QM, QMMM and MM energy terms!
>
>  ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.):
> -696.223035107415399
>
> Which gives the energy with and without the MM energy - so you can figure
> out the MM energy.
>
>
> On Friday, September 8, 2017 at 6:45:52 AM UTC+1, jts2... at gmail.com
> wrote:
>>
>> Hi, Matt,
>>
>> I did as you suggest, then I typed in the command 'grep energy *.out'.
>> But the results said
>>
>> QMMM | MM energy NOT included in the above term! Check for:
>> FORCE_EVAL(QMMM) that includes both QM, QMMM and MM energy terms !
>>
>> So I still didn't get the MM energy message.
>>
>> As far as my understanding, I should add something else in the &MM
>> section, maybe an additional &FORCE_EVAL to output the information of MM
>> region ?
>> Or there is something important ignored ?
>>
>> 在 2017年9月8日星期五 UTC+8上午4:16:40，Matt W写道：
>>>
>>> At each step of a geo_opt run you should see something like
>>>
>>> ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.):
>>> -696.237954025524573
>>>
>>> after all the QS output, that gives you the total energy of the system
>>> (at least if print_level is medium)
>>>
>>> On Thursday, September 7, 2017 at 6:33:03 PM UTC+1, Jadzia wrote:
>>>>
>>>> I am not sure if the question is really "where the file is" since it
>>>> will most likely be nowhere. And to be honest I don't know how to write a
>>>> similar file for the energies for geo_opt as for MD simulations since only
>>>> in the MD section there seems to be this print option, which might not be
>>>> used during geo_opt (not sure about it).
>>>>
>>>> But a workaround might be as follows: One can run cp2k with the -o
>>>> option to store the output of the geometry optimization in a file, and then
>>>> one could grep the energy out of that file.
>>>>
>>>>
>>>>
>>>> On Thursday, September 7, 2017 at 5:05:04 PM UTC+2, jts2... at gmail.com
>>>> wrote:
>>>>>
>>>>> Thanks for your suggestion, which works well in a example in official
>>>>> website, but fails in another case.
>>>>>
>>>>> I run a GEO_OPT simulation using QMMM method,  the original motion.inc
>>>>> is as follows
>>>>> &MOTION
>>>>>   &GEO_OPT
>>>>>      OPTIMIZER LBFGS
>>>>>   &END
>>>>>   &CONSTRAINT
>>>>>      &FIXED_ATOMS
>>>>>      LIST 1..16
>>>>>      EXCLUDE_MM .TRUE.
>>>>>      EXCLUDE_QM .FALSE.
>>>>>      &END FIXED_ATOMS
>>>>>   &END CONSTRAINT
>>>>> &END MOTION
>>>>>
>>>>> Then I added the MD section, they became
>>>>> &MOTION
>>>>>   &GEO_OPT
>>>>>      OPTIMIZER LBFGS
>>>>>   &END
>>>>>   &CONSTRAINT
>>>>>      &FIXED_ATOMS
>>>>>      LIST 1..16
>>>>>      EXCLUDE_MM .TRUE.
>>>>>      EXCLUDE_QM .FALSE.
>>>>>      &END FIXED_ATOMS
>>>>>   &END CONSTRAINT
>>>>>   &MD
>>>>> &PRINT
>>>>> &ENERGY
>>>>> FILENAME=total.ener
>>>>>  &EACH
>>>>>    GEO_OPT 1
>>>>>  &END EACH
>>>>> &END ENERGY
>>>>> &END PRINT
>>>>>   &END MD
>>>>> &END MOTION
>>>>>
>>>>> The strange thing is that there wasn't any file named *total.ener* in
>>>>> the current directory. Where is the question ?
>>>>> The &EACH section is not correct ?
>>>>>
>>>>> Expect for your kind reply !
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 在 2017年9月7日星期四 UTC+8下午12:13:16，Jadzia写道：
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> To my understanding if you want to write the total energy to a file
>>>>>> for instance for an MD simulation you need to add a section similar to:
>>>>>>
>>>>>>  &MOTION
>>>>>>    &MD
>>>>>>     &PRINT
>>>>>>       &ENERGY
>>>>>>         FILENAME =cp2k.out.energy
>>>>>>           &EACH
>>>>>>             MD 10
>>>>>>           &END EACH
>>>>>>       &END ENERGY
>>>>>>     &END PRINT
>>>>>>   &END MD
>>>>>> &END MOTION
>>>>>>
>>>>>> In this example the energy of every tenth step is written to the
>>>>>> file, and is independent of the type of force evaluation (MM, QM, QM/MM,
>>>>>> ...).
>>>>>>
>>>>>> Here is the corresponding section in the manual:
>>>>>> https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD/PRINT/ENERGY/EACH.html
>>>>>>
>>>>>> Hope this helps,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wednesday, September 6, 2017 at 8:31:10 AM UTC+2,
>>>>>> jts2... at gmail.com wrote:
>>>>>>>
>>>>>>> Dear researchers and developers,
>>>>>>>
>>>>>>> I am not so familiar with CP2K. After I run a QMMM simulation of KCl
>>>>>>> just as here: https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm, I
>>>>>>> want to know the energy of the whole system not just the energy of the QM
>>>>>>> region, how to achieve it in the input setting?
>>>>>>>
>>>>>>> I'll appreciate for your apply !
>>>>>>>
>>>>>>
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