[CP2K:3119] Re: Something about MC project
Igor Ying Zhang
wenx... at gmail.com
Wed Mar 2 12:44:26 UTC 2011
Of course, your detailed explanation help me greatly! I will try it
following your suggestion right now.
Igor Ying Zhang
On 03/02/2011 03:02 PM, Matt McGrath wrote:
> Hello Igor.
> I have looked a little more closely at the MC section of your input
> file, and I've noticed a couple things.
> First, it's strange that everything dies without an error message.
> Can you run the tests in tests/MC/regtests? In particular, try to run
> MC_QS.inp. If you can't, there is something wrong with your
> installation. If you can, try changing MC_QS.inp to be the input file
> you want (for example, first try to change the electronic structure
> part, then change the molecules, and then change the MC section).
> This will help narrow down where the problem is arising.
> Secondly, I noticed that the ensemble you have chosen is GEMC_NVT. No
> doubt you choose that because of the NVT in the name, but this isn't
> the ensemble you want. GEMC stands for Gibbs Ensemble Monte Carlo,
> which is a method that uses at least two simulation boxes to simulate
> phase equilibria. So, you're telling MC that you want to do something
> with two simulation boxes, but it's only finding the file for one
> simulation box. This would cause it to crash. "traditional" is the
> one you are looking for (this allows you to run both NVT and NpT...the
> only difference is the percentage of volume moves tried). Take a look
> at the canonical.inp regtest, which is also a single box run in the
> NVT ensemble.
> Something that is also very important is these _MOL keywords you
> alluded to. There are a number of input keywords that don't really
> have good default values, and so I made them "required" in the input
> file (CP2K should die if they are not there). These _MOL keywords are
> among them. If you have more than one molecule type, the MC routines
> need to know how often you want to sample each type with each move.
> For example, PMROT_MOL. If you are doing a simulation of water and
> argon, you don't want to waste time trying to rotate argon. So, if
> water is molecule type 1 and argon is molecule type 2, the PMROT_MOL
> line would look like
> PMROT_MOL 1.0 1.0
> Now when MC chooses a random number to perform a move on, if it's less
> than the first number, it will select a molecule of type 1. If it's
> between the first and the second number, it will choose type 2. In
> this case, nothing is between 1.0 and 1.0, and all random numbers are
> less than 1.0, so it will always choose molecule type 1 to perform a
> rotation on. In your system, let's suppose you want to rotate water
> 30% of the time and glycine 70% of the time. Then, you would have a
> line that looks like this:
> PMROT_MOL 0.7 1.0
> These _MOL keywords are required, because there really is no good
> default value, and it can really impact the efficiency of your
> simulation. Does that make a little more sense? I would recommend
> starting with MC_QS.inp, since it has all the required keywords. You
> can look at one of the other input files that has two molecule types
> to see which keywords require a value for each molecule type (there's
> a few of them).
> I hope this helps!
> Cheers, Matt
> On Mar 1, 10:59 am, Igor Ying Zhang<wenx... at gmail.com> wrote:
>> Hi Matt:
>> Thank you for your kindly and quick reply!
>> I adopt your suggestion to split the psf file. However the situation
>> doesn't change. The seperated psf files and the corresponding input and
>> output files could be found in the attachment.
>> By the way, what does difference between the keywords of "PMTRANS"
>> and "PMTRANS_MOL"? I
>> could not understand them clearly based on the brief information in the
>> CP2K_INPUT manual.
>> Best wishes!
>> On 03/01/2011 03:42 PM, Matt McGrath wrote:
>>> Hello Igor. It seems to me that the problem is arising because you
>>> have two molecules in the PSF file. Due to some of the quirks of MC,
>>> each molecule must be in its own PSF file (see some of the example
>>> inputs in tests/MC/regtest to see how multiple molecules are dealt
>>> with). In addition, there should be only one molecule in the .psf
>>> file even if there are multiple types of that molecule in the
>>> simulation (NMOL tells CP2K to use the molecule specification in
>>> the .psf file NMOL times). The TOPOLOGY section should be something
>>> like this:
>>> CONNECTIVITY MOL_SET
>>> NMOL 1
>>> CONN_FILE_NAME topology_atoms_GLY.psf
>>> NMOL 1
>>> CONN_FILE_NAME topology_atoms_H2O.psf
>>> where the glycine molecule comes first in the COORD section, followed
>>> by the water (if you have multiple molecules of water, they all come
>>> after the glycine...if you have multiple glycine molecules, they all
>>> come before the water). This is so that MC knows which coordinates
>>> belong to which molecule number (since MC moves choose a molecule type
>>> at random, and then a molecule number at random, it cares much more
>>> about molecules than MD). The molecule name in the .psf file should
>>> match the molecule name in the title of the psf file. The psf file
>>> will not change, no matter how many molecules of that type you have in
>>> the simulation.
>>> I hope this helps.
>>> Cheers, Matt
>>> On Feb 28, 10:22 am, Igor Ying Zhang<wenx... at gmail.com> wrote:
>>>> Dear all:
>>>> Recently, I want to use the Montecarlo module of CP2K to do some
>>>> comformation analysis. At first time, I try a system only contains 1
>>>> glycine and 1 water. However, the cp2k terminated abnormally without any
>>>> error information. The attachment pleas find the input file and the
>>>> corresponding psf file.
>>>> Any suggestions are wellcome :)
>>>> Best wishes!
>>>> Igor Ying Zhang.
>> < 1KViewDownload
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