[CP2K:107] Re: psf problems
Teodoro Laino
teodor... at gmail.com
Fri Jun 1 12:15:16 UTC 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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