[CP2K:100] Re: psf problems

Teodoro Laino teodor... at gmail.com
Wed May 30 08:12:19 CEST 2007


PSF is a CHARMM standard format.. you won't find any place around  
where they specify the format..
all the available programs reading PSF have +/- hacked the original  
format..
so we do..

teo

On 30 May 2007, at 08:00, Toon wrote:

>
> Hi Teo,
>
> Thanks for your help. I'll update my copy of cp2k. Is there a standard
> specification for the PSF format availlable on the internet? In the
> (very) long run, I'd like to update my scripts to generate standard
> psf files.
>
> cheers,
>
> Toon
>
> On 29 mei, 19:40, Teodoro Laino <teodor... at gmail.com> wrote:
>> Toon,
>>
>> from your input file I see you're using not an up2date version of
>> cp2k.. at least 1-2 months old..
>> I cannot offer any help for the code you are using..
>>
>> BUT if you update to the new one and use this section:
>>
>>      &TOPOLOGY
>>        CONNECTIVITY MOL_SET
>>        &MOL_SET
>>          &MOLECULE
>>            NMOL 8
>>            CONN_FILE_NAME single.psf
>>            CONNECTIVITY UPSF
>>          &END
>>        &END
>>      &END TOPOLOGY
>>
>> your example works..
>>
>> Bytheway.. yours is not a standard PSF.. me and Axel were working
>> for a couple of weeks and at the moment
>> cp2k supports the EXT standard of the PSF.. everytime you have a psf
>> that is not standard you need to specify
>> that its connectivity is UPSF (mostly you don't care about the  
>> format..)
>>
>> teo
>>
>> On 29 May 2007, at 15:11, Toon wrote:
>>
>>
>>
>>> Hi,
>>
>>> I've been trying to run an mc simulation with the input given below.
>>> I'm just trying to understand how this should work in cp2k. The  
>>> input
>>> is just a dummy example. When I try to run this example (with
>>> cp2k.sdbg), I got this error:
>>
>>> ...
>>>  PSF_INFO| Parsing the NATOM section
>>>  PSF_INFO| NATOM =        5
>>>  PSF_INFO| Parsing the NBOND section
>>>  PSF_INFO| NBOND =        4
>>>  PSF_INFO| Parsing the NTHETA section
>>>  PSF_INFO| NTHETA =        6
>>>  PSF_INFO| Parsing the NPHI section
>>>  PSF_INFO| NPHI =        0
>>> At line 886 of file /home/toon/tmp/build/cp2k/makefiles/../src/
>>> topology_util.F
>>> Traceback: (Innermost first)
>>>    Called from line 498 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/topology_psf.F
>>>    Called from line 359 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/topology.F
>>>    Called from line 206 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/topology.F
>>>    Called from line 279 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/qs_environment.F
>>>    Called from line 111 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/qs_main.F
>>>    Called from line 729 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/f77_interface.F
>>>    Called from line 268 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/cp2k_runs.F
>>>    Called from line 847 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/cp2k_runs.F
>>>    Called from line 248 of file /home/toon/tmp/build/cp2k/
>>> makefiles/../
>>> src/cp2k.F
>>> Fortran runtime error: Array element out of bounds: 31 in (1:5),  
>>> dim=1
>>
>>> The psf file is also given below. It describes the topology of  
>>> exactly
>>> one of the eight methane molecules. I believe the psf file is  
>>> correct,
>>> is it? I did take a look at the part of the code where the error
>>> occurs but I don't really understand what it is expected to do. (It
>>> reads the psf file, something goes wrong when processing the one- 
>>> four
>>> pairs, but I don't get the details.) Is there something wrong in the
>>> input/psf file or is this a bug? The examples from the regtests work
>>> on my machine.
>>
>>> best regards,
>>
>>> Toon
>>
>>> the input file:
>>
>>> &FORCE_EVAL
>>
>>>   METHOD Quickstep
>>>   &DFT
>>>     &QS
>>>       METHOD PM3
>>>       EPS_DEFAULT 1.0E-12
>>>       EPS_GVG 1.0E-6
>>>       EPS_PGF_ORB 1.0E-6
>>>     &END QS
>>>     &SCF
>>>       EPS_SCF 1.0E-6
>>>       MAX_SCF 150
>>>       SCF_GUESS atomic
>>>     &END SCF
>>>   &END DFT
>>
>>>   &SUBSYS
>>>     &CELL
>>>       ABC 7.800000 7.800000 7.800000
>>>       UNIT ANGSTROM
>>>     &END CELL
>>>     &COORD
>>>   C         7.1545135964        0.2916147406        0.6622232680
>>>   H         6.6668950468        1.1504609369        1.1033507689
>>>   H         7.6334667531        0.6233226102       -0.2564860726
>>>   H         6.4208845485       -0.4795931637        0.4356274201
>>>   H         7.9005900072       -0.1048244889        1.3410306662
>>>   C         6.8528101393        3.6807499565        1.5744193983
>>>   H         6.4514929741        2.8349587584        2.1188989803
>>>   H         7.7679317225        3.4073223315        1.0559592149
>>>   H         7.0709998781        4.4961704973        2.2881955953
>>>   H         6.1341098685        4.0308814768        0.8225903997
>>>   C         1.9813613499        6.7192653419        5.8763727299
>>>   H         2.0321973418        7.4196170794        6.7046158757
>>>   H         1.2903991153        7.1400631283        5.1330330349
>>>   H         1.5834916118        5.7941607545        6.2462624125
>>>   H         2.9782222352        6.5700588933        5.4382607646
>>>   C         6.8935808834       10.9042343214        4.8896018240
>>>   H         6.9090027651       10.0556726408        5.5732300957
>>>   H         7.1082178538       11.7975226536        5.4836337927
>>>   H         5.9106655806       10.9864139714        4.4468607567
>>>   H         7.6585223681       10.7854616816        4.0984669623
>>>   C         3.4097928887        4.5767446702        2.2242443860
>>>   H         3.0529585247        4.4184677018        1.2009363529
>>>   H         3.2785552112        3.6406911435        2.7889006394
>>>   H         2.8302525350        5.3840010296        2.6917414739
>>>   H         4.4528957985        4.8811323379        2.2007501082
>>>   C         2.9805519373        8.2006034213        9.5372130039
>>>   H         3.3335722902        9.0450868984       10.1155313292
>>>   H         2.1188103649        7.7275659069       10.0272973693
>>>   H         3.7804325728        7.4372375456        9.4173176654
>>>   H         2.6890775746        8.5348163384        8.5285057129
>>>   C         6.0352120743        6.4801397125        4.0960140077
>>>   H         6.5874102060        7.3836880272        3.9041291362
>>>   H         5.4489916745        6.2452884244        3.2172777054
>>>   H         5.3670640659        6.6104228115        4.9504368037
>>>   H         6.7521214494        5.6814792763        4.3123759997
>>>   C         3.2928814788        2.5582719306        5.8498575291
>>>   H         3.0860227820        2.3159397213        6.8922542536
>>>   H         3.5005462509        3.6199393877        5.7655448415
>>>   H         2.4455631533        2.3255776287        5.2113735329
>>>   H         4.1684058503        1.9781743596        5.5368454612
>>>     &END COORD
>>>     &TOPOLOGY
>>>       CONNECTIVITY MOL_SET
>>>       &MOL_SET
>>>         NMOL 8
>>>         CONN_FILE_NAME single.psf
>>>       &END
>>>     &END TOPOLOGY
>>>     &PRINT
>>>       &TOPOLOGY_INFO
>>>         EACH 1
>>>         PSF_INFO T
>>>       &END TOPOLOGY_INFO
>>>     &END PRINT
>>>   &END SUBSYS
>>> &END FORCE_EVAL
>>
>>> &GLOBAL
>>>   FFT_LIB FFTW3
>>>   PROJECT mc
>>>   RUN_TYPE MC
>>> &END GLOBAL
>>
>>> &MOTION
>>>   &MC
>>>     IUPTRANS 6400000
>>>     IUPVOLUME 3200000
>>>     LBIAS no
>>>     LSTOP yes
>>>     NMOVES 8
>>>     NSTEP 2
>>>     PMSWAP 0.0
>>>     PMTRAION 0.00
>>>     PMTRANS 0.00
>>>     PMVOLUME 1.00
>>>     PMVOL_BOX 1.00
>>>     PRESSURE 1
>>>     ENSEMBLE traditional
>>>     RESTART no
>>>     RESTART_FILE_NAME mc_restart_1
>>>     RMDIHEDRAL 3.0
>>>     RMANGLE 3.0
>>>     RMBOND 0.074
>>>     RMROT 26.0
>>>     RMTRANS 0.38
>>>     RMVOLUME 0.5
>>>     TEMP 101.055000
>>>     AVBMC_RMIN 1.0
>>>     AVBMC_RMAX 5.0
>>>     AVBMC_ATOM 1
>>>     PBIAS 0.5
>>>     PMAVBMC_MOL 1.0
>>>     PMSWAP_MOL 1.0
>>>     PMROT_MOL 1.0
>>>     PMTRANS_MOL 1.0
>>>     PMTRAION_MOL 1.0
>>>   &END MC
>>>   &PRINT
>>>     &TRAJECTORY
>>>       EACH 5
>>>     &END TRAJECTORY
>>>   &END PRINT
>>> &END MOTION
>>
>>> The file single.psf looks like this:
>>
>>> PSF
>>
>>>       1 !NTITLE
>>> None
>>
>>>       5 !NATOM
>>>       1 NAME    1 NAME  C     C 0.0    12.010700 0
>>>       2 NAME    1 NAME  H     H 0.0     1.007940 0
>>>       3 NAME    1 NAME  H     H 0.0     1.007940 0
>>>       4 NAME    1 NAME  H     H 0.0     1.007940 0
>>>       5 NAME    1 NAME  H     H 0.0     1.007940 0
>>
>>>       4 !NBOND
>>>       2       1       3       1       4       1       5       1
>>
>>>       6 !NTHETA
>>>       4      1      2      5      1      2      3      1      2
>>>       5      1      4      4      1      3      5      1      3
>>
>>>       0 !NPHI
>>
>>>       0 !NIMPHI
>>
>>>       0 !NDON
>>
>>>       0 !NACC
>>
>>>       0 !NNB
>
>
> >




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