[CP2K:100] Re: psf problems
Teodoro Laino
teodor... at gmail.com
Wed May 30 06:12:19 UTC 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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