[CP2K:95] psf problems
Teodoro Laino
teodor... at gmail.com
Tue May 29 17:40:22 UTC 2007
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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