Dear Steve,


ok thank you, I think I got it now, how lammps calculates maxbonds/atom. I saw it also by a printout I made today from the source code. One last thing I need to be sure of: I hope I understood your email from yesterday correctely. There you mentioned it has no influence on the results to which atom the bond is assigned. This means list 1 and 2 below lead to the same result despite the differences in maxbonds/atoms. Is this what you meant?    


list 1:


1       8       4       8  # NH3 CT1> >        

2      10       5       4  # HC   NH3 > >        

3      10       6       4  # HC   NH3 > >        

4      10       7       4  # HC   NH3


list2:


 1       8       4       8  # NH3 CT1> >        

2     10       4       5  # NH3   HC> >        

3      10       4       6  # NH3  HC> >        

4      10       4       7  # NH3  HC

Best regards

Sabine


>>> Steve Plimpton <sjplimp@gmail.com> 9/1/2009 4:23 PM >>>
Again, if you have newton bond on, which is the default, then
a bond is stored with only one atom, not with both atoms in the
bond.  And it will be stored only with the first atom of the 2 listed.
So your examples all make sense to me; they are getting the
right answer.

Steve

On Mon, Aug 31, 2009 at 9:50 AM, Sabine Leroch<sabine.leroch@boku.ac.at> wrote:
> By the way if I partly exchange columns in the list below  i.e.
>
>
>       1       5       1       3  # CC   OC
>
>        2       5       1       2  # CC   OC
>
>        3       4       1       8  # CC   CT1
>
>        4       8       4       8  # CT1  NH3
>
>        5      10       4       5  # HC   NH3
>
>        6      10       4       6  # HC   NH3
>
>        7      10       4       7  # HC   NH3
>
>        8       7       8       9  # CT1  HB
>
>        9       6      10       8  # CT1  CT2
>
>       10       9      10      11  # CT2  HA
>
>       11       9      10      12  # CT2  HA
>
> I receive max bonds/atom=4.  Normally there should by no difference for both
> lists. There must be a bug.
>
> Best regards
>
> Sabine
>
>>>> "Sabine Leroch" <sabine.leroch@boku.ac.at> 8/31/2009 4:36 PM >>>
>
> Hi Steve.
>
> Thank you for responding. I really carefully checked  whether the bonds in
> both files are the same (the atomID are, as you say just names and can be
> assigned arbitrarily as long as both files  give the same bonds per atom).
> Below there is an excerpt of the Bonds part of the data.file. I thought
> lammps (read.data.cpp) would scan the third and forth column and count how
> often a certain atomID is present. In this special case for example atomId 4
> should be counted 4 times. So maxbonds/atom should be 4, is not it?  But
> lammps counts only 3 bonds/atom!!!!!!!!!
>
>        1       5       1       3  # CC   OC
>
>        2       5       1       2  # CC   OC
>
>        3       4       1       8  # CC   CT1
>
>        4       8       4       8  # CT1  NH3
>
>        5      10       5       4  # HC   NH3
>
>        6      10       6       4  # HC   NH3
>
>        7      10       7       4  # HC   NH3
>
>        8       7       8       9  # CT1  HB
>
>        9       6      10       8  # CT1  CT2
>
>       10       9      10      11  # CT2  HA
>
>       11       9      10      12  # CT2  HA
>
> Best regards
>
> Sabine
>
>
>
> eve Plimptosjplimp@gmail.com> 8/31/2009 3:50 PM >>>
> One additional thought.  If you have newton bond on (the default),
> then a bond is assigned to one of the 2 atoms in it.  If the
> 2 data files reversed the order of bonds then you could see a different
> tally of which bonds are assigned to which atoms and thus the
> count of max bonds per atom.  But it wouldn't make a difference
> since which atom a bond is assigned to is actually arbitrary.
>
> Steve
>
> On Mon, Aug 31, 2009 at 7:49 AM, Steve Plimpton<sjplimp@gmail.com> wrote:
>>> But the discrepancy concerning the max bonds/atoms remains.
>>
>> This value is important and is computed by LAMMPS by scanning your
>> data file and counting bonds on each atom.  So if it is different
>> for 2 different runs using 2 different data files, it is certainly the
>> case that something in those data files is causing it.  You mentioned
>> something about atom IDs being changed.  If that's the case, then
>> it may be that the bonds assigned to a particular atom are different.
>>
>> Steve
>>
>> On Fri, Aug 28, 2009 at 8:39 AM, Sabine Leroch<sabine.leroch@boku.ac.at>
>> wrote:
>>> Hi
>>>
>>> I found the first difference by myself. The first block in the msi
>>> log.file
>>> is not missing. Just copied the log.file entry reading from restart not
>>> from
>>> data. Sorry
>>>
>>> But the discrepancy concerning the max bonds/atoms remains.
>>>
>>> Greetings
>>>
>>> Sabine
>>>
>>>>>> "Sabine Leroch" <sabine.leroch@boku.ac.at> 8/28/2009 2:25 PM >>>
>>>
>>> Dear lammps users
>>>
>>> Up to now I created data files with msi2lpm using .car and .mdf files.
>>> Now I
>>> switched to the ch2lmp tool using pdb and psf data. Although the molecule
>>> geometries, force parameters, bonds, angles, box sizes, surrounding water
>>> molecules etc. are exactely the same in the two data files (only the
>>> atom,
>>> typeIDs etc. are differently distributed among the atoms), there are
>>> small
>>> differences in the resulting structures.
>>>
>>> So I looked at the log.files and the strange thing about it is :although
>>> I
>>> used the same in. files, Lammps versions and machine its header is not
>>> the
>>> same (have a look below). What is most confusing the max numbers of bonds
>>> and dihedrals are to low in the ch2lmp log.file. The calculated numbers
>>> (for
>>> instance max bonds/atom=3)  cant be true as can be seen by comparison
>>> with
>>> the Bonds list in the ch2lpm data file (for instance atomId 10 has 4 next
>>> neighbors).
>>>
>>> What is going on here? Why differences in the logfiles? Has the
>>> difference
>>> in max bond consequences on the results, or is it just an information not
>>> used any more later?
>>>
>>> Hope somebody can help me.
>>>
>>> Best regards
>>>
>>> Sabine
>>>
>>> head of log.file for the msi datafile:
>>>
>>> LAMMPS (9 Jan 2009)
>>>
>>> Scanning data file ...
>>>
>>>   4 = max bonds/atom
>>>
>>>   6 = max angles/atom
>>>
>>>   15 = max dihedrals/atom
>>>
>>>   2 = max impropers/atom
>>>
>>> Reading data file ...
>>>
>>>   orthogonal box = (0 -10 0) to (32 32 32.86)
>>>
>>> from data.file:
>>>
>>> Bonds
>>>
>>>      1   1      1      5      # CT1  NH3
>>>
>>>      2   2      1      2      # HC   NH3
>>>
>>>      3   2      1      3      # HC   NH3
>>>
>>>      4   2      1      4      # HC   NH3
>>>
>>>      5   3      5      6      # CT1  HB
>>>
>>>      6   4      5      7      # CC   CT1
>>>
>>>      7   5      5      8      # CT1  CT2
>>>
>>>      8   6      7     23     # CC    OC
>>>
>>>      9   6      7     22     # CC    OC
>>>
>>>     10   7      8      9     # CT2   HA
>>>
>>>     11   7      8     10    # CT2   HA
>>>
>>>     12   8      8     11    # CA     CT2
>>>
>>>     13   9     11     12   # CA     CA
>>>
>>>     14   9     11     20   # CA     CA
>>>
>>>     15  10     12     13  # CA     HP
>>>
>>>     16   9     12     14   # CA     CA
>>>
>>>     17  10     14     15  # CA     HP
>>>
>>>     18   9     14     16   # CA     CA
>>>
>>>     19  10     16     17  # CA     HP
>>>
>>>     20   9     16     18   # CA    CA
>>>
>>>     21  10     18     19  # CA    HP
>>>
>>>     22   9     18     20   # CA    CA
>>>
>>>     23  10     20     21  # CA    HP
>>>
>>> head for the ch2lmp data.file:
>>>
>>> LAMMPS (9 Jan 2009)
>>>
>>> units           real
>>>
>>> atom_style      full
>>>
>>> boundary        p p f
>>>
>>> pair_style      lj/charmm/coul/long 15.0 16.0 16.0
>>>
>>> bond_style      harmonic
>>>
>>> angle_style     charmm
>>>
>>> dihedral_style  charmm
>>>
>>> improper_style  harmonic                               ## this block is
>>> missing in the above version
>>>
>>> kspace_style    pppm 0.0001
>>>
>>> kspace_modify   slab 3.0
>>>
>>> read_data       phe_car.data                           # here is the name
>>> of
>>> the file above just sanning data file
>>>
>>>   3 = max bonds/atom                                 # wrong output !!!!!
>>>
>>>   6 = max angles/atom
>>>
>>>   12 = max dihedrals/atom                          # wrong output
>>>
>>>   2 = max impropers/atom
>>>
>>>   orthogonal box = (0 -10 0) to (32 32 32.86)
>>>
>>> data.file:
>>>
>>> Bonds
>>>
>>>        1       5       1       3  # CC   OC
>>>
>>>        2       5       1       2  # CC   OC
>>>
>>>        3       4       1       8  # CC   CT1
>>>
>>>        4       8       4       8  # CT1  NH3
>>>
>>>        5      10       5       4  # HC   NH3
>>>
>>>        6      10       6       4  # HC   NH3
>>>
>>>        7      10       7       4  # HC   NH3
>>>
>>>        8       7       8       9  # CT1  HB
>>>
>>>        9       6      10       8  # CT1  CT2
>>>
>>>       10       9      10      11  # CT2  HA
>>>
>>>       11       9      10      12  # CT2  HA
>>>
>>>       12       2      13      10  # CA   CT2
>>>
>>>       13       3      14      15  # CA   HP
>>>
>>>       14       1      14      13  # CA   CA
>>>
>>>       15       1      16      14  # CA   CA
>>>
>>>       16       3      16      17  # CA   HP
>>>
>>>       17       1      18      22  # CA   CA
>>>
>>>       18       1      18      16  # CA   CA
>>>
>>>       19       3      18      19  # CA   HP
>>>
>>>       20       1      20      13  # CA   CA
>>>
>>>       21       3      20      21  # CA   HP
>>>
>>>       22       1      22      20  # CA   CA
>>>
>>>       23       3      22      23  # CA   HP
>>>
>>>
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