[DFTB-Plus-User] A MD process including three molecules has failed

张海杰 xuannuo5 at 163.com
Fri May 22 11:59:24 CEST 2015



Dear Ben:


Thank you for your nice guidance. I have  pre-optimised my geometry to a
good minimum before starting the MD by the M06-2X method. What I am describing
is a common three body collision effect in the atmosphere particle formation. So I have 
set the temperature as 200K to simulate the atmosphere condition. The energy at the start
of the calculation and after dissociation has been show in the following picture. The
dissociation happens at about 13ps. The steady state after about 25ps stands for sulfuric-ammonia 
cluster.Here I attached the geom-opt.gen. I am not sure whether I have set some wrong parameter? 
Thank you again for your help.


Best regards,
Haijie Zhang






At 2015-05-22 16:16:28, dftb-plus-user-request at mailman.zfn.uni-bremen.de wrote:
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>Today's Topics:
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>   1. Re: How to generate s-k files? (??)
>   2. A MD process including three molecules has failed (???)
>   3. Re: A MD process including three molecules has	failed
>      (Ben Hourahine)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 22 May 2015 00:25:02 -0400
>From: ?? <lijielile at gmail.com>
>To: "User list for DFTB+ related questions"
>	<dftb-plus-user at mailman.zfn.uni-bremen.de>
>Subject: Re: [DFTB-Plus-User] How to generate s-k files?
>Message-ID:
>	<CAL-rKC_S-+11MtrqmSaoYiVKUoagj8wJDDe2-1OMsc=R+eMuGw at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Thank you very much for your reply. BTW, there was one email before that
>regarding the question of generating the s-k files. I am not sure if you
>have seen it.  I appreciate it a lot if you can give me some suggestions on
>this. Below is a copy of that email.
>
>"Dear Dr. Aradi
>Thank you very much for sending me the files and I appreciate it a lot for
>your help. I will try to do some calculations of the system I am studying
>using the the files you sent me and see what will the result looks like.
>
>BTW, correct me if I am wrong, my understanding is that the s-k files for
>any element are highly dependable on the environment the element resides
>in. For example, the s-k files for Cu and C should be different in an
>environment where there are only Cu and C atoms (in case such a system
>exists) to those in an environment where there are  Cu, C, H, and O in the
>system.
>
>If the statement above is true, the system I am studying indeed contains
>Cu, C, H and O and the s-k files I don't have is between Cu and C. To
>generate s-k files for Cu and C which can best fit my system, I was
>wondering to start with some simple compound like CuHCO3 which includes all
>the elements I need but are much simpler in structure and use Material
>Studio to generate the s-k files. Please let me know if this is the right
>approach to proceed or if there is anything I am doing wrong?
>
>Thanks again for your help.
>
>Best,
>
>Jie"
>
>On Fri, May 22, 2015 at 12:15 AM, MF <foster362 at gmail.com> wrote:
>
>> Hi Jie,
>>
>> The regular version, DFTB+ 1.2, can use all the CPUs within a node
>> (openMP). You need to set the environment variable OMP_NUM_THREADS to the
>> number of threads/cores you want to use in your run script. You should be
>> able to find ample information online about this. The mpi version is for
>> running on multiple nodes and is only really useful for very large systems
>> and computer systems with fast network connections (i.e. Infiniban)
>>
>> Cheers
>>
>> Sent from my iPhone
>>
>> On May 21, 2015, at 8:37 PM, ?? <lijielile at gmail.com> wrote:
>>
>> Dear Dr Aradi,
>>
>> The other question I have is regarding the version of DFTB I use. The DFTB+
>> 1.2 version I believe is the standard version but it is not a parallel
>> version (Correct me if I am wrong). I guess with this version I can't use
>> all the cores of my computer's processors in parallel which could
>> potentially compromise the calculation speed. Is it true that I have do
>> download the DFTB+MPI or the DFTB+MPI-NEGF version for parallel computing
>> and get the maximum out of all the cores?
>>
>> Thanks for your help.
>>
>> Best,
>>
>> Jie
>>
>> On Thu, May 21, 2015 at 8:46 PM, ?? <lijielile at gmail.com> wrote:
>>
>>> Dear Dr. Aradi
>>> Thank you very much for sending me the files and I appreciate it a lot
>>> for your help. I will try to do some calculations of the system I am
>>> studying using the the files you sent me and see what will the result looks
>>> like.
>>>
>>> BTW, correct me if I am wrong, my understanding is that the s-k files for
>>> any element are highly dependable on the environment the element resides
>>> in. For example, the s-k files for Cu and C should be different in an
>>> environment where there are only Cu and C atoms (in case such a system
>>> exists) to those in an environment where there are  Cu, C, H, and O in the
>>> system.
>>>
>>> If the statement above is true, the system I am studying indeed contains
>>> Cu, C, H and O and the s-k files I don't have is between Cu and C. To
>>> generate s-k files for Cu and C which can best fit my system, I was
>>> wondering to start with some simple compound like CuHCO3 which includes all
>>> the elements I need but are much simpler in structure and use Material
>>> Studio to generate the s-k files. Please let me know if this is the right
>>> approach to proceed or if there is anything I am doing wrong?
>>>
>>> Thanks again for your help.
>>>
>>> Best,
>>>
>>> Jie
>>>
>>>
>>> On Wed, May 20, 2015 at 7:17 AM, B?lint Aradi <aradi at uni-bremen.de>
>>> wrote:
>>>
>>>> Dear Jie,
>>>>
>>>> > Thank you very much for your reply and information. I definitely would
>>>> > like to try those files you mentioned but I can't find them from the
>>>> > link you sent. I appreciate it a lot if you can let me know how can I
>>>> > get them? We will definitely acknowledge your contribution in any
>>>> > resulting publications.
>>>>
>>>> attached you find the Cu-C files we have used in the mentioned article.
>>>>
>>>>   Best regards,
>>>>
>>>>   B?lint
>>>>
>>>> --
>>>> Dr. B?lint Aradi
>>>> Bremen Center for Computational Materials Science, University of Bremen
>>>> http://www.bccms.uni-bremen.de/cms/people/b_aradi/
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
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>Message: 2
>Date: Fri, 22 May 2015 15:15:14 +0800 (CST)
>From: ??? <xuannuo5 at 163.com>
>To: dftb-plus-user at mailman.zfn.uni-bremen.de
>Subject: [DFTB-Plus-User] A MD process including three molecules has
>	failed
>Message-ID: <7e6d6e04.1eb3a.14d7a79d712.Coremail.xuannuo5 at 163.com>
>Content-Type: text/plain; charset="gbk"
>
>Dear All:
>
>
>We have done a MD process including a sulfuric acids and two ammonia with the DFTB.
>These three molecules contact with each other through hydrogen bonds. The time scale of 
>MD is 100ps. The result shows that after 50ps only one  ammonia contact with sulfuric acids
>through hydrogen bonds. The another ammonia has gone further away from the sulfuric making
>the distance several tens angstrom or even more. I attached the dftb_in.hsd to search help.I
>would be really thankful for any help.
>
>
>Best regards.
>Haijie Zhang
>
>
>Geometry = GenFormat { <<< "geom-opt.gen" } Driver = VelocityVerlet { Steps = 100000 TimeStep [Femtosecond] = 1.000000000000000 Thermostat = NoseHoover { Temperature [Kelvin] = 200 CouplingStrength [cm^-1] = 800 } OutputPrefix = "geom.out" } Hamiltonian = DFTB { SCC = Yes SCCTolerance = 1.0E-005 # Identical to Fan MaxSCCIterations = 9999 Mixer = Broyden { MixingParameter = 5.000000000000000E-002 CachedIterations = 8 } MaxAngularMomentum = { O = "p" H = "s" N = "p" S = "p" } Charge = 0.000000000000000E+000 SpinPolarisation = {} Eigensolver = Standard {} # Slow! Dispersion = LennardJones { Parameters = UFFParameters {} } Filling = Fermi { Temperature [Kelvin] = 1.000000000000000E-008 } SlaterKosterFiles = { O-O = "/home/lt/3ob-2-1/O-O.skf" O-H = "/home/lt/3ob-2-1/O-H.skf" O-N = "/home/lt/3ob-2-1/O-N.skf" O-S = "/home/lt/3ob-2-1/O-S.skf" H-O = "/home/lt/3ob-2-1/O-H.skf" H-H = "/home/lt/3ob-2-1/H-H.skf" H-N = "/home/lt/3ob-2-1/N-H.skf" H-S = "/home/lt/3ob-2-1/S-H.skf" N-O = "/home/lt/3ob
> -2-1/N-O.skf" N-H = "/home/lt/3ob-2-1/N-H.skf" N-N = "/home/lt/3ob-2-1/N-N.skf" N-S = "/home/lt/3ob-2-1/N-S.skf" S-O = "/home/lt/3ob-2-1/S-O.skf" S-H = "/home/lt/3ob-2-1/S-H.skf" S-N = "/home/lt/3ob-2-1/S-N.skf" S-S = "/home/lt/3ob-2-1/S-S.skf" } ReadInitialCharges = No } Options = { WriteAutotestTag = Yes RandomSeed = 12321 } ParserOptions = { ParserVersion = 4 }
>
>
>
>
>
>
>
>
>
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>------------------------------
>
>Message: 3
>Date: Fri, 22 May 2015 09:16:16 +0100
>From: Ben Hourahine <benjamin.hourahine at strath.ac.uk>
>To: User list for DFTB+ related questions
>	<dftb-plus-user at mailman.zfn.uni-bremen.de>
>Subject: Re: [DFTB-Plus-User] A MD process including three molecules
>	has	failed
>Message-ID: <555EE5D0.3070804 at strath.ac.uk>
>Content-Type: text/plain; charset="utf-8"
>
>Dear Zhang,
>
>did you pre-optimise your geometry to a good minimum before starting the
>MD? What you are describing (but please include the geometry to specify
>the full code input), sounds like a common three body collision effect.
>What are the energy components (kinetic and Mermin energy) at the start
>of the calculation and after dissociation? Also remember that your
>boundary conditions are for the three molecules in vacuum - is a bound
>system at 200 K?
>
>Regards
>
>Ben
>
>On 22/05/15 08:15, ??? wrote:
>> Dear All:
>>
>> We have done a MD process including a sulfuric acids and two ammonia
>> with the DFTB.
>> These three molecules contact with each other through hydrogen
>> bonds. The time scale of 
>> MD is 100ps. The result shows that after 50ps only
>> one  ammonia contact with sulfuric acids
>> through hydrogen bonds. The another ammonia has gone further away from
>> the sulfuric making
>> the distance several tens angstrom or even more.I attached the
>> dftb_in.hsd to search help.I
>> would be really thankful for any help.
>>
>> Best regards.
>> Haijie Zhang
>>
>> Geometry = GenFormat { <<< "geom-opt.gen" } Driver = VelocityVerlet {
>> Steps = 100000 TimeStep [Femtosecond] = 1.000000000000000 Thermostat =
>> NoseHoover { Temperature [Kelvin] = 200 CouplingStrength [cm^-1] = 800
>> } OutputPrefix = "geom.out" } Hamiltonian = DFTB { SCC = Yes
>> SCCTolerance = 1.0E-005 # Identical to Fan MaxSCCIterations = 9999
>> Mixer = Broyden { MixingParameter = 5.000000000000000E-002
>> CachedIterations = 8 } MaxAngularMomentum = { O = "p" H = "s" N = "p"
>> S = "p" } Charge = 0.000000000000000E+000 SpinPolarisation = {}
>> Eigensolver = Standard {} # Slow! Dispersion = LennardJones {
>> Parameters = UFFParameters {} } Filling = Fermi { Temperature [Kelvin]
>> = 1.000000000000000E-008 } SlaterKosterFiles = { O-O =
>> "/home/lt/3ob-2-1/O-O.skf" O-H = "/home/lt/3ob-2-1/O-H.skf" O-N =
>> "/home/lt/3ob-2-1/O-N.skf" O-S = "/home/lt/3ob-2-1/O-S.skf" H-O =
>> "/home/lt/3ob-2-1/O-H.skf" H-H = "/home/lt/3ob-2-1/H-H.skf" H-N =
>> "/home/lt/3ob-2-1/N-H.skf" H-S = "/home/lt/3ob-2-1/S-H.skf" N-O =
>> "/home/lt/3ob-2-1/N-O.skf" N-H = "/home/lt/3ob-2-1/N-H.skf" N-N =
>> "/home/lt/3ob-2-1/N-N.skf" N-S = "/home/lt/3ob-2-1/N-S.skf" S-O =
>> "/home/lt/3ob-2-1/S-O.skf" S-H = "/home/lt/3ob-2-1/S-H.skf" S-N =
>> "/home/lt/3ob-2-1/S-N.skf" S-S = "/home/lt/3ob-2-1/S-S.skf" }
>> ReadInitialCharges = No } Options = { WriteAutotestTag = Yes
>> RandomSeed = 12321 } ParserOptions = { ParserVersion = 4 }
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
>-- 
>      Dr. B. Hourahine, SUPA, Department of Physics,
>    University of Strathclyde, John Anderson Building,
>            107 Rottenrow, Glasgow G4 0NG, UK.
>    +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
>2013/4 THE Awards Entrepreneurial University of the Year
>      2012/13 THE Awards UK University of the Year
>
>   The University of Strathclyde is a charitable body,
>        registered in Scotland, number SC015263
>
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