[CP2K:107] Re: psf problems

Teodoro Laino teodor... at gmail.com
Fri Jun 1 14:15:16 CEST 2007


please send input file and all files needed to run the job..
Without it's difficult to give any kind of help,

teo
On 1 Jun 2007, at 13:50, Toon wrote:

>
> Hi, I have a related question. Is it normal that
>
>       COORDINATE XYZ
>       COORD_FILE_NAME geometry.xyz
>
> can not be used with MC simumations, or is this a problem with my
> compilation of cp2k?
>
> cheers,
>
> Toon
>
> On 30 mei, 08:12, Teodoro Laino <teodor... at gmail.com> wrote:
>> 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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