psf problems
Toon
Toon.Ver... at gmail.com
Wed May 30 06:00:03 UTC 2007
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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