[DFTB-Plus-User] Mulliken analysis along the trajectory

Wed Feb 28 18:20:38 CET 2024

Dear Bálint,

Thank you very much!
And are the last three columns from the xyz output velocities?
With the Electrostatic Potential option, I can only get the ESP values for fixed points along the trajectory, is that correct? In another words, it's impossible to change the points according to the atomic positions during the simulation?

Best regards,
Dongyu

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________________________________
发件人: DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> 代表 Bálint Aradi <aradi at uni-bremen.de>
发送时间: Wednesday, February 28, 2024 5:17:49 PM
收件人: User list for DFTB+ related questions <dftb-plus-user at mailman.zfn.uni-bremen.de>
主题: Re: [DFTB-Plus-User] Mulliken analysis along the trajectory

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Dear Dongyu,

sorry, to be more precise, the xyz output contains the mulliken
population, not the gross charge, so you would have to substract the nr.
of electrons in the neutral state.

As for the ESP, we have this quantity, but we do not print it currently.
It should not be compplicated, but we did not implement it yet. As a
workaround for the moment, you use the ElectrostaticPotential option,
and specify the atomic positions as Points.

Best regards,

Bálint

On 28.02.24 16:54, Lyu, Dongyu wrote:
> Dear Bálint,
>
> Thanks for your reply.
> For the charges, why the printed charges in the xyz output file for the
> last frame are different from the atomic gross charges written in the
> detailed.out? Are they the same property?
> Regarding EPS, Is it possible to extract the value of the electrostatic
> potential at the position of the atom for each frame during the simulation?
>
> Best regards,
> Dongyu
>
>
> ------------------------------------------------------------------------
> *From:* DFTB-Plus-User
> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> on behalf of Bálint
> Aradi <aradi at uni-bremen.de>
> *Sent:* Wednesday, February 28, 2024 4:14 PM
> *To:* dftb-plus-user at mailman.zfn.uni-bremen.de
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* Re: [DFTB-Plus-User] Mulliken analysis along the trajectory
> [You don't often get email from aradi at uni-bremen.de. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification> ]
>
> Dear Donyu,
>
> you can find the atomic gross charges in the xyz output file, just after
> the coordinates, for every atom. This is a convention several programs
> understand.
>
> What do you mean by ESP? The value of the electrostatic potential at the
> position of the atom?
>
> Best regards,
>
> Bálint
>
> On 27.02.24 16:30, Lyu, Dongyu wrote:
>> Dear DFTB-plus-User group,
>>
>> I am trying to perform the ground state dynamics of a molecule in gas
>> phase and run the Mulliken Analysis. In the output files I can find the
>> atomic gross charges in detailed.out , which contains the detailed
>> information for the last frame only. Is it possible to do this analysis
>> along the trajectory and print out the Mulliken charges for each step
>> during the simulation? What should I change in the input file?
>> Also, is it possible to print out the ESP of each atom during the
>> simulation?
>> Here is the input file I used:
>> Geometry = GenFormat {
>>   <<< "TMP.gen"
>> }
>>
>> Driver = VelocityVerlet{
>>   TimeStep [fs] = 1.0
>>   Thermostat = NoseHoover {
>>     Temperature [Kelvin] = 300
>>     CouplingStrength [cm^-1] = 3200
>>   }
>>   Steps = 10000
>>   MovedAtoms = 1:-1
>>   MDRestartFrequency = 1
>> }
>>
>> Hamiltonian = DFTB {
>>   Charge = 4
>>   SCC = Yes
>>   SCCTolerance = 1e-7
>>   MaxAngularMomentum {
>>     C = "p"
>>     N = "p"
>>     H = "s"
>>   }
>>   SlaterKosterFiles = Type2FileNames {
>>     Prefix = "/people/FMO/slko/slko/"
>>     Separator = "-"
>>     Suffix = ".skf"
>>   }
>>   ThirdOrderFull = Yes
>>   HubbardDerivs {
>>     C = -0.1492
>>     N = -0.1535
>>     H = -0.1857
>>   }
>> HCorrection = Damping {
>>     Exponent = 4.0
>>   }
>>
>>   Filling = Fermi {
>>     Temperature [ Kelvin ] = 300.0
>>   }
>> }
>>
>> Analysis = {
>>   MullikenAnalysis = Yes
>>   WriteNetCharges = Yes
>>   CalculateForces = Yes
>> }
>> Options = {
>>   WriteDetailedOut = Yes
>> }
>>
>> ParserOptions = {
>> IgnoreUnprocessedNodes = Yes
>> }
>>
>> I would appreciate it if you could help!
>>
>> Best regards,
>> Donyu
>>
>>
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Dr. Bálint Aradi
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